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  • Title: Molecular dynamics simulations of LysRS: an asymmetric state.
    Author: Hughes SJ, Tanner JA, Miller AD, Gould IR.
    Journal: Proteins; 2006 Mar 15; 62(3):649-62. PubMed ID: 16317719.
    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.
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