Validation of the GROMOS 54A7 Force Field with Respect to β-Peptide Folding

被引:231
作者
Huang, Wei [1 ]
Lin, Zhixiong [1 ]
van Gunsteren, Wilfred F. [1 ]
机构
[1] ETH, Phys Chem Lab, Swiss Fed Inst Technol, CH-8093 Zurich, Switzerland
基金
瑞士国家科学基金会; 欧洲研究理事会;
关键词
MOLECULAR-DYNAMICS SIMULATIONS; HELICAL SECONDARY STRUCTURE; BIOMOLECULAR SIMULATION; WATER MIXTURES; NUCLEIC-ACIDS; ENERGY; PROTEIN; MODEL; PARAMETRIZATION; HEPTAPEPTIDE;
D O I
10.1021/ct100747y
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070305 [高分子化学与物理];
摘要
The recently developed GROMOS 54A7 force field, a modification of the 53A6 force field, is validated by simulating the folding equilibrium of two beta-peptides which show different dominant folds, i.e., a 3(14)-helix and a hairpin, using three different force fields, i.e., GROMOS 45A3, 53A6, and 54A7. The 54A7 force field stabilizes both folds, and the agreement of the simulated NOE atom-atom distances with the experimental NMR data is slightly improved when using the 54A7 force field, while the agreement of the (3)J couplings with experimental results remains essentially unchanged when varying the force field. The 54A7 force field developed to improve the stability of a-helical structures in proteins can thus be safely used in simulations of beta-peptides.
引用
收藏
页码:1237 / 1243
页数:7
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