集体重新包装揭示了蛋白质核心的结构是由空间排斥性相互作用唯一指定的

Jennifer C. Gaines, Alejandro Virrueta, D. A. Buch, S. Fleishman, C. O’Hern, Lynne Regan
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引用次数: 9

摘要

摘要蛋白质核心重包装是蛋白质建模软件的一项标准测试。最近对六种不同的建模软件包的研究表明,与表面残留物相比,它们在预测核心侧链构象方面更成功。所有测试的建模软件都具有多组分能量函数,除了基于观察到的蛋白质结构的统计术语外,通常还包括来自溶剂化、静电、氢键和Lennard-Jones相互作用的贡献。我们研究了仅包括立体化学约束和排斥硬球相互作用的简化能量函数在多大程度上可以正确地重新包装蛋白质核心。对于单个残基和集体重包装,硬球模型准确地概括了观察到的Ile、Leu、Phe、Thr、Trp、Tyr和Val的侧链构象。这一结果表明,核心残基不存在可替代的、空间允许的侧链构象。使用Rosetta软件套件对同一组蛋白核进行分析显示,硬球模型和Rosetta在Ile、Leu、Phe、Thr和Val上的表现相同;硬球模型在Trp和Tyr上表现更好,而Rosetta在Ser上表现更好。我们得出结论,通过蛋白质建模软件和我们的简化硬球方法获得的蛋白质核的高预测精度反映了蛋白质核的高密度和空间排斥的优势。
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Collective repacking reveals that the structures of protein cores are uniquely specified by steric repulsive interactions
Abstract Protein core repacking is a standard test of protein modeling software. A recent study of six different modeling software packages showed that they are more successful at predicting side chain conformations of core compared to surface residues. All the modeling software tested have multicomponent energy functions, typically including contributions from solvation, electrostatics, hydrogen bonding and Lennard–Jones interactions in addition to statistical terms based on observed protein structures. We investigated to what extent a simplified energy function that includes only stereochemical constraints and repulsive hard-sphere interactions can correctly repack protein cores. For single residue and collective repacking, the hard-sphere model accurately recapitulates the observed side chain conformations for Ile, Leu, Phe, Thr, Trp, Tyr and Val. This result shows that there are no alternative, sterically allowed side chain conformations of core residues. Analysis of the same set of protein cores using the Rosetta software suite revealed that the hard-sphere model and Rosetta perform equally well on Ile, Leu, Phe, Thr and Val; the hard-sphere model performs better on Trp and Tyr and Rosetta performs better on Ser. We conclude that the high prediction accuracy in protein cores obtained by protein modeling software and our simplified hard-sphere approach reflects the high density of protein cores and dominance of steric repulsion.
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