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Significance of triple torsional correlations in proteins

机译：蛋白质三重扭转相关性的意义

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摘要

The free energy landscape (FEL) of a given complex molecular system is fundamentally the joint probability density of its many comprising degrees of freedom (DOFs). Computation of a complete FEL at atomistic scale is unfortunately intractable for a typical biomolecular system. The challenge of entropy calculation comes from various correlations among different DOFs. The common strategy to treat such complexity is expansion of the full correlation into various orders of local correlations. In reality, expansion is usually cut off at the second order (i.e. pairwise interactions) for protein torsional correlations without reliable estimation of the resulting error. Here, we estimated the mutual information of different torsion sets and found that triple correlations were significant for both local/distant residue pairs and consecutive backbone torsional segments. As expected, the third order approximations were found to be consistently better than the second order approximations. These findings were true for all analyzed proteins with different folds, were independent of the two different force fields utilized to generate trajectory sets, and were therefore likely to be of general importance for proteins. Additionally, binning strategies are of universal importance for numerical computation of correlations, we here provided a detailed comparison between equal-width and equal-sample binning for different bin numbers and demonstrated the impact of binning strategies on variances and biases of calculated mutual information. Our observation suggested that caution should be taken when quantitative comparison of correlations were intended between different studies with different binning strategies.
机译：给定复杂的分子系统的自由能景观（FEL）基本上是其许多包括自由度（DOF）的联合概率密度。遗憾的是，在原始尺度上计算完整的FEL对于典型的生物分子系统是棘手的。熵计算的挑战来自不同的DOF之间的各种相关性。治疗这种复杂性的共同策略是扩大与各种局部相关性的完全相关性。实际上，扩增通常在第二阶（即成对相互作用）上切断蛋白质扭转相关性，而无需可靠地估计所产生的误差。这里，我们估计了不同扭转集的相互信息，发现三重相关性对于局部/远处残留物对和连续的骨架扭转段具有重要意义。正如预期的那样，发现第三阶近似度始终比二阶近似更好。这些发现对于具有不同折叠的所有分析的蛋白质是真实的，与用于产生轨迹组的两个不同的力场无关，因此可能对蛋白质一般重要性。此外，融合策略对相关性的数值计算具有普遍重要性，我们在这里提供了不同箱数的等宽和等于样本排放之间的详细比较，并展示了融合策略对计算的互信息的差异和偏差的影响。我们的观察表明，应当在不同的融合策略之间的不同研究之间进行定量比较时注意谨慎。

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  • 来源
    《RSC Advances》 |2019年第24期|共10页
  • 作者

    Long Shiyang; Wang Jianwei; Tian Pu;

  • 作者单位

    Jilin Univ Sch Chem Changchun Jilin Peoples R China;

    Jilin Univ Sch Life Sci Changchun Jilin Peoples R China;

    Jilin Univ Sch Life Sci Sch Artificial Intelligence 2699 Qianjin St Changchun 130012 Jilin Peoples R China;

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  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类 化学;
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