a coarse-grained approach to protein design learning from design to understand folding一个粗粒度的蛋白质设计方法学习从设计到理解折叠.pdfVIP

A Coarse-Grained Approach to Protein Design: Learning from Design to Understand Folding Ivan Coluzza* Department of Physics, University of Vienna, Vienna, Austria Abstract Computational studies have given a great contribution in building our current understanding of the complex behavior of protein molecules; nevertheless, a complete characterization of their free energy landscape still represents a major challenge. Here, we introduce a new coarse-grained approach that allows for an extensive sampling of the conformational space of a large number of sequences. We explicitly discuss its application in protein design, and by studying four representative proteins, we show that the method generates sequences with a relatively smooth free energy surface directed towards the target structures. Citation: Coluzza I (2011) A Coarse-Grained Approach to Protein Design: Learning from Design to Understand Folding. PLoS ONE 6(7): e20853. doi:10.1371/ journal.pone.0020853 Editor: Annalisa Pastore, National Institute for Medical Research, Medical Research Council, London, United Kingdom Received March 17, 2011; Accepted May 10, 2011; Published July 1, 2011 Copyright: 2011 Ivan Coluzza. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The author acknowledges financial supported by the Austrian Science Foundation (FWF) within the SFB ViCoM (F 41), and Intra-European mobility grant FP6 Project No.: 24496. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The author has declared that no competing interests exist.