Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.
Proteins. 2010 Feb 15;78(3):506-17. doi: 10.1002/prot.22573.
The interdependence of the concept of allostery and enzymatic catalysis, and they being guided by conformational mobility is gaining increased prominence. However, to gain a molecular level understanding of allostery and hence of enzymatic catalysis, it is of utter importance that the networks of amino acids participating in allostery be deciphered. Our lab has been exploring the methods of network analysis combined with molecular dynamics simulations to understand allostery at molecular level. Earlier we had outlined methods to obtain communication paths and then to map the rigid/flexible regions of proteins through network parameters like the shortest correlated paths, cliques, and communities. In this article, we advance the methodology to estimate the conformational populations in terms of cliques/communities formed by interactions including the side-chains and then to compute the ligand-induced population shift. Finally, we obtain the free-energy landscape of the protein in equilibrium, characterizing the free-energy minima accessed by the protein complexes. We have chosen human tryptophanyl-tRNA synthetase (hTrpRS), a protein responsible for charging tryptophan to its cognate tRNA during protein biosynthesis for this investigation. This is a multidomain protein exhibiting excellent allosteric communication. Our approach has provided valuable structural as well as functional insights into the protein. The methodology adopted here is highly generalized to illuminate the linkage between protein structure networks and conformational mobility involved in the allosteric mechanism in any protein with known structure.
变构和酶催化概念的相互依存关系，以及它们受构象灵活性的指导，正变得越来越重要。然而，为了从分子水平上理解变构作用，从而理解酶催化作用，解析参与变构的氨基酸网络至关重要。我们的实验室一直在探索网络分析方法与分子动力学模拟相结合的方法，以在分子水平上理解变构作用。我们之前已经概述了获得通信路径的方法，然后通过网络参数（如最短相关路径、团和社区）来映射蛋白质的刚性/柔性区域。在本文中，我们将方法推进到根据相互作用（包括侧链）形成的团/社区来估计构象群体，并计算配体诱导的群体转移。最后，我们得到蛋白质在平衡时的自由能景观，描绘蛋白质复合物所达到的自由能最小值。我们选择人类色氨酰-tRNA 合成酶（hTrpRS）作为这项研究的对象，该蛋白在蛋白质生物合成过程中负责将色氨酸加载到其同源 tRNA 上。这是一种表现出极好变构通讯的多功能蛋白。我们的方法为该蛋白提供了有价值的结构和功能见解。这里采用的方法具有高度的通用性，可以阐明任何具有已知结构的蛋白质中变构机制涉及的蛋白质结构网络和构象灵活性之间的联系。
