Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation
Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation
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DOI：
10.1016/j.sbi.2007.03.016
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发表时间：
2007-04-01
影响因子：
6.8
通讯作者：
Meirovitch, Hagai
中科院分区：
文献类型：
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作者：
Meirovitch, Hagai
亥姆霍兹自由能F在蛋白质中扮演着重要的角色，因为它们的势能面崎岖，被大量的局部势垒(表示为微态，m)“装饰”。F控制蛋白质折叠，而差值F-mm决定柔性环肽或柔性蛋白质片段(例如表面环)所访问的微态的相对数量。最近发展起来的计算增量F-mm(和熵差，增量S-mN)的方法主要使用热力学积分和计算绝对F；这些类别中有趣的新方法分别是自适应积分法和假设扫描分子动力学方法。
The Helmholtz free energy, F, plays an important role in proteins because of their rugged potential energy surface, which is 'decorated' with a tremendous number of local wells (denoted microstates, m). F governs protein folding, whereas differences Delta F-mm determine the relative populations of microstates that are visited by a flexible cyclic peptide or a flexible protein segment (e.g. a surface loop). Recently developed methodologies for calculating Delta F-mm (and entropy differences, Delta S-mn) mainly use thermodynamic integration and calculation of the absolute F; interesting new approaches in these categories are the adaptive integration method and the hypothetical scanning molecular dynamics method, respectively.