NMR Approaches To Understanding Protein Specificity

Abstract

The biological functions of proteins all depend on their highly specific interactions with other molecules, and the understanding of the molecular basis of the specificity of these interactions is an important part of the effort to understand protein structure-function relationships. NMR spectroscopy can provide information on many different aspects of protein-ligand interactions, ranging from the determination of the complete structure of a protein-ligand complex to focussing on selected features of the interactions between the ligand and protein by using “reporter groups” on the ligand or the protein. It has two particular advantages: the ability to study the complex in solution, and the ability to provide not only structural, but also dynamic, kinetic and thermodynamic information on ligand binding. Early analyses of ligand binding (Jardetzky and Roberts, 1981) focused on measurements of relaxation times, chemical shifts and coupling constants, which gave relatively limited, although valuable, structural information. More recently, it has become possible to obtain much more detailed information, due to the extensive use of nuclear Overhauser effect measurements and isotope-labeled proteins and ligands; a number of reviews of this area are available (Feeney and Birdsall, 1993; Lian et al, 1994; Wand and Short, 1994; Petros and Fesik, 1994; Wemmer and Williams, 1994). In this article, we describe some recent work from our laboratory which illustrates the use of NMR spectroscopy to obtain structural and mechanistic information on relatively large enzyme-substrate and proteinprotein complexes. A number of species of pathogenic bacteria, notably Streptococci and Staphylococci, have proteins on their surface that bind immurioglobulins (reviewed in Boyle (1990)). Protein A from S. aureus and protein G from species of Streptococci are widely used as imrnunological tools and are the most extensively studied of these antibody-binding proteins. A detailed understanding of the binding mechanisms of these proteins is important, not only for providing us with the structural basis for their functions, but also as a contribution toward understanding the general rules of protein-protein interactions.