"Case Studies in the Stereo-electronic Consequences of Protein/Ligand Interactions: i. The Structure and Substrate Specificity of Glycogen Branching Enzyme and the Mechanism of Color Perception in Vision"
Abstract: The interaction between proteins and small molecules are centrally important to all aspects of biology. In most cases the most important determinants involve direct and specific bonding between atoms of the protein and ligand, be they salt bridge, hydrogen bonding or dispersive interactions. Two case studies will be presented where such direct interactions are not the most important role players in determining the specificity or functional significance of the protein/ligand interaction. In the case of the interaction between glycogen branching enzyme and its polymeric substrate, it will be shown that the part of the ligand not interacting with the protein can play as important a role as that which does, because the substrate binding site is displaced from the enzyme active site by many angstroms. In the case of visual perception, a single chromophore, 11-cis-retinal, bound to a variety of opsin proteins, is responsible for perception throughout the visual spectrum. It will be shown, using a designed opsin protein mimic, that the localized projection of electrostatic potential by the protein onto the ligand accounts for virtually all of the observed tuning of the absorption profile of the ligand and requires no direct interaction between protein and ligand.