Literature DB >> 26426424

Multi-probe relaxation dispersion measurements increase sensitivity to protein dynamics.

R Bryn Fenwick1, David Oyen1, Peter E Wright1.   

Abstract

Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion measurements are a valuable tool for the characterization of structural transitions on the micro-millisecond timescale. While the measurement of (15)N relaxation dispersion is now routine, the measurements with alternative nuclei remain limited. Here we report (15)N as well as (1)H R2 relaxation dispersion measurements of the N23PP/S148A "dynamic knockout" mutant of dihydrofolate reductase. The (1)H dispersion measurements are complementary to (15)N data as many additional residues are observed to have dispersive behavior for the (1)H nucleus. Simultaneous fitting of the dispersion profiles for the two nuclei increases the accuracy of exchange parameters determined for individual residues and clustered groups of residues. The different sensitivity of the two nuclei to changes in backbone torsional angles, ring currents, and hydrogen bonding effects provides important insights into the nature of the structural changes that take place during the exchange process. We observe clear evidence of direct and indirect hydrogen bond effects for the (15)N and (1)H chemical shift changes in the active-site, modulation of ring current shielding in the CD-loop and backbone torsional changes in a cluster of residues associated with the C-terminus. This work demonstrates the power of combined (1)H and (15)N probes for the study of backbone dynamics on the micro-millisecond timescale though the analysis of chemical shift changes.

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Year:  2016        PMID: 26426424      PMCID: PMC4758882          DOI: 10.1039/c5cp04670j

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  37 in total

1.  Increasing the exchange time-scale that can be probed by CPMG relaxation dispersion NMR.

Authors:  Pramodh Vallurupalli; Guillaume Bouvignies; Lewis E Kay
Journal:  J Phys Chem B       Date:  2011-11-11       Impact factor: 2.991

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Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

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Authors:  O Zhang; J D Forman-Kay
Journal:  Biochemistry       Date:  1997-04-01       Impact factor: 3.162

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Authors:  J Yao; H J Dyson; P E Wright
Journal:  FEBS Lett       Date:  1997-12-15       Impact factor: 4.124

6.  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

7.  Millisecond timescale fluctuations in dihydrofolate reductase are exquisitely sensitive to the bound ligands.

Authors:  David D Boehr; Dan McElheny; H Jane Dyson; Peter E Wright
Journal:  Proc Natl Acad Sci U S A       Date:  2010-01-08       Impact factor: 11.205

8.  Carbonyl carbon transverse relaxation dispersion measurements and ms-micros timescale motion in a protein hydrogen bond network.

Authors:  Rieko Ishima; James Baber; John M Louis; Dennis A Torchia
Journal:  J Biomol NMR       Date:  2004-06       Impact factor: 2.835

9.  Fast and accurate fitting of relaxation dispersion data using the flexible software package GLOVE.

Authors:  Kenji Sugase; Tsuyoshi Konuma; Jonathan C Lansing; Peter E Wright
Journal:  J Biomol NMR       Date:  2013-06-11       Impact factor: 2.835

Review 10.  Chemical shifts and three-dimensional protein structures.

Authors:  E Oldfield
Journal:  J Biomol NMR       Date:  1995-04       Impact factor: 2.835

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  6 in total

Review 1.  Applications of NMR and computational methodologies to study protein dynamics.

Authors:  Chitra Narayanan; Khushboo Bafna; Louise D Roux; Pratul K Agarwal; Nicolas Doucet
Journal:  Arch Biochem Biophys       Date:  2017-05-05       Impact factor: 4.013

2.  Slow Dynamics of Tryptophan-Water Networks in Proteins.

Authors:  R Bryn Fenwick; David Oyen; H Jane Dyson; Peter E Wright
Journal:  J Am Chem Soc       Date:  2018-01-03       Impact factor: 15.419

3.  General Expressions for Carr-Purcell-Meiboom-Gill Relaxation Dispersion for N-Site Chemical Exchange.

Authors:  Hans Koss; Mark Rance; Arthur G Palmer
Journal:  Biochemistry       Date:  2018-07-30       Impact factor: 3.162

4.  Modeling of Hidden Structures Using Sparse Chemical Shift Data from NMR Relaxation Dispersion.

Authors:  R Bryn Fenwick; David Oyen; Henry van den Bedem; H Jane Dyson; Peter E Wright
Journal:  Biophys J       Date:  2020-12-08       Impact factor: 4.033

5.  Role of Active Site Loop Dynamics in Mediating Ligand Release from E. coli Dihydrofolate Reductase.

Authors:  Amrinder Singh; R Bryn Fenwick; H Jane Dyson; Peter E Wright
Journal:  Biochemistry       Date:  2021-08-24       Impact factor: 3.321

6.  Defining the Structural Basis for Allosteric Product Release from E. coli Dihydrofolate Reductase Using NMR Relaxation Dispersion.

Authors:  David Oyen; R Bryn Fenwick; Phillip C Aoto; Robyn L Stanfield; Ian A Wilson; H Jane Dyson; Peter E Wright
Journal:  J Am Chem Soc       Date:  2017-08-03       Impact factor: 15.419

  6 in total

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