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Incorporating into a Cα Go model the effects of geometrical restriction on Cα atoms caused by side chain orientations

Authors


Correspondence to: Takeshi Kikuchi, Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan. E-mail: tkikuchi@sk.ritsumei.ac.jp

ABSTRACT

Coarse-grained Go models have been widely used for studying protein-folding mechanisms. Despite the simplicity of the model, these can reproduce the essential features of the folding process of a protein. However, it is also known that side chains significantly contribute to the folding mechanism. Hence, it is desirable to incorporate the side chain effects into a coarse-grained Go model. In this study, to distinguish the effects of side chain orientation and to understand how these effects contribute to folding mechanisms, we incorporate into a Cα Go model not only heterogeneous contact energies but also geometrical restraints around two Cα atoms in contact with each other. We confirm that the heterogeneity of contact energies governs the folding pathway of a protein and that the geometric constraints attributed to side chains reproduce cooperative transitions in folding. Proteins 2013; 81:1434–1445. © 2013 Wiley Periodicals, Inc.

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