Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics

International Journal of Molecular Sciences

Ronald D. Hills¹ 

[1] Department of Molecular Biology and Kellogg School of Science and Technology, The Scripps Research Institute, 10550 N. Torrey Pines Rd. TPC6 La Jolla, CA 92037, USA

关键词: Protein folding;    Gō models;    coarse-graining;    energy landscape;    conformational transitions;   

DOI  :  10.3390/ijms10030889

来源: mdpi

【 摘 要 】

Exploring the landscape of large scale conformational changes such as protein folding at atomistic detail poses a considerable computational challenge. Coarse-grained representations of the peptide chain have therefore been developed and over the last decade have proved extremely valuable. These include topology-based Gō models, which constitute a smooth and funnel-like approximation to the folding landscape. We review the many variations of the Gō model that have been employed to yield insight into folding mechanisms. Their success has been interpreted as a consequence of the dominant role of the native topology in folding. The role of local contact density in determining protein dynamics is also discussed and is used to explain the ability of Gō-like models to capture sequence effects in folding and elucidate conformational transitions.

【 授权许可】

CC BY   
© 2009 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland. This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).