Conformational Transition Pathways Explored by Monte Carlo Simulation Integrated with Collective Modes

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 angstrom and 3.55 angstrom, respectively). Target conformations are reached by root mean-square deviations of 2.27 angstrom and 1.90 angstrom for AK and hemoglobin, respectively. The intermediate conformations overlap with crystal structures from the AK family within a 3.0-angstrom root mean-square deviation. In the case of hemoglobin, the transition of tense-to-relaxed passes through the relaxed state. In both cases, the lowest-frequency modes are effective during transitions. The targeted Monte Carlo approach is used without the application of collective modes. Both the ANM-MC and targeted Monte Carlo techniques can explore sequences of events in transition pathways with an efficient yet realistic conformational search.