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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Quantitative Criteria For Native Energetic Heterogeneityinfluences In The Prediction Of Protein Folding Kinetics
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Quantitative Criteria For Native Energetic Heterogeneityinfluences In The Prediction Of Protein Folding Kinetics

机译：天然能量异质性影响蛋白质折叠动力学预测的定量标准

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摘要

Energy landscape theory requires that the protein-folding mechanism is generally globally directed or funneled toward the native state. The collective nature of transition state ensembles further suggests that sufficient averaging of the native interactions can occur so that the knowledge of the native topology may suffice for predicting the mechanism. Nevertheless, while simple homogeneously weighted native topology-based models predict the folding mechanisms for many proteins, for other proteins knowledge of the native topology, by itself, seems not to suffice in determining the folding mechanism. Simulations of proteins with differing topologies reveal that the failure of homogeneously weighted topology-based models can, however, be completely understood within the framework of a funneled energy landscape and can be quantified by comparing the fluctuation of entropy cost for forming contacts to the expected fluctuations in contact energy. To be precise, we find the transition state ensembles of proteins with all-α topologies, which are more uniform in the specific entropy cost of contact formation, have transition state ensembles that are more readily perturbed by differences in energetic weights than are the transition state ensembles of proteins with significant amounts of β-structure, where the specific entropy costs of contact formation are more widely distributed. This behavior is consistent with a random-field Ising model analogy that follows from the free energy functional approach to folding.
机译：能量格局理论要求蛋白质折叠机制通常是全局导向的或朝向天然状态漏斗。过渡状态集合的集体性质进一步表明，可以发生本机交互的足够平均，因此，本机拓扑的知识可能足以预测该机制。然而，尽管简单的基于均匀加权的基于天然拓扑的模型预测了许多蛋白质的折叠机制，但对于其他蛋白质而言，关于天然拓扑的知识本身似乎不足以确定折叠机制。对具有不同拓扑结构的蛋白质的仿真表明，基于均质加权拓扑结构的模型的失败可以在漏斗能量格局的框架内完全理解，并且可以通过将形成接触的熵代价波动与预期波动进行比较来量化接触能量。确切地说，我们发现具有全α拓扑结构的蛋白质的过渡态集成体在接触形成的特定熵成本上更均匀，并且具有过渡态集成体，该过渡态集成体比过渡态更容易受到能量权重差异的干扰大量具有β结构的蛋白质的集合体，其中接触形成的特定熵代价分布更为广泛。这种行为与从自由能功能方法到折叠的随机场Ising模型相似。

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  • 作者

    Samuel S. Cho; Yaakov Levy; Peter G. Wolynes;

  • 作者单位

    Center for Theoretical Biological Physics University of California at San Diego 9500 Gilman Drive, La Jolla, CA 92093 Departments of Chemistry and Biochemistry University of California at San Diego 9500 Gilman Drive, La Jolla, CA 92093;

    Center for Theoretical Biological Physics University of California at San Diego 9500 Gilman Drive, La Jolla, CA 92093 Departments of Physics, University of California at San Diego 9500 Gilman Drive, La Jolla, CA 92093;

    Center for Theoretical Biological Physics University of California at San Diego 9500 Gilman Drive, La Jolla, CA 92093 Departments of Chemistry and Biochemistry University of California at San Diego 9500 Gilman Drive, La Jolla, CA 92093 Departments of Physics, University of California at San Diego 9500 Gilman Drive, La Jolla, CA 92093;

  • 收录信息 美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    energy landscape theory; random-field ising model; native topology-based models;

    机译：能源景观理论;随机场消散模型;基于自然拓扑的模型;

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