Enhanced conformational sampling in Monte Carlo simulations of proteins: application to a constrained peptide.
A Monte Carlo simulation method for globular proteins, called extended-scaled-collective-variable (ESCV) Monte Carlo, is proposed. This method combines two Monte Carlo algorithms known as entropy-sampling and scaled-collective-variable algorithms. Entropy-sampling Monte Carlo is able to sample a large configurational space even in a disordered system that has a large number of potential barriers. In contrast, scaled-collective-variable Monte Carlo provides an efficient sampling for a system whose dynamics is highly cooperative. Because a globular protein is a disordered system whose dynamics is characterized by collective motions, a combination of these two algorithms could provide an optimal Monte Carlo simulation for a globular protein. As a test case, we have carried out an ESCV Monte Carlo simulation for a cell adhesive Arg-Gly-Asp-containing peptide, Lys-Arg-Cys-Arg-Gly-Asp-Cys-Met-Asp, and determined the conformational distribution at 300 K. The peptide contains a disulfide bridge between the two cysteine residues. This bond mimics the strong geometrical constraints that result from a protein's globular nature and give rise to highly cooperative dynamics. Computation results show that the ESCV Monte Carlo was not trapped at any local minimum and that the canonical distribution was correctly determined.
Kidera
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Protein Engineering Research Institute, Osaka, Japan.
D000465:Algorithms; D000595:Amino Acid Sequence; D015815:Cell Adhesion Molecules / Q000737:chemistry; D003198:Computer Simulation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D009842:Oligopeptides / Q000737:chemistry*; D011336:Probability; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D015815:Cell Adhesion Molecules; D009842:Oligopeptides; D011506:Proteins; C047981:arginyl-glycyl-aspartic acid