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Structure and Dynamics of tRNAMet Containing Core Substitutions
Ryan C Godwin1, Lindsay M Macnamara2, Rebecca W Alexander1
1Department of Physics and Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27106, United States.
ACS Omega
|October 6, 2018
Summary
Single nucleotide substitutions in transfer RNA (tRNA)Met D-loop alter flexibility and communication. These changes impact secondary structure, revealing interconnectedness within tRNA, crucial for protein synthesis accuracy.
Area of Science:
- Molecular Biology
- Biochemistry
- Structural Biology
Background:
- Protein synthesis fidelity relies on accurate aminoacyl-tRNA synthetase-tRNA recognition.
- Aminoacylation of tRNAMet is essential for both initiation and elongation in protein synthesis.
- Understanding tRNAMet structure-function relationships is key to investigating enzyme-tRNA complexes.
Purpose of the Study:
- To investigate the impact of single nucleotide substitutions in the D-loop of tRNAMet on its structure and function.
- To probe structure/function relationships through molecular dynamics simulations of tRNAMet variants.
- To understand the role of the tRNA core in mediating communication between anticodon and acceptor ends.
Main Methods:
- Molecular dynamics (MD) simulations of *Escherichia coli* tRNAMet.
- Analysis of single nucleotide substitutions (G15A, G18A, G19A) in the tRNAMet D-loop.
- Network-based analysis of hydrogen bond structure and correlated motion.
Main Results:
- MD simulations revealed altered tRNA flexibility and long-range communication, particularly in the G18A variant.
- Overall tertiary structure of tRNAMet remained intact, but secondary structures showed perturbations.
- Network analysis indicated intraconnected secondary structure elements, loosely interconnected.
Conclusions:
- Single nucleotide substitutions in the tRNAMet D-loop can perturb secondary structure without disrupting overall tertiary structure.
- Nucleotides U8 and G22 appear to stabilize mutated tRNAMet structures.
- These findings provide insights into tRNA structure-function dynamics and identify potential sites for future modification.
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