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

Vincenzo Venditti; Nicolas L Fawzi

doi:10.1007/978-1-4939-7386-6_12

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

Methods Mol Biol. 2018:1688:243-255. doi: 10.1007/978-1-4939-7386-6_12.

Authors

Vincenzo Venditti^{1

2}, Nicolas L Fawzi³

Affiliations

¹ Department of Chemistry, Iowa State University, 0219 Hach Hall, 2438 Pammel Drive, Ames, IA, 50011, USA. venditti@iastate.edu.
² Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 0219 Hach Hall, 2438 Pammel Drive, Ames, IA, 50011, USA. venditti@iastate.edu.
³ Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Box G-E, 171 Meeting Street, Providence, RI, 02912, USA. Nicolas_Fawzi@brown.edu.

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.

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

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

Magnetic Resonance Spectroscopy / methods*
Models, Molecular*
Protein Binding
Protein Conformation*

Grants and funding

R01 GM118530/GM/NIGMS NIH HHS/United States