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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach.
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Identifying residue-residue clashes in protein hybrids by using a second-order mean-field approach.

机译：通过使用二阶均值场方法识别蛋白质杂种中的残基-残基冲突。

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摘要

In this article, a second-order mean-field-based approach is introduced for characterizing the complete set of residue-residue couplings consistent with a given protein structure. This information is subsequently used to classify protein hybrids with respect to their potential to be functional based on the presenceabsence and severity of clashing residue-residue interactions. First, atomistic representations of both the native and denatured states are used to calculate rotamer-backbone, rotamer-intrinsic, and rotamer-rotamer conformational energies. Next, this complete conformational energy table is coupled with a second-order mean-field description to elucidate the probabilities of all possible rotamer-rotamer combinations in a minimum Helmholtz free-energy ensemble. Computational results for the dihydrofolate reductase family reveal correlation in substitution patterns between not only contacting but also distal second-order structural elements. Residue-residue clashes in hybrid proteins are quantified by contrasting the ensemble probabilities of protein hybrids against the ones of the original parental sequences. Good agreement with experimental data is demonstrated by superimposing these clashes against the functional crossover profiles of bidirectional incremental truncation libraries for Escherichia coli and human glycinamide ribonucleotide transformylases.
机译：在本文中，引入了基于二阶均值场的方法来表征与给定蛋白质结构一致的残基-残基偶联的完整集合。该信息随后用于根据杂合残基-残基相互作用的存在和严重程度，根据功能性潜力对蛋白质杂种进行分类。首先，原始状态和变性状态的原子表示都用于计算rotamer-主干，rotamer-本征和rotamer-rotamer构象能。接下来，将此完整的构象能表与二阶均值场描述相结合，以阐明最小亥姆霍兹自由能系中所有可能的旋转异构体-旋转异构体组合的概率。二氢叶酸还原酶家族的计算结果表明，不仅接触而且远端的二阶结构元素之间的取代模式也相关。通过将蛋白质杂种与原始亲本序列中的杂种的集合概率进行对比，可以量化杂合蛋白中的残基-残基冲突。通过将这些冲突与大肠杆菌和人甘氨酰胺核糖核苷酸转化酶的双向增量截短文库的功能交换图谱叠加，证明了与实验数据的良好一致性。

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