Reconstruction of Protein Side-Chain Conformational Free Energy Surfaces From NMR-Derived Methyl Axis Order Parameters

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• 作者：Marimuthu Krishnan ; Jeremy C. Smith
• 刊名：The Journal of Physical Chemistry B
• 出版年：2012
• 出版时间：April 12, 2012
• 年：2012
• 卷：116
• 期：14
• 页码：4124-4133
• 全文大小：599K
• 年卷期：v.116,no.14(April 12, 2012)
• ISSN：1520-5207

文摘

An analytical approach is developed for reconstructing site-specific methyl-bearing protein side-chain conformational energy surfaces from NMR methyl axis order parameters (O_axis²). 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_axis² and the populations of rotamer states of protein side-chains, permitting the rotamer populations to be extracted directly from O_axis². The analytical approach yields side-chain conformational distributions that are in excellent agreement with those obtained from the enhanced-sampling MD results.