Aminoacylation reaction in the histidyl-tRNA synthetase: fidelity mechanism of the activation step

The Journal of Physical Chemistry. B
Sindrila Dutta Banik, Nilashis Nandi

Abstract

Aminoacylation is a vital step of natural biosynthesis of peptide. Correct aminoacylation is a necessary prerequisite for the elimination of noncognate amino acids such as D-amino acids. In the present work, we studied the fidelity mechanism of histidine (His) activation (first step of aminoacylation reaction) using a combined quantum mechanical/semiempirical method based on a model of crystal structure of the oligomeric complex of histidyl-tRNA synthetase (HisRS) from Escherichia coli. The study of the variation in the energy during the mutual approach of the His and ATP to form adenylate shows that the surrounding nanospace of synthetase confines the reactants (L-His and ATP) and proximally places in a geometry suitable for the in-line nucleophilic attack. The significantly higher energy of the energy surface of the model containing D-His is due to unfavorable interaction of D-His with ATP and surrounding residues. This indicates that the network of interaction (principally electrostatic) is highly unfavorable when D-amino acid is incorporated. The reorganization of the surrounding nanospace can lower the unfavorable nature of the intermolecular energy surface of D-His and surrounding residues. However, such a rearrangement r...Continue Reading

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Citations

Jun 27, 2012·Journal of Biomolecular Structure & Dynamics·Sindrila Dutta Banik, Nilashis Nandi
Mar 21, 2015·The Journal of Physical Chemistry. B·Saheb Dutta, Nilashis Nandi
Mar 21, 2017·Journal of Biomolecular Structure & Dynamics·Saheb DuttaNilashis Nandi
Jan 10, 2020·PLoS Computational Biology·Vaitea OpuuThomas Simonson
Nov 1, 2012·EcoSal Plus·Richard Giegé, Mathias Springer
Oct 15, 2021·The Journal of Physical Chemistry. B·Paweł KędzierskiW Andrzej Sokalski

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