GENERAL THOUGHTS ON REGULATION. Lecture 16: Enzymes & Kinetics IV Regulation and Allostery REGULATION IS KEY TO VIABILITY

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1 GENERAL THOUGHTS ON REGULATION Lecture 16: Enzymes & Kinetics IV Regulation and Allostery Margaret A. Daugherty Fall ). Enzymes slow down as product accumulates 2). Availability of substrates determines reaction rate 3). Enzymes are controlled at the level of DNA 4). Many enzymes are regulated via reversible covalent modification 5). Many enzymes regulated via non-covalent interactions with small molecules REGULATION IS KEY TO VIABILITY REGULATION OF ENZYME ACTIVITY? How does the cell know when enough is enough? First step in glycolysis: hexokinase REGULATION OF ENZYME ACTIVITY? Problem: Most metabolic pathways involve many enzymes that act sequentially E1 E2 E3 E4 E5 A B C D threonine dehydratase hexokinase threonine leucine Substrate-level control Feedback inhibition

2 FEEDBACK CONTROL: INHIBITION & ACTIVATION The same substrate can act as an inhibitor of one pathway, and an activator of a second pathway. + Increase in G can inhibit formation of D, activate formation of K. REGULATORY ENZYMES: THREE GENERAL CLASSES Regulatory enzymes: enzymes that control key metabolic points in a pathway. Usually located at the first committed step to a pathway. 1). Enzymes regulated via reversible covalent modification; 2). Enzymes regulated via proteolytic cleavage. 3). Other types: isozymes, modulator proteins 4). Allosteric enzymes (1) (3) and (4) tend to be multi-subunit proteins; Regulatory site and active sites usually on separate subunits ENZYMES REGULATED VIA COVALENT MODIFICATION 30-50% Modification AA residue ENZYMES REGULATED VIA COVALENT MODIFICATION Glycogen synthase: multiple phosphorylation sites, that can act independently, or in concert. (p) of any or all of these sites moderately affects activity (p) of all sites dramatically affects activity (p) of site 5 does not affect activity

3 ACTIVATION OF INTESTINAL PROTEASES ENZYMES REGULATED VIA PROTEOLYSIS: THE BLOOD CLOTTING CASCADE NOTE: These all work on one another, so they all must be activated in a short time span! Regulation is key in everything! ISOZYMES: LACTATE DEHYDROGENASE MODULATOR PROTEINS: Influence activity of an enzyme camp regulatory protein: dimer of C (catalytic subunit) and R (regulatory subunit). Dissociation of R allows activation of C Isomer: one or more quaternary forms; differ in ratios of catalytic subunits that make up the quaternary structure. Modulator proteins interact directly with an enzyme Can either upregulate or downregulate activity

4 ALLOSTERIC ENZYMES: KEY FACTS Multi-subunit proteins that can have different quaternary structures (T - low affinity; R - high affinity) Situated at key steps in metabolic pathways (1rst step) Allosteric Enzymes: Substrate Binding Enzymes that are regulated by the binding of an effector molecule, i.e., a signal molecule that can influence the action of the enzyme. Effectors bind at an allosteric site. (Site that is not the active site) Allosteric effectors can be; Postive effectors - increase enzyme rate Negative effectors - decrease enzyme rate Enzymes can posses both positive and negative regulatory sites Symmetry Model: MWC Monod - Wyman - Changeux Model State 1: unligated state Sigmoidal curve - homo-allostery (cooperative binding) Lineweaver-Burke plot is non-linear Symmetry Model: MWC Monod - Wyman - Changeux Model State 1: unligated state In R: All subunits have R conformation In T: All subunits have T conformation equilibrium constant for 4 o switch R: conformation is high-affinity; favors binding T: conformation is low-affinity; disfavors binding K T and K R : substrate dissociation constants K T = [E][S]/[ES] Model assumes K T >> K R ;This means R has greater affinity for substrate - doesn t dissociate as easily

5 Symmetry Model: MWC Monod - Wyman - Changeux Model Two types of equilibrium constants: L and K T /K R R <--> T State 2: Ligated state S= substrate binding site F = effector binding site L: equilibrium constant for quaternary switch R <--> T Binding of one substrate: 4 o shifts to favor R R is the high affinity structure All binding sites now high affinity Makes binding of next ligand easier High affinity <--> low affinity L = [T o ]/[R o ] POSITIVE COOPERATIVITY! Homotropic: that like molecules influence binding of like molecules Increasing L favors T; Harder to switch; More sigmoidal Two types of equilibrium constants: L and K T /K R ES <--> E + S K: equilibrium dissociation constantfor ES ES <--> E + S bound <--> free K =[E][S]/[ES] c = K R /K T *A larger c means that substrate dissociates more from R than T; T state binding favored -- hence looks like a simple binding system -more hyperbolic Symmetry Model: MWC Monod - Wyman - Changeux Model Heterotropic effectors: small molecules that influence the binding of substrate; work by binding at a site other than the substrate binding site; Effector binding site Positive effectors: molecules that favor the high affinity R conformation Negative effectors: molecules that favor the low affinity T conformation

6 Effect of positive & negative effectors on binding curves SEQUENTIAL MODEL: THE KNF MODEL Koshland, Nemethy, Filmer Model Substrate binding at site 1 alters intrasubunit contacts; these changes affect the affinity for subsequent binding at the neighboring subunits, and so on. KNF Model: Accounts for negative cooperativity! K vs. V Systems V system: Vmax changes +/- allosteric effectors K 0.5 is unchanged *K system: The K 0.5 changes +/- allosteric effectors; Vmax is unchanged T and R have same affinity for substrate; Differ in catalytic ability Differ in affinities for activator and inhibitor T and R have different affinities for substrate, activator and inhibitor

7 An example: Glycogen phosphorylase Role: breaks glycogen down to glucose Where: liver and muscle When: Times of energy need (mild starvation, exercise) Dimer: 2 copies of each site 1). Active site (PLP); Pi 2). Glycogen storage site 3). Allosteric effector site 4). Regulatory site Control of GP v vs. S curves for glycogen phosphorylase 1). Response to fuel needs: High fuel state: Enzyme off high ATP high Glucose high G6P Low fuel state: Enzyme on high AMP low ATP 2). Covalent modification Stress situation! Molecule on! Binding of substrate, Pi, shows positive homotropic cooperativity Binding of activator favors high affinity R quaternary structure without altering Vmax Binding of inhibitor, ATP, favors low affinity T quaternary structure, but doesn t affect Vmax.

8 HORMONAL ACTIVATION OF GLYCOGEN PHOSPHORYLASE GP needs to be phosphorylated (Ser 14) to activate it adrenaline The difference between phosphorylase b and phosphorylase a is a dramatic rearrangement of the N-terminal domain. Change from intrasubunit contacts to intersubunit contacts. flight or fight response Structure of AMP-activated phosphorylase b is almost identical to phosphorylationactivated phosphorylase a. Review 1). The induced fit model accounts for enzymatic catalysis better than the lock and key model. 2). Regulation of enzymes occurs on many levels: Level of DNA synthesis: enzyme is made according to need substrate level control: product directly inhibits enzyme Feedback inhibition: endproduct of pathway inhibits enzyme Reversible covalent modification Cleavage of zymogens Isozymes, modulator proteins Allosteric proteins 3). Allosteric enzymes have two quaternary forms: A low affinity T form with it s own substrate binding constant, K T A high affinity R form with its own substrate binding constant, K R 4). Allosteric enzymes are regulated by effector molecules, either positively or negatively. 5). Velocity vs. Substrate binding curves are sigmoidal. Negative effectors favor more sigmoidicity; positive effectors favor more hyperbolic curves.

9 Review 6). Substrate binding to allosteric enzymes is cooperative; binding of one molecule enhances the binding of subsequent molecules. This is a consequence of the T to R quaternary transition. 7). Allosteric systems can be classified as V systems or K systems 8). Glycogen phosphorylase is a paradigm for understanding allosteric enzymes. 9). Glycogen phosphorylase has two forms: phosphorylase b: mostly inactive due to high concentrations of glucose and ATP (negative heterotropic effectors). Activated when the cell is in a state of energy need (low ATP, hence high AMP). AMP is a positive heterotropic effector phosphorylase a: active form. Covalent phosphorylation due to stress or exercise. In response to an enzyme cascade initiated by an extracellular hormone signal. --The structural basis for activation of both phosphorylase b and phosphorylase a appears to be the same!

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