Mechanisms of Enzyme Action

1. Mechanisms of Enzyme Action

2. What You Need to Know • Understand the importance of and need for enzymes in biological reactions. • Understand how an enzyme’s effect on the transition state and destabilization of the enzyme-substrate complex can affect reaction rates. • What role does transition-state stabilization play in enzyme catalysis? • Why is protein motion important in enzyme catalysis? • Understand importance of near attack conformations in catalysis. • How does destabilization of ES affect enzyme catalysis? • What factors influence enzymatic activity? • Have a general understanding of the 4 basic types of enzyme catalysis discussed in this lecture.

3. In chemical reactions all reacting atoms or molecules pass through a state that is intermediate in structure between the reactant and product. An Enzyme accelerates the reaction rate of a chemical reaction.

4. For the rate of a reaction to be accelerated: • Rate acceleration by an enzyme means that the energy barrier between ES and EX ‡ must be smaller than the barrier between S and X‡ • The enzyme must stabilize the transition-state complex (EX‡) ΔGe‡ < ΔGu‡

5. KS=[E][S]/[ES]; KT=[E][X++]/[EX++] KT<KS • Enzymatic rate enhancement is approximately equal to: ke/ku ~ KS/KT

6. How Does Destabilization of ES Affect Enzyme Catalysis? Raising the energy of ES increases the rate • For a given energy of EX‡, raising the energy of ES will increase the catalyzed rate • This is accomplished by a) loss of entropy due to formation of ES b) destabilization of ES by • strain • distortion • desolvation

7. How Does Destabilization of ES Affect Enzyme Catalysis? Due to favorable interactions of S and AAs on enzyme The intrinsic binding energy of ES is compensated by entropy loss due to binding of E and S and by destabilization due to strain, distortion & desolvation.

8. How Does Destabilization of ES Affect Enzyme Catalysis? Due to 1) Loss of entropy binding of S to E and 2) destabilization of ES due to: strain, distortion , desolvation Favorable interactions of S and AAs on enzyme • Catalysis does not occur if ES and X‡ are equally stabilized. • Catalysis will occur if X‡ is stabilized more than ES.

9. How Does Destabilization of ES Affect Enzyme Catalysis? (a) Formation of the ES complex results in entropy loss. The ES complex is a more highly ordered, low-entropy state for the substrate.

10. How Does Destabilization of ES Affect Enzyme Catalysis? (b) Substrates typically lose waters of hydration in the formation in the formation of the ES complex. Desolvation raises the energy of the ES complex, making it more reactive.

11. How Does Destabilization of ES Affect Enzyme Catalysis? (c) Electrostatic destabilization of a substrate may arise from juxtaposition of like charges in the active site. If charge repulsion is relieved in the reaction, electrostatic destabilization can result in a rate increase.

12. How Tightly Do Transition-State Analogs Bind to the Active Site? • The affinity of the enzyme for the transition state may be 10 -20 to 10-26 M! • Can we see anything like that with stable molecules? • Transition state analogs (TSAs) are stable molecules that are chemically and structurally similar to the transition state • They bind do the enzyme more tightly than does the substrate but not as tightly as the natural substrate already in the transition state

13. Purineriboside inhibits adenosine deaminase. The hydrated form is an analog of the transition state of the reaction.

14. Transition-State Analogs and Drug Discovery • Enzymes are often targets for drugs and other beneficial agents • Transition state analogs often make ideal enzyme inhibitors

15. Enalapril and Aliskiren lower blood pressure Statins lower serum cholesterol Protease inhibitors are AIDS drugs Juvenile hormone esterase is pesticide target Tamiflu is a viral neuraminidase inhibitor

17. USP2a Deubiquitinates Mdm2 ubiquitin Mdm2 p53 ubiquitinLigase Mdm2 p53 ubiquitinLigase p53 Tumor Suppressor P53 Ubiquitination ubiquitin ubiquitin Degradation of p53 Tumor Suppressor

19. Expression Purification and Crystallization of USP2a Core Domain 195 142 USP2a 40 kDa 96 71 48 33 28 22 12 7.6 100mM HEPES pH7.8 5mM DTT, 10% Isopropanol 5% PEG 4000 100mM Pipes pH7.8 5% PEG 4000 100mM HEPES pH7.8 5mM DTT 5% PEG 4000 • Expression: preformed in Ecoli strain Rosetta (DE3) pLysS • Purification: • Affinity chromatography (Ni column) • Size exclusion (Superdex 75) • Total yield (2 liters)≈ 60 mg USP2a. • Crystallization: • Screened with/without Ubiquitin (8.5 kDa Boston Biochem)

20. Catalytic triad: 214-229 Cys-box; 292-305 QDE-box; 446-520 His-box 218 oxyanion hole • USP2a and ubiquitin have complementary shapes • Of the 20 USP residues within 4 angstroms of the C-terminal penta-peptide 14 are conserved • However, USP residues interacting with the ubiquitin core are poorly conserved

21. 1.26Å Structure of USP2-ubiquitin Complex: Active Site and Vicinity • Active site residues shown on left (colored as in previous slide) • Two sites where interruption of ubiquitinin – USP2a interaction disrupts binding: • Large pocket in proximity of active site (C-terminus of ubiquitinin inserts here) • Second large pocket is visible on the right (area of Lys48 [colored in magenta] of ubiquitinin) • USP2 is shown in green, ubiquitin is shown in cyan, water molecules are shown as blue spheres

22. How many other drug targets might there be? • The human genome contains approximately 20,000 genes • How many might be targets for drug therapy? • More than 3000 experimental drugs are presently under study and testing • These and many future drugs will be designed as transition-state analog inhibitors

23. How to read and write mechanisms • In written mechanisms, a curved arrow shows the movement of an electron pair • And thus the movement of a pair of electrons from a filled orbital to an empty one • A full arrowhead represents an electron pair • A half arrowhead represents a single electron • For a bond-breaking event, the arrow begins in the middle of the bond

24. How to read and write mechanisms

25. How to read and write mechanisms • It is important to appreciate that a proton transfer can change a nucleophile into an electrophile, and vice versa. • Thus, it is necessary to consider: • The protonation states of substrate and active-site residues • How pKa values can change in the environment of the active site • For example, an active-site histidine, which might normally be protonated, can be deprotonated by another group and then act as a base, accepting a proton from the substrate

26. How to read and write mechanisms Proton transfer can change a nucleophile into an electrophile, and vice versa. Example: An active-site histidine, which might normally be protonated, can be deprotonated by another group and then act as a base, accepting a proton from the substrate.

27. How to read and write mechanisms Water can often act as an acid or base at the active site through proton transfer with an assisting active-site residue.

28. Mechanisms of Catalysis • Enzymes facilitate formation of near-attack complexes • Protein motions are essential to enzyme catalysis • Covalent catalysis • General acid-base catalysis • Low-barrier hydrogen bonds • Metal ion catalysis

29. How Do Active-Site Residues Interact to Support Catalysis? • About half of the amino acids engage directly in catalytic effects in enzyme active sites • Other residues may function in secondary roles in the active site: • Raising or lowering catalytic residue pKa values • Orientation of catalytic residues • Charge stabilization • Proton transfers via hydrogen tunneling

30. Enzymes facilitate formation of near-attack complexes The energy separation between the NAC and the transition state is approximately the same in the presence and absence of the enzyme.

31. Enzymes Facilitate Formation of NAC • Precise positioning • Reacting atoms are in van der Waals contact • Angle resembling bond to be formed in T-state • NACs are precursors to reaction transition states • Without enzyme, molecules adopt NAC ~0.0001% of the time • NACs form in enzyme active sites 1%-70% of the time

32. The active site of liver alcohol dehydrogenase – a near-attack complex.

33. Protein Motions Are Essential to Enzyme Catalysis • Proteins are constantly moving • Enzymes depend on such motions to provoke and direct catalytic events • Protein motions support catalysis in several ways. Active site conformation changes can: • Assist substrate binding • Bring catalytic groups into position • Induce formation of NACs • Assist in bond making and bond breaking • Facilitate conversion of substrate to product

34. Protein Motions Are Essential to Enzyme Catalysis The active site of cyclophilin with a bound peptide containing proline in cis and trans conformations. Motion by active site residues promote catalysis in cyclophilin.

35. Proteins are on the Move

36. Covalent Catalysis • Some enzymes derive much of their rate acceleration from formation of covalent bonds between enzyme and substrate • Amino acids side chains offer variety of nucleophilic centers for catalysis • These groups readily attack electrophilic centers of substrates, forming covalent enzyme-substrate complexes • The covalent intermediate can be attacked in a second step by water or by a second substrate, forming the desired product

37. Covalent Catalysis Example of covalent bond formation between enzyme and substrate. A nucleophilic center X: on an enzyme attacks a phosphorus atom to form a phosphoryl enzyme intermediate.

38. General Acid-base Catalysis Catalysis in which a proton is transferred in the transition state • "Specific" acid-base catalysis involves H+ or OH- that diffuses into the catalytic center • "General" acid-base catalysis involves acids and bases other than H+ and OH- • These other acids and bases facilitate transfer of H+ in the transition state

39. General Acid-base Catalysis Catalysis of p-nitrophenylacetate hydrolysis can occur either by specific acid hydrolysis or by general base catalysis.