Related ArticlesProtein Dynamics revealed by NMR Relaxation Methods.
Emerg Top Life Sci. 2020 Apr;2(1):93-105
Authors: Chao FA, Byrd RA
Abstract
Structural biology often focuses primarily on three-dimensional structures of biological macromolecules, deposited in the Protein Data Bank (PDB). This resource is a remarkable entity for the world-wide scientific and medical communities, as well as the general public, as it is a growing translation into three-dimensional space of the vast information in genomic databases, e.g. GENBANK. There is, however, significantly more to understanding biological function than the three-dimensional coordinate space for ground-state structures of biomolecules. The vast array of biomolecules experiences natural dynamics, interconversion between multiple conformational states, and molecular recognition and allosteric events that play out on timescales ranging from picoseconds to seconds. This wide range of timescales demands ingenious and sophisticated experimental tools to sample and interpret these motions, thus enabling clearer insight into functional annotation of the PDB. NMR spectroscopy is unique in its ability to sample this range of timescales at atomic resolution and in physiologically relevant conditions using spin relaxation methods. The field is constantly expanding to provide new creative experiments, to yield more detailed coverage of timescales, and to broaden the power of interpretation and analysis methods. This review highlights the current state of the methodology and examines the extension of analysis tools for more complex experiments and dynamic models. The future for understanding protein dynamics is bright, and these extended tools bring greater compatibility with developments in computational molecular dynamics, all of which will further our understanding of biological molecular functions. These facets place NMR as a key component in integrated structural biology.
[NMR paper] Impact of the Hereditary P301L Mutation on the Correlated Conformational Dynamics of Human Tau Protein Revealed by the Paramagnetic Relaxation Enhancement NMR Experiments.
Impact of the Hereditary P301L Mutation on the Correlated Conformational Dynamics of Human Tau Protein Revealed by the Paramagnetic Relaxation Enhancement NMR Experiments.
Related Articles Impact of the Hereditary P301L Mutation on the Correlated Conformational Dynamics of Human Tau Protein Revealed by the Paramagnetic Relaxation Enhancement NMR Experiments.
Int J Mol Sci. 2020 May 30;21(11):
Authors: Kawasaki R, Tate SI
Abstract
Tau forms intracellular insoluble aggregates as a neuropathological hallmark of Alzheimer's disease....
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[NMR paper] Global Dynamics and Exchange Kinetics of a Protein on the Surface of Nanoparticles Revealed by Relaxation-Based Solution NMR Spectroscopy.
Global Dynamics and Exchange Kinetics of a Protein on the Surface of Nanoparticles Revealed by Relaxation-Based Solution NMR Spectroscopy.
Global Dynamics and Exchange Kinetics of a Protein on the Surface of Nanoparticles Revealed by Relaxation-Based Solution NMR Spectroscopy.
J Am Chem Soc. 2016 Apr 25;
Authors: Ceccon A, Tugarinov V, Bax A, Clore GM
Abstract
The global motions and exchange kinetics of a model protein, ubiquitin, bound to the surface of negatively charged lipid-based nano-particles (liposomes) are derived from...
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[NMR paper] Water scaffolding in collagen: Implications on protein dynamics as revealed by solid-state NMR.
Water scaffolding in collagen: Implications on protein dynamics as revealed by solid-state NMR.
Water scaffolding in collagen: Implications on protein dynamics as revealed by solid-state NMR.
Biopolymers. 2013 Jun 19;
Authors: Aliev AE, Courtier-Murias D
Abstract
Solid-state NMR studies of collagen samples of various origin confirm that the amplitude of collagen backbone and sidechain motions increases significantly on increasing the water content. This conclusion is supported by the changes observed in three different NMR...
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[NMR paper] Glassy dynamics of protein methyl groups revealed by deuteron NMR.
Glassy dynamics of protein methyl groups revealed by deuteron NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Glassy dynamics of protein methyl groups revealed by deuteron NMR.
J Phys Chem B. 2013 Jan 31;117(4):1051-61
Authors: Vugmeyster L, Ostrovsky D, Penland K, Hoatson GL, Vold RL
Abstract
We investigated site-specific dynamics of key methyl groups in the hydrophobic core of chicken villin headpiece subdomain (HP36) over the temperature range between 298 and 140 K...
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The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation
The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation
Available online 13 December 2012
Publication year: 2012
Source:Current Opinion in Structural Biology</br>
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Historically it has been virtually impossible to experimentally determine the contribution of residual protein entropy to fundamental protein activities such as the binding of ligands. Recent progress has illuminated the possibility of employing NMR relaxation methods to quantitatively determine the role of changes in conformational...
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02-03-2013 10:13 AM
[NMR paper] Differential dynamics in the G protein-coupled receptor rhodopsin revealed by solutio
Differential dynamics in the G protein-coupled receptor rhodopsin revealed by solution NMR.
Related Articles Differential dynamics in the G protein-coupled receptor rhodopsin revealed by solution NMR.
Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3409-13
Authors: Klein-Seetharaman J, Yanamala NV, Javeed F, Reeves PJ, Getmanova EV, Loewen MC, Schwalbe H, Khorana HG
G protein-coupled receptors are cell-surface seven-helical membrane proteins that undergo conformational changes on activation. The mammalian photoreceptor, rhodopsin, is the...
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[NMR paper] Riboflavin synthase of Schizosaccharomyces pombe. Protein dynamics revealed by 19F NM
Riboflavin synthase of Schizosaccharomyces pombe. Protein dynamics revealed by 19F NMR protein perturbation experiments.
Related Articles Riboflavin synthase of Schizosaccharomyces pombe. Protein dynamics revealed by 19F NMR protein perturbation experiments.
BMC Biochem. 2003 Dec 23;4:18
Authors: Fischer M, Schott AK, Kemter K, Feicht R, Richter G, Illarionov B, Eisenreich W, Gerhardt S, Cushman M, Steinbacher S, Huber R, Bacher A
BACKGROUND: Riboflavin synthase catalyzes the transformation of 6,7-dimethyl-8-ribityllumazine into riboflavin in...
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[NMR paper] Protein-protein interaction revealed by NMR T(2) relaxation experiments: the lipoyl d
Protein-protein interaction revealed by NMR T(2) relaxation experiments: the lipoyl domain and E1 component of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus.
Related Articles Protein-protein interaction revealed by NMR T(2) relaxation experiments: the lipoyl domain and E1 component of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus.
J Mol Biol. 2000 Jan 28;295(4):1023-37
Authors: Howard MJ, Chauhan HJ, Domingo GJ, Fuller C, Perham RN
T(2) relaxation experiments in combination with...