Department of Chemistry and Biochemistry, Institute of Computational Engineering and Sciences (ICES), 1 University Station, ICES, C0200, The University of Texas at Austin, Austin, TX 78712, USA.
Curr Opin Struct Biol. 2010 Apr;20(2):162-7. doi: 10.1016/j.sbi.2010.01.002. Epub 2010 Jan 29.
Computer simulations in molecular biophysics describe in atomic detail the structure, dynamics, and function of biological macromolecules. To assess the quality of these models and to pick up new mechanisms, comparisons with experimental measurements are made. Most comparisons examine thermodynamic and average structural properties. Here we discuss studies of dynamics and fluctuations in a protein. The diffusion of a small ligand between internal cavities in myoglobin, and its escape to solvent are considered. Qualitative and semi-quantitative agreements between experiment and simulation are obtained for the identities of the cavities that physically trap the ligand and for the connections between them. However, experimental and computational 'doors' are at significant variance. Simulations suggest multiple gates while kinetic experiments point to one dominant exit.
计算机分子生物物理学模拟能够详细描述生物大分子的结构、动力学和功能。为了评估这些模型的质量并发现新的机制，我们将它们与实验测量进行比较。大多数比较都检查热力学和平均结构特性。在这里，我们讨论了蛋白质动力学和波动的研究。我们考虑了小分子配体在肌红蛋白内部腔室之间的扩散及其逃逸到溶剂中的情况。实验和模拟之间在物理上捕获配体的腔室的身份以及它们之间的连接方面得到了定性和半定量的一致。然而，实验和计算的“门”存在显著差异。模拟表明存在多个门，而动力学实验则指出只有一个主要出口。
