This is an illustration of the researchers' target protein crystal. Credit: Christopher MacDermaid, University of Pennsylvania

Protein design is technique that is increasingly valuable to a variety of fields, from biochemistry to therapeutics to materials engineering. University of Pennsylvania chemists have taken this kind of design a step further; using computational methods, they have created the first custom-designed protein crystal.

Picking an ambitious design target with challenging features, the researchers' success bodes well for the technique's use in better understanding proteins' makeup or using their self-assembling properties in making new materials with unique properties.

The research was conducted by professor Jeffrey G. Saven, postdoctoral fellow Christopher J. Lanci and graduate student Christopher M. MacDermaid, all of the Department of Chemistry in Penn's School of Arts and Sciences. Also contributing to the work were Seung-gu Kang and Xi Yang, formerly of the chemistry department, and Rudresh Acharya, Benjamin North, X. Jade Qiu and William F. DeGrado, formerly of Penn's Perelman School of Medicine's Department of Biochemistry and Biophysics.

The team's research was published in the journal Proceedings of the National Academy of Sciences.

Proteins are folded strings of molecular building blocks known as amino acids; their different functions are determined by their sequences of amino acids and the shapes they take when folded. As proteins are involved in most biological processes, determining sequences and structures is crucial to many scientific undertakings, such as understanding disease mechanisms or designing drugs to disrupt them.

To determine protein structures, scientists use crystals, which consist of many copies of a single protein lined up and stacked together. By irradiating the crystal with powerful X-rays, they can measure the way the light diffracts off the atoms and piece together the protein's overall three-dimensional shape and composition. Most proteins don't naturally crystalize, however, and making crystals of sufficient quality to do diffraction studies is a hit-or-miss process that can take years of painstaking work.

Protein crystals are also attractive as a nano-scale building material, as their properties, particularly their exterior surfaces, are highly customizable. However, bioengineers run into the same hurdles as crystallographers; making a protein crystal with a particular structure is a complex, hard-to-predict task.

"People have designed crystals out of smaller, much less complex molecules than proteins, but protein design is much more subtle," Saven said. "It's a complicated symphony of intermolecular interactions."

As accounting for these many interactions is one of the principal challenges behind designing a protein crystal, the researchers selected a complicated, honeycomb-shaped target to show their process could be widely applied.

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Researchers create first custom designed protein crystal