ArticleThe journal of physical chemistry. A2006
Protein dynamics from NMR: the slowly relaxing local structure analysis compared with model-free analysis.
Article in The journal of physical chemistry. A, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Predicting NMR Relaxation Using a First-Principles Brownian Dynamics Approach.Journal of chemical theory and computation · 2026Article
- Detecting anisotropic segmental dynamics in disordered proteins by cross-correlated spin relaxation.Magnetic resonance (Gottingen, Germany) · 2021Article
- Conformational Entropy from Restricted Bond-Vector Motion in Proteins: The Symmetry of the Local Restrictions and Relation to NMR Relaxation.The journal of physical chemistry. B · 2020Article
- Local ordering and dynamics in anisotropic media by magnetic resonance: from liquid crystals to proteins.Liquid crystals · 2020Article
- Distance-independent Cross-correlated Relaxation and Isotropic Chemical Shift Modulation in Protein Dynamics Studies.Chemphyschem : a European journal of chemical physics and physical chemistry · 2019Review
- Local Ordering at Mobile Sites in Proteins from Nuclear Magnetic Resonance Relaxation: The Role of Site Symmetry.The journal of physical chemistry. B · 2016Article
- Protein Dynamics in the Solid State from (2)H NMR Line Shape Analysis. II. MOMD Applied to C-D and C-CD3 Probes.The journal of physical chemistry. B · 2015Article
- Protein dynamics in the solid state from 2H NMR line shape analysis: a consistent perspective.The journal of physical chemistry. B · 2015Article
- Analysis of 15N-1H NMR relaxation in proteins by a combined experimental and molecular dynamics simulation approach: picosecond-nanosecond dynamics of the Rho GTPase binding domain of plexin-B1 in the dimeric state indicates allosteric pathways.The journal of physical chemistry. B · 2013Article
- Coupling between internal dynamics and rotational diffusion in the presence of exchange between discrete molecular conformations.The Journal of chemical physics · 2012Article
- NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion.Journal of biomolecular NMR · 2011Article
- Methyl dynamics of a Ca2+-calmodulin-peptide complex from NMR/SRLS.The journal of physical chemistry. B · 2011Article
- Integrated computational approach to the analysis of NMR relaxation in proteins: application to ps-ns main chain 15N-1H and global dynamics of the Rho GTPase binding domain of plexin-B1.The journal of physical chemistry. B · 2011Article
- Backbone dynamics of deoxy and carbonmonoxy hemoglobin by NMR/SRLS.The journal of physical chemistry. B · 2011Article
- Comment on "The physical basis of model-free analysis of NMR relaxation data from proteins and complex fluids" [J. Chem. Phys. 131, 224507 (2009)].The Journal of chemical physics · 2010Article
- Structural dynamics of bio-macromolecules by NMR: the slowly relaxing local structure approach.Progress in nuclear magnetic resonance spectroscopy · 2010Review
- Electron-nuclear interactions as probes of domain motion in proteins.The Journal of chemical physics · 2010Article
- Influence of the coupling of interdomain and overall motions on NMR relaxation.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Re-evaluation of the model-free analysis of fast internal motion in proteins using NMR relaxation.The journal of physical chemistry. B · 2008Article
- An improved picture of methyl dynamics in proteins from slowly relaxing local structure analysis of 2H spin relaxation.The journal of physical chemistry. B · 2007Article
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4 authors.
Funding
Abstract
(15)N-(1)H spin relaxation is a powerful method for deriving information on protein dynamics. The traditional method of data analysis is model-free (MF), where the global and local N-H motions are independent and the local geometry is simplified. The common MF analysis consists of fitting single-field data. The results are typically field-dependent, and multifield data cannot be fit with standard fitting schemes. Cases where known functional dynamics has not been detected by MF were identified by us and others. Recently we applied to spin relaxation in proteins the slowly relaxing local structure (SRLS) approach, which accounts rigorously for mode mixing and general features of local geometry. SRLS was shown to yield MF in appropriate asymptotic limits. We found that the experimental spectral density corresponds quite well to the SRLS spectral density. The MF formulas are often used outside of their validity ranges, allowing small data sets to be force-fitted with good statistics but inaccurate best-fit parameters. This paper focuses on the mechanism of force-fitting and its implications. It is shown that MF analysis force-fits the experimental data because mode mixing, the rhombic symmetry of the local ordering and general features of local geometry are not accounted for. Combined multifield multitemperature data analyzed with the MF approach may lead to the detection of incorrect phenomena, and conformational entropy derived from MF order parameters may be highly inaccurate. On the other hand, fitting to more appropriate models can yield consistent physically insightful information. This requires that the complexity of the theoretical spectral densities matches the integrity of the experimental data. As shown herein, the SRLS spectral densities comply with this requirement.
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