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Protein Functional Sites

Functional Design of Proteins

A protein’s function depends on its ability to bind other molecules, its ligands. The proteins’ ligand binding site and its corresponding ligand are topologically and chemically complementary. The strength of binding between the protein and its ligand is referred to as the proteins’ affinity; its specificity, to the restriction of binding to one or a few preferred ligands. Catalytic proteins are called enzymes which accelerate the rate of cellular reactions by lowering the activation energy for a reaction to occur and stabilizing transition-state intermediates. The active site of enzymes are made up of two functional parts: 1) A region where the substrate binds 2) A catalytic region. The amino acids composing the active site are not necessarily adjacent in the amino acid sequence, but are brought into proximity in the native conformation. The Michealis-Menton equation describes the kinetics of many enzymes. From plots of reaction rate versus substrate concentration, two characterisitic parameters of an enzyme can be determined: the Michaelis constant Km a measure of the enzyme’s affinity for substrate, and the maximal velocity Vmax. Allostery is exhibited in many enzymes and proteins that are multimeric. The binding of one ligand molecule (a substrate, activator, or inhibitor) induces a conformational change, or allosteric transition, that alters the protein’s activity or affinity for other ligands. When multimeric proteins bind multiple ligands, binding of one ligand molecule may increase or decrease the binding affinity for subsequent ligand molecules. Enzymes that cooperatively bind substrates exhibit sigmoidal kinetics. These allosteric mechanisms at times act like switches, turning protein activity on and off. Cyclic phosphorylation and dephosphorylation of amino acid side chains can have the same regulatory effect. Proteolytic cleavage irreversibly converts inactive zymogens into active enzymes.


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