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Biophys J. 2008 Dec 15;95(12):5862-73. doi: 10.1529/biophysj.107.128447. Epub 2008 Aug 1.

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

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  • 1Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek 34342, Istanbul, Turkey.


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-square deviations of 2.27 A and 1.90 A for AK and hemoglobin, respectively. The intermediate conformations overlap with crystal structures from the AK family within a 3.0-A 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.

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