Regulation Through Conformational Changes

In the previous lecture, we discussed the mechanisms of regulating enzymes through inhibitors. Now, we will start this lecture by discussing regulation through conformational changes. Regulation Through Conformational Changes It occurs by changing the conformation of an enzyme in a certain way to rapidly affect the activity of the enzyme from an inactive form to a fully active form, or vice versa. These regulatory mechanisms include: 1) Allosteric activation and inhibition 2) Phosphorylation or other covalent modifications 3) Protein - Protein interactions between regulatory & catalytic subunits or between two proteins 4) Proteolytic cleavage Allosteric Regulation Allosteric enzymes are multi-subunit enzymes with catalytic (active site) and regulatory subunits. The binding of a regulatory molecule (Allosteric modifier) triggers conformational changes by modifying non-covalent interactions; this results in an apparent change in the binding affinity at a different binding site. Note: All Allosteric proteins have a quaternary structure. Allosteric Modifiers They are molecules that bind non-covalently to the Allosteric site (a physically separate site from the active site). Types of modifiers: 1) Negative Allosteric Modifier (inhibitor): Causes the enzyme to be less active by making the active site less fitting for the substrate. 2) Positive Allosteric Modifier (activator): Causes the enzyme to be more active by making the active site more fitting for the substrate. Modifiers can also be: 1) Homotropic: The modifier is the substrate itself. The binding of the substrate causes the enzyme to become more active and causes the binding to a second substrate at a different active site to be easier. This is known as Positive Cooperativity. Example: O₂ is a homotropic allosteric modulator of hemoglobin. 2) Heterotropic: The modifier is different from the substrate. Does the Michaelis-Menten model explain the kinetic properties of Allosteric enzymes? No, because Allosteric enzymes do not show a hyperbolic plot since they have multiple active sites. Michaelis-Menten (Other enzymes) Allosteric Enzymes These multiple active sites exhibit the property of Cooperativity, where the binding of one active site affects the affinity of other active sites on the enzyme; these affected active sites result in a sigmoidal plot that has both Vmax and K50. (K50 is the same concept of KM in other enzymes; where 50% of the effectors are bound to the Allosteric enzyme). Adding an Inhibitor to the Allosteric Enzyme → Disables the conversion of the subunits to the active form → Lowers the reactions’ rates → Does not change Vmax → Increases K50, which means that we need more substrate concentration to reach K50 → Lowers affinity The plot shifts to the right and becomes more sigmoidal. Adding an Activator to the Allosteric Enzyme → → → → Increases the conversion of the subunits to the active form Does not change Vmax Decreases K50, which means that we need less substrate concentration to reach K50 Increases affinity The plot shifts to the left and becomes close to a hyperbolic plot. Note: Vmax does not change in allosteric inhibition, unlike in competitive inhibition. Why? Because increasing the [S] induces conformational changes in the enzyme, the affinity of the enzyme towards the inhibitor decreases until it is almost negligible. Therefore, we reach the normal Vmax. The curve (only substrate) in the previous graph (in the middle) is hypothetical Question: If only activation occurred, which of the following curves would be the substrate alone? Since activation occurred, the plot will be shifted to the left. Therefore, the normal state will be the farthest to right (red curve) and any other curves are just varying activation states. (We cannot say the one on the right is inhibited since inhibition did not occur; only activation did.) Question: If inhibition occurred, which of the following curves would be the substrate alone? Since inhibition occurred, the plot will be shifted to the right. Therefore, the normal state will be the farthest to left (blue curve) and any other curves are just varying inhibition states. (We cannot say the one on the left is activated since activation did not occur; only inhibition did) Aspartate Transcarbamoylase (ATCase) Reaction ATCase is a highly regulated enzyme that catalyzes the first step in pyrimidine biosynthesis. ATCase controls the rate of pyrimidine biosynthesis by changing its catalytic velocity in response to cellular levels of both pyrimidines and purines concentrations. ATCase structure: ATCase consists of two units (12 polypeptides in total): 1) Catalytic unit: 6 subunits organized into 2 trimers. 2) Regulatory unit: 6 subunits organized into 3 dimers. ATCase exists in two forms: 1) T state (taut): less active 2) R state (relaxed): more active The end-products of the reactions' pathway roles: 1) CTP: Cytidine triphosphate, a pyrimidine. High Concentration of CTP inhibits ATCase activity (feedback inhibition). → Decreases the affinity for Asp (substrate) / Increases K50 → Decreases enzymatic activity Binding of CTP to the regulatory subunits results in an equilibrium shift towards the T state (Inhibits ATCase). 2) ATP: The end-product of a parallel pathway, a purine. High concentrations of ATP activate ATCase because ATP is a source for nucleotides synthesis. Binding of ATP to the regulatory subunits results in an equilibrium shift towards the R state (Activates ATCase). Notes: • Allosteric inhibitors usually have a much stronger effect on an enzyme’s velocity than competitive and noncompetitive inhibitors. • Allosteric enzymes do not only regulate through inhibition, but also through activation, since Allosteric regulators (effectors) may also function as activators. • The Allosteric effector does not necessarily need to resemble the substrate or the product of the enzyme. Regulation Through Modulators Small molecule modulators can have dramatic effects on the enzymes. Example: cAMP (structurally modified AMP) activates protein kinase A. Till now, we talked about regulation through allosteric behavior; another way for regulation is: Reversible Covalent Modification Covalent Modification (Phosphorylation) A common mechanism in which an enzyme molecule accepts a phosphate group (covalent addition) into one of its amino acids’ side chains, changing its activity. Usually a serine, threonine or tyrosine residue (amino acids that contain hydroxide). ATP is mostly the phosphoryl donor in these reactions, which are catalyzed by protein kinases. Dephosphorylation by hydrolysis is catalyzed by protein phosphatases. Note: Dephosphorylation is not the reversal of phosphorylation. Note: The addition/removal of the phosphate group from an enzyme may activate or inactivate it. Note: Kinases are transferases, and phosphatases are hydrolases Why is phosphorylation effective (most common)? • Rapid and transient regulation of an enzyme’s activity (reversible). • Adds two negative charges (from the phosphate group). → New electrostatic interactions and accordingly changing conformation. • Can form three or more hydrogen bonds, altering substrate binding and catalytic activity. • Can take place in only less than a second or over a span of hours. • Often causes highly amplified effects. Protein Kinase A Structure When inactive, PKA is a tetramer consisting of: • Two regulatory (R) subunits with high affinity for cAMP. Each regulatory subunit binds to two cAMP molecules (4 cAMPs total). • Two catalytic (C) subunits. The binding of two cAMPs to each regulatory subunit leads to the dissociation of the R2C2 → R2 + two active C subunits. Protein Kinase A (serine/threonine protein kinase) phophorylates many enzymes that regulate different metabolic pathways. Note: The effect of PKA is amplified. Example of an enzyme regulated by PKA: Glycogen phosphorylase kinase (GP) GP catalyzes the removal of glucose molecules from glycogen. The enzyme exists in two forms: 1) Phosphorylase B (inactive state). It shifts between the R and T state in equilibrium, and it favors the T state. 2) Phosphorylase A (active state). It shifts between the R and T state in equilibrium, and it favors the R state. Note: Allosteric Enzymes are influenced by substrate concentration. For example, at high concentrations of substrate / activator, more enzymes are found in the R state. The T state is favored when there is an insufficient amount of substrate to bind to the enzyme or when an inhibitor is present. In other words, the T and R state equilibrium depends on the concentration of the substrate. The transition of phosphorylase B between the T and the R state is controlled by the energy charge (ATP and AMP) of the muscle cell. How? • High concentrations of AMP → Phosphorylase B is active, and AMP binds to a nucleotide-binding site, stabilizing the conformation into the R state. • ATP acts as a negative allosteric effector by competing with AMP → Phosphorylase B is inactive, favoring the T state. Note: Glucose 6-phosphate also favors the T state (feedback inhibition). Phosphorylation Cascade Note how a single hormone can activate a kinase while inhibiting the other. PKA inhibits Glycogen synthase → Inhibits glycogen synthesis PKA activates Phosphorylase kinase → Phosphorylates glycogen phosphorylase B to A → Promotes glycogen degradation Note: Glucagon is a hormone secreted by the pancreas (glucose level sensor), affecting the tissues. Epinephrine is secreted in fight or flight actions, affecting the muscles. Other Covalent Modifications Besides Phosphorylation 1) Adenylylation (addition of adenylyl group). AMP (from ATP) is transferred to a Tyr s The addition of bulky AMP inhibits certain cytosolic enzymes. 2) Uridylylation (addition of uridylyl group). 3) ADP-ribosylation. Addition of an adenosine diphosphate ribosyl group inactivates key cellular enzymes. 4) Methylation. Masks the negative charge of carboxylate side chains and adds hydrophobicity. 5) Acetylation. Acetyl Co → Lysine Masks positive charges. 6) Conformational changes due to protein-protein interaction : G -proteins: They are trans-membrane proteins that cause changes inside the cell. They receive signals from hormones, neurotransmitters, and other signaling factors. When they are bound to (GTP) → On When they are bound to (GDP) → Off • G-protein: a transmembrane heterotrimer protein made up of α, β and γ subunits. • The α subunit is the active subunit. It can be stimulatory or inhibitory. • β and γ subunits are the regulatory subunits • G-proteins belong to a larger group of enzymes: GTPases. • They are always coupled with GPCRs. • They are the target of 25% of drugs. Monomeric G-proteins Monomeric G proteins have the same mechanisms as the trimeric G-proteins. They differ only in the fact that they are small, with one subunit that works as the alpha subunit. They also do not target adenylyl cyclase like the trimeric G-proteins do. 1) When the monomeric G-protein is bound to GDP, it is inactive. 2) In order to activate the monomeric Gprotein, a guanine exchange factor (GEF) is needed. 3) GEF exchanges GDP with a GTP, making the monomeric G-protein active. The activity of many G-proteins is regulated by: 1. GAPs [GTPase-activating proteins]: Stimulate GTP hydrolysis (decrease the activity of G-proteins) 2. GEFs [guanine nucleotide exchange factors]: Stimulate the exchange of GDP/GTP (increase the activity of G-proteins) Note: GTP → GDP (Hydrolysis), but GDP → GTP (Exchange) 3. GDIs [GDP dissociation inhibitors]: Keep GDP associated (decrease the activity of G-proteins)