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通过过量构象熵的测量来量化蛋白质无序度。

Quantifying Protein Disorder through Measures of Excess Conformational Entropy.

作者信息

Rajasekaran Nandakumar, Gopi Soundhararajan, Narayan Abhishek, Naganathan Athi N

机构信息

Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras , Chennai 600036, India.

出版信息

J Phys Chem B. 2016 May 19;120(19):4341-50. doi: 10.1021/acs.jpcb.6b00658. Epub 2016 May 4.

Abstract

Intrinsically disordered proteins (IDPs) and proteins with a large degree of disorder are abundant in the proteomes of eukaryotes and viruses, and play a vital role in cellular homeostasis and disease. One fundamental question that has been raised on IDPs is the process by which they offset the entropic penalty involved in transitioning from a heterogeneous ensemble of conformations to a much smaller collection of binding-competent states. However, this has been a difficult problem to address, as the effective entropic cost of fixing residues in a folded-like conformation from disordered amino acid neighborhoods is itself not known. Moreover, there are several examples where the sequence complexity of disordered regions is as high as well-folded regions. Disorder in such cases therefore arises from excess conformational entropy determined entirely by correlated sequence effects, an entropic code that is yet to be identified. Here, we explore these issues by exploiting the order-disorder transitions of a helix in Pbx-Homeodomain together with a dual entropy statistical mechanical model to estimate the magnitude and sign of the excess conformational entropy of residues in disordered regions. We find that a mere 2.1-fold increase in the number of allowed conformations per residue (∼0.7kBT favoring the unfolded state) relative to a well-folded sequence, or ∼2(N) additional conformations for a N-residue sequence, is sufficient to promote disorder under physiological conditions. We show that this estimate is quite robust and helps in rationalizing the thermodynamic signatures of disordered regions in important regulatory proteins, modeling the conformational folding-binding landscapes of IDPs, quantifying the stability effects characteristic of disordered protein loops and their subtle roles in determining the partitioning of folding flux in ordered domains. In effect, the dual entropy model we propose provides a statistical thermodynamic basis for the relative conformational propensities of amino acids in folded and disordered environments in proteins. Our work thus lays the foundation for understanding and quantifying protein disorder through measures of excess conformational entropy.

摘要

内在无序蛋白(IDP)以及具有高度无序性的蛋白在真核生物和病毒的蛋白质组中大量存在,并在细胞内稳态和疾病中发挥着至关重要的作用。关于IDP提出的一个基本问题是,它们如何抵消从异构构象集合转变为数量少得多的具有结合能力状态时所涉及的熵罚。然而,这一直是一个难以解决的问题,因为从无序氨基酸邻域固定残基形成类似折叠构象的有效熵成本本身尚不清楚。此外,有几个例子表明无序区域的序列复杂性与折叠良好的区域一样高。因此,这种情况下的无序源于完全由相关序列效应决定的过量构象熵,这是一种尚未被识别的熵编码。在这里,我们通过利用Pbx-同源结构域中螺旋的有序-无序转变以及双熵统计力学模型来估计无序区域中残基过量构象熵的大小和符号,从而探讨这些问题。我们发现,相对于折叠良好的序列,每个残基允许的构象数仅增加2.1倍(0.7kBT有利于未折叠状态),或者对于一个N残基序列有2(N)个额外的构象,就足以在生理条件下促进无序。我们表明,这一估计相当可靠,有助于解释重要调节蛋白中无序区域的热力学特征,对IDP的构象折叠-结合景观进行建模,量化无序蛋白环的稳定性效应及其在确定有序结构域中折叠通量分配方面的微妙作用。实际上,我们提出的双熵模型为蛋白质中折叠和无序环境下氨基酸的相对构象倾向提供了统计热力学基础。因此,我们的工作为通过过量构象熵的测量来理解和量化蛋白质无序奠定了基础。

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