Literature DB >> 26821600

Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data.

Yina Gu1, Alexandar L Hansen2, Yu Peng1, Rafael Brüschweiler3,4,5.   

Abstract

Functional motions of (15)N-labeled proteins can be monitored by solution NMR spin relaxation experiments over a broad range of timescales. These experiments however typically take of the order of several days to a week per protein. Recently, NMR chemical exchange saturation transfer (CEST) experiments have emerged to probe slow millisecond motions complementing R1ρ and CPMG-type experiments. CEST also simultaneously reports on site-specific R1 and R2 parameters. It is shown here how CEST-derived R1 and R2 relaxation parameters can be measured within a few hours at an accuracy comparable to traditional relaxation experiments. Using a "lean" version of the model-free approach S(2) order parameters can be determined that match those from the standard model-free approach applied to (15)N R1, R2 , and {(1)H}-(15)N NOE data. The new methodology, which is demonstrated for ubiquitin and arginine kinase (42 kDa), should serve as an effective screening tool of protein dynamics from picosecond-to-millisecond timescales.
© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Entities:  

Keywords:  CEST; NMR spectroscopy; lean model-free analysis; protein dynamics; spin relaxation

Mesh:

Substances:

Year:  2016        PMID: 26821600      PMCID: PMC5035698          DOI: 10.1002/anie.201511711

Source DB:  PubMed          Journal:  Angew Chem Int Ed Engl        ISSN: 1433-7851            Impact factor:   15.336


  27 in total

1.  A 2D ¹³C-CEST experiment for studying slowly exchanging protein systems using methyl probes: an application to protein folding.

Authors:  Guillaume Bouvignies; Lewis E Kay
Journal:  J Biomol NMR       Date:  2012-06-12       Impact factor: 2.835

2.  NMR Order Parameter Determination from Long Molecular Dynamics Trajectories for Objective Comparison with Experiment.

Authors:  Yina Gu; Da-Wei Li; Rafael Brüschweiler
Journal:  J Chem Theory Comput       Date:  2014-06-10       Impact factor: 6.006

3.  Decoding the Mobility and Time Scales of Protein Loops.

Authors:  Yina Gu; Da-Wei Li; Rafael Brüschweiler
Journal:  J Chem Theory Comput       Date:  2015-03-10       Impact factor: 6.006

4.  The Quest for Simplicity: Remarks on the Free-Approach Models.

Authors:  Łukasz Jaremko; Mariusz Jaremko; Michał Nowakowski; Andrzej Ejchart
Journal:  J Phys Chem B       Date:  2015-08-28       Impact factor: 2.991

5.  Speeding-up exchange-mediated saturation transfer experiments by Fourier transform.

Authors:  Marta G Carneiro; Jithender G Reddy; Christian Griesinger; Donghan Lee
Journal:  J Biomol NMR       Date:  2015-09-09       Impact factor: 2.835

6.  Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding.

Authors:  D Yang; L E Kay
Journal:  J Mol Biol       Date:  1996-10-25       Impact factor: 5.469

7.  Insights into the local residual entropy of proteins provided by NMR relaxation.

Authors:  Z Li; S Raychaudhuri; A J Wand
Journal:  Protein Sci       Date:  1996-12       Impact factor: 6.725

8.  Probing slowly exchanging protein systems via ¹³Cα-CEST: monitoring folding of the Im7 protein.

Authors:  Alexandar L Hansen; Guillaume Bouvignies; Lewis E Kay
Journal:  J Biomol NMR       Date:  2013-02-06       Impact factor: 2.835

9.  Probing exchange kinetics and atomic resolution dynamics in high-molecular-weight complexes using dark-state exchange saturation transfer NMR spectroscopy.

Authors:  Nicolas L Fawzi; Jinfa Ying; Dennis A Torchia; G Marius Clore
Journal:  Nat Protoc       Date:  2012-07-19       Impact factor: 13.491

10.  NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

Authors:  F Delaglio; S Grzesiek; G W Vuister; G Zhu; J Pfeifer; A Bax
Journal:  J Biomol NMR       Date:  1995-11       Impact factor: 2.835

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  7 in total

Review 1.  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

2.  Extreme Nonuniform Sampling for Protein NMR Dynamics Studies in Minimal Time.

Authors:  Gregory Jameson; Alexandar L Hansen; Dawei Li; Lei Bruschweiler-Li; Rafael Brüschweiler
Journal:  J Am Chem Soc       Date:  2019-10-14       Impact factor: 15.419

Review 3.  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

4.  Characterization of Internal Protein Dynamics and Conformational Entropy by NMR Relaxation.

Authors:  Matthew A Stetz; José A Caro; Sravya Kotaru; Xuejun Yao; Bryan S Marques; Kathleen G Valentine; A Joshua Wand
Journal:  Methods Enzymol       Date:  2018-12-08       Impact factor: 1.600

5.  15N CEST data and traditional model-free analysis capture fast internal dynamics of DJ-1.

Authors:  Jonathan Catazaro; Tessa Andrews; Nicole M Milkovic; Jiusheng Lin; Austin J Lowe; Mark A Wilson; Robert Powers
Journal:  Anal Biochem       Date:  2017-11-21       Impact factor: 3.365

6.  Fast evaluation of protein dynamics from deficient 15N relaxation data.

Authors:  Łukasz Jaremko; Mariusz Jaremko; Andrzej Ejchart; Michał Nowakowski
Journal:  J Biomol NMR       Date:  2018-03-28       Impact factor: 2.835

7.  Dynamics in natural and designed elastins and their relation to elastic fiber structure and recoil.

Authors:  Ma Faye Charmagne A Carvajal; Jonathan M Preston; Nour M Jamhawi; T Michael Sabo; Shibani Bhattacharya; James M Aramini; Richard J Wittebort; Ronald L Koder
Journal:  Biophys J       Date:  2021-07-31       Impact factor: 3.699

  7 in total

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