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Protein structures
This graphic shows the structure of a computationally designed protein that incorporates sheet-like structures with pockets, known as beta sheets. The beta sheets are the wavy “noodles” in the diagram. The structure also incorporates curled-up molecular spirals. (UW Institute for Protein Design / AAAS)

Researchers at the University of Washington have cracked the code for producing molecular structures with tiny pockets – structures that are likely to expand the repertoire for custom-designed proteins.

The structures, technically known as beta sheets, are thought to have an effect on metabolic pathways and cell signaling. Knowing how to produce them synthetically in precise configurations could lead to new treatments for maladies such as AIDS, cancer and Alzheimer’s disease.

For years, UW biochemist David Baker and his colleagues at the Institute for Protein Design have been studying the ins and outs of protein folding. That’s the process by which proteins build a wide range of molecular structures using a standard set of amino acids.

A protein’s folded shape determines its function, just as keys can be shaped to open different locks. The molecular pockets in a beta sheet act like the bumps and notches chiseled into the blade of a key, unlocking other molecules known as ligands in specific ways during cellular processes.

Biochemists can sometimes reshape naturally occurring proteins to take advantage of bumpy beta sheets, but they’d be out of luck if they wanted to design a pattern of pockets not found in nature. Until now. The approach described in this week’s issue of the journal Science opens up new possibilities for protein folding.

“This approach will allow scientists to fine-tune the size and shape of these pockets, or cavities, so that custom-designed proteins can bind to and act on specific molecular targets,” Baker said in a news release. “This method opens the door to the design of new proteins capable of entirely new functions, including catalyzing reactions not seen in nature, and has many potential applications, including the development of new diagnostic tests and treatments.”

When beta sheets are built with a uniform structure, they tend to be relatively flat, like a flat noodle or a blank key. “However, by incorporating breaks in this uniformity, it turns out it is possible to bend the sheet to a desired shape,” said Enrique Marcos, the Science paper’s lead author. Marcos is a former postdoctoral fellow from Baker’s lab who is now with the Institute for Research in Biomedicine in Barcelona, Spain.

One method to break the uniformity involves placing two molecular structures that are hydrophilic (water-loving) or hydrophobic (water-repellent) side by side on a beta sheet, resulting in a structural kink. Another method, known as a register shift, calls for terminating the bond between adjacent molecular strands on a beta sheet. That allows one of the strands to bend.

The research team showed that those two methods could be used to produce a variety of stable protein structures with pockets in the places they picked.

To predict how the structures would turn out, Baker and his colleagues turned to Rosetta@Home, a volunteer project that takes advantage of spare cycles on hundreds of thousands of computers to crunch the numbers for protein-folding simulations. The Rosetta platform also serves as the foundation for Foldit, an online protein-folding puzzle game.

Update for 8:50 p.m. PT Jan. 13: In a follow-up email to GeekWire, Baker said the applications for proteins with custom-designed pockets could include “designing enzymes (for new metabolic processes, among other things) and small molecule sensors.”

“The key idea is that given a small molecule of interest, we can now design protein-binding pockets with shapes customized for binding, sensing or doing chemistry,” he wrote.

In addition to Marcos and Baker, the authors of the Science paper, “Principles for Designing Proteins With Cavities Formed by Curved Beta Sheets,” include Benjamin Basanta, Tamuka Chidyausiku, Yuefeng Tang, Gustav Oberdorfer, Gaohua Liu, G.V.T. Swapna, Rongjin Guan, Daniel-Adriano Silva, Jiayi Dou, Jose Henrique Pereira, Rong Xiao, Banumathi Sankaran, Peter Zwart and Gaetano Montelione.

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