title: MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery.
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.
authors.affiliation: Departments of Physics and Computer Science, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27109, USA. lir0@wfu.edu.
authors.forename: Rongzhong
authors.initials: R
authors.lastname: Li
authors.affiliation: Department of Chemistry, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27109, USA. lmacnama@wakehealth.edu.
authors.forename: Lindsay M
authors.initials: LM
authors.lastname: Macnamara
authors.affiliation: Department of Physics, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27109, USA. jessica.leuchter@gmail.com.
authors.forename: Jessica D
authors.initials: JD
authors.lastname: Leuchter
authors.affiliation: Department of Chemistry, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27109, USA. alexanr@wfu.edu.
authors.forename: Rebecca W
authors.initials: RW
authors.lastname: Alexander
authors.affiliation: Departments of Physics and Computer Science, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27109, USA. choss@wfu.edu.
authors.forename: Samuel S
authors.initials: SS
authors.lastname: Cho
mesh_terms: D000494:Allosteric Regulation; D000604:Amino Acyl-tRNA Synthetases / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011789:Quantum Theory; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism*
chemical_list: D012343:RNA, Transfer; D000604:Amino Acyl-tRNA Synthetases
keywords: atomistic; catalytic mechanism; coarse-grained; editing; empirical force field