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Int. J. Mol. Sci. 2015, 16(7), 15872-15902; doi:10.3390/ijms160715872

MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery

1
Departments of Physics and Computer Science, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27109, USA
2
Department of Chemistry, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27109, USA
3
Department of Physics, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27109, USA
*
Author to whom correspondence should be addressed.
Academic Editor: Michael Ibba
Received: 6 June 2015 / Revised: 7 July 2015 / Accepted: 8 July 2015 / Published: 13 July 2015
(This article belongs to the Special Issue Functions of Transfer RNAs)
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Abstract

While tRNA and aminoacyl-tRNA synthetases are classes of biomolecules that have been extensively studied for decades, the finer details of how they carry out their fundamental biological functions in protein synthesis remain a challenge. Recent molecular dynamics (MD) simulations are verifying experimental observations and providing new insight that cannot be addressed from experiments alone. Throughout the review, we briefly discuss important historical events to provide a context for how far the field has progressed over the past few decades. We then review the background of tRNA molecules, aminoacyl-tRNA synthetases, and current state of the art MD simulation techniques for those who may be unfamiliar with any of those fields. Recent MD simulations of tRNA dynamics and folding and of aminoacyl-tRNA synthetase dynamics and mechanistic characterizations are discussed. We highlight the recent successes and discuss how important questions can be addressed using current MD simulations techniques. We also outline several natural next steps for computational studies of AARS:tRNA complexes. View Full-Text
Keywords: coarse-grained; atomistic; empirical force field; catalytic mechanism; editing coarse-grained; atomistic; empirical force field; catalytic mechanism; editing
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Li, R.; Macnamara, L.M.; Leuchter, J.D.; Alexander, R.W.; Cho, S.S. MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery. Int. J. Mol. Sci. 2015, 16, 15872-15902.

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