A common way for proteins to hold themselves together is with disulfide bridges. But scientists don’t completely understand why some proteins need them to “hook up” their structure. Researchers used the DESRES Anton system hosted at PSC to discover the critical role disulfides play in holding together MCoTI-II, a natural pesticide that would fall apart without disulfide bridges.

“Large proteins, when they fold into their native structure … have hydrophobic contacts to stabilize the structure. The protein we studied is too small to have enough hydrophobic contacts … Our study [upheld] the theory that there is actually a frustrated structure, and the disulfide bridges come into play to bring it together.”—Yi Zhang, University of Illinois at Urbana-Champaign

Why it’s important.

Proteins are the workers of the living cell. But to work properly, a protein’s chain of amino acids has to be folded together correctly. It’s a bit like making the right knot from a shoelace. One of the tools that nature uses to hold the chain in place are “disulfide bridges,” in which two sulfur atoms form a bridge that ties together two places on the protein chain that are far apart. The final, folded chain can then form the chemically active sites that make the protein work. A better understanding of how proteins assemble could offer clues in treating diseases associated with faulty protein assembly, which include Alzheimer’s and Parkinson’s diseases, sickle-cell anemia and amyloidosis.

For larger proteins, disulfide bridges stabilize the final structure, but they are only one of many connections holding the protein together. “Hydrophobic contacts” — in which “oily” parts of the protein clump together to avoid mixing with the surrounding water — are another important connection. It’s much the same as how many beams, walls, and other connections can hold a house together: You can take any one out and the house will still stand. But for little proteins— called “peptides”—there aren’t enough amino acids to create large numbers of such connections. Yi Zhang, a graduate student working with Martin Gruebele and the late Klaus Schulten at the University of Illinois Urbana-Champaign, wanted to find out what role disulfides are playing in holding together the small protein MCoTI-II, a natural insecticide produced by some fruits.


How PSC Helped:

Working with PSC’s Phil Blood, Zhang simulated the assembly of MCoTI-II using Anton, a D.E. Shaw Research (DESRES) computer system hosted at PSC, and maintained thanks to a grant from the National Institutes of Health. Anton’s unique ability to simulate molecular motions for much longer time periods than traditional supercomputers gave Zhang the opportunity to watch how the folded structure of the peptide is locked into place.

The little protein, he found, had a chokepoint in its folding process. In its natural form, MCoTI-II has three disulfide bridges holding it together. But Zhang found that the bends in the protein needed for one of these bridges to form made it difficult for the protein to bend back to form another of the bridges. The structure was “frustrated.” Without those bridges, the structure is unstable and flops around. The scientists believe that the role of the disulfide bridges is to lock the proper folding into place on the brief occasions that it happens to bend in just the right way— a rare occurrence that the scientists were able to see because of Anton’s long simulation times. Follow-up work, possibly including the new DESRES Anton 2 system at PSC, will focus on practical uses for MCoTI-II as well as continued study of it to understand protein structure. As part of its role as a natural insecticide, MCoTI-II can invade living cells. Future applications may focus on using this capability to deliver medical treatments in humans.

Figure: When one part of the MCoTI-II protein folds correctly, one disulfide bridge can from (red) but it pulls apart the other half of the protein (left). When the latter half folds correctly, the other disulfide bridge (green) forms at the cost of pulling apart the former half (right). MCoTI-II needs both of those disulfides to lock the “frustrated structure” in place on the rare occasions that the whole protein folds correctly (center).