通过微观模拟研究构象对蛋白-肽复合物热力学结合的贡献。
Conformational contribution to thermodynamics of binding in protein-peptide complexes through microscopic simulation.
机构信息
Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata, India.
出版信息
Biophys J. 2013 Mar 19;104(6):1274-84. doi: 10.1016/j.bpj.2012.12.058.
Abstract
We extract the thermodynamics of conformational changes in biomacromolecular complexes from the distributions of the dihedral angles of the macromolecules. These distributions are obtained from the equilibrium configurations generated via all-atom molecular dynamics simulations. The conformational thermodynamics data we obtained for calmodulin-peptide complexes using our methodology corroborate well with the experimentally observed conformational and binding entropies. The conformational free-energy changes and their contributions for different peptide-binding regions of calmodulin are evaluated microscopically.
摘要
我们从大分子的二面角分布中提取生物大分子复合物构象变化的热力学。这些分布是通过全原子分子动力学模拟生成的平衡构型获得的。我们使用这种方法获得的钙调蛋白-肽复合物的构象热力学数据与实验观察到的构象和结合熵非常吻合。钙调蛋白不同肽结合区域的构象自由能变化及其贡献得到了微观评估。
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本文引用的文献
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J Chem Theory Comput. 2011 Aug 9;7(8):2638-53. doi: 10.1021/ct200216n. Epub 2011 Jul 18.
3
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J Biomol Struct Dyn. 2012;30(1):45-61. doi: 10.1080/07391102.2012.674221.
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Reconstruction of protein side-chain conformational free energy surfaces from NMR-derived methyl axis order parameters.从 NMR 衍生的甲基轴序参数重建蛋白质侧链构象自由能表面。
J Phys Chem B. 2012 Apr 12;116(14):4124-33. doi: 10.1021/jp2104853. Epub 2012 Mar 26.
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Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition.统计力学和分子动力学在评估生物分子识别热力学性质中的应用。
Q Rev Biophys. 2012 Feb;45(1):1-25. doi: 10.1017/S0033583511000096. Epub 2011 Nov 15.
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