Journal article
Conservation of side-chain dynamics within a protein family
Journal of the American Chemical Society, Vol.131(18), pp.6322-6323
05/13/2009
DOI: 10.1021/ja809915a
PMCID: PMC2678171
PMID: 19374353
Abstract
The question of protein dynamics and its relevance to function is currently a topic of great interest. Proteins are particularly dynamic at the side-chain level on the time scale of picoseconds to nanoseconds. Here, we present a comparison of NMR-monitored side-chain motion between three PDZ domains of approximately 30% sequence identity and show that the side-chain dynamics display nontrivial conservation. Methyl (2)H relaxation was carried out to determine side-chain order parameters (S(2)), which were found to be more similar than naively expected from sequence, local packing, or a combination of the two. Thus, the dynamics of a rather distant homologue appears to be an excellent predictor of a protein's side-chain dynamics and, on average, better than current structure-based methods. Fast side-chain dynamics therefore display a high level of organization associated with global fold. Beyond simple conservation, the analysis herein suggests that the pattern of side-chain flexibility has significant contributions from nonlocal elements of the PDZ fold, such as correlated motions, and that the conserved dynamics may directly support function.
Details
- Title: Subtitle
- Conservation of side-chain dynamics within a protein family
- Creators
- Anthony B Law - Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USAErnesto J FuentesAndrew L Lee
- Resource Type
- Journal article
- Publication Details
- Journal of the American Chemical Society, Vol.131(18), pp.6322-6323
- DOI
- 10.1021/ja809915a
- PMID
- 19374353
- PMCID
- PMC2678171
- NLM abbreviation
- J Am Chem Soc
- ISSN
- 0002-7863
- eISSN
- 1520-5126
- Publisher
- United States
- Grant note
- T32 GM008719-01 / NIGMS NIH HHS GM066009 / NIGMS NIH HHS R01 GM066009 / NIGMS NIH HHS R01 GM066009-04S1 / NIGMS NIH HHS T32 GM008719 / NIGMS NIH HHS
- Language
- English
- Date published
- 05/13/2009
- Academic Unit
- Biochemistry and Molecular Biology
- Record Identifier
- 9984024544802771
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