Ligands Turning Around in the Midst of Protein Conformers: The Origin of Ligand-Protein Mating. A NMR View
Abstract:Protein-ligand binding is a puzzling process. Many theories have been devised since the pioneering key-and-lock hypothesis based on the idea that both the protein and the ligand have a rigid single conformation.
Indeed, molecular motion is the essence of the universe. Consequently, not only proteins are characterized by an extraordinary conformational freedom, but ligands too can fluctuate in a rather vast conformational space. In this scenario, the quest to understand how do they match is fascinating.
Recognizing that the inherent dynamics of molecules is the key factor controlling the success of binding and, subsequently, of their chemical/biological function, here we present a view of this process from the NMR stand point.
A description of the most relevant NMR parameters that can provide insights, at atomic level, on the mechanisms of protein- ligand binding is provided in the final section.
Keywords: (R2) a; 15N; CRABPI; CRBP; CRBP type I; CaM-MLCK; Calmodulin; DHFR; Enzymes; HSQC; MUP I; MWC; NAMFIS; NH bonds; NMR; NMR spectroscopy; NOE; PCS; PDF; PRE; Paramagnetic Mapping; R1; RDCs; Rex; S2; SRLS; STD; X-ray crystallography became; bound/unbound states; cofactor; conformation; conformational selection model; cytidylyl-transferase en-zyme; enzyme 1; equilibrium; fine tuning; flexibility; h3JNC; hemophore; heterogeneity; ligand; ligand binding; nduced-fit model; per-turbation; probability distribution of states; protein; reactivity; rigidification; signal transduction; substrate; tr-NOE; ubiquitous protein
Document Type: Research Article
Publication date: January 1, 2011