Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation.
The dielectrically consistent reference interaction site model (DRISM) integral equation theory is applied to determine the potential of mean force (PMF) for an alanine tetramer. A stochastic dynamics simulation of the alanine tetramer using this PMF is then compared with an explicit water molecular dynamics simulation. In addition, comparison is also done with simulations using other solvent models like the extended reference interaction site model (XRISM) theory, constant dielectric and linear distance-dependent dielectric models. The results show that the DRISM method offers a fairly accurate and computationally inexpensive alternative to explicit water simulations for studies on small peptides.
Prabhu
N V
NV
Department of Chemistry, University of Houston, TX 77204-5641, USA.
Perkyns
J S
JS
Blatt
H D
HD
Smith
P E
PE
Pettitt
B M
BM
D000465:Algorithms; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003198:Computer Simulation; D004563:Electrochemistry; D006241:Haptens / Q000737:chemistry*; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D013269:Stochastic Processes; D014867:Water / Q000737:chemistry
D006241:Haptens; D009842:Oligopeptides; D014867:Water; C026593:alanyl-alanyl-alanyl-alanine