Literature DB >> 31407202

Exchange saturation transfer and associated NMR techniques for studies of protein interactions involving high-molecular-weight systems.

Vitali Tugarinov1, G Marius Clore2.   

Abstract

A brief overview of theoretical and experimental aspects of the Dark state Exchange Saturation Transfer (DEST) and lifetime line broadening ([Formula: see text]) NMR methodologies is presented from a physico-chemical perspective. We describe how the field-dependence of [Formula: see text] can be used for determining the exchange regime on the transverse spin relaxation time-scale. Some limitations of DEST/[Formula: see text] methodology in applications to molecular systems with intermediate molecular weights are discussed, and the means of overcoming these limitations via the use of closely related exchange NMR techniques is presented. Finally, several applications of DEST/[Formula: see text] methodology are described from a methodological viewpoint, with an emphasis on providing examples of how kinetic and relaxation parameters of exchange can be reliably extracted from the experimental data in each particular case.

Entities:  

Keywords:  Dark state exchange saturation transfer; Exchanging systems; High molecular weight; Lifetime line broadening

Mesh:

Year:  2019        PMID: 31407202      PMCID: PMC6819251          DOI: 10.1007/s10858-019-00244-6

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


  27 in total

1.  Flexibility and ligand exchange in a buried cavity mutant of T4 lysozyme studied by multinuclear NMR.

Authors:  F A Mulder; B Hon; D R Muhandiram; F W Dahlquist; L E Kay
Journal:  Biochemistry       Date:  2000-10-17       Impact factor: 3.162

2.  Reconstructing NMR spectra of "invisible" excited protein states using HSQC and HMQC experiments.

Authors:  Nikolai R Skrynnikov; Frederick W Dahlquist; Lewis E Kay
Journal:  J Am Chem Soc       Date:  2002-10-16       Impact factor: 15.419

3.  Probing the transient dark state of substrate binding to GroEL by relaxation-based solution NMR.

Authors:  David S Libich; Nicolas L Fawzi; Jinfa Ying; G Marius Clore
Journal:  Proc Natl Acad Sci U S A       Date:  2013-06-24       Impact factor: 11.205

4.  Decorrelating Kinetic and Relaxation Parameters in Exchange Saturation Transfer NMR: A Case Study of N-Terminal Huntingtin Peptides Binding to Unilamellar Lipid Vesicles.

Authors:  Alberto Ceccon; G Marius Clore; Vitali Tugarinov
Journal:  J Phys Chem B       Date:  2018-09-12       Impact factor: 2.991

5.  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

6.  Probing Conformational Exchange in Weakly Interacting, Slowly Exchanging Protein Systems via Off-Resonance R Experiments: Application to Studies of Protein Phase Separation.

Authors:  Tairan Yuwen; Jacob P Brady; Lewis E Kay
Journal:  J Am Chem Soc       Date:  2018-01-31       Impact factor: 15.419

7.  Characterizing methyl-bearing side chain contacts and dynamics mediating amyloid β protofibril interactions using ¹³C(methyl)-DEST and lifetime line broadening.

Authors:  Nicolas L Fawzi; David S Libich; Jinfa Ying; Vitali Tugarinov; G Marius Clore
Journal:  Angew Chem Int Ed Engl       Date:  2014-08-11       Impact factor: 15.336

8.  Kinetics of amyloid beta monomer-to-oligomer exchange by NMR relaxation.

Authors:  Nicolas L Fawzi; Jinfa Ying; Dennis A Torchia; G Marius Clore
Journal:  J Am Chem Soc       Date:  2010-07-28       Impact factor: 15.419

9.  Visualizing transient dark states by NMR spectroscopy.

Authors:  Nicholas J Anthis; G Marius Clore
Journal:  Q Rev Biophys       Date:  2015-02       Impact factor: 5.318

10.  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

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  7 in total

1.  Unraveling the structure and dynamics of the human DNAJB6b chaperone by NMR reveals insights into Hsp40-mediated proteostasis.

Authors:  Theodoros K Karamanos; Vitali Tugarinov; G Marius Clore
Journal:  Proc Natl Acad Sci U S A       Date:  2019-10-07       Impact factor: 11.205

Review 2.  NMR methods for exploring 'dark' states in ligand binding and protein-protein interactions.

Authors:  Vitali Tugarinov; Alberto Ceccon; G Marius Clore
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2021-11-02       Impact factor: 9.795

3.  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

4.  NMR spectroscopy, excited states and relevance to problems in cell biology - transient pre-nucleation tetramerization of huntingtin and insights into Huntington's disease.

Authors:  G Marius Clore
Journal:  J Cell Sci       Date:  2022-06-15       Impact factor: 5.235

5.  Probing the Interaction of Huntingtin Exon-1 Polypeptides with the Chaperonin Nanomachine GroEL.

Authors:  Marielle A Wälti; Samuel A Kotler; G Marius Clore
Journal:  Chembiochem       Date:  2021-04-07       Impact factor: 3.461

Review 6.  Large Chaperone Complexes Through the Lens of Nuclear Magnetic Resonance Spectroscopy.

Authors:  Theodoros K Karamanos; G Marius Clore
Journal:  Annu Rev Biophys       Date:  2022-01-19       Impact factor: 19.763

7.  Quantitative NMR Study of Insulin-Degrading Enzyme Using Amyloid-β and HIV-1 p6 Elucidates Its Chaperone Activity.

Authors:  Bhargavi Ramaraju; Spencer L Nelson; Wenwei Zheng; Rodolfo Ghirlando; Lalit Deshmukh
Journal:  Biochemistry       Date:  2021-08-03       Impact factor: 3.162

  7 in total

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