Lecture 5 - Protein Structure II Protein Interactions...

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Unformatted text preview: Protein Structure II Protein Interactions Molecule bound reversibly to a protein is called a ligand. Ligand can be any molecule including other protein. Ligandprotein interactions are transient and fast. Ligand binds at the site on the protein called: the binding site. The binding site is usually complementary to the ligand in size, shape, charge, and hydrophobic and hydrophilic character. Proteins are dynamic and flexible Subtle changes in conformation which reflect molecular vibrations and small movement of amino acid residues is called "breathing" Changes in conformation can be dramatic accompanied by a movement of major amino acid structures. Conformational changes are essential to protein function. Enzymes Enzymes bind and chemically transform other molecules. For enzymes: ligand is substrate. Binding site is catalytic site or active site. Ka Association constant P + L PL Ka Units (M1) Ka = [PL]/[P][L] Ka [L] = [PL]/[P] Usually [L] is much greater then binding sites [P] and in most cases [L] is a constant. = Binding sites occupied/total binding sites = [PL]/([PL]+[P])=[L]/([L] + 1/ Ka) KdDissociation constant Kd= 1/ Ka Kd = [P][L]/[PL] [PL]= [P][L]/Kd = [L]/([L] + K ) Binding of oxygen to myoglobin. = [L]/([L] +Kd) = [O2]/([O2] +Kd) As for any ligand, Kd = [O2] at which half of the sites are occupied, or [O2]0.5 Hemoglobin undergoes a structural change on binding oxygen Rstate: relaxed state higher affinity by O2. Tstate: tense state (greater number of ion pairs at the (1 2 and 2 1 ) interfaces lower affinity by O2. Binding of O2 to the T state changes conformation to the R state. Binding of the first O2 molecule increases the affinity for the rest of O2 molecules to bind. Hemoglobin binds oxygen cooperatively Oxygen is not soluble in blood and must be transported to the rest of the body. Myoglobin is a poor candidate for oxygen transport. Hemoglobin will bind oxygen in lungs and release in the muscle. Hemoglobin is an allosteric protein, binding of ligand to one site affects binding at the other site. Hill equation If protein has n sites, then, P + nL PLn Ka = [PLn]/[P][L]n = [L] n /([L]n +Kd) /(1 ) = [L]n/Kd log ( /(1 ) ) = n log[L] logKd Cooperative ligand binding can be described quantitatively Hemoglobin also transports H and CO2 + Oxidation of organic fuels results in: CO2 + H2O H+ + HCO3 Oxygen and H+ are not bound to the same sites. Oxygen binds to the heme, whereas, H+ binds to the HIS146 side chain (pKa= 7.56). When protonated HIS146 residue forms an ion bond with ASP94 it stabilizes the T state. As H+ concentration in the muscle rises other residues are protonated. This stabilizes the T state, and therefore, enhances the release of O2 due to decreased affinity. CO2 is bound by the amino terminal residues. Oxygen binding to Hemoglobin is regulated by 2,3biphosphoglycerate 2,3biphosphoglycerate BPG Heterotropic allosteric modulation of oxygen binding. BPG binds at a distant site and regulates affinity by conformational change. BPG reduces the affinity of hemoglobin for O2. At high altitude BPG in increased, affinity for oxygen is reduced... Recombinant antibodies Single chain antibodies ...
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