Enzyme Mechanisms and Regulation
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Enzyme Mechanisms and Regulation

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10/28/2008. Biochemistry: Mechanisms. p. 2 of 56. How do enzymes reduce activation energies?. We can illustrate mechanistic principles by looking at specific examples; we can also recognize enyzme regulation when we see it.. 10/28/2008. Biochemistry: Mechanisms. p. 3 of 56. Mechanism Topics. RegulationThermodynamicsEnzyme availabilityAllostery, revisited.
Enzyme Mechanisms and Regulation

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1. 10/28/2008 Biochemistry: Mechanisms 1 Enzyme Mechanisms and Regulation Andy Howard Introductory Biochemistry, Fall 2008 Tuesday 28 October 2008

2. 10/28/2008 Biochemistry: Mechanisms p. 2 of 56 How do enzymes reduce activation energies? We can illustrate mechanistic principles by looking at specific examples; we can also recognize enyzme regulation when we see it.

3. 10/28/2008 Biochemistry: Mechanisms p. 3 of 56 Mechanism Topics Regulation Thermodynamics Enzyme availability Allostery, revisited Mechanisms Induced-fit Tight Binding of Ionic Intermediates Serine proteases Other proteases Lysozyme

4. 10/28/2008 Biochemistry: Mechanisms p. 4 of 56 Examining enzyme mechanisms will help us understand catalysis Examining general principles of catalytic activity and looking at specific cases will facilitate our appreciation of all enzymes.

5. 10/28/2008 Biochemistry: Mechanisms p. 5 of 56 Binding modes: proximity We describe enzymatic mechanisms in terms of the binding modes of the substrates (or, more properly, the transition-state species) to the enzyme. One of these involves the proximity effect, in which two (or more) substrates are directed down potential-energy gradients to positions where they are close to one another. Thus the enzyme is able to defeat the entropic difficulty of bringing substrates together.

6. 10/28/2008 Biochemistry: Mechanisms p. 6 of 56 Binding modes: efficient transition-state binding Transition state fits even better (geometrically and electrostatically) in the active site than the substrate would. This improved fit lowers the energy of the transition-state system relative to the substrate. Best competitive inhibitors of an enzyme are those that resemble the transition state rather than the substrate or product.

7. 10/28/2008 Biochemistry: Mechanisms p. 7 of 56 Proline racemase Pyrrole-2-carboyxlate resembles planar transition state

8. 10/28/2008 Biochemistry: Mechanisms p. 8 of 56 Yeast aldolase Phosphoglycolohydroxamate binds much like the transition state to the catalytic Zn2+

9. 10/28/2008 Biochemistry: Mechanisms p. 9 of 56 Adenosine deaminase with transition-state analog Transition-state analog: Ki~10-8 * substrate Km Wilson et al (1991) Science 252: 1278

10. 10/28/2008 Biochemistry: Mechanisms p. 10 of 56 ADA transition-state analog 1,6 hydrate of purine ribonucleoside binds with KI ~ 3*10-13 M

11. 10/28/2008 Biochemistry: Mechanisms p. 11 of 56 Induced fit Refinement on original Emil Fischer lock-and-key notion: both the substrate (or transition-state) and the enzyme have flexibility Binding induces conformational changes

12. 10/28/2008 Biochemistry: Mechanisms p. 12 of 56 Example: hexokinase Glucose + ATP ? Glucose-6-P + ADP Risk: unproductive reaction with water Enzyme exists in open & closed forms Glucose induces conversion to closed form; water can?t do that Energy expended moving to closed form

13. 10/28/2008 Biochemistry: Mechanisms p. 13 of 56 Hexokinase structure Diagram courtesy E. Marcotte, UT Austin

14. 10/28/2008 Biochemistry: Mechanisms p. 14 of 56 Tight binding of ionic intermediates Quasi-stable ionic species strongly bound by ion-pair and H-bond interactions Similar to notion that transition states are the most tightly bound species, but these are more stable

15. 10/28/2008 Biochemistry: Mechanisms p. 15 of 56 Serine protease mechanism Only detailed mechanism that we?ll ask you to memorize One of the first to be elucidated Well studied structurally Illustrates many other mechanisms Instance of convergent and divergent evolution

16. 10/28/2008 Biochemistry: Mechanisms p. 16 of 56 The reaction Hydrolytic cleavage of peptide bond Enzyme usually works on esters too Found in eukaryotic digestive enzymes and in bacterial systems Widely-varying substrate specificities Some proteases are highly specific for particular aas at position 1, 2, -1, . . . Others are more promiscuous

17. 10/28/2008 Biochemistry: Mechanisms p. 17 of 56 Mechanism Active-site serine ?OH ? Without neighboring amino acids, it?s fairly non-reactive becomes powerful nucleophile because OH proton lies near unprotonated N of His This N can abstract the hydrogen at near-neutral pH Resulting + charge on His is stabilized by its proximity to a nearby carboxylate group on an aspartate side-chain.

18. 10/28/2008 Biochemistry: Mechanisms p. 18 of 56 Catalytic triad The catalytic triad of asp, his, and ser is found in an approximately linear arrangement in all the serine proteases, all the way from non-specific, secreted bacterial proteases to highly regulated and highly specific mammalian proteases.

19. 10/28/2008 Biochemistry: Mechanisms p. 19 of 56 Diagram of first three steps

20. 10/28/2008 Biochemistry: Mechanisms p. 20 of 56 Diagram of last four steps

21. 10/28/2008 Biochemistry: Mechanisms p. 21 of 56 Chymotrypsin as example Catalytic Ser is Ser195 Asp is 102, His is 57 Note symmetry of mechanism: steps read similarly L? R and R ? L

22. 10/28/2008 Biochemistry: Mechanisms p. 22 of 56 Oxyanion hole When his-57 accepts proton from Ser-195: it creates an R?O- ion on Ser sidechain In reality the Ser O immediately becomes covalently bonded to substrate carbonyl carbon, moving - charge to the carbonyl O. Oxyanion is on the substrate's oxygen Oxyanion stabilized by additional interaction in addition to the protonated his 57: main-chain NH group from gly 193 H-bonds to oxygen atom (or ion) from the substrate, further stabilizing the ion.

23. 10/28/2008 Biochemistry: Mechanisms p. 23 of 56 Oxyanion hole cartoon Cartoon courtesy Henry Jakubowski, College of St.Benedict / St.John?s University

24. 10/28/2008 Biochemistry: Mechanisms p. 24 of 56 Modes of catalysis in serine proteases Proximity effect: gathering of reactants in steps 1 and 4 Acid-base catalysis at histidine in steps 2 and 4 Covalent catalysis on serine hydroxymethyl group in steps 2-5 So both chemical (acid-base & covalent) and binding modes (proximity & transition-state) are used in this mechanism

25. 10/28/2008 Biochemistry: Mechanisms p. 25 of 56 Specificity Active site catalytic triad is nearly invariant for eukaryotic serine proteases Remainder of cavity where reaction occurs varies significantly from protease to protease. In chymotrypsin ? hydrophobic pocket just upstream of the position where scissile bond sits This accommodates large hydrophobic side chain like that of phe, and doesn?t comfortably accommodate hydrophilic or small side chain. Thus specificity is conferred by the shape and electrostatic character of the site.

26. 10/28/2008 Biochemistry: Mechanisms p. 26 of 56 Chymotrypsin active site Comfortably accommodates aromatics at S1 site Differs from other mammalian serine proteases in specificity

27. 10/28/2008 Biochemistry: Mechanisms p. 27 of 56 Divergent evolution Ancestral eukaryotic serine proteases presumably have differentiated into forms with different side-chain specificities Chymotrypsin is substantially conserved within eukaryotes, but is distinctly different from elastase

28. 10/28/2008 Biochemistry: Mechanisms p. 28 of 56 iClicker quiz! Why would the nonproductive hexokinase reaction H2O + ATP -> ADP + Pi be considered nonproductive? (a) Because it needlessly soaks up water (b) Because the enzyme undergoes a wasteful conformational change (c) Because the energy in the high-energy phosphate bond is unavailable for other purposes (d) Because ADP is poisonous (e) None of the above

29. 10/28/2008 Biochemistry: Mechanisms p. 29 of 56 iClicker quiz, question 2: Why are proteases often synthesized as zymogens? (a) Because the transcriptional machinery cannot function otherwise (b) To prevent the enzyme from cleaving peptide bonds outside of its intended realm (c) To exert control over the proteolytic reaction (d) None of the above

30. 10/28/2008 Biochemistry: Mechanisms p. 30 of 56 Question 3: what would bind tightest in the TIM active site? (a) DHAP (substrate) (b) D-glyceraldehyde (product) (c) 2-phosphoglycolate (Transition-state analog) (d) They would all bind equally well

31. 10/28/2008 Biochemistry: Mechanisms p. 31 of 56 Convergent evolution Reappearance of ser-his-asp triad in unrelated settings Subtilisin: externals very different from mammalian serine proteases; triad same

32. 10/28/2008 Biochemistry: Mechanisms p. 32 of 56 Subtilisin mutagenesis Substitutions for any of the amino acids in the catalytic triad has disastrous effects on the catalytic activity, as measured by kcat. Km affected only slightly, since the structure of the binding pocket is not altered very much by conservative mutations. An interesting (and somewhat non-intuitive) result is that even these "broken" enzymes still catalyze the hydrolysis of some test substrates at much higher rates than buffer alone would provide. I would encourage you to think about why that might be true.

33. 10/28/2008 Biochemistry: Mechanisms p. 33 of 56 Cysteinyl proteases Ancestrally related to ser proteases? Cathepsins, caspases, papain Contrasts: Cys ?SH is more basic than ser ?OH Residue is less hydrophilic S- is a weaker nucleophile than O-

34. 10/28/2008 Biochemistry: Mechanisms p. 34 of 56 Papain active site

35. 10/28/2008 Biochemistry: Mechanisms p. 35 of 56 Hen egg-white lysozyme Antibacterial protectant of growing chick embryo Hydrolyzes bacterial cell-wall peptidoglycans ?hydrogen atom of structural biology? Commercially available in pure form Easy to crystallize and do structure work Available in multiple crystal forms Mechanism is surprisingly complex (14.7)

36. 10/28/2008 Biochemistry: Mechanisms p. 36 of 56 Mechanism of lysozyme Strain-induced destabilization of substrate makes the substrate look more like the transition state Long arguments about the nature of the intermediates Accepted answer: covalent intermediate between D52 and glycosyl C1 (14.39B)

37. 10/28/2008 Biochemistry: Mechanisms p. 37 of 56 The controversy

38. 10/28/2008 Biochemistry: Mechanisms p. 38 of 56 Regulation of enzymes The very catalytic proficiency for which enzymes have evolved means that their activity must not be allowed to run amok Activity is regulated in many ways: Thermodynamics Enzyme availability Allostery Post-translational modification Protein-protein interactions

39. 10/28/2008 Biochemistry: Mechanisms p. 39 of 56 Thermodynamics as a regulatory force Remember that ?Go? is not the determiner of spontaneity: ?G is. Therefore: local product and substrate concentrations determine whether the enzyme is catalyzing reversible reactions to the left or to the right Rule of thumb: ?Go? < -20 kJ mol-1 is irreversible

40. 10/28/2008 Biochemistry: Mechanisms p. 40 of 56 Enzyme availability The enzyme has to be where the reactants are in order for it to act Even a highly proficient enzyme has to have a nonzero concentration How can the cell control [E]tot? Transcription (and translation) Protein processing (degradation) Compartmentalization

41. 10/28/2008 Biochemistry: Mechanisms p. 41 of 56 Transcriptional control mRNAs have short lifetimes Therefore once a protein is degraded, it will be replaced and available only if new transcriptional activity for that protein occurs ? Many types of transcriptional effectors Proteins can bind to their own gene Small molecules can bind to gene Promoters can be turned on or off

42. 10/28/2008 Biochemistry: Mechanisms p. 42 of 56 Protein degradation All proteins have finite half-lives; Enzymes? lifetimes often shorter than structural or transport proteins Degraded by slings & arrows of outrageous fortune; or Activity of the proteasome, a molecular machine that tags proteins for degradation and then accomplishes it

43. 10/28/2008 Biochemistry: Mechanisms p. 43 of 56 Compartmentalization If the enzyme is in one compartment and the substrate in another, it won?t catalyze anything Several mitochondrial catabolic enzyme act on substrates produced in the cytoplasm; these require elaborate transport mechanisms to move them in Therefore, control of the transporters confers control over the enzymatic system

44. 10/28/2008 Biochemistry: Mechanisms p. 44 of 56 Allostery Remember we defined this as an effect on protein activity in which binding of a ligand to a protein induces a conformational change that modifies the protein?s activity Ligand may be the same molecule as the substrate or it may be a different one Ligand may bind to the same subunit or a different one These effects happen to non-enzymatic proteins as well as enzymes

45. 10/28/2008 Biochemistry: Mechanisms p. 45 of 56 Substrates as allosteric effectors (homotropic) Standard example: binding of O2 to one subunit of tetrameric hemoglobin induces conformational change that facilitates binding of 2nd (& 3rd & 4th) O2?s So the first oxygen is an allosteric effector of the activity in the other subunits Effect can be inhibitory or accelerative

46. 10/28/2008 Biochemistry: Mechanisms p. 46 of 56 Other allosteric effectors (heterotropic) Covalent modification of an enzyme by phosphate or other PTM molecules can turn it on or off Usually catabolic enzymes are stimulated by phosphorylation and anabolic enzymes are turned off, but not always Phosphatases catalyze dephosphorylation; these have the opposite effects

47. 10/28/2008 Biochemistry: Mechanisms p. 47 of 56 Cyclic AMP-dependent protein kinases Enzymes phosphorylate proteins with S or T within sequence R(R/K)X(S*/T*) Intrasteric control: regulatory subunit or domain has a sequence that looks like the target sequence; this binds and inactivates the kinase?s catalytic subunit When regulatory subunits binds cAMP, it releases from the catalytic subunit so it can do its thing

48. 10/28/2008 Biochemistry: Mechanisms p. 48 of 56 Kinetics of allosteric enzymes Generally these don?t obey Michaelis-Menten kinetics Homotropic positive effectors produce sigmoidal (S-shaped) kinetics curves rather than hyperbolae This reflects the fact that the binding of the first substrate accelerates binding of second and later ones

49. 10/28/2008 Biochemistry: Mechanisms p. 49 of 56 T ? R State transitions Many allosteric effectors influence the equilibrium between two conformations One is typically more rigid and inactive, the other is more flexible and active The rigid one is typically called the ?tight? or ?T? state; the flexible one is called the ?relaxed? or ?R? state Allosteric effectors shift the equilibrium toward R or toward T


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