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Globular Protein Functions Functions Examples I Storage of tons molecules myoglobin ferritin 2 Transport 10ns molecules hemoglobin serotonin transporter 3 Defense against pathogens antibodies cytokines 4 Muscle contraction actin myosin 5 Biological catalysts chymotrypsin lysozyme keys to Function 1 Reversible binding of ligands 2 Specific ligands binding sites 3 Induced fit Ligand binding conformational dramatic changes 4 Cooperatively Multi subunit proteins conformational changes in one subunit that affects others 5 Regulated interactions AB a B Ligands Molecule that binds proteins Reversible transient process of equilibrium protein Ligand Binding Interaction Basics Ty EA f i cid 15483 s cid 15483 g E cid 15483 E EH 2 g Ba Examples Of Binding Strength Ligand binds 10 same Non covalent interactions dictating protein structure I cid 15482 Binding site Region in protein that binds ligands typically small noncovalent bonds transient Site r typc at r gandnterac 10nsse9uence spec fpr ein DNA Biotin avidin A n io FY TY TTL TY o Ff TT 2 high affinity Kd M low affinity Specificity Induced Fit Specificity Lock and Key Model proteins high specificity explained by complementary of the binding site ligand Complementary in Size Shape Charge hydrophobic hydrophilic Lock and key model by Emil Fisher 1894 complementary surfaces are performed Ligand and protein change conformations Conformational Changes ligand binding lDaniel Koshland 1958 Induced fit tighter binding variable affinity of different ligands y f cid 15482 Y R Em cid 15482 FINE Binding Quantitative Description CHEEK cid 15482 ligand CL binds reversibly to a site in Protein P ka Kd Described quantitatively by the association rate Process will reach equilibrium association dissociation P L PL Equilibrium constant equilibrium association constant ka or the equilibrium constant Kd Binding Analysis in Terms of the Bound Fraction Fraction of occupied binding sites ka CPL 5s Substituting PL with Ka L P eliminate PL Eliminating P rearranging causes equilibrium association constant equilibrium dissociation constant Binding Graphical Analysis Fraction of bound sites depends on free ligand concentration and ka ka P CL Kd PL Ka P g P L PL PL P Experimentally ligand concentration known I L d L a Ka L P P Kd determined graphically least squares regression 1 0 it ka i I L arbitrary units L L cid 15482 a G L L Ka

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