Dynamics of the Active Sites of Dimeric Seryl tRNA Synthetase from Methanopyrus kandleri

The Journal of Physical Chemistry. B
Saheb Dutta, Nilashis Nandi

Abstract

Aminoacyl tRNA synthetases (aaRSs) carry out the first step of protein biosynthesis. Several aaRSs are multimeric, and coordination between the dynamics of active sites present in each monomer is a prerequisite for the fast and accurate aminoacylation. However, important lacunae of understanding exist concerning the conformational dynamics of multimeric aaRSs. Questions remained unanswered pertaining to the dynamics of the active site. Little is known concerning the conformational dynamics of the active sites in response to the substrate binding, reorganization of the catalytic residues around reactants, time-dependent changes at the reaction center, which are essential for facilitating the nucleophilic attack, and interactions at the interface of neighboring monomers. In the present work, we carried out all-atom molecular dynamics simulation of dimeric (mk)SerRS from Methanopyrus kandleri bound with tRNA using an explicit solvent system. Two dimeric states of seryl tRNA synthetase (open, substrate bound, and adenylate bound) and two monomeric states (open and substrate bound) are simulated with bound tRNA. The aim is to understand the conformational dynamics of (mk)SerRS during its reaction cycle. While the present results pro...Continue Reading

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Citations

Jul 18, 2015·International Journal of Molecular Sciences·Rongzhong LiSamuel S Cho
Mar 21, 2017·Journal of Biomolecular Structure & Dynamics·Saheb DuttaNilashis Nandi
Jan 5, 2020·Journal of Biomolecular Structure & Dynamics·C RamakrishnanM Michael Gromiha
Jun 27, 2019·Journal of Biomolecular Structure & Dynamics·Amrita SahaNilashis Nandi

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