SIMPLIFIED MODELS FOR PROTEIN FOLDING KINETICS & THERMODYNAMICS & MECHANISM

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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. This project is directed toward the development of rapid low-resolution models for protein folding studies exploring both folding kinetics and thermodynamics. Progress has been made in addressing questions relating to protein folding kinetics and mechanisms using simple models. A procedure has been developed to distill an all-atom protein structure into a set of potentials, which then are applied to a simple protein representation. These simplified protein models have been characterized in detail for over 20 proteins to date, and have proved particularly helpful in identifying the origins of experimentally observed qualitative differences in the folding of proteins of shared topology. These models have also been shown to offer considerable advantage over a related class of Ising-like models that depend only on the protein topology. The algorithm for generating such potentials has been implemented as a web-based tool (http://mmtsb.scripps.edu/webservices/gomodel.html), offering users a set of potentials for studying their protein of interest.