[NMR paper] Geometric approximation: a new computational approach to characterize protein dynamics from NMR adiabatic relaxation dispersion experiments.
Related ArticlesGeometric 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 with the analysis of NMR adiabatic relaxation dispersion experiments to reveal biomolecular dynamics. When an analytical solution to the theoretical equations describing a physical process is not available, the new approach can significantly accelerate the computational speed of the conventional numerical integration up to 105 times. NMR adiabatic relaxation dispersion experiments, enhanced with optimized proton-decoupled pulse sequences, although extremely powerful, have previously been refractory to quantitative analysis. Both simulations and experimental validation demonstrate detectable "slow" (?s-ms) conformational exchange rates from 102 sec-1 to 105 sec-1. This greatly expanded timescale range enables characterization of a wide array of conformational fluctuations for individual residues, which correlate with biomolecular function and were previously inaccessible. Moreover, the new computational method can be potentially generalized for analyzing new types of relaxation dispersion experiments to characterize the various dynamics of biomolecular systems.
PMID: 27225523 [PubMed - as supplied by publisher]
[NMR paper] 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.
Related Articles Extracting 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...
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10-20-2015 09:44 PM
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 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
Heteronuclear Adiabatic Relaxation Dispersion (HARD) for Quantitative Analysis of Conformational Dynamics in Proteins
Heteronuclear Adiabatic Relaxation Dispersion (HARD) for Quantitative Analysis of Conformational Dynamics in Proteins
Publication year: 2012
Source:Journal of Magnetic Resonance</br>
Nathaniel J. Traaseth, Fa-An Chao, Larry R. Masterson, Silvia Mangia, Michael Garwood, Shalom Michaeli, Burckhard Seelig, Gianluigi Veglia</br>
NMR relaxation methods probe biomolecular motions over a wide range of timescales. In particular, the rotating frame spin-lock R1? and Carr-Purcell-Meiboom-Gill (CPMG) R2 experiments are commonly used to characterize ?sec-msec dynamics, which...
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04-08-2012 08:53 AM
Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion [Biophysics and Computational Biology]
Measurement of protein unfolding/refolding kinetics and structural characterization of hidden intermediates by NMR relaxation dispersion
Meinhold, D. W., Wright, P. E....
Date: 2011-05-31
Detailed understanding of protein function and malfunction hinges on the ability to characterize transiently populated states and the transitions between them. Here, we use 15N, , and 13CO NMR R2 relaxation dispersion to investigate spontaneous unfolding and refolding events of native apomyoglobin. Above pH 5.0, dispersion is dominated by processes involving fluctuations of the F-helix region, which...
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...
Geometric approximation: a new computational approach to characterize protein dynamics from NMR adiabatic relaxation dispersion experiments.
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