The SAAP force field: development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides.
Molecular simulation by using force field parameters has been widely applied in the fields of peptide and protein research for various purposes. We recently proposed a new all-atom protein force field, called the SAAP force field, which utilizes single amino acid potentials (SAAPs) as the fundamental elements. In this article, whole sets of the SAAP force field parameters in vacuo, in ether, and in water have been developed by ab initio calculation for all 20 proteinogenic amino acids and applied to Monte Carlo molecular simulation for two short peptides. The side-chain separation approximation method was employed to obtain the SAAP parameters for the amino acids with a long side chain. Monte Carlo simulation for Met-enkephalin (CHO-Tyr-Gly-Gly-Phe-Met-NH2) by using the SAAP force field revealed that the conformation in vacuo is mainly controlled by strong electrostatic interactions between the amino acid residues, while the SAAPs and the interamino acid Lennard-Jones potentials are predominant in water. In ether, the conformation would be determined by the combination of the three components. On the other hand, the SAAP simulation for chignolin (H-Gly-Tyr-Asp-Pro-Glu-Thr-Gly-Thr-Trp-Gly-OH) reasonably reproduced a native-like beta-hairpin structure in water although the C-terminal and side-chain conformations were different from the native ones. It was suggested that the SAAP force field is a useful tool for analyzing conformations of polypeptides in terms of intrinsic conformational propensities of the single amino acid units.
Iwaoka
Michio
M
Department of Chemistry, School of Science, Tokai University, Kitakaname, Hiratsuka-shi, Kanagawa 259-1292, Japan. miwaoka@tokai.ac.jp
Kimura
Naoki
N
Yosida
Daisuke
D
Minezaki
Toshiya
T
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D003198:Computer Simulation; D004745:Enkephalins / Q000737:chemistry; D004986:Ether / Q000737:chemistry; D015394:Molecular Structure; D009010:Monte Carlo Method; D009842:Oligopeptides / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D000596:Amino Acids; D004745:Enkephalins; D009842:Oligopeptides; D010455:Peptides; C506175:chignolin; D014867:Water; D004986:Ether