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Molecular dynamics simulations of LysRS: An asymmetric state
Author(s) -
Hughes Samantha J.,
Tanner Julian A.,
Miller Andrew D.,
Gould Ian R.
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20609
Subject(s) - transfer rna , in silico , asymmetry , molecular dynamics , benchmark (surveying) , flexibility (engineering) , computational biology , protocol (science) , computer science , biological system , chemistry , biology , physics , biochemistry , computational chemistry , rna , mathematics , medicine , alternative medicine , pathology , statistics , geodesy , quantum mechanics , gene , geography
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. Proteins 2006. © 2005 Wiley‐Liss, Inc.