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BP: Fachverband Biologische Physik

BP 14: Posters: Protein Structure and dynamics

BP 14.8: Poster

Tuesday, April 1, 2014, 09:30–12:30, P1

Thermodynamic characterization of protein folding using Monte Carlo methods — •Nana Heilmann, Moritz Wolf, Julia Setzler, and Wolfgang Wenzel — INT, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany

The study of protein folding has been a difficult challenge in molecular biology and simulation science. Up-to-date research showed reproducible folding of small protein using molecular dynamics simulations. These results can be only achieved by using time-consuming, specialized supercomputers [1]. In contrast to molecular dynamics simulations, Monte Carlo based simulations are not constrained solving Newton's equation of motion and therefore protein folding simulations can be compute on conventional computer architectures. In this study, we show reproducible all-atom folding transition of the villin headpiece 1VII, which was simulated by using SIMONA[2], a Monte Carlo based simulation package for nanoscale simulations including a variant of the Amber99SB*-ILDN[3]. The results of these simulations demonstrate that Monte Carlo simulation techniques are generally applicable to the investigation of large-scale conformational changes of protein on conventional computer architectures. The thermodynamic characterization of simulated proteins can be compared with the experimental results while the computing time for observing folding/refolding events can be significantly reduced in comparison with molecular dynamics simulations. [1] Shaw et al. Science 330 (2010). [2] Wolf et al. J Comput Chem (2012). [3] Lindorff-Larsen et al. Science 334 (2011).