How to solve a protein structure by nuclear magnetic resonance - The Connexin43 carboxyl terminal domain

Nuclear magnetic resonance, or NMR, as it is usually called, has become a power tool in biology for solving protein structures at atomic resolution. Since the first NMR derived three-dimensional (3D) solution structure of a small protein was determined in 1985, over 2,000 structures have been deposited in the Protein Data Base. The 2002 Nobel Prize in chemistry was given to Kurt Wuthrich for his work on "Three dimensional Structure of Biomolecules". New advancements for structural determination by NMR (i.e. higher field magnets and cryoprobe technology) have increased the molecular weight threshold close to 100 kDa. Liquid-state NMR has other far-reaching applications in chemical and biological research. Some of these applications include the constitution and conformation of organic molecules, 3D structure of nucleic acids, conformational dynamics and mobility of biomacromolecules in solution, chemical and conformational exchange, enzyme mechanism and chemical reactions, mapping protein-protein interactions, folding studies, and rational drug design. While many laboratories can utilize these applications, I believe a major hurdle for most scientists is the "black box" between a purified protein on an SDS-PAGE gel and the answer to their particular scientific question, i.e. the NMR. What I hope to accomplish in this chapter, is explain how spectroscopists go about solving a protein structure by NMR methods. This overview will incorporate a sampling of theory, sample preparation, data collection, processing, analysis, structure generation, and deposition into the appropriate data banks, thus defining what is inside the "black box." The solution structure of the carboxyl terminal domain from the cardiac gap junction protein Connexin43 (Cx43CT) will be used as the test sample. Cx43CT examples are embedded in the descriptions of methods to better illustrate what is to be expected from each step during structure determination by NMR.