Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes.

ABSTRACT: Conformational transitions between open/closed or free/bound states in proteins possess functional importance. We propose a technique in which the collective modes obtained from an anisotropic network model (ANM) are used in conjunction with a Monte Carlo (MC) simulation approach, to investigate conformational transition pathways and pathway intermediates. The ANM-MC technique is applied to adenylate kinase (AK) and hemoglobin. The iterative method, in which normal modes are continuously updated during the simulation, proves successful in accomplishing the transition between open-closed conformations of AK and tense-relaxed forms of hemoglobin (C(alpha)-root mean square deviations between two end structures of 7.13 A and 3.55 A, respectively). Target conformations are reached by root mean-

SUBMITTER: Kantarci-Carsibasi N 

PROVIDER: S-EPMC2599820 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature