Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase.

ABSTRACT: Many proteins function through conformational transitions between structurally disparate states, and there is a need to explore transition pathways between experimentally accessible states by computation. The sizes of systems of interest and the scale of conformational changes are often beyond the scope of full atomic models, but appropriate coarse-grained approaches can capture significant features. We have designed a comprehensive knowledge-based potential function based on a C alpha representation for proteins that we call the virtual atom molecular mechanics (VAMM) force field. Here, we describe an algorithm for using the VAMM potential to describe conformational transitions, and we validate this algorithm in application to a transition between open and closed states of adenylate kinas

SUBMITTER: Korkut A 

PROVIDER: S-EPMC2731797 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature