Molecular Dynamics Simulations of Lysrs: an Asymmetric State.
From: Imperial College Genetic Therapies Centre, Department of Chemistry, Imperial College London.
Proteins
- Publish Date: Mar 2006
- ISSN: 1097-0134
- Volume: 62
- Issue: 3
- Pages: 649-62
- Medium: Internet
- Language: English
- Citation (JAMA): Hughes Samantha J, Tanner Julian A, Miller Andrew D, et al. Molecular Dynamics Simulations of Lysrs: an Asymmetric State.. Proteins Mar 2006;62:649-62
Abstract
We report molecular dynamics simulations of the Escherichia coli Lysyl-tRNA synthetase LysU isoform carried out as a benchmark for mutant simulations in in silico protein engineering efforts. Unlike previous studies of aminoacyl-tRNA synthetases, LysU is modelled in its full dimeric form with explicit solvent. While developing a suitable simulation protocol, we observed an asymmetry that persists despite improvements to the model. This prediction has directly led to experiments that establish a functional asymmetry in nucleotide binding by LysU. The development of a simulation protocol and validation of the model are presented here. The observed asymmetry is described and the role of protein flexibility in developing the asymmetry is discussed.
Mesh Headings (Keywords): Adenosine Triphosphate, Amino Acid Sequence, Binding Sites, Computer Simulation, Crystallography, X-Ray, Dimerization, Escherichia coli Proteins, Hydrogen Bonding, Kinetics, Lysine, Lysine-tRNA Ligase, Models, Molecular, Models, Theoretical, Protein Binding, Protein Structure, Secondary
Check for Full Text / PubMed Unique Identifier (PMID): 16317719
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