The alanine dipeptide free energy surface in solution

被引:130
作者
Smith, PE [1 ]
机构
[1] Kansas State Univ, Dept Biochem, Manhattan, KS 66506 USA
关键词
D O I
10.1063/1.479860
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
Molecular dynamics (MD) simulations have been used to determine the two dimensional free energy surface of the alanine dipeptide in solution. The intramolecular dipeptide interactions were described by the CHARMM22 force field. Three models of solvation were considered; (i) a simple scaling of electrostatic interactions, (ii) solvation energies determined by finite difference Poisson-Boltzmann calculations, and (iii) inclusion of explicit TIP3P solvent molecules. All three solvation models produced qualitatively similar effects, but differed significantly in their quantitative values. In particular, the continuum based models predicted the beta (extended) conformation to be most stable, whereas the explicit solvent model favored the alpha(R) (folded) conformation. Comparison with experimental data for the H-N-C-alpha-H-alpha coupling constant, helix-coil transition thermodynamics, and polypeptide infinite chain length characteristic ratios was performed. The explicit solvent surface produced the strongest agreement with experiment, although there is no unambiguous data to support any of the solvent models. (C) 1999 American Institute of Physics. [S0021-9606(99)50336-X].
引用
收藏
页码:5568 / 5579
页数:12
相关论文
共 45 条
  • [21] All-atom empirical potential for molecular modeling and dynamics studies of proteins
    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
    [J]. JOURNAL OF PHYSICAL CHEMISTRY B, 1998, 102 (18) : 3586 - 3616
  • [22] SOLVENT-DEPENDENT CONFORMATIONAL DISTRIBUTIONS OF SOME DIPEPTIDES
    MADISON, V
    KOPPLE, KD
    [J]. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1980, 102 (15) : 4855 - 4863
  • [23] Comparison of continuum and explicit models of solvation: Potentials of mean force for alanine dipeptide
    Marrone, TJ
    Gilson, MK
    McCammon, JA
    [J]. JOURNAL OF PHYSICAL CHEMISTRY, 1996, 100 (05) : 1439 - 1441
  • [24] McQuarrie D. A., 1976, Statistical Mechanics
  • [25] A THERMODYNAMIC SCALE FOR THE HELIX-FORMING TENDENCIES OF THE COMMONLY OCCURRING AMINO-ACIDS
    ONEIL, KT
    DEGRADO, WF
    [J]. SCIENCE, 1990, 250 (4981) : 646 - 651
  • [26] Potentials of mean force for biomolecular simulations: Theory and test on alanine dipeptide
    Pellegrini, M
    GronbechJensen, N
    Doniach, S
    [J]. JOURNAL OF CHEMICAL PHYSICS, 1996, 104 (21) : 8639 - 8648
  • [27] CONFORMATIONAL FREE-ENERGY OF HYDRATION FOR THE ALANINE DIPEPTIDE - THERMODYNAMIC ANALYSIS
    PETTITT, BM
    KARPLUS, M
    [J]. JOURNAL OF PHYSICAL CHEMISTRY, 1988, 92 (13) : 3994 - 3997
  • [28] Press W. H., 1989, Numerical Recipes, V1st
  • [29] A COMPARISON OF THE CHARMM, AMBER AND ECEPP POTENTIALS FOR PEPTIDES .2. PHI-PSI MAPS FOR N-ACETYL ALANINE N'-METHYL AMIDE - COMPARISONS, CONTRASTS AND SIMPLE EXPERIMENTAL TESTS
    ROTERMAN, IK
    LAMBERT, MH
    GIBSON, KD
    SCHERAGA, HA
    [J]. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 1989, 7 (03) : 421 - 453
  • [30] THE CALCULATION OF THE POTENTIAL OF MEAN FORCE USING COMPUTER-SIMULATIONS
    ROUX, B
    [J]. COMPUTER PHYSICS COMMUNICATIONS, 1995, 91 (1-3) : 275 - 282