Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations

Poramaet Laowanapiban 1 Maryna Kapustina 1 Clemens Vonrhein 2 Marc Delarue 3 Patrice Koehl 4 Charles Carter 1
1 UNC - University of North Carolina [Chapel Hill]
2 Global Phasing Ltd
3 DSM - Dynamique Structurale des Macromolécules
4 UC Davis - University of California [Davis]
Abstract : Two new crystal structures of Bacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) afford evidence that a closed interdomain hinge angle requires a covalent bond between AMP and an occupant of either pyrophosphate or tryptophan subsite. They also are within experimental error of a cluster of structures observed in a nonequilibrium molecular dynamics simulation showing partial active-site assembly. Further, the highest energy structure in a minimum action pathway computed by using elastic network models for Open and Pretransition state (PreTS) conformations for the fully liganded TrpRS monomer is intermediate between that simulated structure and a partially disassembled structure from a nonequilibrium molecular dynamics trajectory for the unliganded PreTS. These mutual consistencies provide unexpected validation of inferences drawn from molecular simulations.
Keywords : conformational transition statedomain movement induced fit minimum action pathway nonequilibrium molecular dynamics
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Journal articles
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Submitted on : Friday, July 5, 2019 - 12:49:10 PM
Last modification on : Monday, January 13, 2020 - 5:08:07 PM

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Poramaet Laowanapiban, Maryna Kapustina, Clemens Vonrhein, Marc Delarue, Patrice Koehl, et al.. Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations. Proceedings of the National Academy of Sciences of the United States of America , National Academy of Sciences, 2009, 106 (6), pp.1790-1795. ⟨10.1073/pnas.0812752106⟩. ⟨pasteur-02174885⟩

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