Exploration of Transferability in Multiscale Coarse-Grained Peptide Models

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• 作者：Ian F. Thorpe ; David P. Goldenberg ; Gregory A. Voth
• 刊名：Journal of Physical Chemistry B
• 出版年：2011
• 出版时间：October 20, 2011
• 年：2011
• 卷：115
• 期：41
• 页码：11911-11926
• 全文大小：1291K
• 年卷期：v.115,no.41(October 20, 2011)
• ISSN：1520-5207

文摘

Coarse-grained models can facilitate the efficient simulation of complex biological systems. In earlier studies the multiscale coarse-graining (MS-CG) method was employed to examine the folding landscape for two small peptides. In those studies, MS-CG force fields specific to each peptide were employed. We extend here the scope of that work with the goal of obtaining a transferable MS-CG force field which can be used to simulate the folded conformations of peptides with disparate structural motifs. Information obtained via MS-CG modeling was used to understand the characteristics of CG interactions which govern their capacity to be transferred between different peptide systems. We find that polar CG groups are least transferable in general, with interactions between CG sites representing the CO and NH groups on the peptide backbone being particularly resistant to facile transfer. Our results additionally suggest that, while there are limitations to the approach, the MS-CG method may provide a systematic path toward obtaining rigorously defined CG interactions with at least some degree of transferability. These studies also indicate that it may be possible to enhance the transferability of the MS-CG approach by identifying novel ways to combine information from different MS-CG force fields.