Related ArticlesExtracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy.
J Biomol NMR. 2015 Oct 17;
Authors: Konuma T, Harada E, Sugase K
Abstract
Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.
PMID: 26476958 [PubMed - as supplied by publisher]
Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy
Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy
Abstract
Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate...
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10-18-2015 09:10 AM
[NMR paper] The Energetics of a Three-State Protein Folding System Probed by High-Pressure Relaxation Dispersion NMR Spectroscopy.
The Energetics of a Three-State Protein Folding System Probed by High-Pressure Relaxation Dispersion NMR Spectroscopy.
Related Articles The Energetics of a Three-State Protein Folding System Probed by High-Pressure Relaxation Dispersion NMR Spectroscopy.
Angew Chem Int Ed Engl. 2015 Sep 14;54(38):11157-11161
Authors: Tugarinov V, Libich DS, Meyer V, Roche J, Clore GM
Abstract
The energetic and volumetric properties of a three-state protein folding system, comprising a metastable triple mutant of the Fyn SH3 domain, have been...
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09-10-2015 02:01 PM
[NMR paper] Ligand-Detected Relaxation Dispersion NMR Spectroscopy: Dynamics of preQ1 -RNA Binding.
Ligand-Detected Relaxation Dispersion NMR Spectroscopy: Dynamics of preQ1 -RNA Binding.
Related Articles Ligand-Detected Relaxation Dispersion NMR Spectroscopy: Dynamics of preQ1 -RNA Binding.
Angew Chem Int Ed Engl. 2014 Nov 17;
Authors: Moschen T, Wunderlich CH, Spitzer R, Levic J, Micura R, Tollinger M, Kreutz C
Abstract
An NMR-based approach to characterizing the binding kinetics of ligand molecules to biomolecules, like RNA or proteins, by ligand-detected Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiments is...
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11-19-2014 04:32 PM
Specific 12C?D212C?D2S13C?HD2 IsotopomerLabeling of Methionine ToCharacterize Protein Dynamics by 1H and 13CNMR Relaxation Dispersion
Specific 12C?D212C?D2S13C?HD2 IsotopomerLabeling of Methionine ToCharacterize Protein Dynamics by 1H and 13CNMR Relaxation Dispersion
Ulrich Weininger, Zhihong Liu, Deane D. McIntyre, Hans J. Vogel and Mikael Akke
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja309294u/aop/images/medium/ja-2012-09294u_0005.gif
Journal of the American Chemical Society
DOI: 10.1021/ja309294u
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/9TseQlKMjfM
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11-03-2012 12:26 AM
Measuring (1)H (N) temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy.
Measuring (1)H (N) temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy.
Measuring (1)H (N) temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy.
J Biomol NMR. 2011 Mar 18;
Authors: Bouvignies G, Vallurupalli P, Cordes MH, Hansen DF, Kay LE
A method based on the Carr-Purcell-Meiboom-Gill relaxation dispersion experiment is presented for measuring the temperature coefficients of amide proton chemical shifts of low populated 'invisible' protein states that exchange...
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03-23-2011 05:41 PM
Measuring 1HN temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy
Measuring 1HN temperature coefficients in invisible protein states by relaxation dispersion NMR spectroscopy
Abstract A method based on the Carr-Purcell-Meiboom-Gill relaxation dispersion experiment is presented for measuring the temperature coefficients of amide proton chemical shifts of low populated â??invisibleâ?? protein states that exchange with a â??visibleâ?? ground state on the millisecond time-scale. The utility of the approach is demonstrated with an application to an I58D mutant of the Pfl6 Cro protein that undergoes exchange between the native, folded state and a cold...
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03-22-2011 07:32 PM
[NMR paper] Slow internal dynamics in proteins: application of NMR relaxation dispersion spectros
Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme.
Related Articles Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme.
J Am Chem Soc. 2002 Feb 20;124(7):1443-51
Authors: Mulder FA, Hon B, Mittermaier A, Dahlquist FW, Kay LE
Recently developed carbon transverse relaxation dispersion experiments (Skrynnikov, N. R.; et al. J. Am. Chem. Soc. 2001, 123, 4556-4566) were...
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11-24-2010 08:49 PM
Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states
Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states
D. Flemming Hansen, Pramodh Vallurupalli and Lewis E. Kay
Journal of Biomolecular NMR; 2008; 41(3); pp 113 - 120
Abstract:
Currently the main focus of structural biology is the determination of static three-dimensional representations of biomolecules that for the most part correspond to low energy (ground state) conformations. However, it is becoming increasingly well recognized that higher energy structures often play important roles in function as well. Because these conformers...