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- Publisher Website: 10.1007/s10858-005-5366-0
- Scopus: eid_2-s2.0-23344451429
- PMID: 16034666
- WOS: WOS:000230694100005
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Article: Relating side-chain mobility in proteins to rotameric transitions: Insights from molecular dynamics simulations and NMR
Title | Relating side-chain mobility in proteins to rotameric transitions: Insights from molecular dynamics simulations and NMR |
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Authors | |
Keywords | Molecular dynamics simulation NMR Order parameter Rotamer populations Saxis2 Side-chain dynamics |
Issue Date | 2005 |
Publisher | Springer 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? |
Abstract | The 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 Identifier | http://hdl.handle.net/10722/167945 |
ISSN | 2023 Impact Factor: 2.4 2023 SCImago Journal Rankings: 0.817 |
ISI Accession Number ID | |
References |
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Hu, H | en_US |
dc.contributor.author | Hermans, J | en_US |
dc.contributor.author | Lee, AL | en_US |
dc.date.accessioned | 2012-10-08T03:13:14Z | - |
dc.date.available | 2012-10-08T03:13:14Z | - |
dc.date.issued | 2005 | en_US |
dc.identifier.citation | Journal Of Biomolecular Nmr, 2005, v. 32 n. 2, p. 151-162 | en_US |
dc.identifier.issn | 0925-2738 | en_US |
dc.identifier.uri | http://hdl.handle.net/10722/167945 | - |
dc.description.abstract | The 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.language | eng | en_US |
dc.publisher | Springer Verlag Dordrecht. The Journal's web site is located at http://springerlink.metapress.com/openurl.asp?genre=journal&issn=0925-2738 | en_US |
dc.relation.ispartof | Journal of Biomolecular NMR | en_US |
dc.subject | Molecular dynamics simulation | - |
dc.subject | NMR | - |
dc.subject | Order parameter | - |
dc.subject | Rotamer populations | - |
dc.subject | Saxis2 | - |
dc.subject | Side-chain dynamics | - |
dc.subject.mesh | Carbon | en_US |
dc.subject.mesh | Computer Simulation | en_US |
dc.subject.mesh | Magnetic Resonance Spectroscopy | en_US |
dc.subject.mesh | Models, Molecular | en_US |
dc.subject.mesh | Protein Conformation | en_US |
dc.subject.mesh | Ubiquitin - Chemistry | en_US |
dc.title | Relating side-chain mobility in proteins to rotameric transitions: Insights from molecular dynamics simulations and NMR | en_US |
dc.type | Article | en_US |
dc.identifier.email | Hu, H:haohu@hku.hk | en_US |
dc.identifier.authority | Hu, H=rp00707 | en_US |
dc.description.nature | link_to_subscribed_fulltext | en_US |
dc.identifier.doi | 10.1007/s10858-005-5366-0 | en_US |
dc.identifier.pmid | 16034666 | - |
dc.identifier.scopus | eid_2-s2.0-23344451429 | en_US |
dc.relation.references | http://www.scopus.com/mlt/select.url?eid=2-s2.0-23344451429&selection=ref&src=s&origin=recordpage | en_US |
dc.identifier.volume | 32 | en_US |
dc.identifier.issue | 2 | en_US |
dc.identifier.spage | 151 | en_US |
dc.identifier.epage | 162 | en_US |
dc.identifier.isi | WOS:000230694100005 | - |
dc.publisher.place | Netherlands | en_US |
dc.identifier.scopusauthorid | Hu, H=7404097564 | en_US |
dc.identifier.scopusauthorid | Hermans, J=7201896483 | en_US |
dc.identifier.scopusauthorid | Lee, AL=7405629964 | en_US |
dc.identifier.citeulike | 265548 | - |
dc.identifier.issnl | 0925-2738 | - |