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

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.

SUBMITTER: Laowanapiban P

PROVIDER: S-EPMC2644116 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature

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

Laowanapiban Poramaet P Kapustina Maryna M Vonrhein Clemens C Delarue Marc M Koehl Patrice P Carter Charles W CW

Proceedings of the National Academy of Sciences of the United States of America 20090127 6

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 ela ...[more]

PMID: 19174517

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

Publications

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

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