Structure and Dynamics of tRNAMet Containing Core Substitutions Article Swipe
Ryan C. Godwin
,
Lindsay Macnamara
,
Rebecca W. Alexander
,
Freddie R. Salsbury
·
YOU?
·
· 2018
· Open Access
·
· DOI: https://doi.org/10.1021/acsomega.8b00280
YOU?
·
· 2018
· Open Access
·
· DOI: https://doi.org/10.1021/acsomega.8b00280
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.
Related Topics
Concepts
Transfer RNA
Aminoacylation
Genetic code
T arm
Aminoacyl tRNA synthetase
Amino Acyl-tRNA Synthetases
Amino acid
Nucleotide
Biology
RNA
Computational biology
Biochemistry
Gene
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1021/acsomega.8b00280
- OA Status
- gold
- Cited By
- 8
- References
- 45
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2891757443
All OpenAlex metadata
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https://openalex.org/W2891757443Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1021/acsomega.8b00280Digital Object Identifier
- Title
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Structure and Dynamics of tRNAMet Containing Core SubstitutionsWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2018Year of publication
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2018-09-05Full publication date if available
- Authors
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Ryan C. Godwin, Lindsay Macnamara, Rebecca W. Alexander, Freddie R. SalsburyList of authors in order
- Landing page
-
https://doi.org/10.1021/acsomega.8b00280Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
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https://doi.org/10.1021/acsomega.8b00280Direct OA link when available
- Concepts
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Transfer RNA, Aminoacylation, Genetic code, T arm, Aminoacyl tRNA synthetase, Amino Acyl-tRNA Synthetases, Amino acid, Nucleotide, Biology, RNA, Computational biology, Biochemistry, GeneTop concepts (fields/topics) attached by OpenAlex
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8Total citation count in OpenAlex
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2025: 1, 2024: 2, 2023: 4, 2022: 1Per-year citation counts (last 5 years)
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45Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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