Optimizing Protein-Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides

被引:133
作者
Nerenberg, Paul S. [1 ]
Head-Gordon, Teresa [1 ,2 ]
机构
[1] Univ Calif Berkeley, Calif Inst Quantitat Biosci QB3, Berkeley, CA 94720 USA
[2] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA
基金
美国国家科学基金会;
关键词
MOLECULAR-DYNAMICS SIMULATIONS; PARTICLE MESH EWALD; HYDRATION FREE-ENERGIES; HELIX-COIL TRANSITION; J COUPLINGS; DISORDERED PROTEINS; WATER MODELS; CHARGE; MECHANICS; CONSTRAINTS;
D O I
10.1021/ct2000183
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
While most force field efforts in biomolecular simulation have focused on the parametrization of the protein, relatively little attention has been paid to the quality of the accompanying solvent model. These considerations are especially relevant for simulations of intrinsically disordered peptides and proteins, for which energy differences between conformations are small and interactions with water are enhanced. In this Work, we investigate the accuracy Of the AMBER ff99SB force field when combined with the standard TIP3P model or the more recent TIP4P-Ew water model, to generate conformational ensembles for disordered trialanine (Ala(3)), triglycine (Gly(3)), and trivaline (Val(3)) peptides. We find that the TIP4P-Ew water model yields significantly better agreement with experimentally measured scalar couplings-and therefore more accurate-conformational ensembles-for both Ala(3) and Gly(3). For Val(3), however, we find that the TIP3P and TIP4P-Ew ensembles are equivalent in: their performance. To further the e protein water force field combination and obtain more accurate. intririsic conformational preferences, we derive a straightforward perturbation to the phi' backbone dihedral potential that shifts the beta-PPII equilibrium. We find that the revised phi' backbone dihedral potential yields improved conformational ensembles for a variety of small peptides and maintains the stability of the globular ubiquitin protein in TIP4P-Ew water.
引用
收藏
页码:1220 / 1230
页数:11
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