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Water and Biomolecules pp 97–121Cite as

Protein Folding and Binding: Effective Potentials, Replica Exchange Simulations, and Network Models

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Abstract

Advances in computational biophysics depend on the development of accurate effective potentials and powerful sampling methods to traverse rugged energy landscapes. We have developed an approach that makes use of the combined power of replica exchange simulations and a network model for kinetics. We carry out replica exchange simulations to generate a very large set of states using an all-atom effective potential function and construct a kinetic model for the folding, using an ansatz that allows kinetic transitions between states based on structural similarity. We are also using replica exchange simulations to study the binding of ligands to proteins such as cytochrome P450. A better understanding of the relationship between the physical kinetics of the systems being studied to their “kinetics” in the replica exchange ensemble is needed to use this new technology to maximum advantage. To illustrate some of the challenges, we will discuss the results using a network model to “simulate” replica exchange simulations of protein folding.

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Authors and Affiliations

  1. Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology Rutgers University, Piscataway, NJ, 08854, USA

    A. K. Felts, M. Andrec, E. Gallicchio & R. M. Levy

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Editor information

Editors and Affiliations

  1. Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, 444-8787, Japan

    Kunihiro Kuwajima

  2. Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan

    Yuji Goto

  3. Institute for Molecular Science Department for Theoretical and Computational Molecular Science, National Institutes of Natural Sciences, 38 Nishigo-Naka, Myodaiji, Okazaki, 444-8585, Japan

    Fumio Hirata

  4. Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-6 Takayama, Ikoma, Nara, 630-0192, Japan

    Mikio Kataoka

  5. Graduate School of Science, Department of Chemistry, Kyoto University, Oiwakecho, Kitashirakawa, Kyoto, 606-8502, Japan

    Masahide Terazima

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© 2009 Springer-Verlag Berlin Heidelberg

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Felts, A.K., Andrec, M., Gallicchio, E., Levy, R.M. (2009). Protein Folding and Binding: Effective Potentials, Replica Exchange Simulations, and Network Models. In: Kuwajima, K., Goto, Y., Hirata, F., Kataoka, M., Terazima, M. (eds) Water and Biomolecules. Biological and Medical Physics, Biomedical . Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88787-4_5

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