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Chapter 5 Protein Function Taq DNA Polymerase Protein Function - Definitions • A Ligand is a molecule that binds specifically and reversibly to a larger one. – Examples of ligand interactions include: • Hormones/Receptors • Antigen/Antibody • Substrate/Enzyme • These molecules interact with proteins at the binding site, which is complimentary to the ligand in size, charge, hydrophobicity and shape • Proteins are highly flexible, allowing them to change their conformations if needed – The interaction is highly specific. – The flexibility allows the fit between the binding partners to be an induced fit (conformational change) or a lock and key fit (no change) • Interactions between ligands and proteins is usually regulated through a different binding interaction • For enzymes, the ligand is termed the substrate and the binding site is called the catalytic site or active site Chapter 5 2 1 Protein Function Ligand Binding is Similar to Ionization • The term Kd is the dissociation constant and is the inverse of the Keq (or the association constant, Ka) • As the Kd value decreases in value, the affinity of the ligand for the protein is increasing. • For most binding equilibria in cells, the [L] is much greatly than the number of binding sites K eq = • Therefore, the binding of L to the protein does not appreciably effect the [L] so it is considered a constant [M - L] [M][L] Kd = Kd = [M][L] [M - L] 1 K eq Chapter 5 3 Protein Function Fraction of Binding Sites Occupied (θ) θ= [L] Bound [M]tot = [M - L] [M] + [M - L] [M - L] = [M][L] Kd θ= [L] K + [L] The Langmuir Isotherm d Chapter 5 4 2 Protein Function Kd is a Measure of Binding Strength Chapter 5 5 Reversible Binding of a Protein to a Ligand Classic Examples: O2 Binding to Myoglobin and Hemoglobin • • • • Myoglobin Reversible binding and storage of O2 in muscles Monomeric protein structure (16.7 kDa) 153 AAs Contains one heme group Chapter 5 • • • • Hemoglobin Reversible binding and transport of O2 in erythrocytes Tetrameric protein structure (α2β2) (64.5 kDa) α chain 141 AAs; β chain 145 AAs Contains four heme groups 6 3 Reversible Binding of a Protein to a Ligand Heme: Protoporphyrin IX and Fe2+ Chapter 5 7 Reversible Binding of a Protein to a Ligand The Hexa-Coordination of Fe2+ in Mb #1-4 are N-atoms from the porphyrin ring #5-6 are to…? Chapter 5 8 4 Reversible Binding of a Protein to a Ligand Histidines Coordinate the Iron and Help Bind O2 Binding orientation with free heme Distal His 64 How does the Histidine help with the binding of the O2 molecule? His 93 Proximal How would this Histidine affect CO binding? Chapter 5 9 Reversible Binding of a Protein to a Ligand O2 Binding to Myoglobin θ= [O ] K + [O ] 2 d θ= 2 [O ] [O ] + [O ] 2 2 2 0.5 θ= Chapter 5 pO 2 pO 2 + P50 10 5 Reversible Binding of a Protein to a Ligand Now Let’s Look at Hemoglobin • Unlike myoglobin, which is a monomer, hemoglobin is a tetramer. • It has two identical alpha and two identical beta subunits; its quaternary structure is thus an α2β2 heterotetramer • The primary structures of all four subunits are similar to each other, and to myoglobin, suggesting evolution by gene duplication Chapter 5 11 Reversible Binding of a Protein to a Ligand Oxygen Binding to Hemoglobin • Sigmoidal binding curve suggesting allosteric effects for Hb [Gr. “allo”=other, “steros”=shape] • Meaning that something is effecting the binding of O2 to the four subunits of Hb Chapter 5 12 6 Reversible Binding of a Protein to a Ligand O2 Binding in Hb Leads to Local Conformational Changes Near the Heme… No oxygen Chapter 5 What has happened to the heme plane upon O2 binding? 13 Reversible Binding of a Protein to a Ligand ….and Global Conformational Changes in the Tetramer 1BBB Fig. 5-10 Stabilized without oxygen Stabilized by oxygen binding by numerous ion pairs 1HGA Chapter 5 Note shift in HC3 Histidines! 14 7 Reversible Binding of a Protein to a Ligand A Closer View of Some Stabilizing Ionic Contacts in the T-State (Deoxyferrous) Chapter 5 15 Reversible Binding of a Protein to a Ligand Many Ionic Contacts Help Stabilize Hb’s T-State Chapter 5 16 8 Reversible Binding of a Protein to a Ligand • • • • Cooperativity Leads to a Sigmoid (Allosteric) Binding Curve Deoxyhemoglobin: T-state R-state picks up O2 in the lungs, where pO2 is high, Converting Hb into the Rstate, so it readily picks up more O2 As loaded oxyhemoglobin (RT-state state) moves back to tissues, where pO2 is lower, it begins to lose its O2, Which facilitates the transition back to the T-state Chapter 5 17 Reversible Binding of a Protein to a Ligand Cooperativity (Allosteric) Binding [M][L] = [M - L ] n Kd [L] K + [L ] n n θ= n The Langmuir Isotherm d • Here, θ is defined as the number of moles of ligand bound per mole of macromolecule and can vary from 0 to n. Chapter 5 18 9 Reversible Binding of a Protein to a Ligand The Hill Plot • If there are multiple binding sites in a protein, we need to determine if the binding of ligands is cooperative. • For many proteins (like Hb), the binding of the first ligand can change the affinity for the second ligand. For our two site example: Positive Cooperativity if K2 > K1 i.e. the second binding is higher in affinity Negative Cooperativity if K2 < K1 i.e. the fist binding is higher in affinity • We can use a Hill Plot to determine the cooperativity and the average K-d value for the binding. This Hill equation is derived from ν and θ and the [L]: Chapter 5 ⎛ θ ⎞ log⎜ ⎟ = log K n + nh log [L] The Hill Equation ⎝ 1- θ ⎠ 19 Reversible Binding of a Protein to a Ligand The Hill Plot ⎛ θ ⎞ log⎜ ⎟ = log K n + nh log [L] The Hill Equation ⎝ 1- θ ⎠ • Kn is the average Kd value for all the binding sites and nh is the Hill coefficient which characterizes the degree of cooperativity: nh > 1 The system shows positive cooperativity nh = N The cooperativity is infinite with N total number of ligand bound nh = 1 The system is non-cooperative nh < 1 The systems shows negative cooperativity Chapter 5 20 10 Reversible Binding of a Protein to a Ligand The Hill Plot ⎛ θ ⎞ log⎜ ⎟ = log K n + nh log [L] The Hill Equation ⎝ 1- θ ⎠ By plotting the log (θ/1-θ) versus the log [L] can yield a linear or curved plot. The shape of the plot is dependent on: – When cooperativity is not complete (i.e., n-h < N), the Hill plot is not linear. – At the extremes of [L], the line has a slope of ~1.0. – At low ligand concentrations, there is no cooperativity. Thus the Hill plot will represent single-site binding (binding of the first ligand molecule). – At high ligand concentrations, all sites are filled but one. Thus this region of the Hill plot should also represent single-site binding for the last ligand. Chapter 5 21 Reversible Binding of a Protein to a Ligand Sigmoid Binding Curve Notice how the Kd changes from the highaffinity T-state to the low-affinity R-state. Why would pure “R” or “T” forms function less well in erythrocytes?? Kd Chapter 5 Kd 22 11 Reversible Binding of a Protein to a Ligand Hemoglobin and the Bohr Effect • In its R-state, Hb is capable of 66% saturation by O2 • Not too good if you want to function at full capacity • The Bohr Effect deal with the effect of pH and CO2 concentration on the binding and release of oxygen by hemoglobin • The interaction of H+ and CO2 with Hb results in allosteric changes in the tetramer • These changes interrelate the physiological parameters in tissues, blood, and lungs (pH!) with the ability of Hb to bind oxygen • This effect results in the movement of H+ and CO2 away from tissue and back to the lungs and the movement of O2 in the opposite direction. Chapter 5 23 Reversible Binding of a Protein to a Ligand Carbon Dioxide, a product of Respiration, is an Acid! • Carbon dioxide released in respiring tissues is insoluble until hydrated and converted to bicarbonate (VERY slow rxn!) • In erythrocytes, the rate of this reaction is increased by the enzyme carbonic anhydrase • But this releases equivalent amounts of H+ (causing the pH in the tissues and blood to fall) • This process is reversed in the lungs, but requires that protons be available in an area of higher pH So, where to they come from? Chapter 5 24 12 Reversible Binding of a Protein to a Ligand Blo od pla sm a • The binding of H+ and CO2 are inversely related to the binding of O2 Lu ng s pH Dependence of O2 Binding to Hemoglobin: The “Bohr Effect” • Do the Kd values reflect this? ss u Ti • At high pH (lungs): Low [H+] & [CO2] so high affinity for O2 es • At low pH (peripheral tissues): High [H+] & [CO2] so low affinity for O2 Chapter 5 25 Reversible Binding of a Protein to a Ligand Recall Those Stabilizing Ionic Contacts in the Deoxy T-State Fig. 7-9 • H+ and O2 do not bind in the same site. • When protonated, His HC3 (H146) forms an ion pair with Asp FG1 (D94) that helps to stabilize the Tstate of Hb • This interaction gives H146 a higher pKa than normal and thus it is readily protonated at pH values found in tissues & the blood • Back at the lungs, the pH rises and H146 is deprotonated, meaning the ion pair cannot form and H146 moves into its Rstate location. What does the stabilization of the T state mean for O2 binding? Chapter 5 26 13 Reversible Binding of a Protein to a Ligand Hemoglobin interaction with CO2 • The amino-termini of the four chains become carbamylated at the low pH (7.2) in the tissues: O C O H+ H + H2N C C R O Amino-terminal residue - H O C H N C C O R O Carbamino-terminal residue • The binding of CO2 to the amino group results in the release of H+, which adds to the Bohr Effect • These anionic groups can also form additional salt bridges that help stabilize the T-state of Hb • This interaction helps to transport ~ 20% of the CO2 formed in the tissues to the lungs and kidneys Chapter 5 Where does the rest go? 27 Reversible Binding of a Protein to a Ligand Oxygen Carrying Capacity of Hemoglobin • Carrying capacity (oxygen delivery) between 13 kPA (100 Torr) O2 and 4 kPA (20 Torr): – Hemoglobin (non-cooperative) …….. 38%* – Hemoglobin (cooperative) ………….. 66% – Hemoglobin + Bohr pH effect ………. 77% – Hemoglobin + Bohr pH effect + CO2.. 88% Chapter 5 *Percent of maximum carrying capacity. (See Stryer: page 273) 28 14 Reversible Binding of a Protein to a Ligand O2 Binding is Also Regulated by BPG D-2,3-bisphosphoglycerate (BPG) can bind in a small pocket in the center of the hemo-globin tetramer – but only to the T-state! • This hole is lined with cationic AAs that interact with the anionic BPG • Only one BPG per Hb tetramer • The conformation change in the R-state closes up the internal “hole”, thereby excluding BPG from binding O- • - O P C CH O O O OH2 C O O P O- O- T Fig. 5-18 R Chapter 5 29 Reversible Binding of a Protein to a Ligand The circular interplay of factors associated with Hb in binding or releasing oxygen: • • • • • Why is the pH in the lungs high? What does that do to protonation of His HC3? How does that help get rid of CO2? How does eliminating CO2 help O2 binding? How would the release of O2 vary in tissues undergoing strenuous aerobic exercise? • How does BPG help in acclimatization to high altitude? • What is the main difference between adult and fetal Hb? See text discussion, pgs. 170-172 Chapter 5 30 15 Sickle-Cell Anemia SCA is due to a mutation that converts Glu-6 in the βchains to Val (E6V mutation). • This substitution creates hydrophobic “sticky” patches on the normally charged surface of the β-chains. • The oxygenated molecules are soluble, but upon deoxygenation, the conformation of HbS differs considerably from HbA, and it aggregates into insoluble fibers (as diagrammed on the next slide). • These fibers deform the RBCs into spiny or sickle-shaped cells. Chapter 5 31 The Tortuous Tale of Hemoglobin S Chapter 5 32 16 Reversible Binding of a Protein to a Ligand Some questions about sickle cell anemia: • Where in the tissues will “sickling” occur? • Why is it homozygous lethal? • Does it tell you anything about conformation changes in hemoglobin? • Why should heterozygous individuals be more resistant to malaria? • What does sickle cell anemia tell you about the importance of protein primary structure? Chapter 5 33 Reversible Binding of a Protein to a Ligand Key Points About Ligand Binding • Proteins may change conformation when ligands bind (allosteary); in a multimer, other subunits can be affected • For a monomer like myoglobin, the simple reversible binding of oxygen may be described by a dissociation constant, KD • Hemoglobin is an α2β2 heterotetramer, in which oxygen binding shifts the stability of the T-state to the R-state • Oxygen binding to hemoglobin causes both allosteric conformational changes and cooperative effects due to subunitsubunit interactions between the subunits • Hemoglobin also binds H+ and CO2, forming ion pairs that lessen the affinity for oxygen (Bohr effect); the binding of 2,3bisphosphoglycerate also prevents efficient oxygen binding • A genetic mutation of β E6V causes sickle-cell anemia because of the hydrophobic patch that leads to aggregation of the deoxyhemoglobin form. Chapter 5 34 17 The Immune System and Immunoglobulins • Oxygen binding proteins demonstrated how conformations of Mb and Hb affect and are affected by the binding of small ligands to the heme group • However, most protein-ligand interactions do not involve a prosthetic group • Rather, the binding site of a ligand within a protein is like that seen for BPG in Hb, a cleft lined with complimentary AAs • The immune system utilizes this type of complimentary binding to distinguish “self” from “non-self” then to destroy the “non-self” entities. Chapter 5 35 The Immune System and Immunoglobulins • Immunity is controlled by a variety of leukocytes (white blood cells) all developed from undifferentiated stem cells in the bone marrow. • These cells can leave the bloodstream and patrol the tissues, looking for molecules that might indicate an infection • There are two complimentary immune systems: – Humoral IS is directed at bacterial and extracellular infections – Cellular IS destroys host cells infected by viruses, and some parasites and foreign tissues Chapter 5 36 18 The Immune System and Immunoglobulins • The proteins at the center of the Humoral IS are the immunoglobulins (Ig) or the antibodies • These proteins bind bacteria, viruses or large molecules identified as “non-self” and target them for destruction • These proteins are produces by the B Lymphocytes (B cells) and make up 20% of the blood protein • The proteins at the center of the Cellular IS are the cytotoxic T cells (TC; killer T cells) and the helper T cells (TH cells) • Recognition of infected cells or parasites involves proteins on the surface of the killer T cells called T-cell receptors • The TH cells produce soluble signaling proteins called cytokines that interact with other proteins and cells of the immune system Chapter 5 37 The Immune System and Immunoglobulins • Any substance capable of initiating an immune response is called an antigen (antibody generator) • This antigen could be a virus, a bacterial cell wall component, an individual protein or any other foreign entities • An antibody or T-cell receptor binds only to a particular portion of the antigen called its epitope • Some epitopes include: – Proteins containing an N-terminus formylated methionine (only found in procaroytes) – Cell exterior molecules and/or features such as flagella, lipopolysaccharides, and cell wall components – Short sequences of bacterial DNA: the unmethylated “CpG motif” Chapter 5 38 19 The Immune System and Immunoglobulins Immunological Memory • The adaptive immune system, like the nervous system, can remember prior experiences. • This is why we develop lifelong immunity to many common infectious diseases after our initial exposure to the pathogen, and it is why vaccination works. Fig 24-10, Molecular Biology of the Cell, 4th Ed., Alberts et al. • When an animal is immunized with antigen A, an immune response appears after several days, rises rapidly and exponentially, and then, more gradually, declines. • This is the characteristic course of a primary immune response, occurring on an animal's first exposure to an antigen. • If the animal is reinjected with antigen A, it will usually produce a secondary immune response that is very different from the primary response: the lag period is shorter, and the response is greater. • These differences indicate that the animal has "remembered" its first exposure to antigen A. Chapter 5 39 The Immune System and Immunoglobulins Immunological Memory • In an adult animal, the peripheral lymphoid organs contain a mixture of cells in at least three stages of maturation: naïve cells, effector cells and memory cells. • When naïve cells encounter antigen for the first time, some of them are stimulated to proliferate and differentiate into effector cells, which are actively engaged in making a response • Effector B cells secrete antibody, while effector T cells kill infected cells or help other cells fight the infection. • Instead of becoming effector cells, some naïve cells are stimulated to multiply and differentiate into memory cells cells that are not themselves engaged in a response but are more easily and more quickly induced to become effector cells by a later encounter with the same antigen. • Memory cells, like naïve cells, give rise to either effector cells or more memory cells Chapter 5 40 Fig 24-11, Molecular Biology of the Cell, 4th Ed., Alberts et al. 20 The Immune System and Immunoglobulins Major Histocompatibility Complex • The immune systems must not only be able to identify and destroy “non-self” but also recognize and NOT destroy “self” • Detection of protein antigens in the host is mediated by Major Histocompatibility Complex (MHC) – MHC bind peptide fragments of digested proteins and present them on the outside surface of the cell – These peptides are normally “self” but during a viral infection, viral proteins are also digested and presented – These “non-self” peptides serve as antigens for T-cell receptors resulting in the launch of the immune response. • There are two types of MHCs: Class I and Class II – They differ in the type of cell on which they present antigens Chapter 5 41 The Immune System and Immunoglobulins Major Histocompatibility Complex • Class I MHCs are found on the surface of nearly all vertebrate cells • These are highly polymorphic proteins with each individual producing up to 6 class I MHCs • They display peptides derived from the breakdown of protein that occur randomly within the cell • These complexes serve as targets for the T-cell receptors of TC cells • These proteins are heterodimers with a small, invariant β chain and a highly polymorphic α chain • Antigen binding occurs in the hypervariant region on the outside of the cell Chapter 5 42 21 The Immune System and Immunoglobulins Major Histocompatibility Complex • Class II MHCs occur on the surfaces of a few types of specialized cells, including macrophages and B lymphocytes that take up foreign antigens • These are also highly polymorphic proteins with each individual producing up to 12 class II MHCs • They display peptides derived from the breakdown of external proteins ingested by the cells • These complexes serve as targets for the T-cell receptors of TH cells • These proteins are heterodimers with highly variant β and α chains • Antigen binding occurs in the amino terminal region on the outside of the cell Chapter 5 43 The Immune System and Immunoglobulins Immunoglobulin G (IgG) • Immunoglobulin G is the major class of antibody, and one of the most abundant proteins in the blood serum • IgG has heterotetramer, with two heavy chains and two light chains • These chains are linked to one another by disulfide bonds into a complex with a MW of 150 kDa • The constant domains all have a characteristic structure called the immunoglobulin fold • The variable domain (one heavy, one light) creat the antigen-binding site. Chapter 5 44 22 The Immune System and Immunoglobulins Other Immunoglobulins • There are five classes of Ig, each having a characteristic type of heavy chain • IgA is found primarily in secretions (saliva, tears, etc) IgA • IgM is the first Ig prepared by the B lymphocytes and is the major Ig in the initial stages of the immune response ~220 AA ~440 AA Chapter 5 45 The Immune System and Immunoglobulins IgG and the Secondary Immune Response • IgG is the major antibody of the secondary immune response, which is initiated by the memory B lymphocytes • When IgG binds to an invading bacterium or virus, it activates certain leukocytes such as macrophages to ingest and destroy the invader • A different set of cell surface receptors on the surface of the macrophages recognizes the Fc region of the IgG • These receptors bind to the pathogen bound IgGs resulting in phagocytosis Chapter 5 46 23 The Immune System and Immunoglobulins Applications for Antibodies • Affinity Chromatography • Analytical Assays – These assays are used to detect, quantify and characterize antigens • • • • • Immunofluorescence (IFA) Immunoblotting (Western Blotting) Immunoprecipitation Radioimmunosorbant assay (RIA) Enzyme-linked immunosorbent assay (ELISA) – All these assays have two main components: • Formation of the antigen-antibody complex • Detection of this complex Chapter 5 47 The Immune System and Immunoglobulins Immunoprecipitation • Generally a qualitative method used to detect a particular antigen in a biological sample • Can be used in conjunction with SDS-PAGE to determine the molecular weight of the target antigen • Steps include: – Labeling of the antigen (optional) – Solubilization of the antigen – Incubation followed by complex formation with the antibody – Isolation of antigen-antibody complex – Electrophoresis, fluorescence or other detection method Chapter 5 Protein A (or G) are proteins isolated from Staphylococcus areus or Streptococcus that bind to the Fc region of IgG 48 24 The Immune System and Immunoglobulins Immunoblotting (The Western Blot) • Generally a qualitative method used to detect a particular protein in a biological sample • Used in conjunction with electrophoresis (usually SDS-PAGE) for protein separation • Steps include: – Antigen electrophoresis – Transfer to membrane – Blocking of membrane – Incubation with primary antibody followed by wash – Incubation with enzyme-linked secondary antibody – Develop with substrate Chapter 5 49 The Immune System and Immunoglobulins Immunofluorescence • This technique is used to localize antigens to a specific cell type of subcellular compartment • Steps include: – Preparation of cells or tissue – Incubation with primary antibody – Wash to remove non-bound 1° antibody – Incubate with secondary antibody (with fluorophore attached) – Wash again to excess 2° antibody – Detect with UV light Fluorophores include: Fluorescein and rhodamine Chapter 5 50 25 The Immune System and Immunoglobulins ELISA (Enzyme-Linked Immunosorbant Assay) • Can be a qualitative or quantitative method used to detect a particular protein in a biological sample • Steps include: – Antigen binding to plate • Binding is due to a hydrophobic interaction between the antigen and the plastic. – Blocking to eliminate non-specific binding – Incubation with primary antibody followed by wash – Incubation with enzyme-linked secondary antibody – Develop with substrate Chapter 5 51 Actin, Myosin and Molecular Motors • Protein-based molecular motors are responsible for the movement of organisms and cells • These motors are usually fueled by chemical energy derived from the hydrolysis of Adenosine triphosphate (ATP) • Large groups of these motor proteins undergo cyclic conformational changes that accumulate into a unified, directional force • Interactions among motor proteins feature complimentary arrangements of ionic, hydrogen bonding, hydrophobic and van der Waals interactions Chapter 5 52 26 Actin, Myosin and Molecular Motors • The major motor proteins found in your muscles are actin and myosin – Actin • 5% of total protein • 20% of vertebrate muscle mass • G-Actin has 375 amino acids = 42 kDa • G-Actins associate to form polymers (F-actin) • These polymers associate with additional proteins to form filaments • Each actin monomer binds and then hydrolyzes an ATP molecule to ADP • This hydrolysis functions only in the formation of the actin filaments not in the muscle contraction Chapter 5 53 Actin, Myosin and Molecular Motors • The major motor proteins found in your muscles are actin and myosin – Myosin • Hexamer of two heavy subunits (220 kDa) and four light subunits (20 kDa) • At the amino terminus, a large globular domain is responsible for ATP hydrolysis for muscle contraction • Myosin molecules associate to form thick filaments, which serve as the core of the contractile unit Chapter 5 54 27 Actin, Myosin and Molecular Motors • • • The interaction between myosin and actin involves weak bonds. When ATP is not bound to myosin, a face on the myosin head is bound tightly to actin Binding of ATP to myosin results in release from actin and the beginning of the contractile cycle Chapter 5 55 28