L10-Protein_Function_I-Mb

L10-Protein_Function_I-Mb - Lecture 10 Proteins...

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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
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