Protein folding mechanisms and energy landscape of src SH3 domain studied by a structure prediction toolbox
Protein folding mechanisms and energy landscape of src SH3 domain studied by a structure prediction toolbox
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DOI：
10.1016/j.chemphys.2004.06.015
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发表时间：
2004-12-27
期刊：
影响因子：
2.3
通讯作者：
Takada, S
中科院分区：
文献类型：
--
作者：
Chikenji, G;Fujitsuka, Y;Takada, S
利用物理-化学蛋白质模型和可逆片段组装方法，全面探索了src SH3结构域的全球能量格局，并讨论了折叠机制。我们发现在模拟中发现的最低能量结构与自然状态非常相似，在变性态和自然状态之间存在明显的自由能垒，并且计算的折叠过渡态系综与实验数据吻合得很好。有趣的是，在折叠的早期阶段发现了非天然的α -螺旋内容物，这似乎也与最近的一项实验相一致。这些结果表明，最初用于结构预测的片段组装方法也可用于研究折叠机制。(C) 2004年Elsevier B.V.出版
The global energy landscape of src SH3 domain is comprehensively explored and folding mechanisms are discussed by using a physico-chemical protein model and the reversible fragment assembly method. We found that the lowest energy structure found in simulations is quite similar to the native, an apparent free energy barrier exists between the denatured and native states, and the computed folding transition state ensemble is well consistent with experimental data. Interestingly, non-native alpha-helical contents are found at early stage of folding, which also seems to be consistent with a recent experiment. These results suggest that the fragment assembly method, originally developed for structure prediction, can be used for studying folding mechanisms as well. (C) 2004 Published by Elsevier B.V.