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Free‐energy landscape of kinesin by a realistic lattice model
Author(s) -
Kenzaki Hiroo,
Kikuchi Macoto
Publication year - 2008
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21707
Subject(s) - kinesin , energy landscape , monte carlo method , microtubule , physics , lattice (music) , folding (dsp implementation) , statistical physics , thermal fluctuations , biophysics , biology , condensed matter physics , thermodynamics , mathematics , statistics , engineering , acoustics , microbiology and biotechnology , electrical engineering
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Gō interactions. By means of the multi‐self‐overlap ensemble Monte Carlo method and the principal component analysis, the free‐energy landscape is obtained. It is shown that kinesins have two subdomains that exhibit partial folding/unfolding at functionally important regions: one is located around the nucleotide binding site and the other includes the main microtubule binding site. These subdomains are consistent with structural variability that was reported recently based on experimentally‐obtained structures. On the other hand, such large structural fluctuations have not been captured by B‐factor or normal mode analyses. Thus, they are beyond the elastic regime, and it is essential to take into account chain connectivity for studying the function of kinesins. Proteins 2008. © 2007 Wiley‐Liss, Inc.