Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field.

ABSTRACT: Protein folding is a hierarchical process where structure forms locally first, then globally. Some short sequence segments initiate folding through strong structural preferences that are independent of their three-dimensional context in proteins. We have constructed a knowledge-based force field in which the energy functions are conditional on local sequence patterns, as expressed in the hidden Markov model for local structure (HMMSTR). Carbon-alpha force field (CALF) builds sequence specific statistical potentials based on database frequencies for alpha-carbon virtual bond opening and dihedral angles, pair-wise contacts and hydrogen bond donor-acceptor pairs, and simulates folding via Brownian dynamics. We introduce hydrogen bond donor and acceptor potentials as alpha-carbon probability f

SUBMITTER: Buck PM 

PROVIDER: S-EPMC4651004 | biostudies-literature | 2009 Aug

REPOSITORIES: biostudies-literature