Chapter 15. Enzyme Regulation. Activity? Part 1 Factors that influence enzymatic activity
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1 Chapter 15 Enzyme Regulation tw/course/106 Reginald H. Garrett Charles M. Grisham Essential Questions Before this class, ask your self the following questions: What are the properties of regulatory enzymes? How do you know this enzyme is a regulatory enzyme? How do regulatory enzymes sense the momentary needs of cells? How signal is delivered? What molecular mechanisms are used to regulate enzyme activity? 2 Outline Part 1 Factors that influence enzymatic activity Zymogen, isozyme and covalent modification! Part 2: The general features of allosteric regulation The mechanisms of allosteric regulation Example of a enzyme controlled by both allosteric regulation and covalent modification Part 3: Special focus on hemoglobin and myoglobin What Factors Influence Enzymatic Activity? 1. The availability of substrates and cofactors! 2. Product accumulates u ates the rate will decrease! ease 3. The amount of enzyme present at any moment Genetic regulation of enzyme synthesis and decay 4. Regulation of Enzyme activity Zymogens, isozymes, and modulator proteins may play a role Enzyme activity can be regulated through covalent modification Allosteric Regulation 4
2 Regulation 1: Zymogen The proteolytic activation of chymotrypsinogen Zymogens are inactive precursors of enzymes. Typically, proteolytic ti cleavage produces the active enzyme. Figure 15.2 Proinsulin is an 86-residue precursor to insulin 5 6 Proteolytic Enzymes of the Digestive Tract How to stop bleeding? How our blood clot? What is clotted? Fibrinogen Fibrin the result of a series of zymogen activations 7 Ann Ny Acad Sci 2001 Mosesson 8
3 Aggregation of Fibrin Two routes to blood clot formation The Cascade activation of seven clotting factors make fibrinogen quickly transformed into fibrin! kallikrein, XIIa, XIa, IXa, VIIa, Xa, and thrombin. Thrombin specifically cleaves R-G peptide bonds Ann Ny Acad Sci 2001 Mosesson 9 Intrinsic i pathway blood physically contact t with abnormal surfaces caused by injury Extrinsic pathway factors released from injured tissue Why Cascade? 10 Isozymes Example of isozymes: lactate dehydrogenase (LDH) Isozymes (also known as isoenzymes) are enzymes that differ in amino acid sequence but catalyze the same chemical reaction. These enzymes usually display different kinetic parameters (i.e. different Km values), or different regulatory properties. How different? Why different? 11 Mammalian lactate dehydrogenase (LDH), which exists as five different isozymes, depending on the tetrameric association of two different subunits, A and B: A4, A3B, A2B2, AB3, and B4 12
4 Regulation 2: Covalent modification Catalytic activities of enzymes can also be altered by reversible, covalent changes to specific amino acid side chains. Converter enzyme 15.4 What Kinds of Covalent Modification o Regulate the Activity of Enzymes? Phosphorylation Most prominent form of covalent modification Reversible by protein kinases / phosphoprotein phosph Target specific of kinase (and phosph p ) Regulating proteins are also a target of regulation Autophosphorylation.. interconvertible enzymes Protein Kinases Target residues on target proteins: Ser ( ), Thr ( ), and Tyr ( ) Typically recognize specific amino acid sequences in their targets But, all kinases share a common catalytic ti mechanism Regulation of kinases (usually, intrasteric control) A regulatory subunit with a pseudosubstrate sequence that t mimics i the target t sequence Inhibitor? What kind? 15 Classificatin of Kinases 16
5 Example of Kinase: PKA Structure of PKA Cyclic AMP-dependent protein kinase (also known as protein kinase A, PKA 150- to 170-kD R2C2 tetramer The two R (regulatory) subunits bind camp R subunits released (Activated) t from the C (catalytic) subunits after camp binding. In other kinases, the regulatory sequence may on the same peptide chain. 17 A conserved core kinase domain of about 260 Protein kinase A (Green) pseudosubstrate peptide, RRGA*I (orange) ATP (red) and two Mn 2+ ions (yellow) 18 Phosphorylation is Not the Only Form of Covalent Modification Types of Protein chemical modification > 100 Only a few of fthese are used dto regulation! reversible conversion Related to the energy state of cell Ask yourself.. EndofPart1 How many ways an enzyme could be regulated? What is a cascade reaction? Is it any good? What is an isozyme? Where is an isozyme came from? What is kinase? What kinds of properties kinases have? 19 20
6 Regulation 3: Allosteric Regulation Action at another site Most key enzymes in metabolic pathways are regulated in this way! Kinetics are sigmoid ("S-shaped") Regulatory Enzymes Have Certain Exceptional Properties Substrate binding is cooperative Allosteric enzymes are usually oligomeric Regulation of allosteric enzyme involved protein conformation change Regulated by allosteric effectors usually produced elsewhere in the pathway may be feed-forward activators or feedback inhibitors Mechanism of allosteric enzymes MWCConcerted Model (1965, Monod, Wyman & Changeux) : The enzyme exists in only two interconvertable states or conformations and all subunits must be in the same state or conformation: KNFmodel (Koshland, Nemethy, and Filmer ) Ligand binding triggers a conformation change in a protein Understand d MWC model: Step 1 The enzyme exists in only two interconvertable states. R State relaxed form T State taut form Molecules l of mixed conformation (having subunits of both R and T states) are not allowed by this model (symmetry model) 23 24
7 Understand MWC model: Step 2 Understand MWC model: Step 3 Most of the enzyme oligomers will assume the homogenous T state in the absence of bound effector molecules If no effector molecule is bound, then the R and T states are indicated as: R and T states are indicated as: R 0 and T 0 The R and the T states have different affinities for substrate. The substrate t dissociation i constant t for the R state is defined as K R (so as K T ). K R E R S E R +S K R = [E R ][S] [E R S] The equilibrium constant L is assumed to be large! 25 Assuming K T >>K R K R /K T = 0 It means most Substrates bind only to R 26 Understand MWC model: Step 4 Most enzyme in T state Most substrates bind to R state Key point is the [R 0 ] and [T 0 ] 2 ways to increase [R 0 ] Understand MWC model: Step
8 Understand MWC model: Step 6 Heterotropic effectors Molecules that influence the binding of something other than themselves Homotropic effectors Ligands such as S are positive homotropic effectors (homotropic activators) S binding increases the population of R, which increases the sites available to S Cooperativity KNF model Based on ligand-induced conformation changes of enzymes If the protein is oligomeric, ligand-induced conformation changes in one subunit may lead to conformation changes in adjacent subunits Explains negative cooperativity Also known as sequential model Explanation of KNF model (a) A subunit changes its conformation after S binding (induced fit) (b) Binding of S to one subunit may cause the other subunit changing its conformation to ( having a greater affinity for S (positive cooperativity) having a less affinity for S (negative cooperativity) 31 Enzymes Controlled by Both Allosteric Regulation and Covalent Modification Use Glycogen phosphorylase (GP) as an example! GP cleaves glucose units from nonreducing ends of glycogen The product, glucose-1-phosphate is a readily usable fuel 32
9 Glucose-1-phosphate Glucose-6-phosphate is the real metabolite for energy production. You will learn the detail in Chapter 18 G-1-P can easily be converted to G-6-P by the phosphoglucomutase Glucose-6-phosphate In muscle glucose-6-phosphate is used to produce energy In the liver it is ultimately transported to other tissues via the circulatory system Structure re of glycogen phosphorylase Muscle GP is a homodimer Each 842 amino acids, ~97 kd Each subunit contains 1. a pyridoxal phosphate * cofactor, covalently linked as a Schiff base ** to Lys an active site (at the center of the subunit) 3. an allosteric effector site near the subunit interface. 4. a regulatory phosphorylation site is located at Ser14 on each subunit * See chap 17 * * Schiff bases are of the general formula R 1 R 2 C=N-R Allosteric Regulation of GP Phosphate (Pi) shows strong positive cooperativity. ATP, glucose-6-p are a feedback inhibitor that affects the affinity of glycogen phosphorylase for its substrates but does not affect Vmax. AMP is a positive heterotropic effector for glycogen phosphorylase (enhances the binding of substrate to glycogen phosphorylase) 36
10 MWC Model of Glycogen Phosphorylase AMP promotes the conversion to the active R state ATP, glucose-6-p, and caffeine favor conversion to the inactive T state Structural explanations: T state, the negatively charged carboxyl group of Asp 283 faces the active site. R state, Asp 283 is displaced from the active site and replaced by Arg 569. Physiological explanataions: ATP and glucose-6-p are abundant, GP activity Cellular energy reserves are low (i.e., high [AMP] and low [ATP] and [G-6-P]), GP activity. Covalent Modification of Glycogen Phosphorylase Two forms of GP Phosphorylase a (more active, phosphorylated) Phosphorylase b (less active, unphosphorylated) Converting enzymes Phosphorylase kinase stimulates GP by phosphorylation p of Ser14 that turns b a Phosphoprotein phosphatase 1 (PP1) inactivates GP 38 A Conformation Change of Glycogen Phosphorylase by Phosphorylation After phosphorylation of Ser 14 (red), the major conformational change occurs in the N-terminal residues. N-terminal conformation of phosphorylated enzyme (phosphorylase a): yellow. N-terminal conformation of unphosphorylated enzyme (phosphorylase b): cyan. Glycogen phosphoryase is activated by a cascade of reactions Secondary messenger Figure The hormone-activated enzymatic cascade that leads to activation of glycogen phosphorylase
11 The Adenylyl Cyclase Reaction Figure The adenylyl cyclase reaction. The reaction is driven forward by subsequent hydrolysis of pyrophosphate by the enzyme inorganic pyrophosphatase. Adenylyl cyclase Adenylyl cyclase, a membrane-bound enzyme that converts ATP to adenosine-3',5' -cyclic monophosphate (cyclic AMP or camp) The hormonal stimulation of adenylyl cyclase is effected by a transmembrane signaling pathway comprising three components (a) membrane-bound hormone receptor (b) GTP-binding protein (G protein ) :have a heterotrimeric ( ) quaternary structure (c) Adenylate cyclase 41 Signaling pathway Step1. G protein is stimulated by a hormonereceptor complex, GDP dissociates and GTP binds to G, causing it to dissociate from G b and to associate with adenylyl cyclase Step2. Binding of G (GTP) activates adenylyl cyclase to form camp from ATP Step3. Intrinsic GTPase activity of G eventually hydrolyzes GTP to GDP, leading to dissociation of G a (GDP) from adenylyl cyclase and reassociation with G b to form the inactive G b complex Guanosine triphosphate (GTP), Guanosine diphosphate (GDP) 43 EndofPart2 Ask yourself.. How to identify an allosteric regulated enzyme? How to explain the mechanism of allosteric regulation? What is MWC model? Still remember the regulation of glycogen phosphorylase? Why it need more than one regulation system? 44
12 Special Focus: Hemoglobin A classic example of allostery Hemoglobin (Hb) and myoglobin (Mb) are oxygen transport and storage proteins Myoglobin Monomeric 153 aa, 17,200 MW Hemoglobin Tetrameric 2 chains of 141 residues, 2 chains of 146 residues 45 Hemoglobin & myoglobin Myoglobin, as an oxygen storage protein Greater affinity for O 2 than Hb at all oxygen pressures. Hemoglobin, as the oxygen carrier Saturated with O 2 in the lungs (po 2 ~100 torr.) Oxygen released from Hb in the capillaries of tissues (po 2 ~40 torr) Some oxygen are bound by Mb in muscle. It will release in case of severe oxygen deprivation, such as during strenuous exercise (po2 is less 20 torr) 46 Hemoglobin & myoglobin Hemoglobin displays sigmoid-shaped shaped O 2 - binding curves Myoglobin s interaction with oxygen obeys classical Michaelis - Menten-type substrate saturation behavior. 47 Structure of Mb Myoglobin consists of 8 helical l segments (designated d A~H) unordered regions are named for the helices they connect, ex. AB region Fe in Mb ferrous iron (Fe 2+ ) is the form that binds oxygen ferric iron (Fe 3+ ) in metmyoglobin does not bind oxygen Fe 3+ :protoporphyrin IX is referred to as hematin. ( ) 48
13 Myoglobin Structure The functions of Mb polypeptide: cradles the heme group protects the heme iron atom from oxidation provides a pocket into which h the O 2 can fit The six liganding positions of an iron ion. Four ligands lie in the same plane His F8 is the 5th ligand; in oxymyoglobin O 2 becomes the 6th. Affinity of Heme changed in Mb Free heme: CO affinity it X greater than O 2 Mb: CO affinity 250 X greater than O 2 Because His E7 force the CO to tilt away! Structures of Hb & Mb What Interactions Exist Between the Subunits of Hemoglobin? Mb: 153 a.a. Hb: chain 146 a.a. H helix is shorter chain 141 a.a. H helix is shorter & Lack D helix 51 -chains contact with - chains more! and helices B G HH and GH corner and helices C G and FG corner (sliding contacts There are fewer - interactions and - interactions 52
14 How Does the Structure of Hemoglobin Change Upon Binding Oxygen? When deoxy-hb crystals are exposed to oxygen, they shatter One alpha-beta pair moves relative to the other by 15 degrees upon oxygen binding This massive change is induced by movement of Fe by nm when oxygen binds ( Mb is nm ) The structure of dexoyhb is stablized Deoxy Hb (T form) is stabilized by specific hydrogen bonds and 8 salt bridges (ion-pair bonds), which will break in OxyHb (R form) H bonds: In deoxyhb Phenolic -OH groups of Tyr 140 and Tyr 145 form intrachain H bonds to Val FG5. (Val FG5 is 93 and 98, respectively.) chain chain 54 The Bohr Effect Why Blood Becomes Acid? CO 2 hydration by the enzyme carbonic anhydrase. Saturation curve of Hb for O 2 is displaced to the right as acidity increases. This phenomenon is called the Bohr effect (by Christian Bohr) DeoxyHb has a higher affinity for proton than oxyhb HbO 2 + H + HbH + +O 2 Other effectors: Protons,carbon dioxide, chloride ions and metabolite 2,3- bisphosphoglycerate (BPG) Many of the are picked up by Hb as O 2 dissociates and HCO 3- are transported with the blood back to the lungs. Hb becomes oxygenated in the lungs, H + is released and reacts with HCO 3- to re-form H 2 CO 3, from which CO 2 is liberated. 56
15 Hb and CO 2 Transportation? CO 2 is directly transported by Hb in the form of carbamate ( NHCOO - ) R NH 2 + CO 2 R NH COO - + H + This reaction to right: in tissues by the high CO 2 concentration; to left in the lungs where [CO 2 ] is low. Note: Carbamylation of N-terminus converts it to a negatively charged functional group that forms a salt bridge to Arg-141 ( chain) stabilizing deoxyhemoglobin (T-State) 57 Effect of 2,3-BPG The binding of 2,3 -bisphosphoglycerate (2,3- BPG) to Hb promotes the release of O 2 Erythrocytes (red blood cells) normally contain about 4.5 mm BPG 4.5 mm BPG equivalent to that of tetrameric hemoglobin molecules. Tetrameric Hb molecule has but one binding site for BPG. This site is situated within the central cavity formed by the association of the four subunits. 58 Binding of 2,3-BPG The strongly gynegative BPG molecule is electrostatically bound via interactions with the positively charged functional groups of each Lys 82, His 2, His 143, and the NH3+-terminal group of each -chain. Oxygen-binding curves of blood In the absence of 2,3-BPG, oxygen binding to Hb follows a rectangular hyperbola The sigmoid binding curve is only observed in the presence of 2,3- BPG BPG bind better to deoxyhb than to oxyhb, causing a shift in equilibrium in favor of O 2 release
16 Fetal hemoglobin Fetal hemoglobin exists as an 2 2 tetramer Gamma has a serine substituted for histidine at AA 143 (lack two of the positive charges in the central BPG-binding cavity. ) Decreased BPG binding in fetal hemoglobin gives it a higher affinity for oxygen than maternal Abnormal Hb Sickle-cell anemia patients have abnormally-shaped red blood cells The erythrocytes are crescent-shaped instead of disc-shaped The sickle cells pass less freely through the capillaries, impairing circulation and causing tissue damage The Cause of sickle-cell cell anemia A single amino acid substitution in the -chains of Hb causes sickle-cell anemia Glu at position 6 of the -chains is replaced by Val As a result, Hb S molecules l aggregate into long, chainlike polymeric structures The polymerization of Hb S via the interactions between the hydrophobic Val side chains at position b6 and the hydrophobic pockets in the EF corners of b-chains in neighboring Hb molecules. Sickle-Cell Anemia is a Molecular Genetic Disease 64
17 Hemoglobin and Nitric Oxide Nitric oxide (NO ) is a simple gaseous molecule that acts as a neurotransmitter and as a second messenger in signal transduction (see Chapter 32) NO is a high-affinity ligand for Hb, binding to the heme iron 10,000 times more tightly than O 2 But why is NO not bound instantaneously t to Hb, preventing its physiological effects? NO reacts with the SH of Cys 93, forming an S-nitroso derivative: 65 Hemoglobin and Nitric Oxide The S-nitroso group is in equilibrium with other S-nitroso compounds formed by reaction of nitric oxide with small-molecule molecule thiols such as free Cys or glutathione: These small-molecule thiols transfer NO from erythrocytes to endothelial receptors, where it exerts its physiological effects 66 Ask yourself. EndofPart3 What s the similarities and differences of myoglobin and hemoglobin? What is Bohr effect? How many ways the activity of Hb could be regulated? Besides oxygen, what else Hb could carry? End of the class You should learned Common regulation mechanisms of enzymes Phosphorylation modification Allosteric modification MWC model The example of glycogen phosphatase h The properties of hemoglobin Allosteric effects on Hb Cargo of Hb 67 68
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