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• W2073213802 abstract "Pyrrolysyl-tRNA synthetase (PylRS) is an atypical enzyme responsible for charging tRNAPyl with pyrrolysine, despite lacking precise tRNA anticodon recognition. This dimeric protein exhibits allosteric regulation of function, like any other tRNA synthetases. In this study we examine the paths of allosteric communication at the atomic level, through energy-weighted networks of Desulfitobacterium hafniense PylRS (DhPylRS) and its complexes with tRNAPyl and activated pyrrolysine. We performed molecular dynamics simulations of the structures of these complexes to obtain an ensemble conformation–population perspective. Weighted graph parameters relevant to identifying key players and ties in the context of social networks such as edge/node betweenness, closeness index, and the concept of funneling are explored in identifying key residues and interactions leading to shortest paths of communication in the structure networks of DhPylRS. Further, the changes in the status of important residues and connections and the costs of communication due to ligand induced perturbations are evaluated. The optimal, suboptimal, and preexisting paths are also investigated. Many of these parameters have exhibited an enhanced asymmetry between the two subunits of the dimeric protein, especially in the pretransfer complex, leading us to conclude that encoding of function goes beyond the sequence/structure of proteins. The local and global perturbations mediated by appropriate ligands and their influence on the equilibrium ensemble of conformations also have a significant role to play in the functioning of proteins. Taking a comprehensive view of these observations, we propose that the origin of many functional aspects (allostery and half-sites reactivity in the case of DhPylRS) lies in subtle rearrangements of interactions and dynamics at a global level." @default.
• W2073213802 created "2016-06-24" @default.
• W2073213802 creator A5031607667 @default.
• W2073213802 creator A5080298741 @default.
• W2073213802 date "2011-06-23" @default.
• W2073213802 modified "2023-10-16" @default.
• W2073213802 title "Probing the Allosteric Mechanism in Pyrrolysyl-tRNA Synthetase Using Energy-Weighted Network Formalism" @default.
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• W2073213802 doi "https://doi.org/10.1021/bi200306u" @default.
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