Intrinsic energy landscapes of amino acid side-chains.

Journal of Chemical Information and Modeling
Xiao ZhuAlexander D Mackerell

Abstract

Amino acid side-chain conformational properties influence the overall structural and dynamic properties of proteins and, therefore, their biological functions. In this study, quantum mechanical (QM) potential energy surfaces for the rotation of side-chain χ(1) and χ(2) torsions in dipeptides in the alphaR, beta, and alphaL backbone conformations were calculated. The QM energy surfaces provide a broad view of the intrinsic conformational properties of each amino acid side-chain. The extent to which intrinsic energetics dictates side-chain orientation was studied through comparisons of the QM energy surfaces with χ(1) and χ(2) free energy surfaces from probability distributions obtained from a survey of high resolution crystal structures. In general, the survey probability maxima are centered in minima of the QM surfaces as expected for sp(3) (or sp(2) for χ(2) of Asn, Phe, Trp, and Tyr) atom centers with strong variations between amino acids occurring in the energies of the minima indicating intrinsic differences in rotamer preferences. High correlations between the QM and survey data were found for hydrophobic side-chains except Met, suggesting minimal influence of the protein and solution environments on their conformational d...Continue Reading

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Citations

May 6, 2014·Journal of Molecular Graphics & Modelling·Francisco CarrascozaRadu Silaghi-Dumitrescu
Aug 26, 2014·Biochimica Et Biophysica Acta·K Vanommeslaeghe, A D MacKerell
Apr 29, 2016·PLoS Computational Biology·Tatiana MaximovaAmarda Shehu
Mar 19, 2015·Biopolymers·Lynne ReganCorey S O'Hern
Dec 8, 2019·Proceedings of the National Academy of Sciences of the United States of America·Steffen BrünleUlrich Ermler
Feb 25, 2017·Journal of Molecular Recognition : JMR·Megan L PeachMarc C Nicklaus
Jul 25, 2020·PloS One·Yaffa Shalit, Inbal Tuvi-Arad
Aug 26, 2017·Journal of Computational Chemistry·Peter I Maxwell, Paul L A Popelier
Jul 9, 2013·Journal of Computational Chemistry·Jing Huang, Alexander D MacKerell
May 18, 2013·Journal of the American Chemical Society·Jianing LiGregory A Voth
Jan 25, 2014·Journal of Chemical Theory and Computation·Pedro E M LopesAlexander D Mackerell
Apr 14, 2020·Journal of Chemical Theory and Computation·Fang-Yu LinAlexander D MacKerell

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