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Structure and Dynamics of tRNAMet Containing Core Substitutions

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abstract
The fidelity of protein synthesis is largely dominated by the accurate recognition of transfer RNAs (tRNAs) by their cognate aminoacyl-tRNA synthetases. Aminoacylation of each tRNA with its cognate amino acid is necessary to maintain the accuracy of genetic code input. Aminoacylated tRNAMet functions in both initiation and elongation steps during protein synthesis. As a precursor to the investigation of a methionyl-tRNA synthetase–tRNAMet complex, presented here are the results of molecular dynamics (MD) for single nucleotide substitutions in the D-loop of tRNAMet (G15A, G18A, and G19A) probing structure/function relationships. The core of tRNAMet likely mediates an effective communication between the tRNA anticodon and acceptor ends, contributing an acceptor stem rearrangement to fit into the enzyme-active site. Simulations of Escherichia coli tRNAMet were performed for 1 μs four times each. The MD simulations showed changes in tRNA flexibility and long-range communication most prominently in the G18A variant. The results indicate that the overall tertiary structure of tRNAMet remains unchanged with these substitutions; yet, there are perturbations to the secondary structure. Network-based analysis of the hydrogen bond structure and correlated motion indicates that the secondary structure elements of the tRNA are highly intraconnected, but loosely interconnected. Specific nucleotides, including U8 and G22, stabilize the mutated structures and are candidates for substitution in future studies.
subject
Chemical structure
Noncovalent interactions
Monomers
Cluster chemistry
Nucleic acid structure
contributor
Godwin, R. (author)
Macnamara, L. (author)
Alexander, F. (author)
Salsbury, F. (author)
date
2020-03-09T19:04:16Z (accessioned)
2020-03-09T19:04:16Z (available)
9/5/18 (issued)
identifier
Godwin, R. C., Macnamara, L. M., Alexander, R. W., & Salsbury Jr, F. R. (2018). Structure and Dynamics of tRNAMet Containing Core Substitutions. ACS omega, 3(9), 10668-10678. (citation)
https://doi.org/10.1021/acsomega.8b00280 (doi)
http://hdl.handle.net/10339/96053 (uri)
language
en (iso)
publisher
ACS
rights
https://pubs.acs.org/page/policy/authorchoice_termsofuse.html (uri)
source
ACS Omega
title
Structure and Dynamics of tRNAMet Containing Core Substitutions
type
Article

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