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通过松散耦合分子动力学模拟研究SH3结构域折叠核的形成

Formation of the folding nucleus of an SH3 domain investigated by loosely coupled molecular dynamics simulations.

作者信息

Settanni G, Gsponer J, Caflisch A

机构信息

Biochemisches Institut, Universität Zürich, Zürich, Switzerland.

出版信息

Biophys J. 2004 Mar;86(3):1691-701. doi: 10.1016/S0006-3495(04)74238-1.

DOI:10.1016/S0006-3495(04)74238-1
PMID:14990497
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1304005/
Abstract

The experimentally well-established folding mechanism of the src-SH3 domain, and in particular the phi-value analysis of its transition state, represents a sort of testing table for computational investigations of protein folding. Here, parallel molecular dynamics simulations of the src-SH3 domain have been performed starting from denatured conformations. By rescuing and restarting only trajectories approaching the folding transition state, an ensemble of conformations was obtained with a completely structured central beta-sheet and a native-like packing of residues Ile-110, Ala-121, and Ile-132. An analysis of the trajectories shows that there are several pathways leading to the formation of the central beta-sheet whereas its two hairpins form in a different but consistent way.

摘要

src-SH3结构域已通过实验充分确立的折叠机制，尤其是其过渡态的φ值分析，代表了蛋白质折叠计算研究的一种测试平台。在此，从变性构象开始对src-SH3结构域进行了并行分子动力学模拟。通过仅挽救和重新启动接近折叠过渡态的轨迹，获得了一组构象，其具有完全结构化的中央β-折叠以及Ile-110、Ala-121和Ile-132残基的类似天然的堆积。对轨迹的分析表明，有几条途径可导致中央β-折叠的形成，而其两个发夹以不同但一致的方式形成。

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