title: Reconstruction of protein side-chain conformational free energy surfaces from NMR-derived methyl axis order parameters.
abstract: An analytical approach is developed for reconstructing site-specific methyl-bearing protein side-chain conformational energy surfaces from NMR methyl axis order parameters (O(axis)(2)). Application of an enhanced sampling algorithm (adaptive biasing force) to molecular dynamics simulation of a protein, calcium-bound calmodulin, reveals a nonlinear correlation between O(axis)(2) and the populations of rotamer states of protein side-chains, permitting the rotamer populations to be extracted directly from O(axis)(2). The analytical approach yields side-chain conformational distributions that are in excellent agreement with those obtained from the enhanced-sampling MD results.
authors.affiliation: Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India. m.krishnan@iiit.ac.in
authors.forename: Marimuthu
authors.initials: M
authors.lastname: Krishnan
authors.forename: Jeremy C
authors.initials: JC
authors.lastname: Smith
mesh_terms: D000465:Algorithms; D002147:Calmodulin / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D010100:Oxygen / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D002147:Calmodulin; D010100:Oxygen