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Unformatted text preview: 34 Lecture 10 Proteins Function-Ligand Binding Overview • the function of a protein is controlled by its structure • proteins function depend on interaction with other molecules including — other proteins and macromolecules — small organic molecules — metals • the interactions are affected by sometimes small changes in conformation • the interactions are often very short lived and do not occur for any extended period of time Terminology and Principles • ligand: a molecule bound reversibly to a protein — bound through weak (non-covalent) interactions • binding site: the location on the protein that the ligand associates — the whole protein molecule is not used — only a specific portion is used and typically involves interactions with specific amino acid side chains — the site only accepts a specific or limited number of ligands → the binding site is complementary to the ligand o if the ligand is hydrophobic, the binding site will be also o if the ligand is negatively charged, the binding site will likely have a positive charge — a single protein may have several binding sites for several ligands • proteins are not “static” molecules; they are very flexible and exhibit a large degree of “breatheability” (subtle changes in conformation) — the changes in conformation are essential to the protein’s function • induced fit model of protein-ligand interaction: when the ligand binds, the protein undergoes small conformational changes that optimize the interaction between protein and ligand • in multimeric proteins, a conformational change in one subunit often triggers conformational changes in the other subunits. Oxygen binding proteins • oxygen is essential to the survival of aerobic organisms • the properties of oxygen make it seem less than the perfect to be so essential — oxygen is poorly soluble in water → if dissolved in blood serum (liquid portion of blood), the concentration of oxygen is insufficient to support life...
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