蛋白质中的侧链旋转异构化。有溶剂环境的动态模拟。
Sidechain rotational isomerization in proteins. Dynamic simulation with solvent surroundings.
作者信息
Ghosh I, McCammon J A
出版信息
Biophys J. 1987 Apr;51(4):637-41. doi: 10.1016/S0006-3495(87)83388-X.
Abstract
Molecular dynamics simulations are used to study the rotational isomerization of the tyrosine 35 ring in bovine pancreatic trypsin inhibitor immersed in liquid water. Inclusion of the solvent surroundings improves the agreement with experimental results significantly, although the theoretical free energy barrier (13 kcal/mol at 300K) is still approximately 3 kcal/mol below that found by nuclear magnetic resonance studies. This remaining discrepancy will probably be eliminated in future calculations by the use of a more accurate model for the hydrogen atoms on the tyrosine ring. An important finding in the present work is that frictional effects due to solvent damping appear to be small for the tyrosine 35 ring, which is largely but not completely buried in the protein surface.
摘要
分子动力学模拟用于研究浸入液态水中的牛胰蛋白酶抑制剂中酪氨酸35环的旋转异构化。尽管理论自由能垒（300K时为13千卡/摩尔）仍比核磁共振研究结果低约3千卡/摩尔，但包含溶剂环境显著改善了与实验结果的一致性。通过使用更精确的酪氨酸环上氢原子模型，未来的计算可能会消除这一剩余差异。本研究的一个重要发现是，对于主要但并非完全埋在蛋白质表面的酪氨酸35环，溶剂阻尼引起的摩擦效应似乎很小。
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本文引用的文献
1
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Biochemistry. 1980 Nov 11;19(23):5147-57. doi: 10.1021/bi00564a001.
2
3
Dynamical theory of activated processes in globular proteins.球状蛋白质中活化过程的动力学理论。
Proc Natl Acad Sci U S A. 1982 Jul;79(13):4035-9. doi: 10.1073/pnas.79.13.4035.
4
Characterization of the distribution of internal motions in the basic pancreatic trypsin inhibitor using a large number of internal NMR probes.使用大量内部核磁共振探针表征碱性胰蛋白酶抑制剂内部运动的分布情况。
Q Rev Biophys. 1983 Feb;16(1):1-57. doi: 10.1017/s0033583500004911.
5
Computer simulation of the dynamics of hydrated protein crystals and its comparison with x-ray data.水合蛋白质晶体动力学的计算机模拟及其与X射线数据的比较。
Proc Natl Acad Sci U S A. 1983 Jul;80(14):4315-9. doi: 10.1073/pnas.80.14.4315.
6
Rate theories and puzzles of hemeprotein kinetics.血红素蛋白动力学的速率理论与谜题。
Science. 1985 Jul 26;229(4711):337-45. doi: 10.1126/science.4012322.
7
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8
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J Mol Biol. 1977 May 25;112(3):535-42. doi: 10.1016/s0022-2836(77)80200-3.
9
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