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摘要翻译：
我们提出了一个验证的SH3畴跃迁态系综的计算模型。该模型是用全原子蛋白质折叠模拟中的实验s为三个独立的SH3结构域建立的。虽然对所有构象的平均不正确地认为非TS构象是过渡态，但通过测量它们的透射系数（pfold或折叠概率）将结构量化为前TS、TS和后TS允许关于折叠核结构的严格结论和折叠过程的全面机械分析。通过对TS的分析，我们观察到一个高度极化的核，其中许多残留物暴露在溶剂中。机理分析表明，疏水核主要是在早期成核后形成的。SH3为研究成核-缩合机理提供了一个理想的体系，突出了实验与模拟在蛋白质折叠研究中的协同关系。
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英文标题：
《Nucleation and the transition state of the SH3 domain》
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作者：
Isaac A. Hubner, Katherine A. Edmonds, and Eugene I. Shakhnovich
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最新提交年份：
2005
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分类信息：
一级分类：Quantitative Biology 数量生物学
二级分类：Biomolecules 生物分子
分类描述：DNA, RNA, proteins, lipids, etc.; molecular structures and folding kinetics; molecular interactions; single-molecule manipulation.
DNA、RNA、蛋白质、脂类等；分子结构与折叠动力学；分子相互作用；单分子操作。
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一级分类：Quantitative Biology 数量生物学
二级分类：Other Quantitative Biology 其他定量生物学
分类描述：Work in quantitative biology that does not fit into the other q-bio classifications
不适合其他q-bio分类的定量生物学工作
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英文摘要：
We present a verified computational model of the SH3 domain transition state (TS) ensemble. This model was built for three separate SH3 domains using experimental s in all-atom protein folding simulations. While averaging over all conformations incorrectly considers non-TS conformations as transition states, quantifying structures as pre-TS, TS, and post-TS by measurement of their transmission coefficient (pfold, or probability to fold) allows for rigorous conclusions regarding the structure of the folding nucleus and a full mechanistic analysis of the folding process. Through analysis of the TS, we observe a highly polarized nucleus in which many residues are solvent-exposed. Mechanistic analysis suggests the hydrophobic core forms largely after an early nucleation step. SH3 presents an ideal system for studying the nucleation-condensation mechanism and highlights the synergistic relationship between experiment and simulation in the study of protein folding.
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PDF链接：
https://arxiv.org/pdf/q-bio/0503027
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