Solid-state near-rotary-resonance measurements of the spinâ??lattice relaxation rate in the rotating frame (R1Ï?) is a powerful NMR technique for studying molecular dynamics in the microsecond time scale. The small difference between the spin-lock (SL) and magic-angle-spinning (MAS) frequencies allows sampling very slow motions, at the same time it brings up some methodological challenges. In this work, several issues affecting correct measurements and analysis of 15N R1Ï? data are considered in detail. Among them are signal amplitude as a function of the difference between SL and MAS frequencies, â??dead timeâ?? in the initial part of the relaxation decay caused by transient spin-dynamic oscillations, measurements under HORROR condition and proper treatment of the multi-exponential relaxation decays. The multiple 15N R1Ï? measurements at different SL fields and temperatures have been conducted in 1D mode (i.e. without site-specific resolution) for a set of four different microcrystalline protein samples (GB1, SH3, MPD-ubiquitin and cubic-PEG-ubiquitin) to study the overall protein rocking in a crystal. While the amplitude of this motion varies very significantly, its correlation time for all four sample is practically the same, 30â??50Â*μs. The amplitude of the rocking motion correlates with the packing density of a protein crystal. It has been suggested that the rocking motion is not diffusive but likely a jump-like dynamic process.
[NMR paper] Microsecond dynamics in ubiquitin probed by solid-state NMR 15N R1rho relaxation experiments under fast MAS (60-110 kHz).
Microsecond dynamics in ubiquitin probed by solid-state NMR 15N R1rho relaxation experiments under fast MAS (60-110 kHz).
Related Articles Microsecond dynamics in ubiquitin probed by solid-state NMR 15N R1rho relaxation experiments under fast MAS (60-110 kHz).
Chemistry. 2017 Apr 20;:
Authors: Lakomek NA, Penzel S, Lends A, Cadalbert R, Ernst M, Meier BH
Abstract
15N R1? relaxation experiments in solid-state NMR are sensitive to timescales and amplitudes of internal protein motions in the hundreds of ns to µs time window,...
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04-21-2017 03:35 PM
[NMR paper] Model of the Interaction between the NF-?B Inhibitory protein p100 and the E3 ubiquitin ligase ?-TrCP based on NMR and Docking Experiments.
Model of the Interaction between the NF-?B Inhibitory protein p100 and the E3 ubiquitin ligase ?-TrCP based on NMR and Docking Experiments.
Related Articles Model of the Interaction between the NF-?B Inhibitory protein p100 and the E3 ubiquitin ligase ?-TrCP based on NMR and Docking Experiments.
J Chem Inf Model. 2016 Dec 22;:
Authors: Melikian M, Eluard B, Bertho G, Baud V, Evrard-Todeschi N
Abstract
NF-?B is a major transcription factor whose activation is triggered through two main activation pathways: the canonical pathway...
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12-24-2016 08:34 AM
[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...
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10-29-2014 03:51 PM
[NMR paper] NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model Free Framework and Markov State Simulations.
NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model Free Framework and Markov State Simulations.
NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model Free Framework and Markov State Simulations.
J Phys Chem B. 2013 May 2;
Authors: Xia J, Deng NJ, Levy RM
Abstract
Calculating NMR relaxation effects for proteins with dynamics on multiple timescales generally requires very long trajectories based on conventional molecular dynamics simulations. In this report,...
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05-04-2013 09:18 PM
Whole-Body Rocking Motion of a Fusion Peptide in Lipid Bilayers from Size-Dispersed 15N NMR Relaxation
Whole-Body Rocking Motion of a Fusion Peptide in Lipid Bilayers from Size-Dispersed 15N NMR Relaxation
Justin L. Lorieau, John M. Louis and Ad Bax
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja2045309/aop/images/medium/ja-2011-045309_0004.gif
Journal of the American Chemical Society
DOI: 10.1021/ja2045309
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/2aIqfWmdIn4
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08-23-2011 05:30 AM
Whole-Body Rocking Motion of a Fusion Peptide in Lipid Bilayers from Size-Dispersed 15N NMR Relaxation.
Whole-Body Rocking Motion of a Fusion Peptide in Lipid Bilayers from Size-Dispersed 15N NMR Relaxation.
Whole-Body Rocking Motion of a Fusion Peptide in Lipid Bilayers from Size-Dispersed 15N NMR Relaxation.
J Am Chem Soc. 2011 Aug 17;
Authors: Lorieau JL, Louis JM, Bax A
Abstract
Biological membranes present a highly fluid environment and integration of proteins within such membranes is itself highly dynamic: proteins diffuse laterally within the plane of the membrane, and rotationally about the normal vector of this plane. We...
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08-19-2011 02:56 PM
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
[NMR paper] What contributions to protein side-chain dynamics are probed by NMR experiments? A mo
What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis.
Related Articles What contributions to protein side-chain dynamics are probed by NMR experiments? A molecular dynamics simulation analysis.
J Mol Biol. 2005 May 27;349(1):185-203
Authors: Best RB, Clarke J, Karplus M
Molecular dynamics simulations of the structurally homologous proteins TNfn3 and FNfn10 have been used to investigate the contributions to side-chain dynamics measured by NMR relaxation experiments. The...
Microsecond motions probed by near-rotary-resonance R 1Ï? 15 N MAS NMR experiments: the model case of protein overall-rocking in crystals
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