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Literature DB >> 29151213

Probing the Atomic Structure of Transient Protein Contacts by Paramagnetic Relaxation Enhancement Solution NMR.

Vincenzo Venditti^1,2, Nicolas L Fawzi³.

Abstract

Important biological processes, including enzyme catalysis, signaling, and protein folding, proceed through lowly populated (<5%) states that elude structural characterization by conventional techniques. Here, we describe the steps required for visualization of these sparsely populated conformations and transient protein-protein interactions using paramagnetic relaxation enhancement solution NMR. We describe experimental design, sample preparation, data acquisition and processing, and the basics of data analysis of structural ensembles.

Entities: Chemical Disease Species

Keywords: Dark states; Encounter complex; Lowly populated states; NMR spectroscopy; Protein-protein interactions; Site-directed spin-labeling; Transient interactions

Mesh：

Year: 2018 PMID： 29151213 PMCID： PMC5823026 DOI： 10.1007/978-1-4939-7386-6_12

Source DB: PubMed Journal: Methods Mol Biol ISSN： 1064-3745

20 in total

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Authors: I Bertini; C Luchinat; M Piccioli
Journal: Methods Enzymol Date: 2001 Impact factor: 1.600

2. Structural characterization of proteins with an attached ATCUN motif by paramagnetic relaxation enhancement NMR spectroscopy.

Authors: L W Donaldson; N R Skrynnikov; W Y Choy; D R Muhandiram; B Sarkar; J D Forman-Kay; L E Kay
Journal: J Am Chem Soc Date: 2001-10-10 Impact factor: 15.419

3. Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear Overhauser enhancement spectroscopy.

Authors: Vincenzo Venditti; Nicolas L Fawzi; G Marius Clore
Journal: J Biomol NMR Date: 2011-09-04 Impact factor: 2.835

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Authors: Charles D Schwieters; John J Kuszewski; Nico Tjandra; G Marius Clore
Journal: J Magn Reson Date: 2003-01 Impact factor: 2.229

5. Visualization of transient encounter complexes in protein-protein association.

Authors: Chun Tang; Junji Iwahara; G Marius Clore
Journal: Nature Date: 2006-10-15 Impact factor: 49.962

6. Structure and dynamics of a conformationally constrained nitroxide side chain and applications in EPR spectroscopy.

Authors: Mark R Fleissner; Michael D Bridges; Evan K Brooks; Duilio Cascio; Tamás Kálai; Kálmán Hideg; Wayne L Hubbell
Journal: Proc Natl Acad Sci U S A Date: 2011-09-12 Impact factor: 11.205

7. 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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Authors: H Cheng; J L Markley
Journal: Annu Rev Biophys Biomol Struct Date: 1995

9. An efficient protocol for incorporation of an unnatural amino acid in perdeuterated recombinant proteins using glucose-based media.

Authors: Vincenzo Venditti; Nicolas L Fawzi; G Marius Clore
Journal: J Biomol NMR Date: 2012-02-17 Impact factor: 2.835

Review 10. Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering.

Authors: Vincenzo Venditti; Timothy K Egner; G Marius Clore
Journal: Chem Rev Date: 2016-01-07 Impact factor: 60.622

5 in total

Probing the Atomic Structure of Transient Protein Contacts by Paramagnetic Relaxation Enhancement Solution NMR.

Review 1. Paramagnetic probes in metalloproteins.

2. Structural characterization of proteins with an attached ATCUN motif by paramagnetic relaxation enhancement NMR spectroscopy.

3. Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear Overhauser enhancement spectroscopy.

4. The Xplor-NIH NMR molecular structure determination package.

5. Visualization of transient encounter complexes in protein-protein association.

6. Structure and dynamics of a conformationally constrained nitroxide side chain and applications in EPR spectroscopy.

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

Review 8. NMR spectroscopic studies of paramagnetic proteins: iron-sulfur proteins.

9. An efficient protocol for incorporation of an unnatural amino acid in perdeuterated recombinant proteins using glucose-based media.

Review 10. Hybrid Approaches to Structural Characterization of Conformational Ensembles of Complex Macromolecular Systems Combining NMR Residual Dipolar Couplings and Solution X-ray Scattering.

1. The LC8-RavP ensemble Structure Evinces A Role for LC8 in Regulating Lyssavirus Polymerase Functionality.

2. Progress toward automated methyl assignments for methyl-TROSY applications.

3. A Chemical Biology Primer for NMR Spectroscopists.

4. Simultaneous detection of intra- and inter-molecular paramagnetic relaxation enhancements in protein complexes.

Review 5. A Double-Armed, Hydrophilic Transition Metal Complex as a Paramagnetic NMR Probe.