Abstract
Recent progress has permitted observation of reproducible folding of small proteins in molecular dynamics simulations(1, 2). Despite the availability of transferable forcefields, these methods remain constrained by the short time-step and availability of specialized hardware. using a new Monte-Carlo based biomolecular simulation code, SIMONA(3), with a modified AMBER forcefield we observe rapid reproducible folding transitions in single-PC simulations of several small proteins, including the villin headpiece and the WW-domain, which can be used to completely characterize the protein folding equilibrium at the all-atom level. These results demonstrate that Monte-Carlo methods can significantly accelerate sampling of large-scale conformational changes of proteins on widely accessible computational resources.1. Lindorff-Larsen, K., et. al. Science 334, 517-520. (2012)2. Shaw, D. E., et.al. Science 330, 341-346 (2010).3. Strunk, T., et. al. SIMONA 1.0: An efficient and versatile framework for stochastic simulations of molecular and nanoscale systems, J. Comp. Chem, DOI: 10.1002/jcc.23089. (2012)View Large Image | View Hi-Res Image | Download PowerPoint Slide
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