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
相关论文
共 49 条
[21]
HECHT E, 2007, FOLDAMERS STRUCTURE
[22]
Hintermann T, 1997, CHIMIA, V51, P244
[23]
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids [J].
Jorgensen, WL ;
Maxwell, DS ;
TiradoRives, J .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1996, 118 (45) :11225-11236
[24]
THE OPLS POTENTIAL FUNCTIONS FOR PROTEINS - ENERGY MINIMIZATIONS FOR CRYSTALS OF CYCLIC-PEPTIDES AND CRAMBIN [J].
JORGENSEN, WL ;
TIRADORIVES, J .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1988, 110 (06) :1657-1666
[25]
CONTACT ELECTRON-SPIN COUPLING OF NUCLEAR MAGNETIC MOMENTS [J].
KARPLUS, M .
JOURNAL OF CHEMICAL PHYSICS, 1959, 30 (01) :11-15
[26]
The effect of using a polarizable solvent model upon the folding equilibrium of different -peptides [J].
Lin, Zhixiong ;
Schmid, Nathan ;
van Gunsteren, Wilfred F. .
MOLECULAR PHYSICS, 2011, 109 (04) :493-506
[27]
Using one-step perturbation to predict the folding equilibrium of differently stereochemically substituted β-peptides [J].
Lin, Zhixiong ;
van Gunsteren, Wilfred F. .
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2010, 12 (47) :15442-15447
[28]
All-atom empirical potential for molecular modeling and dynamics studies of proteins [J].
MacKerell, AD ;
Bashford, D ;
Bellott, M ;
Dunbrack, RL ;
Evanseck, JD ;
Field, MJ ;
Fischer, S ;
Gao, J ;
Guo, H ;
Ha, S ;
Joseph-McCarthy, D ;
Kuchnir, L ;
Kuczera, K ;
Lau, FTK ;
Mattos, C ;
Michnick, S ;
Ngo, T ;
Nguyen, DT ;
Prodhom, B ;
Reiher, WE ;
Roux, B ;
Schlenkrich, M ;
Smith, JC ;
Stote, R ;
Straub, J ;
Watanabe, M ;
Wiórkiewicz-Kuczera, J ;
Yin, D ;
Karplus, M .
JOURNAL OF PHYSICAL CHEMISTRY B, 1998, 102 (18) :3586-3616
[29]
AN ALL-ATOM EMPIRICAL ENERGY FUNCTION FOR THE SIMULATION OF NUCLEIC-ACIDS [J].
MACKERELL, AD ;
WIORKIEWICZKUCZERA, J ;
KARPLUS, M .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (48) :11946-11975
[30]
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6 [J].
Oostenbrink, C ;
Villa, A ;
Mark, AE ;
Van Gunsteren, WF .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2004, 25 (13) :1656-1676