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Article: Relating side-chain mobility in proteins to rotameric transitions: Insights from molecular dynamics simulations and NMR

TitleRelating side-chain mobility in proteins to rotameric transitions: Insights from molecular dynamics simulations and NMR
Authors
Issue Date2005
PublisherSpringer Verlag Dordrecht. The Journal's web site is located at http://springerlink.metapress.com/openurl.asp?genre=journal&issn=0925-2738
Citation
Journal Of Biomolecular Nmr, 2005, v. 32 n. 2, p. 151-162 How to Cite?
AbstractThe dynamic aspect of proteins is fundamental to understanding protein stability and function. One of the goals of NMR studies of side-chain dynamics in proteins is to relate spin relaxation rates to discrete conformational states and the timescales of interconversion between those states. Reported here is a physical analysis of side-chain dynamics that occur on a timescale commensurate with monitoring by 2H spin relaxation within methyl groups. Motivated by observations made from tens-of-nanoseconds long MD simulations on the small protein eglin c in explicit solvent, we propose a simple molecular mechanics-based model for the motions of side-chain methyl groups. By using a Boltzmann distribution within rotamers, and by considering the transitions between different rotamer states, the model semi-quantitatively correlates the population of rotamer states with 'model-free' order parameters typically fitted from NMR relaxation experiments. Two easy-to-use, analytical expressions are given for converting Saxis 2 values (order parameter for C-CH3 bond) into side-chain rotamer populations. These predict that Saxis 2 values below 0.8 result from population of more than one rotameric state. The relations are shown to predict rotameric sampling with reasonable accuracy on the ps-ns timescale for eglin c and are validated for longer timescales on ubiquitin, for which side-chain residual dipolar coupling (RDC) data have been collected. © Springer 2005.
Persistent Identifierhttp://hdl.handle.net/10722/167945
ISSN
2015 Impact Factor: 3.439
2015 SCImago Journal Rankings: 2.043
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorHu, Hen_US
dc.contributor.authorHermans, Jen_US
dc.contributor.authorLee, ALen_US
dc.date.accessioned2012-10-08T03:13:14Z-
dc.date.available2012-10-08T03:13:14Z-
dc.date.issued2005en_US
dc.identifier.citationJournal Of Biomolecular Nmr, 2005, v. 32 n. 2, p. 151-162en_US
dc.identifier.issn0925-2738en_US
dc.identifier.urihttp://hdl.handle.net/10722/167945-
dc.description.abstractThe dynamic aspect of proteins is fundamental to understanding protein stability and function. One of the goals of NMR studies of side-chain dynamics in proteins is to relate spin relaxation rates to discrete conformational states and the timescales of interconversion between those states. Reported here is a physical analysis of side-chain dynamics that occur on a timescale commensurate with monitoring by 2H spin relaxation within methyl groups. Motivated by observations made from tens-of-nanoseconds long MD simulations on the small protein eglin c in explicit solvent, we propose a simple molecular mechanics-based model for the motions of side-chain methyl groups. By using a Boltzmann distribution within rotamers, and by considering the transitions between different rotamer states, the model semi-quantitatively correlates the population of rotamer states with 'model-free' order parameters typically fitted from NMR relaxation experiments. Two easy-to-use, analytical expressions are given for converting Saxis 2 values (order parameter for C-CH3 bond) into side-chain rotamer populations. These predict that Saxis 2 values below 0.8 result from population of more than one rotameric state. The relations are shown to predict rotameric sampling with reasonable accuracy on the ps-ns timescale for eglin c and are validated for longer timescales on ubiquitin, for which side-chain residual dipolar coupling (RDC) data have been collected. © Springer 2005.en_US
dc.languageengen_US
dc.publisherSpringer Verlag Dordrecht. The Journal's web site is located at http://springerlink.metapress.com/openurl.asp?genre=journal&issn=0925-2738en_US
dc.relation.ispartofJournal of Biomolecular NMRen_US
dc.subject.meshCarbonen_US
dc.subject.meshComputer Simulationen_US
dc.subject.meshMagnetic Resonance Spectroscopyen_US
dc.subject.meshModels, Molecularen_US
dc.subject.meshProtein Conformationen_US
dc.subject.meshUbiquitin - Chemistryen_US
dc.titleRelating side-chain mobility in proteins to rotameric transitions: Insights from molecular dynamics simulations and NMRen_US
dc.typeArticleen_US
dc.identifier.emailHu, H:haohu@hku.hken_US
dc.identifier.authorityHu, H=rp00707en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1007/s10858-005-5366-0en_US
dc.identifier.pmid16034666-
dc.identifier.scopuseid_2-s2.0-23344451429en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-23344451429&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume32en_US
dc.identifier.issue2en_US
dc.identifier.spage151en_US
dc.identifier.epage162en_US
dc.identifier.isiWOS:000230694100005-
dc.publisher.placeNetherlandsen_US
dc.identifier.scopusauthoridHu, H=7404097564en_US
dc.identifier.scopusauthoridHermans, J=7201896483en_US
dc.identifier.scopusauthoridLee, AL=7405629964en_US
dc.identifier.citeulike265548-

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