Literature DB >> 33241122

Protein Dynamics revealed by NMR Relaxation Methods.

Fa-An Chao1, R Andrew Byrd1.   

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.

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Year:  2020        PMID: 33241122      PMCID: PMC7685179          DOI: 10.1042/etls20170139

Source DB:  PubMed          Journal:  Emerg Top Life Sci        ISSN: 2397-8554


  80 in total

1.  Heteronuclear Adiabatic Relaxation Dispersion (HARD) for quantitative analysis of conformational dynamics in proteins.

Authors:  Nathaniel J Traaseth; Fa-An Chao; Larry R Masterson; Silvia Mangia; Michael Garwood; Shalom Michaeli; Burckhard Seelig; Gianluigi Veglia
Journal:  J Magn Reson       Date:  2012-04-06       Impact factor: 2.229

2.  Separating degenerate (1)H transitions in methyl group probes for single-quantum (1)H-CPMG relaxation dispersion NMR spectroscopy.

Authors:  Vitali Tugarinov; Lewis E Kay
Journal:  J Am Chem Soc       Date:  2007-07-12       Impact factor: 15.419

Review 3.  Probing conformational dynamics in biomolecules via chemical exchange saturation transfer: a primer.

Authors:  Pramodh Vallurupalli; Ashok Sekhar; Tairan Yuwen; Lewis E Kay
Journal:  J Biomol NMR       Date:  2017-03-19       Impact factor: 2.835

4.  Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study.

Authors:  Rui Huang; Zev A Ripstein; Rafal Augustyniak; Michal Lazniewski; Krzysztof Ginalski; Lewis E Kay; John L Rubinstein
Journal:  Proc Natl Acad Sci U S A       Date:  2016-07-11       Impact factor: 11.205

5.  A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis.

Authors:  Gira Bhabha; Jeeyeon Lee; Damian C Ekiert; Jongsik Gam; Ian A Wilson; H Jane Dyson; Stephen J Benkovic; Peter E Wright
Journal:  Science       Date:  2011-04-08       Impact factor: 47.728

6.  Mapping chemical exchange in proteins with MW > 50 kD.

Authors:  Chunyu Wang; Mark Rance; Arthur G Palmer
Journal:  J Am Chem Soc       Date:  2003-07-30       Impact factor: 15.419

7.  Backbone dynamics of a free and phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation.

Authors:  N A Farrow; R Muhandiram; A U Singer; S M Pascal; C M Kay; G Gish; S E Shoelson; T Pawson; J D Forman-Kay; L E Kay
Journal:  Biochemistry       Date:  1994-05-17       Impact factor: 3.162

8.  Probing slow dynamics in high molecular weight proteins by methyl-TROSY NMR spectroscopy: application to a 723-residue enzyme.

Authors:  Dmitry M Korzhnev; Karin Kloiber; Voula Kanelis; Vitali Tugarinov; Lewis E Kay
Journal:  J Am Chem Soc       Date:  2004-03-31       Impact factor: 15.419

9.  Atomic-resolution dynamics on the surface of amyloid-β protofibrils probed by solution NMR.

Authors:  Nicolas L Fawzi; Jinfa Ying; Rodolfo Ghirlando; Dennis A Torchia; G Marius Clore
Journal:  Nature       Date:  2011-10-30       Impact factor: 49.962

10.  Automated NMR relaxation dispersion data analysis using NESSY.

Authors:  Michael Bieri; Paul R Gooley
Journal:  BMC Bioinformatics       Date:  2011-10-27       Impact factor: 3.169

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  4 in total

1.  Theoretical classification of exchange geometries from the perspective of NMR relaxation dispersion.

Authors:  Fa-An Chao; Yue Zhang; R Andrew Byrd
Journal:  J Magn Reson       Date:  2021-05-11       Impact factor: 2.734

2.  Low-energy electron holography imaging of conformational variability of single-antibody molecules from electrospray ion beam deposition.

Authors:  Hannah Ochner; Sven Szilagyi; Sabine Abb; Joseph Gault; Carol V Robinson; Luigi Malavolti; Stephan Rauschenbach; Klaus Kern
Journal:  Proc Natl Acad Sci U S A       Date:  2021-12-21       Impact factor: 11.205

3.  The transient expression of recombinant proteins in plant cell packs facilitates stable isotope labelling for NMR spectroscopy.

Authors:  Patrick Opdensteinen; Laura E Sperl; Mariam Mohamadi; Nicole Kündgen-Redding; Franz Hagn; Johannes Felix Buyel
Journal:  Plant Biotechnol J       Date:  2022-07-19       Impact factor: 13.263

4.  Unravelling the Time Scale of Conformational Plasticity and Allostery in Glycan Recognition by Human Galectin-1.

Authors:  Sara Bertuzzi; Ana Gimeno; Reyes Núñez-Franco; Ganeko Bernardo-Seisdedos; Sandra Delgado; Gonzalo Jiménez-Osés; Oscar Millet; Jesús Jiménez-Barbero; Ana Ardá
Journal:  Chemistry       Date:  2020-10-29       Impact factor: 5.236

  4 in total

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