Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the flory isolated-pair hypothesis for peptides
Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the flory isolated-pair hypothesis for peptides
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DOI：
10.1016/s0022-2836(03)00765-4
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发表时间：
2003-08-15
影响因子：
5.6
通讯作者：
Sosnick, TR
中科院分区：
文献类型：
--
作者：
Zaman, MH;Shen, MY;Sosnick, TR
人口和Ramachandran盆地之间的过渡进行了研究的标准20个氨基酸的单体，二聚体和三聚体的组合，使用隐式溶剂Langevin动力学算法，并采用7个常用的力场。盆地人口和相互转换率的影响，最近的邻居的构象和身份，相反的弗洛里隔离对假设。这一结论是强大的力场的选择，即使使用不同的力场产生较大的变化，在人口和占主导地位的螺旋，扩展P，和聚脯氨酸11盆地之间的相互转换率。计算的构象和动力学性质的变化与不同的力场超过显式和隐式溶剂计算使用相同的力场之间的差异。对于所有的力场，盆地间的过渡表现出方向的依赖性，大多数过渡通过扩展的P构象，即使它是人口最少的盆地。这些结果的影响在单个残基骨架熵估计以及全原子模拟重现实验蛋白质折叠数据的能力的背景下进行了讨论。(C)2003爱思唯尔有限公司。保留所有权利。
The populations and transitions between Ramachandran basins are studied for combinations of the standard 20 amino acids in monomers, dimers and trimers using an implicit solvent Langevin dynamics algorithm and employing seven commonly used force-fields. Both the basin populations and inter-conversion rates are influenced by the nearest neighbor's conformation and identity, contrary to the Flory isolated-pair hypothesis. This conclusion is robust to the choice of force-field, even though the use of different force-fields produces large variations in the populations and inter-conversion rates between the dominant helical, extended P, and polyproline 11 basins. The computed variation of conformational and dynamical properties with different force-fields exceeds the difference between explicit and implicit solvent calculations using the same force-field. For all force-fields, the inter-basin transitions exhibit a directional dependence, with most transitions going through extended P conformation, even when it is the least populated basin. The implications of these results are discussed in the context of estimates for the backbone entropy of single residues, and for the ability of all-atom simulations to reproduce experimental protein folding data. (C) 2003 Elsevier Ltd. All rights reserved.