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Article: Molecular dynamics simulations of LysRS: An asymmetric state

TitleMolecular dynamics simulations of LysRS: An asymmetric state
Authors
Issue Date2006
Citation
Proteins: Structure, Function And Genetics, 2006, v. 62 n. 3, p. 649-662 How to Cite?
AbstractWe 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. © 2005 Wiley-Liss, Inc.
Persistent Identifierhttp://hdl.handle.net/10722/68074
ISSN
2015 Impact Factor: 2.499
2015 SCImago Journal Rankings: 1.383
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorHughes, SJen_HK
dc.contributor.authorTanner, JAen_HK
dc.contributor.authorMiller, ADen_HK
dc.contributor.authorGould, IRen_HK
dc.date.accessioned2010-09-06T06:01:05Z-
dc.date.available2010-09-06T06:01:05Z-
dc.date.issued2006en_HK
dc.identifier.citationProteins: Structure, Function And Genetics, 2006, v. 62 n. 3, p. 649-662en_HK
dc.identifier.issn0887-3585en_HK
dc.identifier.urihttp://hdl.handle.net/10722/68074-
dc.description.abstractWe 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. © 2005 Wiley-Liss, Inc.en_HK
dc.languageengen_HK
dc.relation.ispartofProteins: Structure, Function and Geneticsen_HK
dc.subject.meshAdenosine Triphosphate - metabolismen_HK
dc.subject.meshAmino Acid Sequenceen_HK
dc.subject.meshBinding Sitesen_HK
dc.subject.meshComputer Simulationen_HK
dc.subject.meshCrystallography, X-Rayen_HK
dc.subject.meshDimerizationen_HK
dc.subject.meshEscherichia coli Proteins - chemistryen_HK
dc.subject.meshHydrogen Bondingen_HK
dc.subject.meshKineticsen_HK
dc.subject.meshLysine - metabolismen_HK
dc.subject.meshLysine-tRNA Ligase - chemistry - metabolismen_HK
dc.subject.meshModels, Molecularen_HK
dc.subject.meshModels, Theoreticalen_HK
dc.subject.meshProtein Bindingen_HK
dc.subject.meshProtein Structure, Secondaryen_HK
dc.titleMolecular dynamics simulations of LysRS: An asymmetric stateen_HK
dc.typeArticleen_HK
dc.identifier.emailTanner, JA:jatanner@hku.hken_HK
dc.identifier.authorityTanner, JA=rp00495en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1002/prot.20609en_HK
dc.identifier.pmid16317719-
dc.identifier.scopuseid_2-s2.0-31944448883en_HK
dc.identifier.hkuros114183en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-31944448883&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume62en_HK
dc.identifier.issue3en_HK
dc.identifier.spage649en_HK
dc.identifier.epage662en_HK
dc.identifier.isiWOS:000235172100009-
dc.identifier.scopusauthoridHughes, SJ=36942170200en_HK
dc.identifier.scopusauthoridTanner, JA=35513993000en_HK
dc.identifier.scopusauthoridMiller, AD=7406230808en_HK
dc.identifier.scopusauthoridGould, IR=36707470300en_HK

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