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首页> 外文期刊>The Journal of Chemical Physics >Understanding protein folding cooperativity based on topologicalconsideration
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Understanding protein folding cooperativity based on topologicalconsideration

机译：基于拓扑考虑了解蛋白质折叠的协同性

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The folding cooperativity is an important issue of protein folding dynamics. Since the nativetopology plays a significant role in determining the folding behavior of proteins, we believe that italso has close relationship with the folding cooperativity. In the present work, we performsimulations on proteins Naf-BBL, QNND-BBL, CI2, and SH3 with the Gō model and compare theirdifferent folding behaviors. By analyzing the weak cooperative folding of protein Naf-BBL in detail,we found that the folding of Naf-BBL shows relatively weak thermodynamic coupling betweenresidues, and such weak coupling is found mainly between the nonlocal native contacts. This findingcomplements our understandings on the source of barrierless folding of Naf-BBL and promotes usto analyze the topological origins of the poor thermodynamic coupling of Naf-BBL. Then, wefurther extend our analysis to other two-state and multistate proteins. Based on the considerations ofthe thermodynamic coupling and kinetic coupling, we conclude that the fraction of scattered nativecontacts, the difference in loop entropy of contacts, and the long range relative contact order are themajor topological factors that influence the folding cooperativity. The combination of these threetertiary structural features shows significant correlations with the folding types of proteins.Moreover, we also discuss the topological factors related to downhill folding. Finally, the genericrole of tertiary structure in determining the folding cooperativity is summarized.
机译：折叠协同性是蛋白质折叠动力学的重要问题。由于自然拓扑学在确定蛋白质的折叠行为中起着重要作用，因此我们认为它也与折叠合作性密切相关。在目前的工作中，我们对具有Gō模型的蛋白Naf-BBL，QNND-BBL，CI2和SH3进行了模拟，并比较了它们不同的折叠行为。通过详细分析蛋白质Naf-BBL的弱协同折叠，我们发现Naf-BBL的折叠在残基之间显示出相对较弱的热力学耦合，而这种弱耦合主要在非本地天然接触之间发现。这一发现补充了我们对Naf-BBL无障碍折叠来源的理解，并促进了我们对Naf-BBL热力学偶联不良的拓扑起源进行分析。然后，我们进一步将分析扩展到其他两种状态和多状态蛋白。基于热力学耦合和动力学耦合的考虑，我们得出结论，分散的自然接触的比例，接触环熵的差异以及远距离相对接触顺序是影响折叠协同性的主要拓扑因素。这些三级结构特征的组合显示出与蛋白质折叠类型的显着相关性。此外，我们还讨论了与下坡折叠有关的拓扑因素。最后，总结了三元结构在确定折叠合作性中的作用。

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