DE NOVO DESIGN OF A BETA SHEET PROTEIN

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We use a combination of computational and experimental methods to design proteins. Central to all of our projects is the Rosetta program for protein modeling. In collaboration with developers from a variety of universities, we are continually adding new features to Rosetta as well as testing it on new problems. As part of an SDSC Strategic Applications Collaboration, we will look at de novo design of beta-sheet proteins. Despite the large number of all-beta proteins in nature, the de novo design of a beta-sheet protein has eluded protein designers. To create a totally novel beta-protein we are using a protocol that iterates between structure refinement and sequence optimization. Our preliminary results showed that we are able to synthesize a protein of mainly beta sheet as the secondary structure. But its not in a monomeric form. One possible reason is that we didnt sample enough conformations. This will require a lot of CPU time. Thats why we want to try out the TeraGrid supercomputer center to do more extensive modeling.