Proteins and nucleic acids are highly dynamic bio-molecules that can populate a variety of conformational states. NMR relaxation dispersion (RD) methods are uniquely suited to quantify the associated kinetic and thermodynamic parameters. Here, we present a consistent suite of 19F-based CPMG, on-resonance R1Ï? and off-resonance R1Ï? RD experiments. We validate these experiments by studying the unfolding transition of a 7.5Â*kDa cold shock protein. Furthermore we show that the 19F RD experiments are applicable to very large molecular machines by quantifying dynamics in the 360Â*kDa half-proteasome. Our approach significantly extends the timescale of chemical exchange that can be studied with 19F RD, adds robustness to the extraction of exchange parameters and can determine the absolute chemical shifts of excited states. Importantly, due to the simplicity of 19F NMR spectra, it is possible to record complete datasets within hours on samples that are of very low costs. This makes the presented experiments ideally suited to complement static structural information from cryo-EM and X-ray crystallography with insights into functionally relevant motions.
Removal of slow-pulsing artifacts in in-phase 15 N relaxation dispersion experiments using broadband 1 H decoupling
Removal of slow-pulsing artifacts in in-phase 15 N relaxation dispersion experiments using broadband 1 H decoupling
Abstract
Understanding of the molecular mechanisms of protein function requires detailed insight into the conformational landscape accessible to the protein. Conformational changes can be crucial for biological processes, such as ligand binding, protein folding, and catalysis. NMR spectroscopy is exquisitely sensitive to such dynamic changes in protein conformations. In particular, Carrâ??Purcellâ??Meiboomâ??Gill (CPMG) relaxation...
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06-03-2018 01:00 AM
[NMR paper] Resolving biomolecular motion and interactions by R2 and R1? Relaxation Dispersion NMR.
Resolving biomolecular motion and interactions by R2 and R1? Relaxation Dispersion NMR.
Related Articles Resolving biomolecular motion and interactions by R2 and R1? Relaxation Dispersion NMR.
Methods. 2018 Apr 25;:
Authors: Walinda E, Morimoto D, Sugase K
Abstract
Among the tools of structural biology, NMR spectroscopy is unique in that it not only derives a static three-dimensional structure, but also provides an atomic-level description of the local fluctuations and global dynamics around this static structure. A battery of...
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05-01-2018 10:20 AM
[NMR paper] Geometric approximation: a new computational approach to characterize protein dynamics from NMR adiabatic relaxation dispersion experiments.
Geometric approximation: a new computational approach to characterize protein dynamics from NMR adiabatic relaxation dispersion experiments.
Related Articles Geometric approximation: a new computational approach to characterize protein dynamics from NMR adiabatic relaxation dispersion experiments.
J Am Chem Soc. 2016 May 26;
Authors: Chao FA, Byrd RA
Abstract
A new computational strategy is reported that provides a fast approximation of numerical solutions of differential equations, in general. The method is demonstrated...
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05-27-2016 06:18 PM
[NMR paper] The Complexity of Protein Energy Landscapes Studied by Solution NMR Relaxation Dispersion Experiments.
The Complexity of Protein Energy Landscapes Studied by Solution NMR Relaxation Dispersion Experiments.
Related Articles The Complexity of Protein Energy Landscapes Studied by Solution NMR Relaxation Dispersion Experiments.
J Phys Chem B. 2015 Feb 13;
Authors: Khirich G, Loria JP
Abstract
The millisecond timescale motions in ribonuclease A (RNase A) were studied by solution NMR CPMG and off-resonance R1? relaxation dispersion experiments over a wide pH and temperature range. These experiments identify three separate protein...
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02-14-2015 03:52 PM
[NMR paper] Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
Related Articles Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
J Phys Chem B. 2014 Oct 28;
Authors: Allnér O, Foloppe N, Nilsson L
Abstract
Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory...
Can Enzyme Engineering Benefit from the Modulation of Protein Motions? Lessons Learned from NMR Relaxation Dispersion Experiments.
Can Enzyme Engineering Benefit from the Modulation of Protein Motions? Lessons Learned from NMR Relaxation Dispersion Experiments.
Can Enzyme Engineering Benefit from the Modulation of Protein Motions? Lessons Learned from NMR Relaxation Dispersion Experiments.
Protein Pept Lett. 2011 Jan 11;
Authors:
Despite impressive progress in protein engineering and design, our ability to create new and efficient enzyme activities remains a laborious and time-consuming endeavor. In the past few years, intricate combinations of rational mutagenesis, directed...
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01-13-2011 12:00 PM
Suite of Six NMR Relaxation Dispersion Experiments to Study Multiple-Site Exchange in Proteins
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Multiple-Site Exchange in Proteins Studied with a Suite of Six NMR Relaxation Dispersion Experiments: An Application to the Folding of a Fyn SH3 Domain Mutant
Dmitry M. Korzhnev, Philipp Neudecker, Anthony Mittermaier, Vladislav Yu. Orekhov, and Lewis E. Kay*
Contribution from the Departments of Medical Genetics, Biochemistry, and Chemistry, The University of Toronto, Toronto, Ontario M5S 1A8, Canada, and Swedish NMR Center at Göteborg University, Box 465, 405 30 Göteborg, Sweden
J. Am. Chem....
A suite of 19 F based relaxation dispersion experiments to assess biomolecular motions
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