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Simulating Protein Folding in Different Environmental Conditions

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Protein Conformational Dynamics

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 805))

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Abstract

Molecular dynamics simulations have become an invaluable tool in investigating the dynamics of protein folding. However, most computational studies of protein folding assume dilute aqueous simulation conditions in order to reduce the complexity of the system under study and enhance the efficiency. Nowadays, it is evident that environmental conditions encountered in vivo (or even in vitro) play a major role in regulating the dynamics of protein folding especially when one considers the highly condensed environment in the cellular cytoplasm. In order to factor in these conditions, we can utilize the high efficiency of well-designed low resolution (coarse-grained) simulation models to reduce the complexity of these added protein-milieu interactions involving different time and length scales. The goal of this chapter is to describe some recently developed coarse-grained simulation techniques that are specifically designed to go beyond traditional aqueous solvent conditions. The chapter also gives the reader a flavor of the things that we can study using such “smart” low resolution models.

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Authors and Affiliations

  1. AMS Department, Khalifa University, 127788, Abu Dhabi, UAE

    Dirar Homouz

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  1. Dirar Homouz
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Correspondence to Dirar Homouz .

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Editors and Affiliations

  1. Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, People's Republic of China

    Ke-li Han

  2. The Scripps Research Institute, La Jolla, California, USA

    Xin Zhang

  3. Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, People's Republic of China

    Ming-jun Yang

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Homouz, D. (2014). Simulating Protein Folding in Different Environmental Conditions. In: Han, Kl., Zhang, X., Yang, Mj. (eds) Protein Conformational Dynamics. Advances in Experimental Medicine and Biology, vol 805. Springer, Cham. https://doi.org/10.1007/978-3-319-02970-2_8

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