A New Map Catalogs the Effects of Coronavirus Mutations – Howard Hughes Medical Institute

Scientists have analyzed every possible mutation to one key part of the coronavirus. The data could help guide vaccine and drug development and hint at how the virus might spread.

HHMI scientists are joining many of their colleagues worldwide in working to combat the new coronavirus. Theyre developing diagnostic testing, understanding the viruss basic biology, modeling the epidemiology, and developing potential therapies or vaccines. Over the next several weeks, we will be sharing stories of some of this work.

As the novel coronavirus spreads, its picking up new mutations for better and for worse.

Now, Howard Hughes Medical Institute Investigator Jesse Bloom and his colleagues have cataloged how nearly 4,000 different mutations alter SARS-CoV-2s ability to bind to human cells.

Their data, publicly available online as an interactive map, is a new resource for researchers developing antiviral drugs and vaccines to fight COVID-19, the infectious disease caused by SARS-CoV-2. The work also reveals how individual mutations may affect the viruss behavior, the team reports August 11, 2020in the journal Cell.

We dont know how the virus will evolve, but now we have a way to look at the mutations that can occur and see their effects, says Bloom, a virologist at the Fred Hutchinson Cancer Research Center.

Each time a virus replicates, it can pick up new genetic mutations. Many of these mutations have no effect on a viruss behavior. Others could make the virus better or worse at infecting people. To what extent mutations might be making SARS-CoV-2 more dangerous has been an open and controversial question. Doctors and scientists have analyzed genetic differences in virus samples collected from COVID-19 patients around the world, hunting for clues to the diseases spread. But until now, no one had comprehensively linked potential mutations to their functional effect on SARS-CoV-2.

We dont know how the virus will evolve, but now we have a way to look at the mutations that can occur and see their effects.

Jesse Bloom, HHMI Investigator at the Fred Hutchinson Cancer Research Center

The new study focused on mutations to a key part of SARS-CoV-2 its spike protein. This protein binds to a protein on human cells called ACE2, a necessary step for infection. Mutations in the spike protein could change how well SARS-CoV-2 sticks to and thus infects human cells.

Blooms team bred yeast cells to display a fragment of the spike protein on their surface. This fragment, called the receptor binding domain, makes direct contact with ACE2. The researchers systematically created thousands of versions of the fragment each with different mutations. Then they measured how well these mutated fragments stuck to ACE2. That let them assess how various mutations might affect the function of the binding domain.

The data show that many possible mutations could make the virus bind to human cells more strongly. But those mutations dont seem to be gaining a foothold in circulating versions of the virus.

This would suggest that theres some sort of sweet spot, where if the virus can bind ACE2 pretty well, then its able to infect humans, Bloom says. Maybe theres no evolutionary need for it to get better.

Other mutations made it harder for the spike protein to bind to cells or prevented the protein from properly folding into its final shape, the team found. Versions of the virus with these mutations might be less likely to gain a foothold because they cant infect cells as effectively. The teams targeted lab tests arent a perfect proxy for how mutations will affect the virus in the wild, where many other factors influence how effectively it can spread but theyre a useful starting place.

The data will also be valuable for researchers designing drugs and vaccines to fight COVID-19, says Tyler Starr, a postdoc in Blooms lab who led the project alongside graduate student Allie Greaney. Understanding the consequences of different mutations can guide the development of drugs that will continue to work as the virus changes over time. Plus, Starr says, its becoming clear that antibodies that stick to this part of the virus are really good, protective antibodies that we would want to elicit with a vaccine.

Study coauthor Neil King and his lab at the University of Washington is already working on such vaccines. His team is designing artificial proteins that mimic components of the virus. As part of a vaccine, such proteins could potentially train peoples immune systems to produce antibodies that target the coronavirus. The researchers modify the artificial proteins to make them more stable and easier to produce in large quantities than the natural versions of the proteins.

The data from Blooms team offers a roadmap to making those modifications. Normally, when were trying to figure out how to make a protein better, were shooting in the dark, says Daniel Ellis, a graduate student in Kings lab. The information theyve given us is kind of like a cheat sheet. It makes our lives amazingly easier.

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Citation

Tyler N. Starr et al. Deep mutationalscanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell. Published online on August 11, 2020. doi:10.1016/j.cell.2020.08.012

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A New Map Catalogs the Effects of Coronavirus Mutations - Howard Hughes Medical Institute

All processors on deck in the race to research COVID-19 – Silicon Prairie News

Sometimes a problem is so urgent and complex, you need the whole world working on it.

Thats COVID-19.

Sometimes you also need the help of a global supercomputer.

Thats Folding@home.

A distributed computing project powering research into SARS-CoV-2, Folding@home seeks to develop effective, patent-free drugs to treat the deadly coronavirus, which has caused over 732,000 deaths worldwide, including more than 163,000 deaths nationally.

But a successful response to this large-scale, generation-defining problem cant be realized without the combined computing resources of millions of ordinary citizens around the world. Thats why Folding@home is inviting everyday computer users to share their excess computing power with researchers. Volunteers can download the necessary software here.

Weve had several million volunteers, citizen scientists that have downloaded the software and helped us out in this, said Anton Thynell, head of collaboration and communication for Folding@home in a recent interview with Dubuque, Iowa radio station KDTH-AM. Were actually the strongest supercomputer in the world.

A self-described moonshot collaboration, Folding@home studies both the virus and the human proteins it interacts with. So far, the project has discovered novel protein structures previously inaccessible to researchers.

With that victory in tow, the team has shifted toward the discovery of new therapies to treat the illnessone that scientists and the medical community are still struggling to figure out.

What Folding@home does is basically trying to map out the entire virus and how it folds and unfolds, Thynell said. But this requires an immense amount of computing.

To that end, Omaha-based cloud provider First National Technology Solutions (FNTS) has joined several other organizations worldwide in the effort, providing access to a phenomenal amount of excess processing power that is then tied together with other processors around the world to create the supercomputer, said FNTS president Kim Whittaker in that same interview. (Whittaker sits on the board of the nonprofit AIM Institute, which operates Silicon Prairie News.)

We wanted to look for ways that we could give back and help other organizations with different supercomputing initiatives that they have underway, Whittaker said.With the technology in place to make these complicated simulations possible through our partnership with Folding@home, this allows scientists to concentrate on research, analysis and finding cures.

FNTS is active in the community, actively supporting organizations such as the AIM Institute.The company is celebrating its 25-year anniversaryin August as a nationally recognized advisor in managed IT services.

Folding@home began at Stanford University in 2000 as a distributed computing project for disease research that simulates protein folding, computational drug design and molecular dynamics. When the pandemic hit, the project shifted to address the mechanics of the novel coronavirus, with unprecedented support from people around the world, Thynell said.

It is really fascinating what theyve been able to accomplish with individuals and companies that have donated time and resources, all for a good cause, to help solve some of these healthcare challenges, Whittaker said.

Thynell gave a direct plea for users to please consider downloading the software from the Folding@home website and running it on both their personal and work computers, if possible.

Youre helping us with a small part of a very large simulation, where were trying to understand better how SARS-CoV-2 works and moves, Thynell said.

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All processors on deck in the race to research COVID-19 - Silicon Prairie News

Nine Cambridge researchers among this year’s Royal Society medal and award winners – Mirage News

He is one of the 25 Royal Society medals and awards winners announced today, nine of whom are researchers at the University of Cambridge. The annual prizes celebrate exceptional researchers and outstanding contributions to science across a wide array of fields.

President of the Royal Society, Venki Ramakrishnan, said:

The Royal Societys medals and awards celebrate those researchers whose ground-breaking work has helped answer fundamental questions and advance our understanding of the world around us. They also champion those who have reinforced sciences place in society, whether through inspiring public engagement, improving our education system, or by making STEM careers more inclusive and rewarding.

This year has highlighted how integral science is in our daily lives, and tackling the challenges we face, and it gives me great pleasure to congratulate all our winners and thank them for their work.

Sir Alan Fersht FMedSci FRS, Emeritus Professor in the Department of Chemistry and former Master of Gonville and Caius College, is awarded the Copley Medal for the development and application of methods to describe protein folding pathways at atomic resolution, revolutionising our understanding of these processes.

Most of us who become scientists do so because science is one of the most rewarding and satisfying of careers and we actually get paid for doing what we enjoy and for our benefitting humankind. Recognition of ones work, especially at home, is icing on the cake, said Sir Alan. Like many Copley medallists, I hail from a humble immigrant background and the first of my family to go to university. If people like me are seen to be honoured for science, then I hope it will encourage young people in similar situations to take up science.

As the latest recipient of the Royal Societys premier award, Sir Alan joins an elite group of scientists, that includes Charles Darwin, Albert Einstein and Dorothy Hodgkin, and more recently Professor John Goodenough (2020) for his research on the rechargeable lithium battery, Peter Higgs (2015), the physicist who hypothesised the existence of the Higgs Boson, and DNA fingerprinting pioneer Alec Jeffreys (2014).

Professor Barry Everitt FMedSci FRS, from the Department of Psychology and former Master of Downing College, receives the Croonian Medal and Lecture for research which has elucidated brain mechanisms of motivation and applied them to important societal issues such as drug addiction.

Professor Everitt said: In addition to my personal pride about having received this prestigious award, I hope that it helps draw attention to experimental addiction research, its importance and potential.

Professor Herbert Huppert FRS of the Department of Applied Mathematics and Theoretical Physics, and a Fellow of Kings College, receives a Royal Medal for outstanding achievements in the physical sciences. He has been at the forefront of research in fluid mechanics. As an applied mathematician he has consistently developed highly original analysis of key natural and industrial processes. Further to his research, he has chaired policy work on how science can help defend against terrorism, and carbon capture and storage in Europe.

In addition to the work for which they are recognised with an award, several of this years recipients have also been working on issues relating to the COVID-19 pandemic.

Professor Julia Gog of the Department of Applied Mathematics and Theoretical Physics and a Fellow of Queens College, receives the Rosalind Franklin Award and Lecture for her achievements in the field of mathematics. Her expertise in infectious diseases and virus modelling has seen her contribute to the pandemic response, including as a participant at SAGE meetings. The STEM project component of her award will produce resources for Key Stage 3 (ages 11-14) maths pupils and teachers exploring the curriculum in the context of modelling epidemics and infectious diseases and showing how maths can change the world for the better.

The Societys Michael Faraday Prize is awarded to Sir David Spiegelhalter OBE FRS, of the Winton Centre for Centre for Risk and Evidence Communication and a Fellow of Churchill College, for bringing key insights from the disciplines of statistics and probability vividly home to the public at large, and to key decision-makers, in entertaining and accessible ways, most recently through the COVID-19 pandemic.

The full list of Cambridges 2020 winners and their award citations:

Copley Medal

Alan Fersht FMedSci FRS, Department of Chemistry, and Gonville and Caius College

He has developed and applied the methods of protein engineering to provide descriptions of protein folding pathways at atomic resolution, revolutionising our understanding of these processes.

Croonian Medal and Lecture

Professor Barry Everitt FMedSci FRS, Department of Psychology and Downing College

He has elucidated brain mechanisms of motivation and applied them to important societal issues such as drug addiction.

Royal Medal A

Professor Herbert Huppert FRS, Department of Applied Mathematics and Theoretical Physics, and Kings College

He has been at the forefront of research in fluid mechanics. As an applied mathematician he has consistently developed highly original analysis of key natural and industrial processes.

Hughes Medal

Professor Clare Grey FRS, Department of Chemistry and Pembroke College

For her pioneering work on the development and application of new characterization methodology to develop fundamental insight into how batteries, supercapacitors and fuel cells operate.

Ferrier Medal and Lecture

Professor Daniel Wolpert FMedSci FRS, Department of Engineering and Trinity College

For ground-breaking contributions to our understanding of how the brain controls movement. Using theoretical and experimental approaches he has elucidated the computational principles underlying skilled motor behaviour.

Michael Faraday Prize and Lecture

Sir David Spiegelhalter OBE FRS, Winton Centre for Risk and Evidence Communication and Churchill College

For bringing key insights from the disciplines of statistics and probability vividly home to the public at large, and to key decision-makers, in entertaining and accessible ways, most recently through the COVID-19 pandemic.

Milner Award and Lecture

Professor Zoubin Ghahramani FRS, Department of Engineering and St Johns College

For his fundamental contributions to probabilistic machine learning.

Rosalind Franklin Award and Lecture

Professor Julia Gog, Department of Applied Mathematics and Theoretical Physics, and Queens College

For her achievements in the field of mathematics and her impactful project proposal with its potential for a long-term legacy.

Royal Society Mullard Award

Professor Stephen Jackson FMedSci FRS, Gurdon Institute, Department of Biochemistry

For pioneering research on DNA repair mechanisms and synthetic lethality that led to the discovery of olaparib, which has reached blockbuster status for the treatment of ovarian and breast cancers.

The full list of medals and awards, including their description and past winners can be found on the Royal Society website: https://royalsociety.org/grants-schemes-awards/awards/

Adapted from a Royal Society press release.

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Nine Cambridge researchers among this year's Royal Society medal and award winners - Mirage News

Life after R&D death: Halozyme CEO Helen Torley on the company’s pivot and path to profitability – FierceBiotech

Halozyme CEO Helen Torley has always been frank about what would happen if the companys foray into drug development failed: The two-pillar company would ditch its internal pipeline and focus solely on providing its drug delivery technology to pharma partners.

Now, nine months after its pancreatic cancer program foundered in phase 3, that transparency, along with lots of planning and quick decision-making, have turned out to be key in keeping the company aliveand profitable.

With the second quarter of 2020, Halozyme delivered its first profitable quarter of what it expects to be many, with earnings per share of $0.19. The company reeled in $25.8 million in income, compared witha loss of $14.6 million during the same quarter last year.

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Part of that gain comes from canning its R&D work. In November 2019, the company announced that its lead program, a PEGylated version of its hyaluronidase enzyme, in tandem with Celgenes Abraxane and the chemo drug gemcitabine, did not extend the lives of patients with pancreatic cancer compared withAbraxane and chemo alone.

Halozyme, which had two plans in its pocketone for an FDA approval and one for a trial failurepulled the trigger on a pivot. It started a reorganization that would lay off more than half of its staffersabout 160and worked to expand its drug delivery business with the 120 employees that remained.

RELATED: Halozyme kills pipeline, cuts 55% of jobs as lead cancer med flops in phase 3

The hardest part was the town hall, where we had to talk about the results being negative. To see almost 300 faces looking at you trying to understand what happened, Torley said. Because we had such conviction; opinion leaders had such a conviction we had a good shot at it.

All told, winding down its development pipeline dropped its R&D spend to $9 million from $33.9 million the same quarter last year.

But saving on R&D costs isnt the whole story. Halozymes revenue jumped to $55.2 million from $39.1 million year over year, largely thanks to payments from partners Janssen and Bristol Myers Squibb totaling $32.3 million.

The companys partnerships are based on Enhanze, its drug delivery technology that uses the enzyme hyaluronidase to break down hyaluronan, a natural sugar chain that forms a gel in the innermost layer of the skin. This allows drugs, like Janssens multiple myeloma med, Darzalex, to be injected just under the skin, saving patients from hours-long intravenous infusions.

In the second quarter alone, Halozyme has seen three new approvals for its partnered drugs: nods from the FDA and European Medicines Agency for the subcutaneous version of Darzalex, and an FDA green light for Roches Phesgo, a combination of breast-cancer drugs Perjeta and Herceptin using the Enhanze technology.

Halozyme now has five partnered drugs on the market, including subcutaneous versions of Roches Herceptin and Rituxan, as well as of Baxaltas HYQVIA, a treatment for primary immunodeficiency. And more are in the works. Janssen is also testing subcutaneous Darzalex in in a protein-folding disorder called light-chain amyloidosis, while Bristol Myers is testing a subcutaneous form of Yervoy in combination with its PD-1 blocker Opdivo in multiple cancers.

This year is mostly about milestones It was important we didnt take the eye off the ball with Enhanze and continued to support our partners with trial initiations and the regulatory back-and-forth as we get ready for approvals, Torley said. If everything like that could go well, we knew we would be profitable in the second quarter.

Between 2020 and 2022, the company expects to pick up $350 million to $450 million in milestone payments as its partnered programs move through the clinic.

We expect three phase 3 starts this year, all of which are associated with milestones, Torley said. The company expects to see nine new studies this year, including one new phase 2 study and five new phase 1 studies.

In 2021, Halozyme expects to add some royalty income, too: Once all the reimbursement is in place for Darzalex in the U.S. and Europe, and for Phesgo in the U.S., we see the opportunity for robust uptake, Torley said. 2020 is a bit of a setup yearwe will see revenues this year, but they will be substantial in 2021.

Although the COVID-19 pandemic threw a wrench in the plan, Halozymes partners have stayed on track. Despite seeing delays of one to two quarters in some partnered programs, its partners have managed to start trials on time. Based on its partners' latest updates, Halozyme anticipates $230 million to $245 million in sales this year.

And to keep growing, Halozyme plans to add new partners to the mix.

Things slowed down certainly in Q2, but were definitely seeing an uptake in the pace of discussions, Torley said. Weve never had as broad an array of conversations as we have at the moment, with both biotech and pharma.

Torley believes the Janssen and Roche approvals have driven this interest.

We had two recent approvals with products early in their life cycle with a lot of growth ahead of them What Enhanze has allowed to happen has grabbed peoples attention: turning a four- to six-hour IV into a three- to -five-minute [subcutaneous injection]. People marvel at that, she said.

Beyond supporting its partners and signing new ones, any growth will come from M&A. It's not an immediate priority, "but if at the right time, we find the right platform," the company would acquire a technology that complements Enhanze and that is "partly or substantially derisked."

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Life after R&D death: Halozyme CEO Helen Torley on the company's pivot and path to profitability - FierceBiotech

Demand Scenario of Zinc Deficiency Treatment Market to Remain Positive Through 2025 – Research Newspaper

Zinc is a micronutrient and essential trace element required for metabolism reactions that catalyze number of enzyme reactions, protein folding, gene expression etc. Deficiency of zinc may cause range of infectious diseases and other complications affecting almost every aspect of health such as delayed or retarded growth in children, hair loss, lack of cognitive function, reduced sense of taste and smell, loss of appetite, immunosuppression, anemia, night blindness, etc. Zinc deficiency may also cause deficiency of vitamin A as zinc is required for vitamin A absorption. Zinc deficiency is the fifth leading factor causing disease across the globe, and according to World Health Organization (WHO) 31% of the global population is experiencing zinc deficiency.

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Underdeveloped countries are facing major problem of death due to childhood diarrhea and pneumonia caused due to zinc deficiency. As per International Zinc Nutrition Consultative Group (IZiNCG) zinc deficiency is expected to cause 176,000 diarrhea deaths, 406,000 pneumonia deaths and 207,000 malaria deaths across the world Regions such as Africa, Middle East and South-East Asia are bearing high burden of zinc deficiency due to poor nutrition, lack of breastfeeding etc. Treatment of zinc deficiency mainly involves intake of zinc rich food and zinc supplements. Mild zinc deficiency requires treatment with zinc supplements at 2-3 times the recommended dietary allowance (RDA) and moderate to severe zinc deficiency requires zinc supplements with 4-5 times the RDA and treatment is continued for at least 6 months.

Oral repletion of zinc in the form of zinc acetate, zinc sulfate, zinc aspartate, zinc orotate and zinc gluconate, multivitamin supplements etc. and zinc supplements are available in the form of oral tablets capsules, syrups or intravenous solutions. National Institute of Health (NIH) recommends daily intake of 20-40 mg zinc for adults orally to avoid complications caused by zinc deficiency. High dose of zinc i.e. more than 50 mg per day is recommended to patients with severe zinc deficiency or patients with irreversible malabsorptive disorders. Intravenous administration of zinc is rarely recommended unless the patient is suffering from intestinal failure or on long-tern treatment with total parenteral nutrition.

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Market for zinc deficiency treatment is primarily driven by increasing occurrence of malnutrition in underdeveloped and developing countries. Increasing incidence of anemia, hypovitaminosis A, etc. are other factors driving demand for zinc supplements across the globe. Zinc supplements are also used as an adjunctive therapy in many disorders such as alopecia, ulcers, electrolyte replenishment therapy for diarrhea, etc.; high incidence of which can propel the demand for zinc supplements over the forecast period. However, unavailability of treatment opportunities in the underdeveloped countries can be the factor which can hamper growth of global zinc deficiency treatment market.

The global market for zinc deficiency treatment is segmented on basis of product types, treatment, dosage form, distribution channel and geography:

Among treatment type, dietary supplements is expected to dominate the global market as dietary zinc supplements are recommended along with drug therapy in every patient suffering from zinc deficiency. Among all four distribution channels of zinc supplements, e-commerce is expected to experience highest growth over the forecast period.

On the basis of geography, global zinc deficiency treatment testing market is segmented into five key regions viz. North America, Latin America, Europe, Asia Pacific, and Middle East & Africa. Asia Pacific is expected to dominate the global market for zinc deficiency treatment due to high level of malnutrition in developing countries such as India, Bangladesh, Sri Lanka, etc. The region is expected to witness robust growth due to growing awareness towards malnutrition and its consequences. North America and Western Europe shows lower occurrence of zinc deficiency as adequate intake of animal food by population in the region. Despite high incidence of zinc deficiency in Middle East and Africa market growth is limited by access to zinc supplements due to low purchasing power and poor health consciousness among general population.

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Some of the key players present in global zinc deficiency treatment market are

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Demand Scenario of Zinc Deficiency Treatment Market to Remain Positive Through 2025 - Research Newspaper

Cryo-EM structures of the air-oxidized and dithionite-reduced photosynthetic alternative complex III from Roseiflexus castenholzii – Science Advances

INTRODUCTION

Photosynthesis transforms solar energy to chemical energy and supports nearly all life on Earth. Sunlight is absorbed by pigments in the light-harvesting (LH) antenna system, and excitation energy is transferred to the reaction center (RC), where photochemistry occurs, initiating an electron transfer process. The electron transport chain (ETC) couples the redox reactions associated with electron donors and acceptors to proton translocation to build up a proton motive force across the membrane, which, in turn, drives the formation of adenosine triphosphate (ATP) and other energy-consuming processes. In photosynthetic and respiratory ETCs, complex III (mitochondrial and bacterial cytochrome bc1, chloroplast and cyanobacterial cytochrome b6f) functions primarily to couple thermodynamically favorable electron transfer to proton translocation across the membrane (13). As quinol:electron acceptor oxidoreductases, these complexes create a transmembrane (TM) proton gradient through the Q-cycle mechanism: Four protons are translocated for every two electrons transferred to cytochrome c (cyt c) or plastocyanin upon quinol oxidation (35).

Notably, a functional counterpart for the cyt bc1 complex, alternative complex III (ACIII), has been identified in a wide range of bacterial taxa, and its presence usually coincides with the absence of the cyt bc1 complex (610). This complex is structurally and compositionally unrelated to the bacterial cyt bc1 complex, but it plays the same central role as a quinol:electron acceptor oxidoreductase in both the respiratory and photosynthetic ETCs (6, 813). In the respiratory chain, ACIII is usually associated with different cyt c oxidases and functions in aerobic electron transfer (14, 15). In the photosynthetic ETC of Chloroflexus aurantiacus, in which ACIII was originally discovered (16), the photosynthetic ACIII catalyzes the oxidation of menaquinol and mediates transfer of the released electrons to a periplasmic blue copper protein auracyanin, which, in turn, completes a cyclic electron transfer back to the RC (9, 12, 13).

Recent studies of the respiratory ACIII from Rhodothermus marinus (17) and Flavobacterium johnsoniae (18) have elucidated the structural features of this complex that are related to quinol coordination, cyt c oxidase association, and putative proton translocation. Regarding the association with different cyt c oxidases and the linear electron transfer mode of respiratory ACIII, the photosynthetic ACIII has a distinct composition and functions in a simple and efficient cyclic ETC using the electron donor menaquinol (8, 12, 13, 19, 20). However, the structure of the photosynthetic ACIII remains unknown. In particular, the fundamental coupling mechanisms underlying the menaquinol oxidation and proton translocation of the respiratory and photosynthetic ACIII complexes have received little research attention. Therefore, a structural investigation of the photosynthetic ACIII is necessary for a deeper understanding of the common coupling mechanism used by the ACIII from diverse bacterial taxa.

Roseiflexus castenholzii is a chlorosome-less filamentous anoxygenic phototroph. It contains a mosaic LH antenna, the type II pheophytin-quinone RC, and a cyclic electron transport system. The LH antenna of R. castenholzii is structurally similar to the LH1, but spectroscopically it resembles the LH2 of purple bacteria (19, 21, 22). Our previous structure of the R. castenholzii core complex (rcRC-LH) revealed a previously unknown architecture and a new type of menaquinone shuttling channel in the bacterial RC-LHs and illustrated the molecular basis underlying the LH and energy transfer mechanisms of early prokaryotes (23). We then extracted and purified R. castenholzii ACIII and its periplasmic electron acceptor auracyanin and revealed that ACIII oxidizes menaquinol-4 or menaquinol-7 and transfers the electrons to the copper ion coordinated in auracyanin (24). Here, we report the structures of the six-subunit R. castenholzii ACIII in air-oxidized and dithionite-reduced states, determined by single-particle cryoelectron microscopy (cryo-EM) at 3.3- and 3.5- resolution, respectively. We elucidated its structural features and here propose a previously unrecognized redox-coupled electron transfer and proton translocation mechanism that apparently links the respiratory and photosynthetic functions of the ACIII.

We purified the ACIII from phototrophically grown R. castenholzii using a modification of previous methods (7, 8, 16). We next used SDSpolyacrylamide gel electrophoresis (PAGE) and blue native PAGE to evaluate the purified ACIII (fig. S1A). Consistent with the molecular size expected from the corresponding gene sequences, we observed that the overall 300-kDa complex was composed of six subunits (ActA, ActB, ActC, ActD, ActE, and ActF), with molecular masses ranging from ~10 to 110 kDa (fig. S1A). Each subunit was confirmed by peptide mass fingerprinting (PMF) (tables S1 and S2). Further, gel filtration analysis (fig. S1B) indicated that the purified ACIII was a monomer containing one copy of each subunit. Spectral analysis indicated that the purified ACIII was air-oxidized: It was reduced via addition of sodium dithionite (fig. S1C). The reduced-minus-oxidized difference spectrum showed two absorbance peaks at 524 and 554 nm, indicating the increase of the c-type heme absorbance after reduction (fig. S1D).

To elucidate the proposed conformational changes that were involved in the redox-driven proton translocation of respiratory ACIII (17), the vitrified air-oxidized and dithionite-reduced ACIII were individually subjected to cryo-EM single-particle analysis. A dataset of 257,815 particles of the air-oxidized ACIII was used to reconstruct an electron potential map with an average resolution of 3.3 and a local resolution extending to 2.5 (fig. S2 and movie S1). The final reconstructed cryo-EM map was resolved and enabled us to build an accurate model of the TM helices with side chains in the air-oxidized ACIII (fig. S3) and all the cofactors and lipid molecules (Table 1 and fig. S4). The cryo-EM map of the dithionite-reduced ACIII was reconstructed from 488,581 particles to 3.5- resolution, the composition and overall structure of which resembles that of the air-oxidized ACIII (Table 1, fig. S5, and movie S2).

Different from the respiratory ACIII from R. marinus that contains seven subunits (ActABCDEFH) and one additional unidentified subunit (17), the photosynthetic ACIII only contains six core subunits (ActA, ActB, ActC, ActD, ActE, and ActF) as in F. johnsoniae (18). Superimposition of R. castenholzii ACIII structure with that of R. marinus and F. johnsoniae gives a main-chain root mean square deviation (RMSD) of 1.5 and 3.2 , respectively. Like the two respiratory ACIII structures, R. castenholzii ACIII is assembled into an L-shaped architecture with dimensions of 141 by 98 by 80 ; a TM arm (42 ) containing 23 TM helices from subunits ActA, ActC, ActD, and ActF; and a peripheral arm comprising the periplasmic subunits ActA, ActB, and ActE. On the periplasmic side, subunit ActB forms extensive contacts with ActE, the penta-heme binding domain of ActA, and the periplasmic region of ActC, ActD, and ActF. The loop between the two TMs of ActD inserts into the interface of ActA, ActB, ActC, and ActF. The globular domain of ActD is located in the cytoplasm (Fig. 1, A and B).

(A) The cryo-EM map of the air-oxidized ACIII is shown from the front (left) and back (right) view and represented with the dimensions of the TM and periplasmic region. Each of the six subunits is labeled with the length of its encoded amino acid. (B) Cartoon representation of the air-oxidized ACIII. The c-type hemes and lipids are shown as sticks, and the iron-sulfur clusters are shown as spheres. (C) Representation of the arrangement of cofactors in the air-oxidized ACIII. (D) Edge-to-edge distance between the iron-sulfur clusters and the hemes in the air-oxidized ACIII. The distances are labeled and shown in dashed lines. Color codes for all panels: lime green, ActA; slate, ActB; wheat, ActC; violet, ActD; yellow orange, ActE; aquamarine, ActF; red, c-type heme; orange brown, iron-sulfur clusters; yellow, lipids.

Similar to R. marinus ACIII, given its known electron transport function, one [3Fe-4S] and three [4Fe-4S] clusters in ActB, and six c-type hemes (five in ActA and one in ActE) were modeled in the density map of R. castenholzii ACIII (Fig. 1C and fig. S4), apparently forming wires of the six hemes and the iron-sulfur clusters (Fig. 1D). The six c-type hemes exemplify identical positions and orientations as that in R. marinus and F. johnsoniae ACIII, but there are only one [3Fe-4S] cluster and one [4Fe-4S] cluster identified at deviated positions in F. johnsoniae ACIII (fig. S6A). The six hemes and four iron-sulfur clusters are all located within reasonable edge-to-edge distances (less than 14 ) to permit direct electron transfer along the wire.

Structural superimposition of the air-oxidized and dithionite-reduced ACIII showed a main-chain RMSD of 0.4 (Fig. 2A), indicating that dithionite reduction does not induce obvious conformational changes at the current resolution. However, the difference map of ACIII (the air-oxidized map minus dithionite-reduced map) showed major electron potential differences at the periplasmic subunits (ActA, ActE, and ActB) and the cytoplasmic side of the TM region of ActA, ActC, and ActD (Fig. 2A). The increased electron potentials were observed at the six heme groups as well as the four iron-sulfur clusters (Fig. 2A and movie S3), indicating that these electron carriers are essentially reduced after dithionite treatment, which is consistent with the increased heme spectral differences upon dithionite reduction (fig. S1D).

(A) The air-oxidized minus dithionite-reduced electron potential difference map (orange) of the ACIII is shown from the front (left) and back (right) view. The structures of the air-oxidized and dithionite-reduced ACIII (white) are superimposed, with the iron-sulfur clusters and heme groups shown in sphere and stick models. The color code for each subunit and cofactors of the air-oxidized ACIII is the same as that in Fig. 1. (B) Ribbon representation of the ActA and ActE subunits bound with pentaheme and monoheme groups (red sticks). The N and C termini of the protein are highlighted with a black dot and labeled. (C) Spatial organization and immobilization of the pentaheme and monoheme groups in ActA and ActE subunits. The residues that axially coordinate the heme iron ions are shown as sticks and labeled; the center-to-center distances of the hemes are shown and labeled. (D) Overall structure of ActB subunit. The B1 and B2 domains are colored in blue and magenta, respectively. The iron-sulfur clusters are shown as spheres. (E) Coordination of the iron-sulfur clusters in the ActB subunit. The conserved cysteine residues that coordinate the iron-sulfur clusters are shown as sticks and labeled, and the B2 domain is shown as a ribbon with 80% transparency.

ActA (Gln9-Arg226) and ActE (Cys33-Asn193) were found to be penta-heme and mono-heme subunits, respectively, which form the main electron transfer wire of the photosynthetic ACIII. ActA is membrane-anchored, with an N-terminal TM helix (1, Gln9-Trp43). Five c-type hemes were bound in the loop regions between its six helices on the periplasmic side (Fig. 2B). The C-terminal mono-heme binding domain of ActE is composed of three helices and two turns (Fig. 2B), and our model showed a lipid anchor that is present at the N terminus of ActE (fig. S4D). This observation suggested the possibility that the consensus lipobox sequence L/V-A/T-G/A-C (M30TAC33) (fig. S6B) in the actE gene sequence may be excised from the transcript or degraded following translation in cells or at some point before the final complex assembly. This phenomenon was also observed in the respiratory ACIII (17).

The six heme groups bound by ActA and ActE are each covalently attached via thioester linkages to cysteine residues of highly conserved heme binding motifs (C-X-X-C-H), and their iron ions are axially coordinated through bi-His or His-Met residue couplets (Fig. 2C and fig. S6B). The five hemes of the ActA subunit are arranged in alternating parallel (heme_2,5 and heme_3,4) and perpendicular pairs (heme_2,3 and heme_4,5) (Fig. 2C). In particular, the heme_3,4 pair adopts typical stacked motif in van der Waals contact (edge-to-edge distance, 4.8 ), whereas heme_2,3 (5.1 ) and heme_4,5 (4.5 ) exemplify the T-shaped heme pairs (Figs. 1D and 2C). The spatial organization of heme_2 to heme_5 resembles that of the tetraheme in Shewanella oneidensis STC, in which the electron transfer between stacked heme pairs is approximately an order of magnitude greater than for the T-shaped heme pairs (25). But the electronic coupling of T-shaped heme pairs would be strongly enhanced by cysteine linkages inserted in the space between these pairs (26). The heme_1 is closest in terms of edge-to-edge distance to [3Fe-4S] (8.3 ), and it is buried in a hydrophobic pocket formed by residues from ActB, ActC, ActD, and ActE (fig. S6C). The porphyrin ring of the mono-heme in ActE is inclined about 60 compared to that of heme_5 in ActA, with an edge-to-edge distance of 9.0 and a center-to-center distance of 16.7 (Figs. 1D and 2C).

No midpoint redox potential data are available for the six hemes and iron sulfur clusters in R. castenholzii ACIII. The heme redox potentials of R. marinus ACIII was shown to range from 45 mV to +230 mV at neutral pH (11). Potentiometric titration of the c hemes in F. johnsoniae ACIII gives redox potentials at +331 mV and +439 mV (18). For C. aurantiacus ACIII, which shares 59% sequence identities with R. castenholzii ACIII, the heme midpoint redox potentials were determined to be 228 mV, 110 mV, +94 mV, and +391 mV (8). With the highest redox potential at +391 mV (8), the monoheme of ActE is believed to be the final electron prosthetic group to accept the electrons transferred from the five hemes in ActA. Regarding the high sequence homology and functional similarity (9) of ActA and ActE with that of C. aurantiacus and respiratory ACIIIs from R. marinus and F. johnsoniae (fig. S6, A to C), as well as the spatial distribution of the six hemes (Fig. 2, A to C), electrons can be sequentially transferred along a wire that begins with the heme_1 in ActA and ends with the monoheme in the ActE subunit, and then eventually to the acceptor auracyanin (13, 24).

The largest subunit, ActB (Gly77-Glu1006), was found to be composed of 26 helices and 17 strands that can be divided into two subdomains: the B1 domain (Gly77-Phe714) and B2 iron-sulfur binding domain (Leu715-Glu1006) (Fig. 2D). The N terminus of ActB was resolved from Gly77, just behind the signal peptidase cleavage site A71LA73. The twin-arginine translocase signal peptide assists with the translocation of ActB to periplasm (27). Superimposition analysis of ActB with PsrA and PsrB subunits of polysulfide reductase (PsrABC), an integral membrane-bound enzyme that performs quinone-coupled reduction of polysulfide substrates (28), revealed that the B2 iron-sulfur binding domain is similar to PsrB and that both the folding and positions of the four iron-sulfur clusters match well between the two subunits (fig. S7A). The analysis also revealed that the B1 domain of ActB forms a fold similar to the known substrate binding pocket of PsrA (fig. S9B), yet the absence of any cofactors in our model suggests that the function of ActB does not mirror the reduction activity of PsrA.

The four iron-sulfur clusters are covalently coordinated by conserved Cys residues (Fig. 2E and fig. S6D), with the largest edge-to-edge distance of 9.7 (Fig. 1D). The [3Fe-4S] is located at the interface with ActC and in the most proximity to the periplasmic side of the four-helix bundle that hosts the menaquinol binding pocket (Fig. 3A). This iron-sulfur cluster is the most probable primary electron acceptor from the menaquinol bound in the ActC subunit. The midpoint redox potential of [3Fe-4S] in R. marinus ACIII was determined to be +140 mV (11, 17), which is sufficient for an uphill electron transfer from menaquinol (70 mV at pH 7) (29). The role of the three [4Fe-4S] clusters in both respiratory and photosynthetic ACIIIs are still unknown. The air-oxidized minus dithionite-reduced electron potential differences at the [3Fe-4S] and three [4Fe-4S] clusters indicate that these iron-sulfur clusters can be reduced upon dithionite treatment (Fig. 2A and movie S3). An edge-to-edge distance of 8.3 was observed between the [3Fe-4S] and heme_1 in the ActC subunit (Fig. 1D), which suggests that the electrons accepted by the [3Fe-4S] cluster are most probably transferred along the heme wire to reduce a periplasmic electron carrier.

(A) Ribbon representation of the side (left) and bottom-up (right) views of the ActC (wheat) and ActF (aquamarine) subunits. The TM helices of ActC and ActF are labeled with numbers, and the iron-sulfur clusters in ActB and heme groups in ActA subunit are shown in spheres and red sticks, respectively. The N and C termini of each subunit are highlighted with a black dot and labeled. (B) Open cavity (bright yellow) between the TM helices of ActA, ActC, and ActD subunits of ACIII, which is equivalent to the menaquinol binding pocket. The cavity inside the TM region of ACIII was calculated using the program HOLLOW (44), and it is shown as a surface model. (C) Zoomed-in view of the putative menaquinol binding pocket, with essential amino acids shown as stick models. (D) Interactions between the modeled menaquinol head (blue stick model) and the menaquinol binding pocket. Residues are shown as stick models, and the hydrogen bonding interactions are shown as dashed lines with distances labeled.

The ActC (Lys8-Ala464) and ActF (Gln4-Ser399) subunits each contain 10 TM helices. The middle eight helices are arranged into two four-helix bundles (TM2-5 and TM6-9 of ActC, and TM2-5 and TM6-9 of ActF), which were sandwiched by the intersection of TM1 (TM1) and TM10 (TM10) (Fig. 3A). The helix bundles of ActC and ActF resemble the structure of PsrC dimer (fig. S7C). Superimposition of the structures of ActC and PsrC gives a main-chain RMSD of 1.1 . The quinone binding pocket of PsrC, which is formed by the N-terminal four-helix bundle and located at the periplasmic side, was identified according to the structures complexed with MK-7, pentachlorophenol, and ubiquinone-1 (28). Although no menaquinol was found in the current structures, we observed an open cavity between the TM helices of ActA, ActD, and TM3/4 of ActC subunits, which is equivalent to the quinol binding pocket of PsrC (Fig. 3B and movie S4).

On the basis of structural analysis and comparison as well as sequence alignment (fig. S8), we identified a menaquinol binding pocket of ACIII at the periplasmic side of the first four-helix bundle in ActC, about 12 away from the [3Fe-4S] cluster (Fig. 3C). Adjacent to [3Fe-4S], a strictly conserved His141 residue replaces the Glu67 of PsrC quinol binding pocket (Fig. 3C and figs. S7D and S8), which is involved in proton transfer from the menaquinol (30). The side chains of Trp84, Ile88, Phe91, Pro138, and Leu168 further form a hydrophobic pocket that is capable of immobilizing the menaquinol head group (Fig. 3D). The two carbonyl oxygen atoms of the modeled menaquinol head are capable of forming hydrogen bonds with the imidazole group of His141 (2.8 ) and the hydroxyl group of Asp171 (2.8 ), which further forms hydrogen bonds with Asp252 (2.9 ) (Fig. 3D). At the bottom of the pocket, Ile249 takes the position of Tyr130 in PsrC, which forms a hydrogen bond (2.6 ) with the O1 carbonyl group of MK-7 (fig. S7D) (28). The menaquinol binding pocket of R. castenholzii ACIII shares high sequence homology and conformational similarity with that of R. marinus and F. johnsoniae ACIII (fig. S7, E and F), indicating that ACIIIs play essentially similar enzymatic function in the photosynthesis and respiration.

On the basis of the structural comparison with the respiratory ACIII, we further identified a putative proton translocation passage in the ActC subunit. The passage begins at the cytoplasmic residues Arg198 and Asp199 and proceeds to the TM region located primarily at the first four-helix bundle of the periplasmic region (Fig. 4, A and C). This passage is composed of 22 proton-carrying residues that provide side chains for hydrogen bonding with protons (Fig. 4A). The air-oxidized minus dithionite-reduced electron potential differences were mainly distributed at the cytoplasmic side of TM1, TM3, TM4, TM5, and TM10 of ActC (Figs. 2A and 4C), where the menaquinol binding pocket and proton translocation passage are absent. Furthermore, we did not observe obvious structural differences at the proton translocation passage between the air-oxidized and dithionite-reduced structures (Fig. 2A).

(A) Organization of the menaquinol binding pocket (highlighted with a green box), [3Fe-4S] cluster, heme_1, and the putative proton translocation passage in ActC (wheat). The distance between [3Fe-4S] and the side chain of Asp171 in the menaquinol binding pocket is 12.2 , and the edge-to-edge distance between the [3Fe-4S] cluster and heme_1 is 8.3 . The residues that constitute the proton translocation passage and menaquinol binding pocket are shown as stick models, and the TM helices of ActC are shown as ribbon with 80% transparency. (B) Zoomed-in view of the hydrogen bonding networks between the menaquinol binding pocket and middle passage residues of the proton translocation passage in the ActC subunit, as well as the residues from the ActD and ActF subunits. Residues are shown as stick models, and the hydrogen bonding interactions are shown as dashed lines with distances labeled. (C) Topology diagram of the ActC subunit. The amino acids that constitute the menaquinol binding pocket and proton translocation pathway are shown in blue and green triangles, respectively.

In the middle of the passage, three strictly conserved residuesArg394, His246, and His99form a hydrogen bonding network that links the menaquinol binding pocket and proton translocation passage (Fig. 4B). The imidazole group of His246 forms hydrogen bonds with the guanidine group of Arg394 (3.1 ) and imidazole nitrogen of His99 (3.3 ), which forms a weak hydrogen bond with the main chain of Ile95 (3.3 ). The main-chain nitrogen of Ile95 is further hydrogen-bonded with the main-chain oxygen of Phe91 (3.1 ), one of the key residues involved in menaquinol coordination. In close proximity to His246, Ile248 forms a hydrogen bond with Asp171 (3.0 ), which is hydrogen-bonded with Asp252 (2.9 ) at the top of the menaquinol binding pocket (Fig. 4B).

Arg394, His246, and His99 are strictly conserved in both the respiratory and photosynthetic ACIII (fig. S8). Superimposition analyses showed that the triplet residues adopt the same side-chain orientations and hydrogen bonding network as that from R. marinus and F. johnsoniae (Fig. 5, A and B), suggesting that these residues share a similar function in the respiratory and photosynthetic ACIII. Asp394 is also conserved in other polysulfide, tetrathionate, nitrate, and dimethyl sulfoxide reductases (30). Mutation of Arg394 in Wolinella succinogenes PsrC resulted in an inactive enzyme, which was suggested that it stabilizes the deprotonated quinol (30). Regarding the sequence conservation, location, and extensive hydrogen bonding interactions with the menaquinol binding pocket, the triplet residues are likely essential for coupling the menaquinol oxidation and proton translocation.

(A) Comparison of the proton translocation passage in R. castenholzii ActC (wheat) with that of the respiratory ActC from R. marinus (PDB 6f0k, white) and F. johnsoniae (PDB 6btm, pink). The [3Fe-4S] cluster, heme_1, and the amino acids are shown as sticks. (B) Middle passage residues that are capable of forming hydrogen bonding networks. (C) Putative proton translocation passage in R. castenholzii ActF subunit (aquamarine) and its superimposition with that of R. marinus (PDB 6f0k, white) and F. johnsoniae (PDB 6btm, pink). (D) The middle passage residues that are capable of forming hydrogen bonds in ActF subunits are shown in stick models.

We observed a similar proton translocation passage in the ActF subunit formed by 20 less conserved amino acids (about 20% identities) from the cytoplasmic to periplasmic side (Fig. 5C and fig. S9). In the middle of the ActF passage, side chains of Glu335, Ser217, and Tyr339 are capable of forming hydrogen bonding interactions, but no menaquinol-binding pocket and similar hydrogen bonding networks as that in ActC were found (Fig. 5C). In addition, Ser217 and Tyr339 are less conserved in both the photosynthetic and respiratory ActF, and Glu335 is replaced by Arg in C. aurantiacus and His residue in the respiratory ActF (Fig. 5D and fig. S9). Minor electron potential differences were only observed at His287, Ala189, and Met65 of the ActF subunit, suggesting that this subunit is not sensitive to the air-oxidized and dithionite-reduced state of ACIII. To be noted, a conserved residue Tyr264F forms a hydrogen bond with the main-chain oxygen of Pro267C (2.8 ), which is close to the periplasmic portion of the proton translocation passage in ActC (Fig. 4B). The distinct conservation of these proton translocation passages indicates that the ActC subunit plays consensus important role in both the respiratory and photosynthetic ACIII.

The function of the ActD subunit in the ACIII remains obscure. We observed hydrogen bonding interactions between Asn100 of ActD and Tyr755 of ActB, as well as between Leu106 of ActD and Tyr753 of ActB (fig. S10A). We also observed extensive hydrophobic interactions between residues located in the ActD loop and subunits ActB, ActF, and ActC. These interactions can stabilize the conformation of TM5, which contributes to the menaquinol binding pocket (fig. S10A). Near the menaquinol binding pocket, a hydrogen bond is formed between the hydroxyl groups of Glu118 of ActD and Ser244 of ActC (2.1 ), which was close to the His246 of ActC that would be essential for coupling the menaquinol oxidation and proton translocation (Fig. 4B). Thus, ActD might play a primary role in stabilizing the TM region of ACIII, which thereby contributes to a stable menaquinol binding pocket and proton translocation passage.

As a functional counterpart of the bc1 complex, ACIII plays a central role in both the photosynthetic and respiratory ETC of a wide range of bacterial taxa (610). It couples quinol oxidation with TM proton translocation to build up a TM proton gradient, which drives the formation of ATP required for bacterial growth. However, the nature of the coupling mechanism(s) for the respiratory and photosynthetic functions of ACIII has not been well discussed.

The photosynthetic bacterium R. castenholzii has evolved a simple but efficient cyclic ETC to transform solar energy into chemical energy that is different from the linear respiratory chain (3133). Our study has revealed the structure of the first photosynthetic ACIII comprising six conserved subunits, in both the air-oxidized and dithionite-reduced states, as well as the nature and position of the cofactors, including six hemes and four iron-sulfur clusters. We also detected a menaquinol binding pocket positioned at the periplasmic side of the TM subunit ActC. This pocket is capable of immobilizing the menaquinol head group via strictly conserved residues (Fig. 3D), which is linked by extensive hydrogen bonding interactions with three proton-carrying residues in the middle of an apparent proton translocation passage. In addition, the ActD subunit is shown to coordinate extensive interactions with subunits ActA, ActB, ActC, and ActF.

Previous enzymatic analyses confirmed the activity of photosynthetic ACIII as a menaquinol:auracyanin or cyt c oxidoreductase (9). Recently, we revealed that R. castenholzii ACIII oxidizes menaquinol-4 or menaquinol-7 and transfers electrons to its periplasmic electron acceptor auracyanin (24). It has been revealed that there is a single quinol binding site in R. marinus ACIII by isothermal titration calorimetry experiments (17). The high sequence and structural similarity among photosynthetic and respiratory ACIIIs would also suggest a single menaquinol binding pocket of R. castenholzii ACIII. Within this pocket, menaquinol binds and is oxidized by the terminal electron acceptor auracyanin, releasing two protons into periplasm. Considering that menaquinone is reduced at the binding site of RC-LH complex (23), accepting two protons from cytoplasm, an apparent efficient quinone shuttling cycle is formed among RC-LH, the membrane quinone pool, and ACIII in the R. castenholzii simple cyclic photosynthetic ETC. As a result, with the reduction of one molecule menaquinone at RC-LH and the oxidation of one shuttled menaquinol at ACIII, two transferred electrons are accompanied with two protons transferred from cytoplasm to periplasm, yielding a H+/e ratio of 2:2.

To date, no experimental data on the H+/e stoichiometry for any ACIII were reported. Previous studies proposed that ACIII could also actively pump additional protons from cytoplasm into periplasm (10, 12, 14, 15), which would yield a different H+/e stoichiometry deduced from above quinone shuttling cycle. However, the detailed mechanism of its active proton translocation has not been elucidated. The lack of any redox-active cofactors in the TM and cytoplasmic regions of ACIII argues against a Q-cycle type H+ pumping mechanism, such as is used in the cyt bc1 and cyt b6f complexes.

Structural comparison and analyses revealed two putative proton translocation passages in ActC and ActF, respectively, for both photosynthetic and respiratory ACIII (Fig. 5, A and C). The side chains of the middle-passage triplet residues Arg394, His264, and His99 of ActC adopt exactly the same conformation for all three ACIIIs (Fig. 5B). However, the proton-carrying residues in the passage of ActF are less conserved than that of ActC (Fig. 5, C and D). Notably, the respiratory ACIIIs from R. marinus (17) and F. johnsoniae (18) contain two conserved His and Asp residues in the middle passage of ActF, but these two residues are replaced by Glu and Tyr in the R. castenholzii ACIII (Fig. 5D and fig. S9). In addition, neither menaquinol binding pocket nor hydrogen bonding network was found in ActF. Less differences of electron potential around ActF between the air-oxidized and dithionite-reduced states (Fig. 2A) suggest that ActF is insensitive to the changes of redox potential. Therefore, most probably, ActF passage lacks a driving force for efficient TM proton translocation. If there exists a redox-coupled active proton translocation in ACIII, it would be mostly located in the ActC subunit and driven by the coupling between menaquinol oxidation and putative proton passage, without the necessary conformational change.

On the basis of the above structural analysis and discussion, we propose a redox-coupled proton translocation mechanism for the photosynthetic ACIII, which occurs within the subunit of ActC (Fig. 6). In the menaquinol binding pocket, at the close-to-neutral pH environment (pH ~6.5) of periplasmic space, both Asp171 and His141 are deprotonated and coordinate the bound menaquinol (MQH2) by hydrogen bonds. The hydroxyl hydrogens of menaquinol can be bound by the hydroxyl oxygen of Asp171 and imidazole nitrogen of His141, respectively. Upon oxidation, the hydroxyl group of menaquinol that faces the side chain of Asp171 is first oxidized to form an intermediate semi-menaquinol. The released hydrogen protonates Asp171. Lacking the coordination by Asp171, the semi-menaquinol would be relocated in the binding pocket and thus enable extraction of one proton from the proximal proton passage of ActC, resulting in one proton translocated from the cytoplasm. The binding of the extracted proton will induce a reorganized electronic structure of semi-menaquinol, releasing another hydroxyl hydrogen to protonate His141. The reorganized semi-menaquinol can be further coordinated by the hydroxyl group of Asp171. Then, the semi-menaquinol is further oxidized to form menaquinone (MQ) and release the exacted proton. After the release of menaquinone and the extracted proton from the menaquinol binding pocket, the two protons from oxidation of menaquinol are released to periplasmic space with the deprotonation of Asp171 and His141. During this proposed process, one instance of menaquinol oxidation is coupled to one proton pumped from the cytoplasm. As a result, three protons are released into the periplasm per two electrons transferred (Fig. 6).

The menaquinol head group and the side chains of the essential amino acids are shown to indicate the coupling mechanism of the photosynthetic ACIII from R. castenholzii. Upon menaquinol oxidation, two electrons are sequentially transferred to the [3Fe-4S] cluster with a time interval, two protons from oxidation of menaquinol are released to periplasmic space, and one proton is pumped from the cytoplasm (colored in red) through hydrogen bonding networking with the essential amino acids in the proton translocation passage. As a result, three protons are released into the periplasm per two electrons transferred during oxidation of one instance of menaquinol.

In both the respiratory and photosynthetic ACIII structures, a [3Fe-4S] cluster in the ActB subunit functions as the primary electron acceptor from menaquinol (17, 18), donating the electrons along the six-heme wire and finally onto the periplasmic electron acceptor. Both the photosynthetic ACIII from R. castenholzii and the respiratory ACIII from R. marinus contain additional three [4Fe-4S] clusters, while only one [4Fe-4S] cluster was identified in the F. johnsoniae ACIII (18). The function of [4Fe-4S] clusters remains largely unknown.

Our observation of the electron potential differences of these [4Fe-4S] clusters between air-oxidized and dithionite-reduced states indicates that these clusters are either accessible to dithionite or connected to the electron transfer wire. In Psr with the absence of heme groups, two electrons released from MK-7 are transferred via five [4Fe-4S] clusters to the bis-MGD (bis-molybdopterin guanine dinucleotide) cofactor and then reduce polysulfide (28). Unfortunately, no cofactors were observed in the B1 domain of ActB subunit (fig. S7B), indicating an electron transfer dead end in these [4Fe-4S] clusters. How they contribute to the electron transfer of ACIII needs to be further considered.

Both heme and iron-sulfur cluster are single electron carriers that are unable to transfer two electrons simultaneously. Thus, a sequential transfer of electrons upon menaquinol oxidation is necessary. In addition, the latency time between the formation of semi-menaquinol and its further oxidation needs long enough to allow extraction of proton from the translocation passage, but it should not be too long to avoid the formation of reactive oxygen species. On the other side, the final periplasmic electron acceptor auracyanin can only accept one electron each time. Therefore, the speed of electron transfer in ACIII should be well controlled. The alternating T-shaped spatial organization of the six hemes in ACIII would limit in one order the electron transfer efficiency of the heme wire, which would increase the steady time of semi-menaquinol. This limitation could be further compensated by the [4Fe-4S] clusters playing as an electron sink. Overall, the possible electron transfer during menaquinol oxidation would look like that, the first electron would quickly sink into the [4Fe-4S] clusters via [3Fe-4S] with the formation of semi-menaquinol, and the second electron could then be transferred to the final periplasmic acceptor auracyanin via the heme wire; with a second auracyanin binding, the sinking electron in the [4Fe-4S] clusters could be further transferred to the final acceptor via the heme wire. As a result, the existence of the [4Fe-4S] clusters would be very important in assisting sequential and efficient transfer of two electrons with an intrinsic time interval.

In summary, our work provides a structural basis and conceptual insight into the coupling mechanism underlying menaquinol oxidation, electron transfer, and proton translocation for the photosynthetic ACIII, which seems likely to play the same role as a menaquinol:electron acceptor oxidoreductase in respiratory ACIIIs. Direct experimental will be required for definitive characterization the proton pumping mechanism of these ACIIIs.

R. castenholzii DSM 13941 was grown in a batch culture anaerobically in modified PE medium at 50C under high-light conditions for 10 days (19). Cells were harvested by centrifugation at 10,000g for 20 min, and the pellet was washed twice with 20 mM tris buffer (pH 7.4) and then stored at 40C.

A suspension of whole membranes [with OD880 (optical density at 880 nm) = 20 cm1] in 20 mM tris-HCl (pH 8.0; buffer A) was treated with 1% -octyl glucoside and stirred for 1 hour at room temperature in the dark. The extraction was centrifuged at 200,000g for 2 hours (Ti 70 rotor, 45,000 rpm) at 4C. The pellets were resuspended in 50 mM sodium acetate (pH 5.0; buffer B) and treated with 0.5% -dodecyl maltoside as above with 1% -octyl glucoside. The supernatant from the second ultracentrifugation was collected and filtered through a 0.22-m Millipore filter and subsequently loaded on a prepacked cation exchange chromatography column (SPHP5, GE Healthcare), which had been equilibrated with buffer B containing 0.04% -dodecyl maltoside (which makes up buffer C). The column was extensively washed with 50 mM NaCl in buffer C until the eluent was colorless. Last, the crude ACIII was eluted from the column by a sodium gradient from 0.1 M NaCl to 0.4 M NaCl with 50 ml of buffer C at 2 ml min1. The collected fractions were concentrated and further purified by Superdex-200 gel filtration in buffer D [100 mM NaCl, 0.02% -dodecyl maltoside, and 20 mM tris-HCl (pH 8.0)]. The fractions with an absorption ratio of A413/A280 higher than 1.38 were pooled and used for cryo-EM analysis.

The polypeptide composition of the purified complex was determined by SDS-PAGE and blue-native PAGE. The sample solubility was optimized by dissolving samples in buffer containing 5% 2-mercaptoethanol for 30 min at 65C; these conditions yielded the sharpest protein bands. The identity of SDS-PAGE and blue-native PAGE bands was confirmed by PMF using matrix-assisted laser desorption/ionizationtime-of-flight (MALDI-TOF) mass spectroscopy.

Stained bands from the SDS-PAGE were excised and destained and washed with 50% acetonitrile in 50 mM aqueous NH4HCO3. Proteins were then reduced with 10 mM dithiothreitol in 100 mM NH4HCO3 for 30 min. Cysteine residues in the proteins were further alkylated by 55 mM iodoacetamide in 100 mM NH4HCO3 for an additional 30 min. Trypsin (Promega Trypsin Gold, TPCK (L-1-tosylamido-2-phenylethyl chloromethyl ketone)treated) in 50 mM NH4HCO3 was added to the gel pieces, and the enzymatic reaction proceeded overnight at 37C. Afterward, peptides were extracted twice with 1% trifluoroacetic acid in 60% acetonitrile for 30 min. Extracted solutions were collected, dried completely in a speed-vac, and then redissolved in 50% acetonitrile containing 0.1% trifluoroacetic acid for mass spectrometry analysis.

The identities of proteins were determined by PMF using an ABI 4700 MALDI-TOF mass spectrometer. A mixture of the peptide sample and freshly prepared matrix solution (10 mg ml1 -cyano-4-hydroxycinnamic acid in 50% acetonitrile) was spotted on a stainless-steel target plate. Peptide mass value searches were performed against the National Center for Biotechnology Information (NCBI) database using Mascot software (www.matrixscience.com). The alkylation of cysteine was included as a possible modification. The mass tolerance for the monoisotopic peptide mass was set to 0.6 Da.

Three-microliter aliquots of air-oxidized ACIII (4 mg ml1) was placed on the glow-discharged GiG R1.2/1.3 300-mesh gold holey carbon grid (Jiangsu Lantuo Biotechnology, China) and blotted for 3.0 s under a blot force of 1 at 100% humidity and 16C before being flash-frozen in liquid ethane with a Mark IV Vitrobot system (FEI). Micrographs were acquired on a Titan Krios microscope (FEI) operated at 300 kV with a K2 Summit direct electron detector (Gatan). SerialEM (34) was used for automatic data collection. A nominal magnification of 22,500 was used for imaging, which yielded a pixel size of 1.04 . The defocus range was between 1.2 and 3.3 m. Each micrograph was dose-fractionated to 32 frames under a dose rate of 9.2 e/2 per second and an exposure time of 6.4 s, which resulted in a total dose of about 59 e/2.

For the sodium dithionitereduced ACIII, 3-l aliquots of a sample (4.5 mg ml1) were placed on the glow-discharged CryoMatrix R1.2/1.3 300-mesh amorphous alloy film (product no. M024-Au300-R12/13, Zhenjiang Lehua Technology Co. Ltd., China) and blotted for 3 s under a blot force of 0 at 100% humidity and 16C before being flash-frozen in liquid ethane with a Mark IV Vitrobot system (FEI). Micrographs were acquired on a Titan Krios microscope (FEI) operated at 300 kV with a K2 Summit direct electron detector (Gatan). SerialEM was used for automatic data collection. A nominal magnification of 22,500 was used for imaging, which yielded a pixel size of 1.04 . The defocus range was between 1.5 and 2.5 m. Each micrograph was dose-fractionated to 32 frames under a dose rate of 9.4 e/2 per second and an exposure time of 6.4 s, which resulted in a total dose of about 60 e/2.

Motion correction and exposure weighting was performed by the MotionCorr2 program (35), and the CTF (contrast transfer function) parameter was estimated using the Gctf program (36). The automatic particle picking was performed by Gautomatch (developed by K. Zhang, MRC Laboratory of Molecular Biology, Cambridge, UK) and Auto-picking module in RELION; an initial model was made by e2initialmodel.py in EMAN2 software package (37), and all other steps were performed using RELION (38). For the air-oxidized ACIII dataset, 600 particles were manually picked and extracted for two-dimensional (2D) classification. The resulting 2D class averages were used as the templates for the automated particle picking, which yielded 257,815 particles from 1700 micrographs. The picked particles were extracted at 2 2 binning and subjected to three rounds of 2D classification. A total of 197,496 particles were finally selected for 3D classification.

Good 2D class averages in different orientations were selected to generate the initial model. A total of 177,489 particles were left after two rounds of 3D classification and re-extracted into the original pixel size of 1.04 . The following 3D refinement and postprocessing yielded an EM map with a resolution of 3.45 . After performing CTF refinement in RELION3, the resolution was increased to 3.24 . Reported resolutions were estimated with a soft-edge mask around the protein complex and micelle densities and based on the gold-standard FSC (Fourier Shell Correlation) = 0.143 criterion. Local resolution was estimated with Resmap (39).

For the reduced ACIII dataset, 1970 unscreened micrographs were subjected to 3D referencebased auto-picking in RELION3; reconstruction of the ACIII dataset was the 3D reference low passfiltered to 20 . The resulting 488,581 particles were used to extract particles at 2 2 binning. After two rounds of 2D classification, 297,122 particles were selected for a 3D refinement and alignment-free 3D classification, and 219,913 particles from the best 3D class were re-extracted without downscaling. The following 3D refinement and postprocessing yielded an EM map with a resolution of 3.68 . CTF refinement and another alignment-free 3D classification improved the resolution to 3.51 and 3.46 , respectively. The final subset had 207,633 particles.

De novo atomic model building was conducted in Coot (40). Sequence assignments were guided by residues with bulky side chains. The starting models of the cofactors were taken from the CCP4 ligand library. The model was real spacerefined by PHENIX (41, 42) with intra-cofactor and protein-cofactor geometric constraints. The refinement and model statistics are listed in Table 1. All figures were prepared in PyMOL (www.pymol.org) or UCSF Chimera (43).

The difference map between air-oxidized and dithionite-reduced ACIII was calculated using EMAN2 (37). First, the cryo-EM map of dithionite-reduced ACIII was fitted to that of air-oxidized ACIII by Chimera and then was clipped into the same box size using e2proc3d.py in EMAN2. Then, the structural amplitudes of both maps were scaled using e2proc3d.py in EMAN2. Last, the difference map between the corrected maps was computed by the e2.py python tool in EMAN2 and further low-passfiltered at a quarter of the Nyquist criterion.

The rest is here:
Cryo-EM structures of the air-oxidized and dithionite-reduced photosynthetic alternative complex III from Roseiflexus castenholzii - Science Advances

Development of a pH-responsive polymersome inducing endoplasmic reticulum stress and autophagy blockade – Science Advances

INTRODUCTION

The important role of autophagy in health and disease has received unprecedented attention (1). As an essential and conservative physiological catabolic process, autophagy is responsible for the removal of protein aggregates, damaged organelles, and foreign bodies that invade cells (2). The autophagy contents are sequestered by double-membraned compartments (autophagosomes). Subsequently, the autophagosomes are fused with lysosomes to form autolysosomes, which degrade and circulate to produce nutrients (amino acids, fatty acids, and nucleotides) to be supplied to cells, and this dynamic process is called autophagic flux (3, 4). The unhindered autophagic flux is of great notable for maintaining homeostasis and protecting cells from attacks (5). The autophagic level is characterized by the amount of autophagy markers (e.g., autophagosomes and autolysosomes) and autophagy protein markers [e.g., LC3 (microtubule-associated protein-1 light chain-3)]. The upstream initiation or downstream blocking of autophagic flux will lead to the increase in autophagy markers (6). Malignant tumors are at a relatively high autophagic level compared with normal tissues to satisfy their metabolic demands, evasion, and resistance and allow tumor growth, survival, and malignancy (7). The involvement of autophagy in the occurrence and development of tumors suggests the reliable prospect of autophagy manipulation as an interventional means for tumor therapy (8). Autophagic flux blockade can disrupt the metabolism cycle of cancer cells, thereby reducing their fitness (9). Hydroxychloroquine (HCQ) and chloroquine (CQ) are the only clinically available autophagic blocking agents and they have been proven to be effective adjuvants for chemotherapeutics to increase their antitumor effects (10). HCQ/CQ, as a lysosomal alkalizing agent, can diffuse into lysosomes, causing the lysosomal pH to rise and dysfunction so that the lysosomes no longer fuse with the autophagosome, thereby blocking autophagic flux (11). However, the use of HCQ/CQ as a monotherapy strategy to block autophagic flux displays limited antitumor activity in clinical treatment (12). However, when HCQ is combined with autophagic stimulus, it can significantly increase its antitumor effect and reduce its dosage (13).

Aberrant endoplasmic reticulum (ER) status triggers autophagy stimulation (14). The ER acts as a reservoir of calcium ions in cells and is responsible for the correct folding and secretion of proteins (15). The accumulation and aggregation of misfolded proteins cause ER stress, triggering unfolded protein response (UPR) to significantly increase the autophagic level to restore homeostasis (16). As an ER stress initiator, tunicamycin (Tuni) blocks N-glycosylation and causes ER stressinduced autophagy to increase the autophagic level through PERK [protein kinase RNAlike ER kinase]/Akt (protein kinase B)/mTOR (mammalian target of rapamycin) signaling pathways, which are also closely related to matrix metalloproteinase-2 (MMP-2) expression (17).

Therefore, the combined application of the autophagic flux blocker HCQ and the ER stress initiator Tuni could cause cancer cells to have a special autophagic stress, which can severely disrupt cell homeostasis and cause cell death, resulting in a better therapeutic effect for tumor treatment. However, for a systemic administration of HCQ and Tuni, challenges such as poor hydrophilicity, poor biodistribution profile, low tumor accumulation, and tumor acid microenvironment prevent the drugs from penetrating the cell membranes, further affecting the application of free drugs in vivo (18). Moreover, high-dose HCQ in clinical application can only produce a moderate blockage of autophagic flux due to its poor efficacy, thus producing capricious therapeutic effects (19). Thus, the drug nanocarrier is considered to solve the above problems (20), as it has the following features: co-encapsulating hydrophilic and hydrophobic drugs, accumulating in tumor tissues through an enhanced permeability and retention (EPR) effect (21), entering the cells through the lysosomal pathway, and stimulating drug release with environment-responsive signals (22).

In addition, metastatic tumors undergo local migration and invasion in the early stage of tumor metastasis, and the migration speed depends on the focal adhesions (FAs) turnover (23). FAs are transmembrane multiprotein complexes containing integrins, paxillin, talin, zyxin, etc. Both cell-cell and cellextracellular matrix (ECM) adhesions form a stable connection via FAs (24). The decomposition of FAs at the cell rear by autophagy is critical for the forward movement and successful migration/invasion of tumor cells (25). In addition, MMPs are also an important factor in the selective regulation of tumor microenvironment to promote tumor metastasis, and are considered to be an inducer of epithelial-mesenchymal transition (26). The ER stress induced by Tuni regulates the PERK/Akt signaling pathway and down-regulates the expression of MMP-2 (27). Both the inhibition of the FAs turnover and the down-regulation of the expression of MMP-2 will reduce tumor metastasis.

Accordingly, in this study, we develop a pH-responsive polymersome for codelivering HCQ and Tuni drugs to simultaneously induce ER stress and block autophagic flux for achieving the antitumor effect and inhibiting tumor metastasis. A dual drugloaded, pH-responsive polymersome, Tuni/HCQ@CS-PAE, was designed to achieve this objective. The amphiphilic polymer chondroitin sulfate (CS)poly(-amino ester) was used to fabricate this polymersome, and hydrophilic HCQ and hydrophobic Tuni were loaded into the inner cavity and outer shell, respectively. Poly(-amino esters) with acid-stimulated responses are a class of highly biocompatible polymers and are believed to satisfy the performance of drug delivery (28). Repeated tertiary amine groups on the poly(-amino esters) are protonated by acid stimulation, thereby converting the hydrophobicity of the segment, resulting in the dissociation of the nanostructure and drug release (29). Simultaneously, the protonation process produces a similar HCQ effect to deacidify the lysosomes, swelling and rupturing the lysosomes, which can help the drugs to escape from the lysosomes and block the autophagic flux together with HCQ (30). Polymersomes with both a hydrophilic inner cavity and a hydrophobic shell are considered promising drug delivery platforms (31). In this work, the hydrophilic CS component can mask the surface positive charges of poly(-amino ester), prolonging the blood circulation time of the polymersomes. These polymersomes reached tumor tissues through the EPR effect, overcoming the nonselective distribution of the Tuni and HCQ drugs in vivo, increasing intratumoral accumulation, entering cells by endocytosis, and remaining in the lysosomes. Because of the pH response of poly(-amino ester), the polymersomes dissociated and produced a similar alkalization effect in lysosomes with HCQ, destroying and rapidly escaping the lysosomes, releasing the drugs Tuni and HCQ. Under the dual action of poly(-amino ester) and HCQ, the lysosomes in the tumor cells were destroyed, resulting in the blockade of autophagic flux. Moreover, the released Tuni triggered ER stress, further regulating the PERK/Akt signaling pathway to enhance the autophagic level and down-regulate the MMP-2 expression. The tumor cells were simultaneously attacked by both the inducement of autophagy due to the ER stress and the blockade of autophagic flux due to lysosomal destruction, resulting in a special autophagic stress, which seriously damaged the cell homeostasis and caused cell death.

The synthetic routes of CS-poly(-amino ester) are shown in fig. S1. The chemical structures of the block copolymers were confirmed using Fourier transform infrared spectra and nuclear magnetic resonance (NMR) spectra (figs. S2 to S4). The number-average molecular weight of CS-poly(-amino ester) was obtained as 8044 g/mol through gel permeation chromatography. The dual drugloaded Tuni/HCQ@CS-PAE polymersome was prepared by dialysis. The encapsulation efficiency (EE) and encapsulation content (EC) of Tuni were 38.5 and 10.5%, while those of HCQ were 56.1 and 11.2%, respectively. The morphologies of the Tuni/HCQ@CS-PAE polymersomes were characterized using transmission electron microscopy (TEM). Apparent vesicle structures with a size of ~180 nm can be observed in Fig. 1A, and the shell thickness of the vesicle in the enlarged image is ~30 nm. The average hydrodynamic size of the Tuni/HCQ@CS-PAE polymersomes was 230.0 9.3 nm, as measured using dynamic light scattering (DLS), with a polydispersity index of 0.156. The potential was 17.2 mV (Fig. 1B), and the negative charge indicated that it is suitable for drug carriers because it cannot be prematurely cleared in the blood circulation (32). The investigation of stability suggested that the polymersomes showed no significant changes (P > 0.05) in particle size when they were placed in phosphate-buffered saline (PBS) buffer and 10% fetal bovine serum (FBS) for 48 hours at 37C (fig. S5), indicating their potential for application in vivo. The pH response of the Tuni/HCQ@CS-PAE polymersomes was evaluated in a lysosomal acidic environment, and the CS-poly(-amino ester) was assayed to determine its pKa (where Ka is the acid dissociation constant) via acid-base titration. The results showed that CS-poly(-amino ester) had a pKa value of 5.4 (Fig. 1C), which was close to the lysosomal acidity (pH = ~5.0) (33). The TEM image obtained after the Tuni/HCQ@CS-PAE polymersomes were stored at pH 5.0 for 4 hours showed that the polymersome structure disappeared (Fig. 1D), indicating that the pH response of CS-poly(-amino ester) successfully caused the dissociation of the polymersomes. The 1H-NMR spectrum of CS-poly(-amino ester) in deuterium chloride at pH 5.0 (fig. S6) showed that the peak of poly(-amino ester) could be observed, indicating that it was hydrophilic at pH 5.0. DLS was further used to detect the pH response of the Tuni/HCQ@CS-PAE polymersomes. As shown in Fig. 1E, after the polymersomes were stored under the three acidic conditions of pH 7.4, pH 6.8, and pH 5.0 for 4 hours, the particle size distribution demonstrated that the polymersomes at both pH 7.4 and pH 6.8 (tumor ECM acidity) were stable; whereas at pH 5.0, the polymersome structure was destroyed, which is consistent with the TEM results. At pH 5.0, the potential of the Tuni/HCQ@CS-PAE polymersomes significantly shifted from 17.2 to 2.08 mV (Fig. 1F), indicating that the protonation of CS-poly(-amino ester) resulted in the capture of strong positive charges. The pH response of the polymersomes imparts them the ability to release drugs on-demand. As shown in Fig. 1 (G and H), the release of HCQ and Tuni at pH 6.8 was not significantly different (P > 0.05) from that at pH 7.4, suggesting that the polymersomes were stable in the tumor ECM and would not be released in advance. However, the 24-hour releases of HCQ and Tuni at pH 5.0 (lysosomal acidity) were 86.5 and 76.6%, respectively, which were 7.52 and 6.66 times the releases at pH 7.4, respectively. This result indicates that the Tuni/HCQ@CS-PAE polymersomes can rapidly release drugs in acidic lysosomes.

(A) TEM images of the Tuni/HCQ@CS-PAE polymersomes at pH 7.4. (B) Measurement results of the Tuni/HCQ@CS-PAE polymersomes by the Malvern laser particle size analyzer at pH 7.4. (C) Acid-base titration curve of CS-poly(-amino ester). (D) TEM images of Tuni/HCQ@CS-PAE at pH 5.0. (E) Hydrodynamic particle size distribution of the Tuni/HCQ@CS-PAE polymersomes at pH 7.4, pH 6.8, and pH 5.0. (F) potential of the Tuni/HCQ@CS-PAE polymersomes at pH 7.4, pH 6.8, and pH 5.0. (G) Release profiles of HCQ from the Tuni/HCQ@CS-PAE polymersomes. (H) Release profiles of Tuni from the Tuni/HCQ@CS-PAE polymersomes.

Before applying the polymersomes to cells and animals, both mouse breast cancer cells (4T1) and human umbilical vein endothelial cells (HUVECs) were used to evaluate the cytocompatibility of the polymersome delivery system. The blank material CS-PAE polymersomes exhibited good cytocompatibility at a concentration of 20 to 400 g/ml (cell viability over 85%, Alamar Blue assay; fig. S7, A and B). Only a small amount of red spots (representing dead cells) was observed in the fluorescence image of cells, with a polymersome concentration of up to 400 g/ml (live-dead cell staining; fig. S7C), also confirming the low cytotoxicity of the polymersomes.

The endocytic pathway of polymersomes was further examined in vitro. Fluorescein isothiocyanate (FITC)labeled (green) polymersomes were cocultured with adherent 4T1 cells, and the locations of the polymersomes in the cells and lysosomes labeled by LysoTracker Red DND-99 (red) were observed using fluorescence microscopy at 1 hour (fig. S8A) and 4 hours (fig. S8C), respectively. A large amount of yellow fluorescence in the cells was observed at 1 hour, which was the result of the overlap between green fluorescence and red fluorescence, suggesting that the polymersomes were in the lysosomes. At 4 hours, the yellow fluorescent signal decreased and the separated green and red fluorescent signals increased, indicating that the polymersomes were separated from the lysosomes. The figures (fig. S8, B and D) show the corresponding fluorescence intensity profiles of the white arrow regions in fig. S8 (A and C) obtained using ImagePro Plus, respectively. It can be observed that there was a large overlap between the two fluorescent signals at 1 hour, and their Pearsons correlation coefficient was calculated to be 0.88, indicating that the polymersomes and the lysosomes were strongly colocalized at 1 hour. At 4 hours, the Pearsons correlation coefficient was reduced to 0.04 according to fig. S8D, indicating that the polymersomes successfully escaped from the lysosomes. This result indicates that the polymersomes were endocytosed into the cells by the lysosomal pathway and could successfully escape the lysosomes at 4 hours in vitro.

The damage to the lysosomes by poly(-amino ester) and HCQ was marked by an increase in the lysosomal pH value. The LysoSensor Green-189 can monitor the acidity of the lysosomes, and its fluorescence reaches the highest value in normal lysosomes and decreases with increasing pH value. As shown in fig. S8E, it was observed via fluorescence microscopy that the green fluorescence in the HCQ, blank material CS-PAE polymersomes, and Tuni/HCQ@CS-PAE treatment groups was weakened to varying degrees. The results of the fluorescence-activated cell sorter (FACS) can be more intuitively observed (fig. S8F), and Tuni did not cause a change in the acidity of the lysosomes compared with that of untreated cells (control). Both the HCQ drug and CS-PAE polymersome had an alkalization ability for lysosomes, but HCQ performed better. This can be ascribed to the fact that CS-PAE polymersomes can only destroy lysosomes involved in endocytosis. The Tuni/HCQ@CS-PAE treatment group performed the best, and the median fluorescence intensity was only 14.3% of the control group, suggesting that the double action of HCQ and the polymersomes caused an increase in the intracellular lysosomal pH.

The relationship between various treatments and autophagy was further examined in vitro. Acridine orange (AO) is an acid-sensitive dye that stains the acidic organelles, including autophagosomes and autolysosomes in the cells red, whereas the DNA and cytoplasm in cells are green. Accordingly, the ratio of red to green signals can be used to evaluate the autophagic level (34). As shown in Fig. 2A, the number of red spots (observed via fluorescence microscopy) is positively correlated with the autophagic level. The red/green ratio calculated using FACS determines the autophagic level in each treatment group (Fig. 2B). The red/green ratios of the treatment groups increased compared with those of the untreated cells (control). The red/green ratio of the Tuni/HCQ@CS-PAE treatment group was approximately 68.0% higher than that of the Tuni/HCQ treatment group and was 1.91 and 2.21 times those of Tuni@CS-PAE and HCQ@CS-PAE, respectively. The red/green ratios of Tuni@CS-PAE and HCQ@CS-PAE also increased by 83.3 and 58.3%, respectively, compared with that of the blank material CS-PAE polymersomes. The red/green ratio of the CS-PAE polymersomes treatment group was also significantly increased by 71.4% compared with that of the control group. The results suggest that both Tuni and HCQ can cause an accumulation of acidic organelles, in addition to CS-PAE polymersomes. Unfortunately, the AO cannot distinguish whether the acidic organelles are autophagosomes or autolysosomes.

(A) Fluorescence images and (B) FACS analysis of AO-stained 4T1 cells after incubation with different treatments for 24 hours; ***P < 0.001. (C) Fluorescence images of mCherry-GFP-LC3 4T1 cells after incubation with different treatments for 48 hours. (D) Quantification of the number of LC3 puncta per cell (autophagosomes, yellow puncta; autolysosomes, red puncta). (E) TEM images of cells treated with saline or Tuni/HCQ@CS-PAE polymersomes (N, nucleus; green arrow, autophagosomes; red arrow, autolysosomes).

To track the autophagic flux, mCherrygreen fluorescent protein (GFP)LC3 adenovirustransfected cells were used. When autophagy occurs, a recognized autophagy marker, LC3, aggregates in both the inner and outer membranes of the autophagosomes. The LC3 in the transfected cells simultaneously expresses red fluorescence (mCherry) and green fluorescence (GFP). Thus, it will be observed in the form of yellow puncta in the autophagosomes. When the autophagosomes and lysosomes eventually fuse to form the autolysosomes, GFP is quenched by lysosomal acidity and only exhibits red puncta. Thus, the yellow and red puncta represent the autophagosomes and autolysosomes in the autophagic flux, respectively (Fig. 2C). The LC3 puncta statistic is shown in Fig. 2D. Comparing the LC3 puncta distribution of the Tuni@CS-PAE treatment group with that of the HCQ@CS-PAE treatment group, the former has more red puncta, indicating that the autophagic flux had entered the final stage, and the autolysosome had been formed. The large yellow puncta of the latter indicate that the autophagic flux mainly remained in the autophagosome stage, suggesting that HCQ@CS-PAE destroyed the lysosomes and prevented the autophagosomes from merging with the lysosomes. In contrast to CS-PAE polymersomes, Tuni@CS-PAE increased the autophagosome puncta and autolysosome puncta, indicating that it effectively increased the autophagic level in the cells. Compared with CS-PAE polymersomes, HCQ@CS-PAE showed a significant increase in the autophagosomes, but there was a decrease in the autolysosomes, which proved that HCQ@CS-PAE has a stronger ability to destroy the lysosomes and block the autophagic flux at the autophagosome stage. The autophagic level of the Tuni/HCQ@CS-PAE treatment group was greatly improved compared with that of Tuni/HCQ, whereas the number of autolysosomes was reduced. This result indicated that the dual drugloaded, pH-responsive polymersomes could increase the autophagic level and block the autophagic flux more evidently than free drugs.

From the TEM images (Fig. 2E), it can be observed that abundant autophagosomes (green arrows) and a few autolysosomes (red arrows) accumulated in the Tuni/HCQ@CS-PAE treatment group, in contrast to the control group (saline treatment). The increase in the autophagosomes and autolysosomes showed that the autophagic level of the Tuni/HCQ@CS-PAE treatment group was significantly enhanced. Furthermore, the amount of autophagosomes was significantly more than the amount of autolysosomes, indicating that the autophagic flux was blocked during the fusion process of the autophagosomes and the lysosomes.

The ability of the polymersomes to resist tumor metastasis was examined. A wound-healing assay (Fig. 3A) and the transwell invasion assay (Fig. 3B) were used to assess the cell migration and invasion in each group of treatments in vitro. The migration area (calculated by ImageJ) in the wound-healing assay is shown in Fig. 3C. The migration area of the Tuni/HCQ@CS-PAE treatment group is only 21.1% (P < 0.001) and 38.4% (P < 0.001) of those of Tuni@CS-PAE and HCQ@CS-PAE, respectively. Matrigel matrix (simulated ECM) was coated in the transwell upper chamber as an in vitro test tool for cell invasion. As shown in Fig. 3D, the number of cells (crystal violet staining) that arrived at the back of the polycarbonate membrane was counted as a quantitative index of invasive ability. The number of invasive cells in the Tuni/HCQ@CS-PAE treatment group was only 6.7% of that in the untreated group, 8.7% of that in the Tuni@CS-PAE treatment group, and 19.3% of that in the HCQ@CS-PAE treatment group. The above results show that the drug delivery system can effectively inhibit cell migration and invasion in vitro. Furthermore, Tuni@CS-PAE has a certain effect in inhibiting cell migration and invasion, but this effect is weaker than that of HCQ@CS-PAE.

(A) Typical images of wound-healing assay. (B) Cell invasion with the transwell assay (bottom). (C) Migration area of the wound-healing assay. (D) Number of invaded cells by the transwell assay. All data are represented as the means SD from three independent experiments; ***P < 0.001.

The in vitro cell viability of different treatment groups was firstly investigated. As shown in fig. S9A, the decrease in cell viability was positively correlated with increased autophagic level and autophagic flux blockade. On the basis of the concentration of fig. S9B, the median effect plots (fig. S9, C and D) of Tuni/HCQ and Tuni/HCQ@CS-PAE can be calculated to obtain their half maximal inhibitory concentration (IC50) values. According to the calculation method in the Supplementary Materials, the IC50 value of the Tuni/HCQ@CS-PAE treatment group is 8.2 M, which is 27.7% lower than that of the Tuni/HCQ treatment group.

The antitumor effect of the pH-responsive polymersome codelivering HCQ and Tuni drugs was further evaluated using the orthotopic luciferase genetransfected 4T1 (4T1-Luc) tumorbearing BALB/c mice. The treatment schedule is shown in Fig. 4A. After 7 days of orthotopic 4T1-Luc tumor implantation, the mice were randomly divided into six groups, and the drugs or drug-loaded polymersomes were administered intravenously at 0, 3, 6, and 9 days. The IVIS imaging system was used to monitor the bioluminescence signals of the tumors at days 0 and 30 (Fig. 4B). Ex vivo tumors were photographed on day 30 (Fig. 4C), and tumor volume was measured once in 3 days (Fig. 4D) and ex vivo tumors weighed on day 30 (Fig. 4E). Tumor growth inhibition (TGI; Fig. 4F) was calculated by tumor weight. The results indicated that three of the 4T1 tumors in the Tuni/HCQ@CS-PAE treatment group had successfully ablated, and the tumor weight was only 9.6% (P < 0.001) and 4.6% (P < 0.001) of those treated with Tuni@CS-PAE and HCQ@CS-PAE, respectively, whereas the TGI was as high as 97.5%. This proves that Tuni/HCQ@CS-PAE has an excellent antitumor effect. The body weight of the mice was monitored every 3 days (Fig. 4G), and it showed no difference in each treatment group on day 30 (P > 0.05), indicating the safety of the polymersome delivery system and the potential for application in vivo. Hematoxylin and eosin (H&E) staining of the main organs (heart, liver, spleen, and kidney) (fig. S10) also revealed no significant morphological changes in all the treatment groups.

(A) Treatment schedule for 4T1 breast tumor in BALB/c mice. (B) Bioluminescence images of 4T1-Luc tumorbearing BALB/c mice were taken on days 0 and 30 after various treatments. (C) Photographs of the tumors removed from the mice in the different treatment groups at the end of the experiment. (D) Tumor volume growth curves of the different treatment groups. (E) Weight of isolated tumors in the different treatment groups. (F) Tumor growth inhibition (TGI) after the different treatments. (G) Body weight changes of mice in the different treatment groups. (H) Hematoxylin and eosin (H&E) staining and immunohistochemical (IHC) analysis of tumor sections after the different treatments. All statistical data are presented as means SD. (n = 5; #P > 0.05; ***P < 0.001). [Photo credit for (B), (C), and (H): Funeng Xu, Southwest Jiaotong University].

H&E staining, terminal deoxynucleotidyl transferasemediated deoxyuridine triphosphate nick end labeling (TUNEL), and immunohistochemical (IHC) analyses (Ki67) were used to characterize the antitumor effects further (Fig. 4H). The H&E staining sections of the Tuni/HCQ@CS-PAE treatment group showed nuclear shrinkage and fragmentation, and the cell contour disappeared. Its TUNEL-positive signal (characterized apoptosis, brown) was the largest, and its Ki67-positive signal (characterized proliferation, brown) was the smallest. These results suggest that the lysosomal pH-responsive polymersomes entrapped with Tuni and HCQ can achieve excellent antitumor effects in tumor-bearing mouse models, demonstrating the success of autophagy regulation in antitumor applications.

The mouse 4T1 tumor is a metastatic tumor, corresponding mainly to lung and bone metastasis (35). The lung of the mouse was excised on day 30, and the lung metastasis of the tumor was observed using the bioluminescence images (Fig. 5A). There was no bioluminescence signal in the Tuni/HCQ@CS-PAE treatment group, indicating that there was no lung metastasis. Moreover, the pulmonary nodules are visualized using a Bouins fixative in Fig. 5B, which also supports this conclusion. The table summarizes the number of metastasis nodes (NOMN) (Fig. 5C), and the lung nodules are categorized by diameter: less than 0.5 mm, 0.5 to 1 mm, 1 to 2 mm, and greater than 2 mm, weighted 1 to 4 in turn. Because of the effective treatment of orthotopic tumors and the effective regulation of autophagy, Tuni/HCQ@CS-PAE has an excellent antimetastatic ability. The results of NOMN are shown in Fig. 5D. The average NOMN of the HCQ@CS-PAE treatment group was 52.89% that of the Tuni@CS-PAE treatment group and 22.49% that of the CS-PAE polymersomes treatment group. This indicates that both HCQ@CS-PAE and Tuni@CS-PAE can inhibit tumor metastasis to a certain extent, but the former performed better than the latter, which is also consistent with the results of in vitro antimetastasis evaluation. The H&E staining of the lungs can also demonstrate the antimetastatic effect (Fig. 5E). The red circle framed the foreign tissues of the lungs, and the foreign tissues were observed to be tumor tissues by comparison with the H&E staining of the tumors. No tumor tissue was observed in the H&E sections of the Tuni/HCQ@CS-PAE treatment group, and the area of the tumor tissue was significantly reduced in the Tuni@CS-PAE and HCQ@CS-PAE treatment groups compared with that in the saline group, which is consistent with the lung metastasis results of Fig. 5 (A and B).

(A) Bioluminescence images of tumor lung metastases in each treatment group in vitro. (B) Photographs of lung tissues; tumor metastasis was visualized by Bouins fixative, and metastatic nodules were white (represented by red arrows). (C and D) Counting the number of lung metastasis nodules, measurement of the diameter of metastatic tumors, and performing classification and counting. Number of metastasis nodes (NOMN) = I 1 + II 2 + III 3 + IV 4 (according to the diameter of the lung nodules for class 4: I < 0.5 mm, 0.5 mm II < 1 mm, 1 mm III 2 mm, and IV > 2 mm). (E) H&E staining of lung tissue after the various treatments. The red circle marks the metastatic tumor tissue. [Photo credit for (A), (B), and (E): Funeng Xu, Southwest Jiaotong University].

The dual drugloaded, pH-responsive polymersomes (Tuni/HCQ@CS-PAE) have made breakthroughs in the antitumor effect and metastasis inhibition effects in tumor-bearing mice. Western blot (WB) and IHC were further used to explore the mechanism of action of Tuni/HCQ@CS-PAE. ER stress and autophagy are closely related (Fig. 6A). It has been reported that the ER stress enhances the autophagic level by negatively regulating the Akt/mTOR pathway (36). In addition, the expression of MMP-2 is down-regulated by the down-regulation of Akt expression. Therefore, it can be concluded that the Tuni/HCQ@CS-PAE polymersome has two important functions in vivo: increasing autophagic levels and decreasing the MMP-2 expression and blocking the autophagic flow at the autophagosome stage by preventing the fusion of the autophagosomes and the lysosomes.

(A) Schematic diagram of Tuni causing ER stress, promoting autophagy, and reducing MMP-2 expression via signaling pathways in vivo. (B) WB analysis of key proteins of ER stress and downstream pathway protein of 4T1 tumor in BALB/c mice. (C) Relative expression level of key proteins in (B); ***P < 0.001 compared with control. (D) Expression of LC3 and p62 lanes of 4T1 tumor in BALB/c mice via WB. (E) Quantification of the ratio of LC3-II to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and p62 to GAPDH expression using ImageJ software. (F) IHC pictures of talin-1, paxillin, and MMP-2 in 4T1 tumorbearing BALB/c mice.

Under normal physiological conditions, GRP78/BiP (78-kDa glucose-regulated protein/immunoglobulin heavy chainbinding protein) acts as an ER chaperone and binds to ER receptors, which is in an inactive state. However, under ER stress, GRP78/BiP dissociates from ER receptors to activate and trigger UPR (37). The dissociation of GRP78/BiP from PERK (ER transmembrane receptor) triggers kinase dimerization and autophosphorylation to generate activated PERK (p-PERK) (38). Therefore, the expression of GRP78/BiP and p-PERK can be used as an indicator of ER stress. The expression of GRP78/BiP and p-PERK of the Tuni/HCQ@CS-PAE treatment group was significantly increased by 59.7% (P < 0.001) and 87.0% (P < 0.001), respectively, compared with that of the control group (Fig. 6, B and C). It indicated that Tuni/HCQ@CS-PAE can strongly trigger ER stress. The expressions of GRP78/BiP and p-PERK of the Tuni/HCQ treatment group were only 71.7% (P < 0.001) and 70.9% (P < 0.001), respectively, of that of the Tuni/HCQ@CS-PAE treatment group, suggesting that the polymersome system is more efficient than the free drugs at the same dose. The occurrence of ER stress triggered a series of downstream signaling pathways. The expressions of p-Akt and p-mTOR proteins in the Tuni/HCQ@CS-PAE treatment group were reduced by 80.0% (P < 0.001) and 67.2% (P < 0.001), respectively, compared to the control group, suggesting that the increase in the upstream event down-regulates Akt and mTOR activity. The expression of MMP-2 was significantly decreased in the Tuni/HCQ@CS-PAE and Tuni@CS-PAE treatment groups, which were only 32.8 and 41.0% of that of the control group, respectively, which was consistent with the trend of p-Akt expression.

When the autophagy occurs, LC3-I, which is in the cytoplasm of cells, is modified and processed to form LC3-II and expressed on the autophagosome membrane. The expression of p62 (sequestosome-1) as an autophagy substrate can characterize the smoothness of the autophagic flux. When the autophagic level is increased and the autophagic flux is smooth, the expression of LC3-II is increased and the expression of p62 is decreased; however, when the autophagy level is increased and the autophagic flux is blocked, the expression of both LC3-II and p62 is increased (39, 40). As shown in Fig. 6 (D and E), the expression of LC3-II and p62 was up-regulated in all the treatment groups compared with that in the control group, suggesting that the autophagic level of each treatment group was increased, and the autophagic flux was blocked to some extent. The highest expression of LC3-II was observed for Tuni/HCQ@CS-PAE and Tuni@CS-PAE, which was consistent with the results of down-regulation of p-mTOR. The expression of LC3-II of HCQ@CS-PAE was also significantly improved, indicating that, when autophagic flux was blocked by lysosomal destruction, the overall autophagic level of the cells also increased, and the autophagic flux mainly remained in the autophagosome stage. The expression of p62 was the highest in the Tuni/HCQ@CS-PAE and HCQ@CS-PAE treatment groups, i.e., 4.67 (P < 0.001) and 4.13 (P < 0.001) times that of the control group, respectively, suggesting that substrate degradation in the autophagosomes was largely blocked.

Talin-1 and paxillin are the constituent proteins of the FAs. The turnover of FAs is the basis of cell movement. The blockade of the autophagic flux leads to the failure of FAs degradation, which reduces the ability of cell movement. As shown in Fig. 6F, the IHC sections of Tuni/HCQ@CS-PAE and HCQ@CS-PAE showed the largest amounts of talin-1 and paxillin, indicating that the blockade of autophagic flux can significantly prevent FAs turnover. In the IHC section analysis of MMP-2, the expression of MMP-2 of the Tuni/HCQ@CS-PAE and Tuni@CS-PAE treatment groups was significantly inhibited, and the results were also consistent with the WB test in Fig. 6B, indicating that the MMP-2 expression was closely related to the ER stress induced by Tuni. It is suggested that based on the results of in vitro and in vivo antimetastasis experiments, it is known that HCQ@CS-PAE has stronger antimetastatic ability than Tuni@CS-PAE, also suggesting that the reduction in FAs turnover by autophagy affects tumor metastasis more than the decrease in the MMP-2 expression. Thus, Tuni/HCQ@CS-PAE achieved a considerable tumor-metastasis inhibition effect under the combined effect of down-regulation of MMP-2 expression and inhibition of FAs turnover.

CS was acetylated to increase its solubility in dimethyl sulfoxide (DMSO). Briefly, CS (1.0 g) was added to a round-bottom flask containing formamide (50.0 ml). The system was heated to 80C to promote dissolution and then cooled to room temperature. Pyridine (557.0 l) and acetic anhydride (500.0 l) were added to the round-bottom flask and magnetically stirred at room temperature for 12 hours. The reaction solution was dialyzed and lyophilized to obtain acetylated CS (Ac-CS; 0.91 g), which was stored for later use.

Ac-CS (0.41 g), 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (0.16 g), and N-hydroxysuccinimide (0.04 g) were dissolved in reverse osmosis (RO) water. Triethylamine (0.08 g) was added to this mixture, and magnetic stirring was performed to activate the carboxyl group in an ice bath. Subsequently, 1,6-hexanediamine (0.63 g) was added, and the mixture was stirred at room temperature for 24 hours. The product Had-Ac-CS (0.49 g) was obtained via the dialysis and lyophilization of the reaction solution.

CS-poly(-amino ester) was prepared via the Michael addition reaction. Had-Ac-CS (0.37 g), Hexane-1,6-dioldiacrylate (HDDA) (0.5 g), and 3-dibutylamino-1-propylamine (DBPA) (0.37 g) were dissolved in 15 ml of DMSO, and the round-bottom flask was purged with N2. The mixture was stirred at 50C for 5 days. CS-poly(-amino ester) (1.1 g) was obtained via the dialysis and lyophilization of the reaction solution.

Dialysis was used to prepare the dual drugloaded polymersomes. First, 20.0 mg of CS-poly(-amino ester) and 7.0 mg of Tuni were codissolved in a beaker containing 5.0 ml of DMSO. Then, 5.0 ml of RO water containing 5.1 mg of HCQ was added dropwise under high-speed stirring, and the system was continuously stirred for 20 min. The system was transferred to a dialysis bag (molecular weight cutoff, 3500) for 48 hours and then lyophilized for the next experiment. EE and EC were calculated by Eqs. 1 and 2, respectivelyEE(%)=Weight of the drug in polymersomesWeight of the drug in feed100(1)EC(%)=Weight of the drug in polymersomesWeight of drug-loaded polymersomes100(2)

CS-poly(-amino ester) was placed in deionized water, and HCl solution was added until it was completely dissolved. Then, 1 to 5 l of 0.1 M NaOH solution was added dropwise, and the pH was measured after each addition. The pKa of the polymer is the pH at which it is half ionized.

The pH response of polymersomes was characterized by DLS, TEM, and 1H-NMR, respectively. The polymersomes were placed at pH 5.0, pH 6.8, and pH 7.4, respectively. After 4 hours, DLS was used to measure the particle size distribution and potential. Samples at pH 5.0 were also used for TEM and 1H-NMR detection.

The release of Tuni and HCQ in Tuni/HCQ@CS-PAE was investigated under three acidity conditions of pH 7.4, pH 6.8, and pH 5.0 at 37C. The release solution was taken 1 ml each time at the planned time point, and the same volume of fresh medium was added. The release solution was treated and analyzed by high-performance liquid chromatography.

Size changes of Tuni/HCQ@CS-PAE polymersomes after incubation in PBS or in cell culture medium [containing 10% FBS (v/v)] were monitored by DLS. The polymersome concentration was 1 mg ml1, and the experimental conditions were 37C.

Alamar Blue assay and live-dead staining were used to determine the cytocompatibility of blank polymersomes. In Alamar Blue assay detection, 1 104 cells per well of 4T1 and HUVECs were seeded in 48-well plates. After 24 hours of culture, polymersomes with 20 to 400 g/ml were added to each well. After 48 hours, the culture medium was removed, and 300 l of Alamar Blue solution [10% Alamar Blue, 80% media 199 (Gibco), and 10% FBS, (v/v)] was added for a further 3-hour incubation. They were then transferred to 96-well plates and detected by automated microplate spectrophotometer. For live-dead staining, 2 104 cells per well of 4T1 and HUVECs were seeded in 24-well plates. The cells were stained by 2 mM calcein acetoxymethylester for 10 min and propidium iodide for 5 min after 48 hours incubation, with different concentrations of polymersomes. Live cells were stained green, and dead cells were stained red when visualized by fluorescence microscopy.

4T1 cells were cultured in confocal dishes for 12 hours in Dulbeccos modified Eagles medium with 10% FBS. FITC-labeled polymersomes were added to two sets of confocal dishes, and then the medium was discarded at 1 and 4 hours, respectively. Cells were washed three times with PBS before staining, and then lysosomes were labeled with the LysoTracker Red DND-99. The fluorescence signal was observed by fluorescence microscopy.

Adherent 4T1 cells were treated with saline, Tuni, HCQ, CS-PAE, and Tuni/HCQ@CS-PAE for 12 hours, and stained with the acid-sensitive dye LysoSensor Green-189. The fluorescence intensity of each group was measured by fluorescence microscope and FACS.

The adherent 4T1 cells were treated with saline, CS-PAE, Tuni/HCQ, Tuni@CS-PAE, HCQ@CS-PAE, and Tuni/HCQ@CS-PAE, respectively. After 24 hours, the cells were stained with AO (1 l) for 15 min and detected by fluorescence microscopy and FACS, respectively.

4T1 cells were inoculated with 5 105 per well in confocal dishes before infection. The density of cells before virus transfection reached 50%, and the amount of virus mother liquor added to the plate was plaque-forming units = cell number multiplicity of infection (MOI). MOI was 20, 24 hours after infection; 2 ml of fresh medium was added to each well to replace the virus-containing medium.

4T1 cells were seeded in culture flasks at a density of 1 106 cells/ml for 18 hours. Then, saline and Tuni/HCQ@CS-PAE were added for 48 hours, respectively. Cells were digested, collected by centrifugation, and then fixed overnight in 2.5% glutaraldehyde. Samples were prepared according to TEM standard procedures and photographed.

Alamar Blue assay was used to assess the in vitro cytotoxicity. 4T1 cells were seeded in 48-well plates at a density of 2 104 cells per well. After the cells were cultured for 24 hours, various preparations were added to the well plates for 48 hours. After the incubation, 300 l of Alamar Blue solution was added for further 3 hours, and then the Alamar Blue solution was transferred to a 96-well plate, and the absorbance was measured with an automated microplate spectrophotometer. The median effect plot was a straight line fit with X = log(D) versus Y = log[fa/(1 fa)] (41). The theoretical IC50 value is the drug concentration corresponding to the x axis intercept of the median effect plot.

4T1 cells were seeded in six-well plates. When the cell confluence reached 100%, scratches were made with a 200-l pipette tip, and cells were washed three times with PBS to remove the delineated cells. The treatments were added to each group. Various therapeutic agents were added to the treated six-well plates and cultured for 36 hours in serum-free medium. The entire process was monitored with a microscope, and the healing area was calculated by ImageJ.

One hundred microliters of the diluted Matrigel was added vertically in the center of the transwell upper chamber and incubated at 37C for 4 hours to form a gel. Six hundred microliters of 10% serum medium was added to the lower chamber, and 100 l of the cell suspension was added to the upper chamber, and incubation was continued for 24 hours. The transwell chamber was removed, fixed in methanol for 30 min, stained with 0.1% crystal violet for 20 min, and the uninjured cells in the upper layer were gently wiped off with a cotton swab, and the count was observed with a microscope.

4T1-Luc cells were injected into the mouse mammary fat pad to establish an orthotopic breast cancer model. The animal experiments were approved by the Institutional Animal Care and Use Committee of Sichuan University and carried out in compliance with its guidelines. When the tumor volume of the mouse reached approximately 35 mm3, it was defined as 0 day of treatment, and the mice were randomly divided into six groups of five mice each. Each group was administered through the tail vein at 0, 3, 6, and 9 days of treatment [Tuni (7.5 mg/kg)]. Tumor volumes were calculated using the following equation: V = 0.5 A B2 (A refers to tumor length, and B refers to the tumor width). TGI was calculated using the following equation: TGI (%) = 100 (mean tumor weight of saline group mean tumor weight of experimental group)/mean tumor weight of saline group.

4T1 tumorbearing BALB/c mice were sacrificed, and the heart, liver, spleen, lung, kidney, and tumor tissues were excised, fixed with 10% formalin, dehydrated with gradient ethanol, and embedded in paraffin block. After denitrification with xylene, 4-m-thick tissue sections were stained with H&E, or for TUNEL detection, or for IHC staining with rabbit antiKi-67 polyclonal antibody and lastly observed with an optical microscope.

The potential association of ER stress with autophagy and antimetastatic mechanisms were analyzed by WB and immunohistochemistry. BIP/GRP78, PERK, Akt, mTOR, LC3, and p62 were used for WB analysis to explore the ER stressautophagy signaling pathway based on relative expression levels. MMP-2, talin, and paxillin were used as indicators of antimetastasis to analyze changes in their expression through WB and immunohistochemistry.

SPSS software was used for the statistical data analysis. Data were presented as means SD. One-way analysis of variance (ANOVA) was performed to determine statistical significance of the data. The differences were considered significant for #P > 0.05, *P < 0.05, **P < 0.01, and ***P < 0.001.

Acknowledgments: We thank the Analytical and Testing Center of the Southwest Jiaotong University. Funding: This work was partially supported by the China National Funds for Distinguished Young Scientists (51725303), the National Natural Science Foundation of China (21574105), and the Sichuan Province Youth Science and Technology Innovation Team (2016TD0026). Author contributions: F.X., Y.W., and S.Z. designed research; F.X., X.L., and X.H. performed research; F.X. and J.P. analyzed data; and F.X. and S.Z. wrote the manuscript. Competing interests: The authors declare that they have no competing interests. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors.

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Development of a pH-responsive polymersome inducing endoplasmic reticulum stress and autophagy blockade - Science Advances

The function of folding | Feature – Chemistry World

Molecules that fold are fundamental to life. If you look at biology as a chemist, you cant escape the conclusion that almost every complicated thing that biology does at the molecular level is carried out by a sequence-specific folded heteropolymer, says Sam Gellman from the University of WisconsinMadison in the US. Chemists have been trying to learn a few of these folding tricks from biology, but according to Jonathan Clayden from the University of Bristol in the UK, rather than just replicating these polymers, the aim now is [to] do better than nature with a bit of chemical ingenuity. Using a wider spectrum of starting blocks he and others are creating molecules called foldamers that might one day beat biology at its own folding game.

The idea of synthesising molecules that could fold into secondary structures stems from work on protein folding carried out in the 1980s. A key contribution was simulations from protein [modelling] specialist Ken Dill, says Gellman, an early adopter of the approach, who came up with the name foldamer.

Dill, now at Stony Brook University in New York state, US, had been working on protein folding and concluded that the process was driven by the juxtaposition of hydrophobic and hydrophilic amino acids in proteins. Before that, the view had been that hydrogen bonding was the magic that dictated how proteins get their structure, says Dill. Work carried out by his collaborator Ron Zuckermann, then at pharma company Chiron, showed this was not the case. He used peptoids made from poly-N-substituted glycines, which have side chains appended to the backbone nitrogen atom rather than the carbon. These molecules could adopt stable helices without the presence of hydrogen bonding, which convinced Dill and Zuckermann that folding was primarily due to the nature of amino acid side chains, with the backbone hydrogen bonding acting only as additional glue.

We walk in proteins footsteps, but we lag far behind

These ideas led Gellman to wonder what other molecules might be able to fold like peptides and he remembers questioning Dill after a conference talk, asking If I could make a polystyrene with a hydrophobic styrene sub-unit and a hydrophilic styrene sub-unit, would they fold? The response was Yes, I think so.

For Dill and collaborator Zuckermann, the folding process is where life started and is responsible for the chemistry to biology transition. While the prevailing theory marks RNA as the first self-replicating molecule, Dill thinks that there must have been a stage before the RNA world where molecules started folding, publishing his foldamer hypothesis in 2017.1 Dividing monomers into those with hydrophilic (polar) and those with hydrophobic side chains, he used a simple computer model to create chains where similar subunits were attracted to each other and found that even short chains can collapse into relatively compact structures.

Theres a natural elongation mechanism that is also selective and auto catalytic, Dill explains. This is because the collapsed structures expose what he calls landing pads for catalysing other nascent polymers, ultimately creating primitive enzymes. What it means is youre going to have a whole ensemble of potential protein functions that are coming out of this soup, just naturally, because of the variability of hydrophobicpolar sequences themselves. For biology you ultimately needed information storage via DNA, but first you needed folding, Dill says.

So if biology is about folding, could chemists also harness this power? Gellman started trying in the 1990s, coming up with the name foldamer for these types of synthetic molecules, typically 1020 monomer units. It turns out, you cant do this with polystyrene because nobody knows how to make a polystyrene where you [can] control which monomer goes where, so a lot of this work has ended up focusing on polyamides, explains Gellman. He has focused on -amino acids which have their amino group bonded to the -carbon rather than the as found in biology, but still fold into helices of various shapes, comparable to those found in proteins.

Others, such as supramolecular chemist Ivan Huc, from the University of Munich in Germany, have designed more exotic structures using aromatic oligoamides, and monomers bearing proteinogenic side chains that provide the folding impetus. Hucs apple peel helical capsule can be tuned in diameter according to monomer size, and specific attractive and repulsive interactions between the amide and the other functional groups can be substituted onto the aromatic rings. These foldamers can house a guest molecule in the resulting cavity.2 These shapes are very trivial to obtain with aromatic amides and they are completely out of the reach of peptides or nucleotides, says Huc.

Designing foldamers is still a mostly trial and error process based on an understanding of local conformational preferences. Computational tools are gaining ground but arent as advanced as tools to model proteins and peptides. We walk in their footsteps, but we lag far behind, says Huc.

One of the obvious dreams is to create catalytic versions [of foldamers], says Gellman, who recently took up this difficult challenge. In some cases, enzymes speed reactions up a million times by organising molecules within enclosed pockets. While Gellman cannot make this sort of tertiary structure yet, he did create a foldamer that allows two functional groups to be arranged in proximity to each other tethered to a helix.3 Gellmans foldamer contained a and amino acids, including residues with five-membered rings, which stabilised the foldamers helical structure by constraining the backbones flexibility.

This was used to catalyse the formation of large macrocycles, which are useful as potential drugs but difficult to make as the two ends of long chain molecules need to be close together to react. Using a primary and secondary amine group each attached to a residue, the foldamer is able to correctly position the ends and form a carboncarbon bond via an aldol condensation, creating 1222 carbon rings. Previous work had shown that such foldamer systems allowed similar reactions to proceed at least 100 times faster than using small molecule catalysts. The foldamers performance is still a long way from that of an enzyme though.

Gellman and others are also working on how foldamers could out-smart biology as drug molecules. There is a whole host of peptides which sometimes are used as drugs but they break down [in the body] very fast, says Dimitri Dimitriou, chief executive of Swiss drug company Immupharma. If you can effectively create a peptide analogue, which is stable, then [foldamers] have the potential to be as big as the monoclonal antibody industry thats the excitement from the commercial side. He is confident that within five years foldamer drugs will be on the market.

Gellman co-founded Longevity Biotech in 2010 to develop peptide drugs incorporating -amino acids.4 These peptides only have a quarter to a third of the residue, but because theyre distributed along the backbone, proteolytic enzymes will cut [them] very slowly, he explains.The company call these helical foldamers hybridtides and are trying to design hybridtide drugs that bind to G protein-coupled receptors (GPCRs), transmembrane proteins that transmit signals inside a cell when stimulated by molecules outside. They are currently conducting a pre-clinical biomarker study for a Parkinsons disease drug candidate.

During the coronavirus shutdown Gellman has continued to work on foldamers that may block the Sars-CoV-2 virus that causes Covid-19. The approach is based on work carried out in 2009 inspired by a drug for HIVAids.5 A 36-residue peptide, enfuvirtide, is effective in blocking the virus attaching itself to cells, but the drug has such a short half-life that patients needed to be injected twice a day. We made variants that were 300-fold less susceptible to proteolysis [digestion] because of the a [backbone] and thats what were trying to do with the coronavirus, says Gellman.

Its a very complicated and difficult challenge but this is what we are trying

Immupharma are also developing foldamer drugs alongside subsidiary company Ureka, based on the work of Giles Guichard at the University of Bordeaux in France. But their foldamers swap some amino acids for ureas, which have two amino groups joined by a carbonyl. Oligourea is particularly good to form helices and those helices are similar to peptide helices you have a good mixture of rigidity coming from the urea [backbone] and some flexibility coming from the sidechain groups, which can be substituted a little bit like an amino acid, explains Sebastien Goudreau, head of research at Ureka.

As proof-of-concept Ureka has started with glucagon-like peptide-1 (GLP-1), the 31-amino-acid hormone found in the pancreas that enhances the secretion of insulin and is used for the treatment of type 2 diabetes and the liver disease non-alcoholic-steatohepatitis. Their foldamer replaces four consecutive GLP-1 amino acids with three urea residues.6 We have shown that it works and proved that it can extend the half-life dramatically [in mice], say Dimitriou. This could mean a dose would only be needed once a month and if resistant enough to digestive enzymes it might be able to be taken orally, although Dimitriou says they have not proven this yet.

Also on the radar are complex proteinprotein interactions, traditionally considered undruggable. Its a very complicated and difficult challenge, says Huc. But this is what we are trying. He has been designing foldamer molecules that can match a binding site in terms of their size, shape and proteinogenic side chains as far they can predict, but the final trick is to tether it to the protein. Using disulfide linkers, foldamers bearing different proteinogenic side chains were attached via a cysteines thiol side chain. Hucs achiral foldamer will resonate between a left-handed and right-handed helix, but if it interacts with the protein surface, one version will become more favourable and predominate; this can be detected using circular dichroism spectroscopy.7 The sign of an interaction doesnt mean tight binding, says Huc, but from these interactions, I can design.

Not only has nature created folded molecules, but also molecules that can change their shapes. For example, GPCRs will undergo conformational switching as they respond to hormones and the molecules that stimulate our senses of taste and smell. Clayden has been using foldamers to try and recreate the action of these receptors. Weve been designing molecules that have exactly the same sort of features when they pick up a ligand for example, they change shape and as a result they transmit information through the structure of the molecule thats what we call dynamic foldamers.

Unlike nature, Clayden starts with an achiral amino acid, -aminoisobutyric acid (AIB). You end up with a helix that can either be left- or right-handed and can actually inter-convert very rapidly between those, he says. The switching mechanism is provided by a large cyclic amino-borate group on the amine end of the foldamer. When a bulky chiral diol ligand is added it will form a boronate ester which then forms a methanol-bridge to the amine group. The steric bulk of the ligand forces the foldamer to switch to one helical sense.8 Clayden has shown these artificial receptors work when embedded in phospho-lipid vesicles.9 [In] the long term we would like to get these things into real cells. Weve done some very preliminary work, he says. These dynamic foldamers could lead to smart drugs that could independently switch enzyme pathways on or off within cells depending on a specific stimulus.

Clayden has used the same approach to imitate our colour vision, which in nature relies on the GPCR receptor rhodopsin in the retinal rods. Our molecule is an azobenzene chromophore and thats attached to an AIB foldamer that changes shape when the azobenzene responds to light, he explains. In UV light the molecule switches to its cis conformation which induces a screw sense in the foldamer making what Clayden calls a conformational photo diode.10 He envisions future smart chemical systems made from dynamic foldamers for example, simply using different coloured lights to turn reactions on and off or switch from one enantiomeric product to another. Were currently working on a system that binds a catalyst, but releases it when its prompted to switch. That sort of idea could be used to release, for example, an enzyme inhibitor.

Dills foldamer hypothesis for the early stages of life supposes a move from secondary folded structures to the proteins we have today, with their complex tertiary structures, combining helices and sheets made from defined peptide sequences. The real power of biology in my view, and where I would love to see foldamers go, is hooking domains together, he says. But chemists are some way from this. Most proteins are over 100 residues thats pretty hard for chemical synthesis, says Gellman.

Most labs are using solid-phase synthetic methods and starting to introduce automation but synthesising the relevant monomers isnt trivial. Small molecule synthesis is not nearly as advanced a field as it should be, says Gellman. For peptide chemistry, many of the starting blocks are commercially available but for foldamers that isnt the case. We can buy some of the amino acids we need, but many of them, particularly when they have rings to constrain their local conformation, we cant, and we dont know how to make [them].

Most proteins are over 100 residues thats pretty hard for chemical synthesis

Nevertheless chemists are attempting some simple tertiary structures. Several groups have produced foldamers that mimic the zinc finger domain (a protein motif that is able to coordination one or more zinc ions and binds a wide variety of biological molecules). Foldamers have also re-created the four-helix bundle motif, with hydrophobic residues buried in the core. Huc has even formed helical bundles in non-polar organic solvents showing these structures can form in very different environments to nature.11

To create larger structures, Huc has suggested borrowing natures solution: ribosomes, the cells protein factory. [My] long term dream is to hijack this machinery, and teach or modify the ribosome to produce [non-natural] chemical entities. This hasnt been done yet and might not be so easy. Ribosomes are complexes of RNA and protein that are able to link amino acids together. They start with a messenger RNA (mRNA) template which base pairs with transfer RNA (tRNA) molecules that carry individual amino acids.

We need to think of other things that nature doesnt do at all

Hucs initial work with ribosomes in 2018 used novel RNA enzymes known as flexizymes, designed by Hiroaki Suga at the University of Tokyo in Japan, that are capable of attaching non-natural amino acids to tRNA. Huc was able to attach a dipeptide-appended aromatic helical foldamer. He then used an E. coli ribosome to synthesise a foldamerpeptide hybrid the foldamer needed to unfold to get through the ribosome exit tunnel.12 While the ribosome is not forming bonds within the foldamer itself, its certainly a small step in that direction.

Going back 30 years the question was whether biological polymers and their ability to fold were unique. Chemists have answered that: we can tell many different types of chemical backbones have a propensity to fold, says Huc. The question is now whether we can make increasingly complex large folded molecules and what can we do with them. Nature has taught us some tricks, but chemists have a wider palette to work from. [We need to] think of other things that nature doesnt do at all, suggests Huc. Perhaps the key developments will be in high temperature materials or micro-processors, who knows?

Rachel Brazil is a science writer based in London, UK

1 E Guseva, R N Zuckermann and K A Dill, Proc. Natl Acad. Sci. USA, 2017, 114, E7460 (DOI: 10.1073/pnas.1620179114)

2 J Garric, J-M Lger and I Huc, Angew. Chem. Int. Ed., 2005, 44, 1954 (DOI: 10.1002/anie.200462898)

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4 R Cheloha et al, Nat. Biotechnol., 2014, 32, 653 (DOI: 10.1038/nbt.2920)

5 S W Horne et al, Proc. Natl Acad. Sci. USA, 2009, 106, 14751 (DOI: 10.1073/pnas.0902663106)

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Protein Engineering Market To Reach USD 4.77 Billion By 2027 | Reports And Data – PR Newswire UK

- The increasing research in protein engineering and rising government funding for new drug discovery are expected to be some major drivers for the market

- Market Size USD 1.86 Billion in 2019, Market Growth CAGR of 12.3%, Market Trends The growing research institutions across developing economies is expected to fuel the market in the forecast period

NEW YORK, July 28, 2020 /PRNewswire/ -- According to the current analysis of Reports and Data, theProtein Engineering marketwas valued at USD 1.86 billion in 2019 and is expected to reach USD 4.77 billion by the year 2027, at a CAGR of 12.3%. Protein engineering is the process of conception and production of unnatural polypeptides, which is achieved through the modification of different amino acid sequences that are found in nature. With the wide application of protein engineering, various synthetic protein structures and functions can now be designed completely using a computer and produced in the laboratory using various methods.

With the advent of technology, the rising demand is expected to provide traction to the market. For instance, computational protein design holds a potential promise to revolutionize protein engineering. Protein engineering is significantly in demand as it can develop useful or valuable proteins. It is known to be an emerging research field that helps researchers in understanding protein folding and recognition used for protein design principles. Protein engineering market is spurred by various reasons such as availability of immense information regarding 3D protein structure, advancement in structural bioinformatics, novel protein design algorithms, and other factors that have made it possible to use computational approaches for research and development in protein engineering. Strategic utilization of approaches that have been discovered with research has enabled better stability and increased catalytic activity of the protein. Moreover, it has increased its applicability in various fields that will further expand the market. Protein engineering has also evolved to become a potent tool contributing considerably to the developments in both synthetic biology and metabolic engineering. The rising funding for synthetic biology by governments and other healthcare institutions may drive the industry extensively in the future. Furthermore, substantial ongoing research in the drug discovery process is expected to fuel the market during the forecast period. Growing technological advancements and innovative instruments useful for protein engineering may drive the market extensively in the future. The emergence of new diseases due to microorganisms may also trigger market growth.

Request free sample of this research report at: https://www.reportsanddata.com/sample-enquiry-form/3369

However, factors such as high cost of instrumentation and lack of skill professional may hamper the protein engineering industry in the forecast period.

COVID-19 Impact:

WHO is focused on the latest scientific findings and knowledge on COVID-19. Various researchers and scientists are discovering new ways to tackle COVID-19 infection. Furthermore, the market of protein engineering is also going to get significantly affected due to the multiple kinds of research which are being carried out in this field. With the advent of technology, improving protein stability is an essential goal for clinical and industrial applications, however no commonly accepted and widely used strategy for efficient engineering is known. Furthermore, during the COVID-19 outbreak, protein engineering market is significantly impacted because many of the procedures involve lab automation. Market players are focusing on a research-based approach that will provide traction to the market. For instance, Vir Biotech identified two antibodies that could be effective in preventing and treating COVID-19. However, the high requirement of funds is expected to hamper the market during this period.

To identify the key trends in the industry, click on the link below:https://www.reportsanddata.com/report-detail/protein-engineering-market

Further key findings from the report suggest

Order Now: https://www.reportsanddata.com/checkout-form/3369

For the purpose of this report, Reports and Data has segmented the Protein Engineering market on the basis of product, type, technology, end use and region:

By Product Outlook (Revenue in Million USD; 2017-2027)

By Type Outlook (Revenue in Million USD; 2017-2027)

By Technology Outlook (Revenue in Million USD; 20172027)

By End Use Outlook (Revenue in Million USD;20172027)

Regional Outlook (Revenue, USD Billion; 2017-2027)

Browse more similar reports on Biotechnology category by Reports And Data

About Reports and Data

Reports and Data is a market research and consulting company that provides syndicated research reports, customized research reports, and consulting services. Our solutions purely focus on your purpose to locate, target and analyze consumer behavior shifts across demographics, across industries and help client's make a smarter business decision. We offer market intelligence studies ensuring relevant and fact-based research across a multiple industries including Healthcare, Technology, Chemicals, Power and Energy. We consistently update our research offerings to ensure our clients are aware about the latest trends existent in the market. Reports and Data has a strong base of experienced analysts from varied areas of expertise.

Contact Us:

John WHead of Business DevelopmentReports And Data | Web:www.reportsanddata.comDirect Line: +1-212-710-1370E-mail: sales@reportsanddata.comLinkedIn | Twitter | Blogs

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Protein Engineering Market To Reach USD 4.77 Billion By 2027 | Reports And Data - PR Newswire UK

Protein Engineering Market To Reach USD 4.77 Billion By 2027 | Reports And Data – PRNewswire

NEW YORK, July 28, 2020 /PRNewswire/ -- According to the current analysis of Reports and Data, theProtein Engineering marketwas valued at USD 1.86 billion in 2019 and is expected to reach USD 4.77 billion by the year 2027, at a CAGR of 12.3%. Protein engineering is the process of conception and production of unnatural polypeptides, which is achieved through the modification of different amino acid sequences that are found in nature. With the wide application of protein engineering, various synthetic protein structures and functions can now be designed completely using a computer and produced in the laboratory using various methods.

With the advent of technology, the rising demand is expected to provide traction to the market. For instance, computational protein design holds a potential promise to revolutionize protein engineering. Protein engineering is significantly in demand as it can develop useful or valuable proteins. It is known to be an emerging research field that helps researchers in understanding protein folding and recognition used for protein design principles. Protein engineering market is spurred by various reasons such as availability of immense information regarding 3D protein structure, advancement in structural bioinformatics, novel protein design algorithms, and other factors that have made it possible to use computational approaches for research and development in protein engineering. Strategic utilization of approaches that have been discovered with research has enabled better stability and increased catalytic activity of the protein. Moreover, it has increased its applicability in various fields that will further expand the market. Protein engineering has also evolved to become a potent tool contributing considerably to the developments in both synthetic biology and metabolic engineering. The rising funding for synthetic biology by governments and other healthcare institutions may drive the industry extensively in the future. Furthermore, substantial ongoing research in the drug discovery process is expected to fuel the market during the forecast period. Growing technological advancements and innovative instruments useful for protein engineering may drive the market extensively in the future. The emergence of new diseases due to microorganisms may also trigger market growth.

Request free sample of this research report at: https://www.reportsanddata.com/sample-enquiry-form/3369

However, factors such as high cost of instrumentation and lack of skill professional may hamper the protein engineering industry in the forecast period.

COVID-19 Impact:

WHO is focused on the latest scientific findings and knowledge on COVID-19. Various researchers and scientists are discovering new ways to tackle COVID-19 infection. Furthermore, the market of protein engineering is also going to get significantly affected due to the multiple kinds of research which are being carried out in this field. With the advent of technology, improving protein stability is an essential goal for clinical and industrial applications, however no commonly accepted and widely used strategy for efficient engineering is known. Furthermore, during the COVID-19 outbreak, protein engineering market is significantly impacted because many of the procedures involve lab automation. Market players are focusing on a research-based approach that will provide traction to the market. For instance, Vir Biotech identified two antibodies that could be effective in preventing and treating COVID-19. However, the high requirement of funds is expected to hamper the market during this period.

To identify the key trends in the industry, click on the link below:https://www.reportsanddata.com/report-detail/protein-engineering-market

Further key findings from the report suggest

Order Now: https://www.reportsanddata.com/checkout-form/3369

For the purpose of this report, Reports and Data has segmented the Protein Engineering market on the basis of product, type, technology, end use and region:

By Product Outlook (Revenue in Million USD; 2017-2027)

By Type Outlook (Revenue in Million USD; 2017-2027)

By Technology Outlook (Revenue in Million USD; 20172027)

By End Use Outlook (Revenue in Million USD;20172027)

Regional Outlook (Revenue, USD Billion; 2017-2027)

Browse more similar reports on Biotechnology category by Reports And Data

About Reports and Data

Reports and Data is a market research and consulting company that provides syndicated research reports, customized research reports, and consulting services. Our solutions purely focus on your purpose to locate, target and analyze consumer behavior shifts across demographics, across industries and help client's make a smarter business decision. We offer market intelligence studies ensuring relevant and fact-based research across a multiple industries including Healthcare, Technology, Chemicals, Power and Energy. We consistently update our research offerings to ensure our clients are aware about the latest trends existent in the market. Reports and Data has a strong base of experienced analysts from varied areas of expertise.

Contact Us:

John WHead of Business DevelopmentReports And Data | Web:www.reportsanddata.comDirect Line: +1-212-710-1370E-mail: [emailprotected]LinkedIn | Twitter | Blogs

SOURCE Reports And Data

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Protein Engineering Market To Reach USD 4.77 Billion By 2027 | Reports And Data - PRNewswire

Explained: How corona of the virus changes into a hairpin shape and why – The Indian Express

Written by Kabir Firaque | New Delhi | Updated: July 24, 2020 10:45:13 am Structure of SARS-CoV-2, including the spike protein. (Source: Wikipedia)

The spike protein of SARS-CoV-2 the corona in the coronavirus that causes Covid-19 disease has just revealed new secrets. Researchers have found that the spike protein changes its form after it attaches itself to a human cell, folding in on itself and assuming a rigid hairpin shape. The researchers have published their findings in the journal Science, and believe the knowledge can help in vaccine development.

It is a protein that protrudes from the surface of a coronavirus, like the spikes of a crown or corona hence the name coronavirus. In the SARS-CoV-2 coronavirus, it is the spike protein that initiates the process of infection in a human cell. It attaches itself to a human enzyme, called the ACE2 receptor, before going on to enter the cell and make multiple copies of itself.

Using the technique of cryogenic electron microscopy (cryo-EM), Dr Bing Chen and colleagues at Boston Childrens Hospital have freeze-framed the spike protein in both its shapes before and after fusion with the cell.

The images show a dramatic change to the hairpin shape after the spike protein binds with the ACE2 receptor. In fact, the researchers found that the after shape can also show itself before fusion without the virus binding to a cell at all. The spike can go into its alternative form prematurely.

Dr Chen suggests that assuming the alternative shape may help keep SARS-CoV-2 from breaking down. Studies have shown that the virus remains viable on various surfaces for various periods of time. Chen suggests that the rigid shape may explain this.

More significantly, the researchers speculate that the postfusion form may also protect SARS-CoV-2 from our immune system.

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The postfusion shape could induce antibodies that do not neutralise the virus. In effect, the spikes in this form may act as decoys that distract the immune system.

Antibodies specifically targeting the postfusion state would not be able to block membrane fusion (viral entry) since it would be too late in the process. This is well established in the field of other viruses, such as HIV, Chen told The Indian Express, by email.

In principle, if both conformations shared neutralising epitopes (the part of the virus targeted by antibodies), then the postfusion form too could induce neutralising antibodies, Chen said. But because the two structures are often very different, in particular, in case of SARS-CoV-2 and HIV, I think it is not very likely that the postfusion form would be useful as an immunogen, he explained.

Yes, both the before and after forms have sugar molecules, called glycans, at evenly spaced locations on their surface. Glycans are another feature that helps the virus avoid immune detection.

The researchers believe the findings have implications for vaccine development. Many vaccines that are currently in development use the spike protein to stimulate the immune system. But these may have varying mixes of the prefusion and postfusion forms, Chen said. And that may limit their protective efficacy.

Chen stressed the need for stabilising the spike protein in its prefusion structure in order to block the conformational changes that lead to the postfusion state. If the protein is not stable, antibodies may be induced but they will be less effective in terms of blocking the virus, he said.

Using our prefusion structure as a guide, we should be able to do better (introducing stabilizing mutations) to mimic the prefusion state, which could be more effective in eliciting neutralizing antibody responses, Chen told The Indian Express. We are in the process of doing this in case the first round of vaccines are not as effective as we all hope.

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Explained: How corona of the virus changes into a hairpin shape and why - The Indian Express

DeepMinds Protein Folding AI Is Going After Coronavirus

In late December last year, Dr. Li Wenliang began warning officials about a novel coronavirus in Wuhan, China, but was silenced by the police before tragically succumbing to the disease two months later. Meanwhile, almost simultaneously, a computer server halfway across the world started issuing worrying alerts of a potential new outbreak. The server runs software by BlueDot, a company based in San Francisco that uses AI to monitor infectious disease outbreaks for signs of early trouble.

Not enough people listened to either human expertise or AI. Then cases skyrocketed in Wuhan and spread across the world, and people had to take note.

Hindsight is 20/20, but it is remarkable that BlueDot and other machine learning-based services are beginning to catch early signs of infectious disease outbreaksalmost within the same time frame as health experts, if just for COVID-19. We often hear about AI as the next second coming of healthcare, where it can catch cases early, accelerate drug development, and personalize treatment. Yet COVID-19 is the first global pandemic to ever hold healthcare AIs feet to the flame in a global, serious, and urgent real-world test case. In a head-to-head race, can AI actually accelerate new anti-virals or vaccines for COVID-19, something the world has never previously seen? Or will traditional biotech measures excel, in turn unveiling that AIs hype massively outstrips reality?

MIT Technology Review recently reported an excellent piece that comprehensively looks at how AIat its current ability levelcan help us predict, diagnose, and treat novel viral threats. Im on board with the general idea: AIs potential is enormous.

Yet for now, dont look to AI to help tackle COVID-19; its simply not ready.

That said, it is enormously helpful to see how major machine learning companies are utilizing or repositioning their technologies for tackling the crisis. People often critique AI tested in toy cases, or standardized, limited datasets that may have limited significance in the real world. With companies working on COVID-19, thats no longer the case.

Ready, player, go? Heres how one major AI player in healthtech, DeepMind, is trying to knee-cap COVID-19.

The promise of AI for accelerating medical drug discovery is almost a universally supported idea. One caveat: so far, though new drugs have been discovered using AI, no AI-based drug candidate has made it through the approval process (yet), or even demonstrated that the tech makes the whole process faster to market (yet).

In very broad strokes, AI could be enormously helpful for initial drug discovery in two main ways: one, screening through millions of chemical compounds for potential drugs in simulation tests, far faster than any human expert; two, identifying targets that new drugs can latch onto, either to reduce their impact (making people less sick), or to slow their spread among people.

For COVID-19, DeepMind is focusing on the second route. Known mostly for its algorithms that beat human players at Go, DOTA, and other games, DeepMind has nevertheless been working directly on solutions for drug discovery. Their secret sauce? AlphaFold, a deep learning system that tries to predict protein structures accurately when no similar proteins exist.

Stay with me. How a protein looks in 3D is essential for developing new drugs, especially for new viruses. COVID-19, for example, has really spikey proteins that jut out from its surface. Normally, human cells dont carethey wont let the virus inside. But COVID-19s spikey proteins also harbor a Trojan Horse that activates it in certain cells with a complementary component. Lung cells have an abundance of these factors, which is why theyre susceptible to invasion.

Bottom line: if a drug is going to fit into a protein like a key into a lock to trigger a whole cascade of nasty reactions, then the first step is to figure out the structure of the lock. Thats what DeepMinds AlphaFold is doing.

Thanks to a surge of global collaboration, China released the genomic blueprint of the COVID-19 virus in open-access databases, whereas others have posted online the structure of some of its proteinseither determined by experiments or through computational modeling. DeepMind is taking these data to the next level by focusing on a few understudied but potentially important proteins that could become drug or vaccine targets using machine learning.

Protein folding has been a decades-long, fundamental problem in biochemistry and drug discovery. Almost all of our existing drugs grab onto certain proteins to work, so identifying protein structure is akin to surveying the enemy landscape and figuring out best attack point simultaneously. The problem is the genetic code doesnt translate to how proteins look. When it comes to a new virus, without predicting protein structures were basically fighting viruses and diseases as if they were the Invisible Man.

Traditional methods use high-tech microscopes, freezing proteins into crystal-looking entities, and other strange and expensive ways to understand their structure. Under the scope, a protein is basically a chain of chemical letters that wrap around itself into intricate structureskinda like how your headphones always tangle into inconceivable structures while youre sleeping. For DeepMind and other protein-folding efforts, the key is to predictand then find methods to decipher drug targets fromthose structures.

AlphaFold stands out as a union of decades of deep learning progress, but guided by expertise from protein structure databases in the public domain. In a nutshell, AlphaFold uses genome sequences (available for COVID-19 and relatively easy to get) to predict the properties of resulting proteins that actually do the work, by looking at the distance of each letter or component that makes up a certain protein. It doesnt predict specific sequences with special powerssuch as those that bind to a cellbut offers a quick police sketch of the virus perp in sight.

Theres no doubt that AlphaFold is new to the protein-folding game. Even DeepMind itself stresses that these structure predictions have not been experimentally verified, but could galvanize efforts at making anti-virals and/or vaccines. For now, its difficult to judge how much AlphaFold will contribute to the pandemic, if at all. But by automating a critical aspect of drug discovery, its also en route to becoming a much larger player in the next epidemic.

Of note: all of this would not be possible without public, open-source databases of protein structures (like UniProt and the Protein Data Bank) thats been building for decades. DeepMinds release, posted with open access, has been lauded by fellow scientists as a way of giving back to the community.

Chinas long-time Google surrogate and AI behemoth, Baidu, is using an algorithm to predict the structure of another important biomolecule, mRNA. mRNA shuttles information from the genome to protein factories, so shoot the mRNA messenger, then the viral proteins are never born. Similarly, AI could one day potentially predict epidemics and how a virus changes over timebut it will only help if theres enough trust to listen to the models.

Various AI companies are also making a play towards efficient diagnosticsidentifying COVID-19 signs in medical scansor other measures to support at-risk and overworked medical frontline heroes. The problem is that with any new outbreak, we dont have enough data to train an AI, which means that they will struggle to find subtle differences in imperfect medical scans, at least for now.

So, is AI our savior? Not in this pandemic. Similar to the 2003 SARS outbreak, the best response is something that has existed for centuries: social distancing. As I mentioned previously, before COVID-19 exploded into a pandemic, science was ready to provide answers for COVID-19 as long as governments were also ready to respond. And because AI is based on scientific data and helping otherwise difficult efforts, machine learning is rapidly learning to do the same.

But perhaps ironically, COVID-19 is exposing both the best and weakest parts of AI in our current society for healthcare: great models that in theory should work, solid predictions that can be tested, but not without any recommendations without a heavy dose of skepticism. COVID-19 presents a brutal test case for AI in healthcare.

But for now, the toughest case is that of government management and what we do in response.

Note: To learn more about the Covid-19 pandemic, tune into Singularity Universitys free virtual summit: Covid-19: The State & Future of Pandemics.

Image Credit: Vektor Kunst from Pixabay

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DeepMinds Protein Folding AI Is Going After Coronavirus

Demand for Syndromes of Progressive Ataxia and Weakness Disorders Market to Witness Rapid Surge – Lake Shore Gazette

Ataxia is a neurological condition, characterized by lack of voluntary coordination of muscle movement. Ataxia causes head trauma, stroke, Transient Ischemic Attack (TIA), tumor and toxic reaction. Progressive ataxia and weakness disorders are related to damage, degeneration or loss of neurons of the brain which leads to muscle coordination disability.

The global market for treatments of syndromes of progressive ataxia and weakness disorders is categorized based on various drugs used for treatment of progressive ataxia syndromes, drugs for progressive weakness syndromes and by technology. The progressive ataxia syndrome segment is further sub-segmented into major diseases, such as Friedreichs ataxia, Gertsman-Straussler-Scheinker disease and Machado-Joseph disease. The progressive weakness syndrome segment includes amyotrophic lateral sclerosis, hereditary spastic paraplegia, hereditary neuropathies, progressive bulbar palsy and multiple sclerosis. The technology segment is further sub-segmented into small molecules based therapies and monoclonal antibody.

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In terms of geography, the U.S. and Canada holds major market share of treatments for syndromes of progressive ataxia and weakness disorders market in North America. In Europe, Germany, France and the U.K are major markets for treatments of syndromes of progressive ataxia and weakness disorders.

Globally, treatments for syndromes of progressive ataxia and weakness disorders market are growing due to novel drug development and rapid technological advancement for treatment of progressive ataxia and weakness disorders. Some of the major technological advancement involved in growth of the market are protein mis-folding, gene mutation and stem cell therapy. In addition, increased collaborations between industry players for development of new therapies is a key trend for the market.

However, patent expiries of major drugs hampers growth of the treatments for syndromes of progressive ataxia and weakness disorders market. Moreover, stringent regulations and standard requires for approval process of new drugs impede growth of the treatments for syndromes of progressive ataxia and weakness disorders market. Several government agencies, such as FDA and European Medicines Agency, are responsible for the approval of every drug. In addition, the approval process takes a very long time to approve a specific drug.

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Some of the major companies operating in the treatment for syndromes of progressive ataxia and weakness disorders market are Abbott Laboratories, Acorda Therapeutics Inc., American Regent Inc., Baxter International Inc., Biogen Idec., Bristol-Myers Squibb, Cadila Healthcare Ltd., Eli Lilly and Company, Glaxosmilthkline Plc., Sanofi, Roche Holding Ltd., Pfizer Inc. and Novartis AG.

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Demand for Syndromes of Progressive Ataxia and Weakness Disorders Market to Witness Rapid Surge - Lake Shore Gazette

Microsoft Executive Vice President Jason Zander: Digital Transformation Accelerating Across the Energy Spectrum; Being Carbon Negative by 2030; The…

WASHINGTON--(BUSINESS WIRE)--Microsoft Executive Vice President Jason Zander says the company has never been more busy partnering with the energy industry on cloud technologies and energy transition; the combination of COVID-19 and the oil market shock has condensed years of digital transformation into a two-month period; the companys return to its innovative roots and its goal to have removed all of the companys historic carbon emissions by 2050 in the latest edition of CERAWeek Conversations.

In a conversation with IHS Markit (NYSE: INFO) Vice Chairman Daniel Yergin, Zanderwho leads the companys cloud services business, Microsoft Azurediscusses Microsofts rapid and massive deployment of cloud-based apps that have powered work and commerce in the COVID-19 economy; how cloud technologies are optimizing business and vaccine research; the next frontiers of quantum computing and its potential to take problems that would take, literally, a thousand years, you might be able to solve in 10 seconds, and more.

The complete video is available at: http://www.ceraweek.com/conversations

Selected excerpts:Interview Recorded Thursday, July 16, 2020

(Edited slightly for brevity only)

Watch the complete video at: http://www.ceraweek.com/conversations

Weve already prepositioned in over 60 regions around the world hundreds of data center, millions and millions of server nodestheyre already there. If you can imagine COVID, if you had to go back and do a procurement exercise and figure out a place to put the equipment, and the supply chains were actually shut down for a while because of COVID. Thats why I say, even three to five years ago we as industries would have been pretty challenged to respond as quickly as we had.

Thats on the more tactical end of the spectrum. On the other end weve also done a lot of things around data sets and advanced data work. How do we find a cure? Weve done things like [protein] folding at home and making sure that those things could be hosted on the cloud. These are thingsthat will be used in the search of a vaccine for the virus. Those are wildly different spectrums from the tactical 'we need to manage and do logistics' to 'we need a search for things that are going to get us all back to basically normal.'

Theres also a whole bunch of stimulus packages and payment systems that are getting created and deployed. Weve had financial services companies that run on top of the cloud. They may have been doing a couple of hundred big transactions a day; weve had them do tens to hundreds of thousands a day when some of this kicked in.

The point is with the cloud I can just go to the cloud, provision it, use it, and eventually when things cool back down, I can just shut it off. I dont have to worry about having bought servers, find a place for them to live, hiring people to take care of them.

There was disruption in supply chain also. Many of us saw this at least in the Statesif you think even the food supply chain, every once in a while, youd see some hiccups. Theres a whole bunch of additional work that weve done around how do we do even better planning around that, making sure we can hit the right levels of scale in the future? God forbid we should have another one of these, but I think we can and should be responsible to make sure that weve got it figured out.

The policy and investment sideit has never been more important for us to collaborate with healthcare, universities, and with others. Weve kicked off a whole bunch of new partnerships and work that will benefit us in the future. This was a good wake up call for all of us in figuring out how to marshal and be able to respond even better in the future.

Weve had a lot of cases where people have been moving out of their own data centers and into ours. Let us basically take care of that part of the system. We can run it cheaply and efficiently. Im seeing a huge amount of data center accelerationfolks that really want to move even faster on getting their workloads removed. Thats true for oil and gas but its also true for the financial sector and retail.

Specifically, for oil and gas, one of the things that were trying to do in particular is bring this kind of cloud efficiency, this kind of AI, and especially help out with places where you are doing exploration. What these have in common is the ability to take software especially from the [independent software vendors] that work in the spacereservoir simulation, explorationand marry that to these cloud resources where I can spin things up and spin things down. I can take advantage of that technology that Ive got, and I am more efficient. I am not spending capex; I can perhaps do even more jobs than I was doing before. That allows me to go do that scale. If youre going to have less resources to do something, you of course want to increase your hit rate; increase your efficiency. Those are some of the core things that were seeing.

A lot of folks, especially in oil and gas, have some of the most sophisticated high-performance computing solutions that are out there today. What we want to be able to do with the cloud is to be able to enable you to do even more of those solutions in a much more efficient way. Weve got cases where people have been able to go from running one reservoir simulation job a day on premises [to] where they can actually go off to the cloud and since we have all of this scale and all of this equipment, you can spin up and do 100 in one day. If that is going to be part of how you drive your efficiency, then being able to subscribe to that and go up and down its helping you do that job much more efficiently than you used to and giving you a lot more flexibility.

Were investing in a $1 billion fund over the next four years for carbon removal technology. We also are announcing a Microsoft sustainability calculator for cloud customers. Basically, you can help get transparency into your Scope 1,2, and 3 carbon emissions to get control. You can think of us as we want to hit this goal, we want to do it ourselves, we want to figure out how we build technology to help us do that and then we want to share that technology with others. And then all along the way we want to partner with energy companies so that we can all be partnering together on this energy transition.

From a corporate perspective weve made pledges around being carbon negative, but then also working with our energy partners. The way that we look at this is youre going to have continued your requirements and improvements in standards of living around the entire planet. One of the core, critical aspects to that is energy. The world needs more energy, not less. There are absolutely the existing systems that we have out there that we need to continue to improve, but they are also a core part of how things operate.

What we want to do is have a very responsible program where were doing things like figuring out how to go carbon negative and figuring out ways that we as a company can go carbon negative. At the same time, taking those same techniques and allowing others to do the same and then partnering with energy companies around energy transformation. We still want the investments in renewables. We want to figure out how to be more efficient at the last mile when we think about the grid. I generally find that when you get that comprehensive answer back to our employees, they understand what we are doing and are generally supportive.

Coming up is a digital feedback loop where you get enough data thats coming through the system that you can actually start to be making smart decisions. Our expectation is well have an entire connected environment. Now we start thinking about smart cities, smart factories, hospitals, campuses, etc. Imagine having all of that level of data thats coming through and the ability to do smart work shedding or shaping of electrical usage, things where I can actually control brownout conditions and other things based on energy usage. Theres also the opportunity to be doing smart sharing of systems where we can do very efficient usage systemsintelligent edge and edge deployments are a core part of that.

How do we keep all the actual equipment that people are using safe? If you think about 5G and additional connectivity, were getting all this cool new technology thats there. You have to figure out a way in which youre leveraging silicon, youre leveraging software and the best in securityand were investing in all three.

The idea of being able to harness particle physics to do computing and be able to figure out things in minutes that would literally take centuries to go pull off otherwise in classical computing is kind of mind-blowing. Were actually working with a lot of the energy companies on figuring out how could quantum inspired algorithms make them more efficient today. As we get to full scale quantum computing then they would run natively in hardware and would be able to do even more amazing things. That one has just the potential to really, really change the world.

The meta point is problems that would take, literally, a thousand years, you might be able to solve in 10 seconds. Weve proven how that kind of technology can work. The quantum-inspired algorithms therefore allow us to take those same kind of techniques, but we can run them on the cloud today using some of the classic cloud computers that are there. Instead of taking 1,000 years, maybe its something that we can get done in 10 days, but in the future 10 seconds.

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About IHS Markit (www.ihsmarkit.com)

IHS Markit (NYSE: INFO) is a world leader in critical information, analytics and solutions for the major industries and markets that drive economies worldwide. The company delivers next-generation information, analytics and solutions to customers in business, finance and government, improving their operational efficiency and providing deep insights that lead to well-informed, confident decisions. IHS Markit has more than 50,000 business and government customers, including 80 percent of the Fortune Global 500 and the worlds leading financial institutions. Headquartered in London, IHS Markit is committed to sustainable, profitable growth.

IHS Markit is a registered trademark of IHS Markit Ltd. and/or its affiliates. All other company and product names may be trademarks of their respective owners 2020 IHS Markit Ltd. All rights reserved.

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Microsoft Executive Vice President Jason Zander: Digital Transformation Accelerating Across the Energy Spectrum; Being Carbon Negative by 2030; The...

Learn the ‘right way’ to make scrambled eggs with this French technique – TODAY

Scrambled eggs are a breakfast staple and everyone seems to have their own particular method for cooking up the fluffiest eggs possible. But the quest for the perfect scrambled eggs may be over, thanks to this French-style recipe by private chef and YouTuber Bruno Albouze.

Unlike traditional scrambled eggs, which are fluffy and form more solid curds, the French style offers a silkier, creamier variation on the breakfast food, Albouze told TODAY.

If (the eggs are) cooked the right way, it changes the texture, the mouthfeel is just incredible, he said. If it's overcooked, you just don't get the same thing. You're pretty much eating chopped omelet.

According to Albouze, the French way of cooking scrambled eggs is the right way.

While Albouze may have mastered this classic technique, he didnt invent it. Chef Brendan Walsh, the dean of the School of Culinary Arts at The Culinary Institute of America, explained that while scrambled eggs have likely been around for thousands of years in places where chickens were first domesticated (like China and Egypt), the French style emerged in the early days of haute or "high cuisine." This term refers to the style of food preparation that blossomed in France during the 16th century, and is still served in many Michelin-starred eateries today.

Eggs are a staple in cooking school," Albouze said. "Cooking eggs is a big thing, because eggs are the trickiest thing to cook. It's composed mostly of water, because the egg white is watery, and the yolk is fat, but it's tricky because it can overcook very fast.

"Scrambled eggs are definitely the item not everyone knows how to cook it properly. And very very few restaurants know how to do it without them being overcooked.

Albouze, 50, has been cooking since he began an apprenticeship at the age of 14 in France, where he learned the art of cooking, baking and pastry making. Growing up, Albouze said he used to walk to nearby farms for fresh, pasture-raised eggs to make omelets and scrambled eggs.

During his career, the chef has worked at the Htel Plaza Athne in Paris under renowned chef Alain Ducasse and as an instructor at the Culinary Institute Lenotre in Houston.

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But the chef, who now lives in San Diego, really found his stride in 2009 when he started his own YouTube channel. Albouze now has over 760,000 subscribers and 70 million total video views. One of his most popular videos, a recipe for ratatouille, has garnered over 10 million views.

In one of his latest cooking demos, Albouze shared his favorite method for cooking scrambled eggs in the French style. In 2015, he showcased how to cook French-style eggs in water bath. Both methods require constant stirring and movement over low heat to achieve the desired creamy texture.

One method Albouze demonstrated uses a nonstick pan, while the other uses a water bath, which is known as a "bain marie in French and culinary terms.

Walsh added that the French way is a technique where "slow and low, patience and respect" result in the creamiest eggs possible. It is a preparation method that is taught at the CIA, although he said he rarely sees the technique used in America outside of fancier hotels and restaurants.

"It is important in egg cookery to create soft and supple textures," Walsh said via email. "Too high of heat will dry out the protein and take away the supple creaminess that the protein can provide.

Cooking is about ingredients, Albouze added. 80% (is) about the ingredients, 10% skills and 10% time. So, it tells us you don't have to be skilled, just if you understand that ingredients are the most important part of cooking.

.

For this reason, he recommends using pasture-raised eggs, which means that the egg-laying hens are allowed to spend plenty of time outside, and feed on grass, bugs or worms instead of a corn- or soy-based diet.

These days, if the egg aisle at your supermarket seems a little empty, it might not be a bad idea to take a road trip out to a local farm, pick up some fresh eggs and try out this fun technique at home.

Said Walsh, Crispy toast and creamy French-style eggs are just the sexiest start to the chefs morning."

This recipes serves two people and takes about 15 minutes from start to finish.

Said Albouze, There's no question that the most important factor when cooking eggs is the cooking technique itself. In the case of scrambled eggs, that means using gentle heat and taking the eggs off the flame a little early to account for carryover cooking.

1. Crack eggs into a bowl and set aside. Do not whisk the eggs. Set flame to medium and allow heat to gently warm the pan prior to adding any fat.

2. Add the olive oil and butter to the pan. Let melt slightly before adding the unbeaten eggs. With a whisk or a rubber spatula, poke the egg yolks and cook slowly on medium heat while constantly stirring, folding and shaking the pan.

3. Continue to cook and move the eggs as they start to scramble. They should yield a soft, delicate and creamy texture in about 5 minutes. As the eggs start to come together, turn off the heat and continue to stir the eggs.

4. To stop the cooking process, whisk in a dash of milk or cream. Season the eggs with salt and a few grinds of pepper before youre ready to serve. Salting the eggs too early may make your eggs watery.

5. If desired, serve the scrambled eggs with some fresh herbs, such as dill or chives. Eggs also pair remarkably well with caviar, salmon roe, truffle, cured salmon or bacon. Either way, these eggs should be served immediately.

Bon apptit!

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Clare Boothe Luce Scholarship Prepares Women Scientists for the Future – St John’s University News

July 15, 2020

Named for the visionary woman who excelled in myriad fields, St. Johns Clare Boothe Luce (CBL) Undergraduate Scholarship encourages gifted women to pursue collegiate studies in the sciences and technologyareas in which women historically are underrepresented. The CBL scholarship is an outgrowth of the UniversitysWomen in Science (WIS) Scholarship Program. St. Johns College of Liberal Arts and Sciences Class of 2020 included three recipients of the prestigious scholarship, each with an inspiring story to tell.

When toxicology major Kathryn Bozell enrolled at St. Johns four years ago, she was not even aware of the CBL scholarship. This fall, the scholarship recipient returns to the University to pursue her masters degree in toxicology as a CBL Graduate Fellow.

During her first year, Kathryn, a native of Louisville, KY, was encouraged to apply for the CBL scholarship by several faculty, who saw great promise in the budding scientist.

Upon learning about the exciting opportunities available through WIS and the CBL scholarship program, I eagerly applied, she recalled. The scholarship program provided me with the opportunity to connect with incredible female mentors and peers. It also inspired me to continue my studies and pursue a masters degree.

The experience also served as a launchpad for her research on the effects of copper dimethyldithiocarbamate (CDDC) on the release of a protein that is known to propagate the inflammation of nervous tissue. Neuronalinflammation has been linked to neurodegenerative diseases, such as Alzheimers disease, Parkinsons disease, and Multiple Sclerosis.

Participating in WIS activities was an integral part of my academic and professional development at St. Johns, she recalled. In addition to the invaluable networking opportunities it offered, it provided me the chance to build personal relationships with other women in science, which greatly enriched my academic experience overall.

Kathryn is excited to return to campus to begin her graduate work and serve as a role model for younger students. As I continue my education and research, I am excited to inspire the next generation of women in science in the same manner, she said. I would highly encourage all young women interested in a career in the sciences to learn more about the Clare Boothe Luce Scholarship program.

For Teagan Sweet, the CBL scholarship was a connection to a welcoming community of female scientists at St. Johns and around the globe.

CBL was such a pivotal experience for me, the native of North Attleborough, MA, recalled. I loved being surrounded byand supported bythe strong women in STEM at St. Johns who became my role models. CBL validated my experience in science.

That experience saw the chemistry major complement her study of the field with minors in photography and international studies. She also explored computational research, focusing on understanding how orientation and the folding of proteins leadto large-scale changes in the cell.

Teagan traveled to Dublin, Irelands Trinity College to work on the development of new green materials, which could one day lead to advances in energy storage, solar cells, and drug delivery.

In addition to her rigorous course load, Teagan was Head Skull of the Skull and Circle Honor Society, St. Johns Colleges highest honor for students, and was awarded the prestigiousJeannette K. Watson Fellowshipa three-year, international internship program funded by the Thomas J. Watson Foundation. She was also an S-STEM scholar and contributed to research in collaboration with the National Science Foundation, which focused on the development of a biodegradable water filter to be used in disaster situations.

Both the WIS and CBL programs assisted Teagan in her graduate school application process, through mentorship, as well as words of wisdom. This fall, she will pursue a Ph.D. in inorganic chemistry at the University of Notre Dame.

Thanks to these programs, I feel especially connected not only to women in STEM at St. Johns, but across the country, as well, she said. I will always be proud to be a part of this elite, intelligent community.

Like many students, Natalie Williams entered her senior year unsure of her postgraduation plans. A chemistry major with a minor in graphic design, Natalie sought the advice of a faculty mentor, who suggested she pursue a career where she could combine her passion for chemistry with her love of the arts.

One of my professors told me about science-related research at art museums, she recalled. I had not given this field any serious thought, but now my goal is to be a scientific researcher at a museum.

In pursuit of that goal, Natalie will attend Yale University this fall, where she will work toward her Ph.D. in material chemistry. While her focus now is on the future, she looks back on her four years at St. Johns with fondness and gratitude.

The CBL scholarship helped me not only financially, but professionally, making the way for new and lasting professional connections, she said. This program introduced me to fellow women in science who will always serve as my inspiration.

Natalie was a member of St. Johns National Science Foundation-funded S-STEM Scholars Program, which introduced her to undergraduate student research, including a research group in the chemistry department that designed, synthesized, and analyzed materials using DNA nanotechnology. There, she was able to combine her chemistry and biotechnology skills with her graphic design knowledge and made nanometer-scale DNA origami objects, which fold themselves into particular shapes.

She was also a member of the American Chemical Societys Scholar Program, an extremely competitive program for underrepresented minority students who plan to pursue careers in chemistry. In addition, Natalie participated in the BIOMOD research competition, an international bio-molecular design competition for students sponsored by the Wyss Institute for Biologically Inspired Engineering at Harvard University.

Natalie is grateful for the support she received as a CBL scholar as St. Johns. Everyone here gave me great advice that helped guide me in the best direction to achieve my goals, she recalled. Conducting research on art is something that truly fascinates me, and I plan to fulfill this dream.

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Clare Boothe Luce Scholarship Prepares Women Scientists for the Future - St John's University News

Global Research report on Molecular Modelling Market Size, Analysis and Growth Forecast by Applications, S … – Adify Media News

Molecular Modelling Market report provides a detailed evaluation of the market by highlighting information on different aspects which include drivers, restraints, opportunities, threats, and global markets including progress trends, competitive landscape analysis, and key regions expansion status.This report is comprehensive numerical analyses of the Molecular Modelling industry and provides data for making strategies to increase the market growth and success. The Report also estimates the market size, Price, Revenue, Gross Margin and Market Share, cost structure and growth rate for decision making.

Molecular Modelling Market provides key analysis on the market status of theMolecular Modelling manufacturers with best facts and figures, meaning, definition, SWOT analysis, expert opinions and the latest developments across the globe. The Report also calculate the market size,Molecular Modelling Sales, Price, Revenue, Gross Margin and Market Share, cost structure and growth rate.

Final Report will add the analysis of the impact of COVID-19 on this industry.

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The research covers the current Molecular Modellingmarket size of the market and its growth rates based on 6-year records with company outline of Key players/manufacturers:

Brief Description about Molecular Modelling market:

Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies.

Molecular modelling methods are now used routinely to investigate the structure, dynamics, surface properties, and thermodynamics of inorganic, biological, and polymeric systems. The types of biological activity that have been investigated using molecular modelling include protein folding, enzyme catalysis, protein stability, conformational changes associated with biomolecular function, and molecular recognition of proteins, DNA, and membrane complexes.

By the product type, the Molecular Modelling marketis primarily split into:

By the end users/application, Molecular Modelling marketreport coversthe following segments:

Get a Sample PDF ofMolecular ModellingMarket Report 2020

The key regions covered in theMolecular Modelling market report are:

Key Reasons to Purchase:

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Table of Contents with Major Points :

Detailed TOC of Global Molecular ModellingMarket Research Report 2020-2026, by Manufacturers, Regions, Types and Applications

1 Molecular Modelling MarketOverview1.1ProductOverviewandScopeof Molecular Modelling1.2 Molecular Modelling SegmentbyType1.3 Molecular Modelling SegmentbyApplication1.4Global Molecular Modelling MarketSizeEstimatesandForecasts1.5 Molecular Modelling Industry1.6 Molecular Modelling MarketTrends

2Global Molecular Modelling MarketCompetitionbyManufacturers2.1Global Molecular Modelling SalesMarketSharebyManufacturers(2015-2020)2.2Global Molecular Modelling RevenueSharebyManufacturers(2015-2020)2.3Global Molecular Modelling AveragePricebyManufacturers(2015-2020)2.4Manufacturers Molecular Modelling ManufacturingSites,AreaServed,ProductType2.5 Molecular Modelling MarketCompetitiveSituationandTrends2.6ManufacturersMergers&Acquisitions,ExpansionPlans2.7PrimaryInterviewswithKey Molecular Modelling Players(OpinionLeaders)

3 Molecular Modelling RetrospectiveMarketScenariobyRegion3.1Global Molecular Modelling RetrospectiveMarketScenarioinSalesbyRegion:2015-20203.2Global Molecular Modelling RetrospectiveMarketScenarioinRevenuebyRegion:2015-20203.3NorthAmerica Molecular Modelling MarketFacts&FiguresbyCountry3.4Europe Molecular Modelling MarketFacts&FiguresbyCountry3.5AsiaPacific Molecular Modelling MarketFacts&FiguresbyRegion3.6LatinAmerica Molecular Modelling MarketFacts&FiguresbyCountry3.7MiddleEastandAfrica Molecular Modelling MarketFacts&FiguresbyCountry

4Global Molecular Modelling HistoricMarketAnalysisbyType4.1Global Molecular Modelling SalesMarketSharebyType(2015-2020)4.2Global Molecular Modelling RevenueMarketSharebyType(2015-2020)4.3Global Molecular Modelling PriceMarketSharebyType(2015-2020)4.4Global Molecular Modelling MarketSharebyPriceTier(2015-2020):Low-End,Mid-RangeandHigh-End

5Global Molecular Modelling HistoricMarketAnalysisbyApplication5.1Global Molecular Modelling SalesMarketSharebyApplication(2015-2020)5.2Global Molecular Modelling RevenueMarketSharebyApplication(2015-2020)5.3Global Molecular Modelling PricebyApplication(2015-2020)

6CompanyProfilesandKeyFiguresin Molecular Modelling Business7 Molecular Modelling ManufacturingCostAnalysis8MarketingChannel,DistributorsandCustomers9MarketDynamics9.1MarketTrends9.2OpportunitiesandDrivers9.3Challenges9.4PortersFiveForcesAnalysis

10GlobalMarketForecast10.1Global Molecular Modelling MarketEstimatesandProjectionsbyType10.2 Molecular Modelling MarketEstimatesandProjectionsbyApplication10.3 Molecular Modelling MarketEstimatesandProjectionsbyRegion10.4NorthAmerica Molecular Modelling EstimatesandProjections(2021-2026)10.5Europe Molecular Modelling EstimatesandProjections(2021-2026)10.6AsiaPacific Molecular Modelling EstimatesandProjections(2021-2026)10.7LatinAmerica Molecular Modelling EstimatesandProjections(2021-2026)10.8MiddleEastandAfrica Molecular Modelling EstimatesandProjections(2021-2026)

11ResearchFindingandConclusion12MethodologyandDataSource

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Europe Protein A Resins Market Research, Recent Trends and Growth Forecast 2025 – CueReport

A Research study on Europe Protein A Resins Market analyzes and offers ideas of exhaustive research on ancient and recent Europe Protein A Resins market size. Along with the estimated future possibilities of the market and emerging trends in the Europe Protein A Resins market.

Rapid expansion of biotechnology and pharmaceutical companies will spur protein A resins market growth. Also, rising funding for protein-based research will augment the market growth. However, availability of alternatives such as crystallization, ultrafiltration, capillary electrophoresis and high pressure folding for purification methods may restrain the industry growth in forthcoming years.

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Europe Protein A Resins MarketSize Estimated To Exceed USD 232.0 Million By 2026. Growing demand for chromatography for purification and discovery of biological entities will escalate the adoption of Protein A resins in Europe over the analysis timeframe. Owing to improved, cost-effective and widely accepted component for purification of biological samples, protein A resins are widely used in chromatography technique. Furthermore, increasing product approvals of monoclonal antibodies from regulatory bodies to cater the increasing demand for immunotherapy will further fuel the industry growth.

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Demand for protein A resins in biopharmaceutical companies will progress at 8.4% CAGR during the projection period. Growing demand for drug development coupled with increase research and development spending will augment the segment share. With rising adoption by biotechnology industries for protein A resins for antibody production, will offer profitable growth in the forecast timeframe.

Antibody purification application segment accounted for more than 77% revenue share in 2019. With rising incidence of chronic diseases such as rheumatoid arthritis, protein A resin kits are developed for purification of antibodies for structural and diagnostic studies. They are also used as molecular probes for research and development activities. Monoclonal antibodies exhibit remarkable results in the management of chronic conditions such as cancer and rheumatoid arthritis. Thus, wide applications and benefits of antibodies will render a lucrative potential for protein A resins market growth in the forthcoming years.

Agarose-based matrix segment is estimated to grow at 8.3% CAGR over the forecast timeframe. Suitable resolution, favorable pH conditions and high flow rate drives the segment growth over the forecast time period. The benefits of using agarose-based matrix include excellent biocompatibility, considerable mechanical resistance, and hydrophobic nature that significantly contribute to product preference, thus increasing segmental growth.

Europe protein A resins industry was led by Germany protein A resins market in 2019 and is estimated to show a positive trend throughout the projection period. UK protein A resins business is forecasted to proceed at more than 7.5% CAGR across the forecast timeframe. Increasing number of pharmaceutical industry and presence of major market players in the country will influence market growth in the future. Furthermore, expanding applications of immunotherapy will augment the UK protein A resins business growth in future.

Recombinant protein A resins market held more than USD 80 million revenue size in 2019. Recombinant protein A is generally formulated in E.coli and functioning is same as that of natural protein A resins. When other sources of production offer less non-specific binding, recombinant protein A resins are generally preferred. Thus, higher inclination towards recombinant protein A resins owing to its advantages will augment the segmental growth.

Major market players in Europe protein A resins market are Thermo Fisher Scientific, EMD Millipore, GE Healthcare, and Bio-Rad Laboratories among other industry participants. These market players are undertaking strategies such as technology advancements and inorganic growth strategies to strengthen their market presence and company expansion. For instance, in June 2018, Purolite introduced advanced protein A agarose resin. The new-generation resins, Praesto Jetted A50 shows improved performance aimed at widening their product and customer base.

A Pin-point overview of TOC of Europe Protein A Resins Market are:

Overview and Scope of Europe Protein A Resins Market

Europe Protein A Resins Market Insights

Industry analysis - Porter's Five Force

Company Profiles

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Europe Protein A Resins Market Research, Recent Trends and Growth Forecast 2025 - CueReport

Global Zinc Deficiency Treatment Market to Witness Heightened Growth During the Period 2017 2025 – My Amazon Echo

Zinc is a micronutrient and essential trace element required for metabolism reactions that catalyze number of enzyme reactions, protein folding, gene expression etc. Deficiency of zinc may cause range of infectious diseases and other complications affecting almost every aspect of health such as delayed or retarded growth in children, hair loss, lack of cognitive function, reduced sense of taste and smell, loss of appetite, immunosuppression, anemia, night blindness, etc. Zinc deficiency may also cause deficiency of vitamin A as zinc is required for vitamin A absorption. Zinc deficiency is the fifth leading factor causing disease across the globe, and according to World Health Organization (WHO) 31% of the global population is experiencing zinc deficiency. Underdeveloped countries are facing major problem of death due to childhood diarrhea and pneumonia caused due to zinc deficiency. As per International Zinc Nutrition Consultative Group (IZiNCG) zinc deficiency is expected to cause 176,000 diarrhea deaths, 406,000 pneumonia deaths and 207,000 malaria deaths across the world Regions such as Africa, Middle East and South-East Asia are bearing high burden of zinc deficiency due to poor nutrition, lack of breastfeeding etc. Treatment of zinc deficiency mainly involves intake of zinc rich food and zinc supplements. Mild zinc deficiency requires treatment with zinc supplements at 2-3 times the recommended dietary allowance (RDA) and moderate to severe zinc deficiency requires zinc supplements with 4-5 times the RDA and treatment is continued for at least 6 months.

Oral repletion of zinc in the form of zinc acetate, zinc sulfate, zinc aspartate, zinc orotate and zinc gluconate, multivitamin supplements etc. and zinc supplements are available in the form of oral tablets capsules, syrups or intravenous solutions. National Institute of Health (NIH) recommends daily intake of 20-40 mg zinc for adults orally to avoid complications caused by zinc deficiency. High dose of zinc i.e. more than 50 mg per day is recommended to patients with severe zinc deficiency or patients with irreversible malabsorptive disorders. Intravenous administration of zinc is rarely recommended unless the patient is suffering from intestinal failure or on long-tern treatment with total parenteral nutrition.

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Market for zinc deficiency treatment is primarily driven by increasing occurrence of malnutrition in underdeveloped and developing countries. Increasing incidence of anemia, hypovitaminosis A, etc. are other factors driving demand for zinc supplements across the globe. Zinc supplements are also used as an adjunctive therapy in many disorders such as alopecia, ulcers, electrolyte replenishment therapy for diarrhea, etc.; high incidence of which can propel the demand for zinc supplements over the forecast period. However, unavailability of treatment opportunities in the underdeveloped countries can be the factor which can hamper growth of global zinc deficiency treatment market.

The global market for zinc deficiency treatment is segmented on basis of product types, treatment, dosage form, distribution channel and geography:

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Among treatment type, dietary supplements is expected to dominate the global market as dietary zinc supplements are recommended along with drug therapy in every patient suffering from zinc deficiency. Among all four distribution channels of zinc supplements, e-commerce is expected to experience highest growth over the forecast period.

On the basis of geography, global zinc deficiency treatment testing market is segmented into five key regions viz. North America, Latin America, Europe, Asia Pacific, and Middle East & Africa. Asia Pacific is expected to dominate the global market for zinc deficiency treatment due to high level of malnutrition in developing countries such as India, Bangladesh, Sri Lanka, etc. The region is expected to witness robust growth due to growing awareness towards malnutrition and its consequences. North America and Western Europe shows lower occurrence of zinc deficiency as adequate intake of animal food by population in the region. Despite high incidence of zinc deficiency in Middle East and Africa market growth is limited by access to zinc supplements due to low purchasing power and poor health consciousness among general population.

Some of the key players present in global zinc deficiency treatment market are Hospira, Inc. (Pfizer Inc.), Metagenics, Inc., Sandoz International GmbH (subsidiary of Novartis AG), Teva Pharmaceutical Industries Ltd., Nu Life Nutrition Ltd., Twin Laboratories Inc., Amway Corp., DSM Nutritional Products, etc. among others.

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First subject dosed with ZF874, a potential disease-modifying treatment for alpha-1-antitrypsin deficiency – Cambridge Network

AATD is a common genetic disorder, affecting around in 1 in 2000 people in Western countries, where a single mistake in the DNA encoding the protein alpha-1-antitrypsin (A1AT) causes both liver and lung disease.

Nearly all of the cases of AATD are caused by just a single mutation in the A1AT gene, known as the Z mutation. The Z mutation causes most of the A1AT to misfold, forming polymers that stay in the liver instead of being secreted into the blood where it plays a key role in protecting the lungs and other organs from the damaging effects of inflammation explained Jim Huntington, Professor at the University of Cambridge and Founder of Z Factor (pictured). The low levels of correctly-folded A1AT in the lungs results in the development of emphysema in nearly all AATD sufferers. At the same time, accumulation of Z-A1AT polymers in the liver can cause liver disease, sometimes manifesting as liver failure in newborns and more commonly cirrhosis and liver cancer as carriers of this mutation age.

ZF874 was developed with the help of a proprietary crystal structure solved by the Huntington lab. It is a novel compound that acts as a molecular patch for the faulty protein, allowing it to fold correctly, thereby simultaneously relieving the liver burden of polymer accumulation and providing fully-functional Z-A1AT in the circulation to protect the lungs. In mice genetically engineered to express human Z-A1AT in their livers, oral doses of ZF874 were able to substantially increase levels of correctly folded protein in the blood and to completely eliminate accumulation of misfolded protein in the liver.

We are excited to have dosed our first human volunteer with ZF874, said Trevor Baglin, Chief Medical Officer for Z Factor. This trial is designed to allow us to determine how safe and effective it is at raising Z-A1AT levels in humans in a short period of time. We expect to have top-line results for this potentially disease-modifying treatment in subjects carrying the Z mutation by the end of this year.

ZF874 has an excellent safety profile in preclinical toxicology studies and is suitable for oral dosing, ideal for the long-term treatment of patients with AATD, and eventually in the 2-3% of the population carrying a single copy of this mutant gene, who are also at increased risk of both liver and lung disease.

Only one other program targeting Z-A1AT folding is currently in the clinic, from the US pharmaceutical company Vertex (NASDAQ: $VRTX), who expect to report data on a similar time-frame to Z Factor.

The burden of disease caused by the Z-A1AT genetic defect has largely gone under the radar, said David Grainger, Executive Chairman at Z Factor. As many as a third of all emphysema and cirrhosis cases in Western countries, amounting to millions of patients, can trace the origins of their disease to this single error in their DNA. There is a huge unmet clinical need here.

Z Factor was founded in 2015, as a spin-out from the University of Cambridge, armed with the worlds first detailed structure of the Z-A1AT polymer from the Huntington laboratory. Cambridge Enterprise, the commercialisation arm of the University of Cambridge, licensed the technology into Z Factor. Cambridge Enterprise also participated in both the seed round and the Series A round, which was led by Medicxi, with Cambridge Innovation Capital participating.

The funding allowed the team to leverage this window onto the folding defect caused by the Z mutation, working in collaboration with the local out-sourced discovery platform company, RxCelerate, to create ZF874. Entry into the clinic marks a significant step in the development pathway for a drug from concept to approval.

We are one important step closer to delivering a drug that will not only treat the diseases associated with AATD, but that, given prophylactically, may ensure carriers of the Z mutation never develop these diseases in the first place said Huntington.

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First subject dosed with ZF874, a potential disease-modifying treatment for alpha-1-antitrypsin deficiency - Cambridge Network