Searching for Global Minima in Protein Folding

KEN DILL
Department of Pharmaceutical Chemistry
University of California, San Francisco
San Francisco 94118, USA
dill@maxwell.ucsf.edu

Abstract:

Proteins are complex heterogeneous polymer molecules. Yet proteins fold -- often very quickly (in microseconds)--to a unique ``native'' structure. Described in terms of energy landscapes, a folding protein can find a global minimum of a bumpy landscape very quickly. Using simple exact statistical mechanical models, it has been found that the basis for this speed is that these energy landscapes are funnel-shaped. We have been exploring ways to make use of information about the shapes of protein energy landscapes to find faster conformational search methods for locating the globally optimal states.