화학공학소재연구정보센터
Journal of Physical Chemistry B, Vol.101, No.38, 7592-7603, 1997
Modern Computational Methodology Applied to the Simulation of Blocked Trialanine Peptide in-Vacuo, Water Clusters, and Bulk Water
The results of computer simulation studies of CH3CO-(Ala)(3)-NHCH3 solvated in bulk computer water, solvated in computer water clusters, and in vacuo (isolated model molecule) at T = 300 K using modern computational methods are reported. The simulations were performed using a new multipurpose molecular dynamics package, PINY_MD, which utilizes recently developed simulation techniques and is capable of evolving the peptide-water system with an integration time step of 6 fs, 6 times the usual value. Specifically, the conformational free energy surface of the peptide is calculated via umbrella sampling using the distance between the carbonyl oxygen of the N-terminal blocking group and the amide hydrogen of the C-terminal blocking group as the reaction coordinate. Comparisons are made between results obtained using the several different force fields, CHARMM22 (MacKerell, A. D., Jr.; et al., unpublished), CHARMM19 (Brooks, B., et al. J. Comput. Chem 1983, 4, 187.) and AMBER95 (Cornell et al. J. Am. Chem. Sec. 1995, 117, 5179.). Contact is made with the early studies on this system under the conditions of constant temperature and volume using the CHARMM19 force field to model the interactions, a small system and spherical cutoff to treat the Coulombic interactions (Tobias, D. J.; Brooks, C. L., III Biochemistry 1991, 30, 6059-6070.). Quantitative results are presented on effects of finite size, the truncation of Coulombic interactions in periodic systems, and external pressure. Physically, the studies demonstrate quantitatively the effects of progressive hydration (moving the peptide from vacuum to clusters and into the bulk) on internal peptide hydrogen bonding.