Coarse kMC-based replica exchange algorithms for the accelerated simulation of protein folding in explicit solvent.
In this paper, we present a coarse replica exchange molecular dynamics (REMD) approach, based on kinetic Monte Carlo (kMC). The new development significantly can reduce the amount of replicas and the computational cost needed to enhance sampling in protein simulations. We introduce 2 different methods which primarily differ in the exchange scheme between the parallel ensembles. We apply this approach on folding of 2 different β-stranded peptides: the C-terminal β-hairpin fragment of GB1 and TrpZip4. Additionally, we use the new simulation technique to study the folding of TrpCage, a small fast folding α-helical peptide. Subsequently, we apply the new methodology on conformation changes in signaling of the light-oxygen voltage (LOV) sensitive domain from Avena sativa (AsLOV2). Our results agree well with data reported in the literature. In simulations of dialanine, we compare the statistical sampling of the 2 techniques with conventional REMD and analyze their performance. The new techniques can reduce the computational cost of REMD significantly and can be used in enhanced sampling simulations of biomolecules.
Institute of Computational Science, Faculty of Informatics, University of Lugano, Switzerland. igor.pivkin@usi.ch.
Emanuel K
EK
Peter
Joan-Emma
JE
Shea
Igor V
IV
Pivkin
D000465:Algorithms; D018554:Avena / Q000737:chemistry; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D010940:Plant Proteins / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D010455:Peptides; D010940:Plant Proteins; D011506:Proteins; C539234:Trpzip2 protein