Literature DB >> 21059410

An introduction to NMR-based approaches for measuring protein dynamics.

Ian R Kleckner1, Mark P Foster.   

Abstract

Proteins are inherently flexible at ambient temperature. At equilibrium, they are characterized by a set of conformations that undergo continuous exchange within a hierarchy of spatial and temporal scales ranging from nanometers to micrometers and femtoseconds to hours. Dynamic properties of proteins are essential for describing the structural bases of their biological functions including catalysis, binding, regulation and cellular structure. Nuclear magnetic resonance (NMR) spectroscopy represents a powerful technique for measuring these essential features of proteins. Here we provide an introduction to NMR-based approaches for studying protein dynamics, highlighting eight distinct methods with recent examples, contextualized within a common experimental and analytical framework. The selected methods are (1) Real-time NMR, (2) Exchange spectroscopy, (3) Lineshape analysis, (4) CPMG relaxation dispersion, (5) Rotating frame relaxation dispersion, (6) Nuclear spin relaxation, (7) Residual dipolar coupling, (8) Paramagnetic relaxation enhancement. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
Copyright © 2010 Elsevier B.V. All rights reserved.

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Year:  2010        PMID: 21059410      PMCID: PMC3061256          DOI: 10.1016/j.bbapap.2010.10.012

Source DB:  PubMed          Journal:  Biochim Biophys Acta        ISSN: 0006-3002


  174 in total

Review 1.  Structural dynamics of bio-macromolecules by NMR: the slowly relaxing local structure approach.

Authors:  Eva Meirovitch; Yury E Shapiro; Antonino Polimeno; Jack H Freed
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2010-05       Impact factor: 9.795

2.  Improvement of duty-cycle heating compensation in NMR spin relaxation experiments.

Authors:  Grover N B Yip; Erik R P Zuiderweg
Journal:  J Magn Reson       Date:  2005-10       Impact factor: 2.229

3.  Signal identification in NMR spectra with coupled evolution periods.

Authors:  Daniel Malmodin; Martin Billeter
Journal:  J Magn Reson       Date:  2005-09       Impact factor: 2.229

4.  Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation.

Authors:  Nikola Trbovic; Byungchan Kim; Richard A Friesner; Arthur G Palmer
Journal:  Proteins       Date:  2008-05-01

5.  The mechanism of rate-limiting motions in enzyme function.

Authors:  Eric D Watt; Hiroko Shimada; Evgenii L Kovrigin; J Patrick Loria
Journal:  Proc Natl Acad Sci U S A       Date:  2007-07-05       Impact factor: 11.205

Review 6.  Recent advances in segmental isotope labeling of proteins: NMR applications to large proteins and glycoproteins.

Authors:  Lenka Skrisovska; Mario Schubert; Frédéric H-T Allain
Journal:  J Biomol NMR       Date:  2009-08-19       Impact factor: 2.835

7.  Internal mobility in the partially folded DNA binding and dimerization domains of GAL4: NMR analysis of the N-H spectral density functions.

Authors:  J F Lefevre; K T Dayie; J W Peng; G Wagner
Journal:  Biochemistry       Date:  1996-02-27       Impact factor: 3.162

8.  Trapping moving targets with small molecules.

Authors:  Gregory M Lee; Charles S Craik
Journal:  Science       Date:  2009-04-10       Impact factor: 47.728

9.  Spectral density function mapping using 15N relaxation data exclusively.

Authors:  N A Farrow; O Zhang; A Szabo; D A Torchia; L E Kay
Journal:  J Biomol NMR       Date:  1995-09       Impact factor: 2.835

10.  The flexibility of a distant loop modulates active site motion and product release in ribonuclease A.

Authors:  Nicolas Doucet; Eric D Watt; J Patrick Loria
Journal:  Biochemistry       Date:  2009-08-04       Impact factor: 3.162

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  157 in total

1.  GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data.

Authors:  Ian R Kleckner; Mark P Foster
Journal:  J Biomol NMR       Date:  2011-12-11       Impact factor: 2.835

2.  Segmental motions, not a two-state concerted switch, underlie allostery in CheY.

Authors:  Leanna R McDonald; Joshua A Boyer; Andrew L Lee
Journal:  Structure       Date:  2012-06-21       Impact factor: 5.006

3.  NMR-based conformational ensembles explain pH-gated opening and closing of OmpG channel.

Authors:  Tiandi Zhuang; Christina Chisholm; Min Chen; Lukas K Tamm
Journal:  J Am Chem Soc       Date:  2013-10-01       Impact factor: 15.419

Review 4.  Advances in coarse-grained modeling of macromolecular complexes.

Authors:  Alexander J Pak; Gregory A Voth
Journal:  Curr Opin Struct Biol       Date:  2018-11-30       Impact factor: 6.809

Review 5.  An introduction to biological NMR spectroscopy.

Authors:  Dominique Marion
Journal:  Mol Cell Proteomics       Date:  2013-07-06       Impact factor: 5.911

6.  NMR studies of the dynamics of nitrophorin 2 bound to nitric oxide.

Authors:  Dhanasekaran Muthu; Robert E Berry; Hongjun Zhang; F Ann Walker
Journal:  Biochemistry       Date:  2013-10-30       Impact factor: 3.162

7.  Two fatty acid-binding proteins expressed in the intestine interact differently with endocannabinoids.

Authors:  May Poh Lai; Francine S Katz; Cédric Bernard; Judith Storch; Ruth E Stark
Journal:  Protein Sci       Date:  2020-04-28       Impact factor: 6.725

8.  TCR scanning of peptide/MHC through complementary matching of receptor and ligand molecular flexibility.

Authors:  William F Hawse; Soumya De; Alex I Greenwood; Linda K Nicholson; Jaroslav Zajicek; Evgenii L Kovrigin; David M Kranz; K Christopher Garcia; Brian M Baker
Journal:  J Immunol       Date:  2014-02-12       Impact factor: 5.422

9.  Protein Interactions with Nanoparticle Surfaces: Highlighting Solution NMR Techniques.

Authors:  Y Randika Perera; Rebecca A Hill; Nicholas C Fitzkee
Journal:  Isr J Chem       Date:  2019-09-19       Impact factor: 3.333

10.  Characterization of Electrospray Ionization (ESI) Parameters on In-ESI Hydrogen/Deuterium Exchange of Carbohydrate-Metal Ion Adducts.

Authors:  O Tara Liyanage; Matthew R Brantley; Emvia I Calixte; Touradj Solouki; Kevin L Shuford; Elyssia S Gallagher
Journal:  J Am Soc Mass Spectrom       Date:  2018-10-23       Impact factor: 3.109

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