Chapter 5 Protein Function Ligand a molecule bound reversibly by a protein where a ligand binds to a protein o Binding site Complementary to the ligand in size shape charge and hydrophobic or hydrophilic character The interaction is specific the structural adaptation that occurs between protein o Induced fit and ligand In a multisubunit protein a conformational change in one subunit often affects the conformation of other subunits Substrates the molecules acted upon by enzymes o Catalytic site or active site the binding site for an enzyme 5 1 Reversible Binding of a Protein to a Ligand Oxygen Binding Proteins Oxygen Can Bind to a Heme Prosthetic Group Iron is a common transporter of oxygen in larger organisms o Oxygen is poorly soluble in aqueous solutions and diffusion over long distances is ineffective o Heme incorporated a protein bound prosthetic group into which iron is often Consist of a complex organic ring structure protoporphyrin to which is bound a single iron atom The iron has six coordination bonds four to nitrogen that are part of the flat porphyrin ring and two perpendicular to the ring Myoglobin Has a Single Binding Site for Oxygen Myoglobin facilitates oxygen diffusion in muscle Myoglobin is a single polypeptide of 153 amino acids and a heme molecule o Typical of the family of globins o Made up of eight helical segments connected by bends Protein Ligand Interactions Can B Described Quantitatively An equilibrium expression can be used to describe the reversible binding of a protein to a ligand K a or the association constant describes the equilibrium between the complex and the unbound components of the complex o Units of M 1 o Provides a measure of the affinity of the ligand for the protein o The higher the Ka the higher the affinity o Also equals the ratio of the rates of the forward and reverse reactions The forward reaction is second order ka The reverse reaction is first order kd o The value of Ka can be found from a plot of versus the concentration of free ligand The concentration of ligand at which half of the available ligand binding sites are occupied corresponds to 1 Ka K d or the dissociation constant the equilibrium constant for the release of ligand o The reciprocal of Ka given in units of molar concentration o The lower the Kd the higher the affinity of a ligand for a protein o Kd equals the concentration of ligand at which half of the available ligand binding sites are occupied Protein Structure Affects How Ligands Bind Binding is often accompanied by conformational changes Binding of O2 to the heme in myoglobin depends on molecular motions breathing Hemoglobin Transports Oxygen in Blood Erythrocytes are incomplete vestigial cells unable to reproduce Hemocytoblasts Hemoglobin is a better oxygen transporter than myoglobin because it has precursor stem cells that form erythrocytes in humans more binding sites of the globin family Hemoglobin Subunits Are Structurally Similar to Myoglobin The chains and the chains in hemoglobin as well as myoglobin are part Hemoglobin Undergoes a Structural Change on Binding Oxygen Two major conformations of hemoglobin o R state o T state o Oxygen has a significantly higher affinity for the R state o Oxygen binding stabilizes the R state o When oxygen is absent the T state is more stable and is thus the predominant conformation of deoxyhemoglobin o Binding O2 in the T state triggers a change to the R state Hemoglobin Binds Oxygen Cooperatively Hemoglobin solves the problem of both releasing oxygen in the tissues and binding it in the lungs where there are pressure differences by transforming from the T state low affinity to the R state high affinity as more O2 molecules are bound An allosteric protein is a protein in which the binding of a ligand to one site affects the binding properties of another site o The ligands that bind to allosteric proteins are called modulators o When the normal ligand and modulator are identical the interaction is homotropic o When the normal ligand is a different molecule than the modulator the interaction is heterotropic Cooperative Ligand Binding Can Be Described Quantitatively Hill equation o Hill plot o Hill coefficient a plot of log 1 versus log L a measure of the degree of cooperativity Greater than one means a positive cooperativity If it equals one ligand binding is not cooperative Less than one means negative cooperativity the binding of one ligand impedes the binding of others Rare Two Models Suggest Mechanisms for Cooperative Binding MWC model or the concerted model assumes that the subunits of a cooperatively binding protein are functionally identical that each subunit can exist in at least two conformations and that all subunits undergo the transition from one conformation to another simultaneously o The subunits still have different affinities for ligands o If a ligand binds to a subunit with low affinity makes a transition to high affinity conformations more likely ligand binding can induce a change of conformation in an Sequential model individual subunit o a change in one subunit triggers a change in a different subunit and makes the binding of a ligand more likely Hemoglobin Also Transports H and CO2 hemoglobin transports H and CO2 from the tissues to the lungs and kidneys where they are excreted carbonic anhydrase catalyzes the hydration of CO2 to make bicarbonate an enzyme particularly abundant in erythrocytes that o prevents the formation of bubbles in the tissues and blood o this reaction decreases the pH in the tissues Bohr effect o At low pH and high CO2 concentration the affinity of hemoglobin for oxygen decreases issues o The affinity of hemoglobin for oxygen increases in the lungs due to a higher pH and lower CO2 concentration Oxygen Binding to Hemoglobin Is Regulated by 2 3 Bisphosphoglycerate BPG is present in high concentrations in erythrocytes BPG greatly reduces the affinity of hemoglobin for oxygen Hypoxia lowered oxygenation of peripheral tissues due to inadequate functioning of the lungs or circulatory system caused by an increase in BPG concentration in erythrocytes BPG binds between the subunits in the T state of hemoglobin Sickle Cell Anemia Is a Molecular Disease of Hemoglobin sickle cell anemia occurs in individuals who inherit the allele for sickle cell hemoglobin from both parents the erythrocytes are fewer and abnormal sickle shaped o when hemoglobin from these cells is deoxygenated it becomes insoluble and forms polymers