A test of AMBER force fields in predicting the secondary structure of α-helical and β-hairpin peptides
A test of AMBER force fields in predicting the secondary structure of α-helical and β-hairpin peptides
复制标题
AMBER 力场预测 α 螺旋和 β 发夹肽二级结构的测试
DOI：
10.1016/j.cplett.2017.04.074
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发表时间：
2017-07-01
影响因子：
2.8
通讯作者：
Zhu, Tong
中科院分区：
文献类型：
--
作者：
Gao, Ya;Zhang, Chaomin;Zhu, Tong
我们用隐式溶剂模型，通过REMD模拟，测试了当前一些琥珀力场，即AMBER03、AMBER99SB、AMBER99SB-ILDN、AMBER99SB-NMR、AMBER12SB、AMBER14SB和AMBER14ipq对两个多肽折叠行为的模拟能力。AMBER99SB-NMR力场提供了最可靠的性能。在考虑了一种新的极化氢键电荷模型后，α-螺旋成功地折叠到其自然状态，而β-发夹没有进一步折叠。这项研究有力地表明，极化效应和正确的扭转项对于研究具有不同二级结构的多肽的动力学和构象性质是重要的。(C)2017爱思唯尔B.V.保留所有权利。
We tested the ability of some current AMBER force fields, namely, AMBER03, AMBER99SB, AMBER99SB-ildn, AMBER99SB-nmr, AMBER12SB, AMBER14SB, and AMBER14ipq, with implicit solvent model in reproducing the folding behavior of two peptides by REMD simulations. AMBER99SB-nmr force field provides the most reliable performance. After a novel polarized hydrogen bond charge model is considered, the alpha-helix successfully folded to its native state, while the further folding of the beta-hairpin is not observed. This study strongly suggests that polarization effect and correct torsional term are important to investigate dynamic and conformational properties of peptides with different secondary structures. (C) 2017 Elsevier B.V. All rights reserved.