Rajasekaran Nandakumar, Suresh Swaathiratna, Gopi Soundhararajan, Raman Karthik, Naganathan Athi N
Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras , Chennai 600036, India.
Center for Biotechnology, Anna University , Chennai 600025, India.
Biochemistry. 2017 Jan 10;56(1):294-305. doi: 10.1021/acs.biochem.6b00798. Epub 2016 Dec 27.
Mutations in the hydrophobic interior of proteins are generally thought to weaken the interactions only in their immediate neighborhood. This forms the basis of protein engineering-based studies of folding mechanism and function. However, mutational work on diverse proteins has shown that distant residues are thermodynamically coupled, with the network of interactions within the protein acting as signal conduits, thus raising an intriguing paradox. Are mutational effects localized, and if not, is there a general rule for the extent of percolation and the functional form of this propagation? We explore these questions from multiple perspectives in this work. Perturbation analysis of interaction networks within proteins and microsecond long molecular dynamics simulations of several aliphatic mutants of ubiquitin reveal strong evidence of the distinct alteration of distal residue-residue communication networks. We find that mutational effects consistently propagate into the second shell of the altered site (even up to 15-20 Å) in proportion to the perturbation magnitude and dissipate exponentially with a decay distance constant of ∼4-5 Å. We also report evidence for this phenomenon from published experimental nuclear magnetic resonance data that strikingly resemble predictions from network theory and molecular dynamics simulations. Reformulating these observations onto a statistical mechanical model, we reproduce the stability changes of 375 mutations from 19 single-domain proteins. Our work thus reveals a robust energy dissipation-cum-signaling mechanism in the interaction network within proteins, quantifies the partitioning of destabilization energetics around the mutation neighborhood, and presents a simple theoretical framework for modeling the allosteric effects of point mutations.
蛋白质疏水内部的突变通常被认为只会削弱其紧邻区域的相互作用。这构成了基于蛋白质工程的折叠机制和功能研究的基础。然而，对多种蛋白质的突变研究表明，远距离残基在热力学上是相互耦合的，蛋白质内部的相互作用网络充当信号传导通道，从而引发了一个有趣的悖论。突变效应是局部化的吗？如果不是，渗流范围和这种传播的功能形式是否存在一般规律？我们在这项工作中从多个角度探讨了这些问题。对蛋白质内部相互作用网络的扰动分析以及对泛素几种脂肪族突变体的微秒级长时间分子动力学模拟揭示了远端残基 - 残基通信网络明显改变的有力证据。我们发现，突变效应始终会按扰动幅度的比例传播到改变位点的第二壳层（甚至可达15 - 20 Å），并以约4 - 5 Å的衰减距离常数呈指数衰减。我们还从已发表的实验核磁共振数据中报告了这一现象的证据，这些数据与网络理论和分子动力学模拟的预测惊人地相似。将这些观察结果重新构建到一个统计力学模型中，我们重现了来自19种单结构域蛋白质的375个突变的稳定性变化。因此，我们的工作揭示了蛋白质内部相互作用网络中一种强大的能量耗散兼信号传导机制，量化了突变邻域周围去稳定化能量学的分配，并提出了一个用于模拟点突变变构效应的简单理论框架。
