Literature DB >> 29188417

Simultaneous determination of fast and slow dynamics in molecules using extreme CPMG relaxation dispersion experiments.

Jithender G Reddy1,2, Supriya Pratihar1, David Ban3, Sebastian Frischkorn1, Stefan Becker1, Christian Griesinger1, Donghan Lee4.   

Abstract

Molecular dynamics play a significant role in how molecules perform their function. A critical method that provides information on dynamics, at the atomic level, is NMR-based relaxation dispersion (RD) experiments. RD experiments have been utilized for understanding multiple biological processes occurring at micro-to-millisecond time, such as enzyme catalysis, molecular recognition, ligand binding and protein folding. Here, we applied the recently developed high-power RD concept to the Carr-Purcell-Meiboom-Gill sequence (extreme CPMG; E-CPMG) for the simultaneous detection of fast and slow dynamics. Using a fast folding protein, gpW, we have shown that previously inaccessible kinetics can be accessed with the improved precision and efficiency of the measurement by using this experiment.

Keywords:  Conformational exchange; Extreme CPMG; Protein dynamics; Relaxation dispersion; µs–ms dynamics

Mesh:

Substances:

Year:  2017        PMID: 29188417     DOI: 10.1007/s10858-017-0155-0

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  43 in total

1.  A phase cycle scheme that significantly suppresses offset-dependent artifacts in the R2-CPMG 15N relaxation experiment.

Authors:  Grover N B Yip; Erik R P Zuiderweg
Journal:  J Magn Reson       Date:  2004-11       Impact factor: 2.229

Review 2.  An NMR perspective on enzyme dynamics.

Authors:  David D Boehr; H Jane Dyson; Peter E Wright
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

3.  Protein folding kinetics: barrier effects in chemical and thermal denaturation experiments.

Authors:  Athi N Naganathan; Urmi Doshi; Victor Muñoz
Journal:  J Am Chem Soc       Date:  2007-04-10       Impact factor: 15.419

Review 4.  Recent developments in (15)N NMR relaxation studies that probe protein backbone dynamics.

Authors:  Rieko Ishima
Journal:  Top Curr Chem       Date:  2012

5.  The energetics of a three-state protein folding system probed by high-pressure relaxation dispersion NMR spectroscopy.

Authors:  Vitali Tugarinov; David S Libich; Virginia Meyer; Julien Roche; G Marius Clore
Journal:  Angew Chem Int Ed Engl       Date:  2015-09-14       Impact factor: 15.336

6.  The dependence of chemical exchange on boundary selection in a fibronectin type III domain from human tenascin.

Authors:  A E Meekhof; S J Hamill; V L Arcus; J Clarke; S M Freund
Journal:  J Mol Biol       Date:  1998-09-11       Impact factor: 5.469

7.  Pervasive conformational fluctuations on microsecond time scales in a fibronectin type III domain.

Authors:  M Akke; J Liu; J Cavanagh; H P Erickson; A G Palmer
Journal:  Nat Struct Biol       Date:  1998-01

8.  Protein dynamics studied by rotating frame 15N spin relaxation times.

Authors:  T Szyperski; P Luginbühl; G Otting; P Güntert; K Wüthrich
Journal:  J Biomol NMR       Date:  1993-03       Impact factor: 2.835

9.  Dynamics of ligand binding from 13C NMR relaxation dispersion at natural abundance.

Authors:  John S Zintsmaster; Brian D Wilson; Jeffrey W Peng
Journal:  J Am Chem Soc       Date:  2008-10-04       Impact factor: 15.419

10.  Visualizing the molecular recognition trajectory of an intrinsically disordered protein using multinuclear relaxation dispersion NMR.

Authors:  Robert Schneider; Damien Maurin; Guillaume Communie; Jaka Kragelj; D Flemming Hansen; Rob W H Ruigrok; Malene Ringkjøbing Jensen; Martin Blackledge
Journal:  J Am Chem Soc       Date:  2015-01-16       Impact factor: 15.419

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  11 in total

1.  Detection of chemical exchange in methyl groups of macromolecules.

Authors:  Michelle L Gill; Andrew Hsu; Arthur G Palmer
Journal:  J Biomol NMR       Date:  2019-08-12       Impact factor: 2.835

2.  Probing the Broad Time Scale and Heterogeneous Conformational Dynamics in the Catalytic Core of the Arf-GAP ASAP1 via Methyl Adiabatic Relaxation Dispersion.

Authors:  Fa-An Chao; Yifei Li; Yue Zhang; R Andrew Byrd
Journal:  J Am Chem Soc       Date:  2019-07-22       Impact factor: 15.419

3.  Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.

Authors:  Dominique Marion; Diego F Gauto; Isabel Ayala; Karine Giandoreggio-Barranco; Paul Schanda
Journal:  Chemphyschem       Date:  2018-12-20       Impact factor: 3.102

4.  The A39G FF domain folds on a volcano-shaped free energy surface via separate pathways.

Authors:  Ved P Tiwari; Yuki Toyama; Debajyoti De; Lewis E Kay; Pramodh Vallurupalli
Journal:  Proc Natl Acad Sci U S A       Date:  2021-11-16       Impact factor: 11.205

5.  A litmus test for classifying recognition mechanisms of transiently binding proteins.

Authors:  Kalyan S Chakrabarti; Simon Olsson; Supriya Pratihar; Karin Giller; Kerstin Overkamp; Ko On Lee; Vytautas Gapsys; Kyoung-Seok Ryu; Bert L de Groot; Frank Noé; Stefan Becker; Donghan Lee; Thomas R Weikl; Christian Griesinger
Journal:  Nat Commun       Date:  2022-07-01       Impact factor: 17.694

Review 6.  Methyl-Based NMR Spectroscopy Methods for Uncovering Structural Dynamics in Large Proteins and Protein Complexes.

Authors:  Zachary K Boswell; Michael P Latham
Journal:  Biochemistry       Date:  2018-10-26       Impact factor: 3.162

7.  The precious fluorine on the ring: fluorine NMR for biological systems.

Authors:  Andras Boeszoermenyi; Barbara Ogórek; Akshay Jain; Haribabu Arthanari; Gerhard Wagner
Journal:  J Biomol NMR       Date:  2020-07-10       Impact factor: 2.835

8.  Efficient Detection of Structure and Dynamics in Unlabeled RNAs: The SELOPE Approach.

Authors:  Judith Schlagnitweit; Emilie Steiner; Hampus Karlsson; Katja Petzold
Journal:  Chemistry       Date:  2018-03-25       Impact factor: 5.236

9.  Coupling between conformational dynamics and catalytic function at the active site of the lead-dependent ribozyme.

Authors:  Neil A White; Minako Sumita; Victor E Marquez; Charles G Hoogstraten
Journal:  RNA       Date:  2018-08-15       Impact factor: 4.942

10.  Functional protein dynamics on uncharted time scales detected by nanoparticle-assisted NMR spin relaxation.

Authors:  Mouzhe Xie; Lei Yu; Lei Bruschweiler-Li; Xinyao Xiang; Alexandar L Hansen; Rafael Brüschweiler
Journal:  Sci Adv       Date:  2019-08-14       Impact factor: 14.136

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