An Introduction to Enzyme and Coenzyme Chemistry, 2nd Ed. T. D. H. Bugg, Blackwell Science, Oxford, 2004

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1 Combinatorial synthesis of linchpin β-turn mimic 1 2 DCC, BT 1 2 n -tbu 1 n -tbu 1) 2 FMC DCC, BT 2) piperidine n -tbu 3 DCC, BT 1 2 n -tbu 3 1) Ph 3 P 2) cyclization 3) CF 3 C n 3 2 Evaluated for omatostatin receptor binding! n= 1,2 x 2 = 34 AA x 3 = 10 = 1292 β-turn mimics! 139 An Introduction to Enzyme and Coenzyme Chemistry, 2nd Ed. T. D.. Bugg, Blackwell cience, xford, 2004 ydrolytic Enzymes: Proteases Phosphatases Chapter 5, pp Chapter 5, pp Cofactors (Coenzymes): redox mutase 2 e - 1 e - or 2 e - 1 e - Thiamin Pyridoxal phosphate icotinamide Flavin coenzyme eme Vitamin B12 Chapter 7, pp Chapter 9, pp Chapter 6, pp Chapter 6, pp Chapter 6, pp Chapter 11, pp

2 Enzymes: all enzymes are proteins catalysts speed up reactions by lowering the activation energy (ΔG ), T by changing the thermodynamics of the reaction (ΔG ) tabilization of the transition state inging reactants together in the proper orientation for the reaction to occur 141 3C C 3C 2-3C C 3 - K rel = 1 M -1 s -1 - Ar - K rel = 220 s -1 effect molarity 220 M C Ar - K rel = 5 x 10 4 s -1 effect molarity 5 x 10 4 M - 2C - Ar - K rel = 2 x 10 6 s -1 effect molarity 2 x 10 6 M C C C Ar - K rel = 1 x 10 7 s -1 effect molarity 1 x 10 7 M

3 - 2 C C 2 - K rel = 5 x 10 4 s -1 reactive conformation for cyclization reaction C 2 - held (pre-organized) in the reactive conformation K rel = 2 x 10 6 s -1-2 C 143 Mechanism: Mechanisms can not be proven absolutely, they can only be disproved (inconsistent with the available data) Accepted mechanism is based on the preponderance of the available evidence consistent with the products - labeling studies intuition: consistent with well-known chemistry and widely accepted mechanistic tenets consistent with modest changes in the substrate kinetic rate expression model reactions - easier to study

4 Enzyme Commission (EC) classification IUBMB #.##.##.X## Class eaction EC 1 xidoreductases calatyzes oxidations and reductions EC 2 Transferases functional group transfer EC 3 ydrolases hydrolysis (overall addition of 2 ) to a substrate to give two products EC 4 Lyases non-hydrolytic addition or removal of groups (i.e., 2, 3, etc) from a substrate. EC 5 Isomerases (mutase) product is a structural isomer of the substrate EC 6 Ligases catalyzes the bond formation reaction of two substrates using ATP to drive the reaction. EC# s define a biochemical reaction, not a specific enzyme imple Enzymes: consists only of the proteins. Complex Enzyme: Protein contains other non-protein group(s) that assistant in the catalysis = coenzyme (vitamins or metal ions) Coenzymes are bound to the protein by non-covalent interactions Prosthetic group: cofactor is covalently bound to the protein oloenzyme: protein coenzyme complex Apoenzyme: protein only, missing the coenzyme

5 ates, equilibria and reaction order Velocity: v = k [] v 1 = k 1 [] v -1 = k -1 [P] k 1 k -1 P K eq = [P] k = 1 [] k -1 eaction rder: P first order reaction v = k [] A B P second order reaction v = k [ A ] [ B ] half-life t ½ = ln2/k (k = first order rate constant) ate-limiting (determining) step: slowest step in a multi-step chemical reaction. The overall rate of a reaction is dependent on the rate-limiting step 147 Plot of substrate concentration versus reaction velocity k 1 E [ E] P E k -1 k 2 k -2 V o = V max [] K m [] teady-state approximation: [ E] is constant V max : the maximum velocity at saturating [] K m : [] at half the V max ; rough estimate of the affinity of the k cat : V max /[E] ; turnover number V max /K m or k cat /K m : catalytic efficiency of the reaction

6 Proteases: catalyzes the hydrolysis of peptide bonds Bugg, Chapter 5, pp C 2 protease C 2 1. erine protease Bugg, p Cysteine protease p Aspartyl protease p Zinc (metallo) protease p. 92 chymotrypsin: cleaves at the C-terminal side of aromatic residues Phe, Tyr, Trp trypsin: cleaves at the C-terminal side of basic residues Arg, Lys but not is 149 erine Protease: Chymotrypsin oxy-anion hole er 195 is 57 Asp 102 C er 195 is 57 Asp 102 C C Bugg, p

7 Catalytic triad of α-chymotrypsin is-57 Asp-102 er-195 pdb code: 5CA 151 Active site of bovine trypsin with a bound inhibitor Asp-102 Asp-189 is-57 er-195 tbu Et B tbu Et Et Et B er-175 pdb code: 1BTX Bugg, p Katz, B. A.; Finer-Moore, J.; Mortezaei,.; ich, D..; troud,. M. Biochemistry 1995, 34,

8 xy-anion hole of trypsin Gly-196 er-195 Asp-194 Gly-193 Gln-192 Gly-196 Asp-194 Gly-193 is-57 er-195 Gln-192 Asp-102 Asp-102 is-57 tbu Et Et B er-175 pdb code: 1BTX Cysteine Protease: Papain (212 amino acids) active-site cysteine and histidine, overall mechanism is similar to serine proteases usually not a digestive enzyme (intracellular) Cys 25 is 159 oxy-anion hole Cys 25 is C Bugg, p

9 tructure of papain with a bound inhibitor Asn 19 is 157 oxyanion hole Cys 25 pdb code: 1BP4 papain Asn 19 Cys 25 oxyanion hole 155 Aspartyl Protease Mechanism: enin, IV protease Bell shaped p vs. rate profile: max rate at p ~ 2.4 indicative of general acid-general base catalysis. Asp ' _ Asp Asp _ ' Asp

10 IV Protease: an Aspartyl Protease Catalytic Asp-25 with a bound inhibitor Ph C 3 C 3 Ph pdb code: 1VJ inhibitor 157 Interaction of the catalytic Asp-25 with the bound inhibitor Ph C 3 C 3 Ph pdb code: 1VJ inhibitor

11 Metallo-protease (zinc): carboxypeptidase: important catalytic groups: Glu-270, Tyr-248 Zn ion coordination: Glu-72, is-196, is-69 General base mechanism ucleophilic mechanism (acyl enzyme complex) Bugg, p Active site of carboxypeptidase Arg-145 Tyr-248 Bound ligand is-69 2 Zn Glu-72 Glu-270 is-196 pdb code: 2CTC

12 Phosphate ester hydrolysis 1. Phosphatases: over transfer (hydrolysis) of a phosphate monoester to water 3. Phosphodiesterases: hydrolysis of a phosphodiester to a phosphate monoester and an alcohol 5. Kinases: transfer of the γ-phosphate group of ATP to an acceptor group Glucose 6-phosphatase -2 3 P glucose-6-phosphate 2-2 P 4-3 (P i ) Fructose 1,6-bisphosphatase: M 2 dependent -2 3P -2 C 2P 3 fructose-1,6- bisphosphate P C 2 P 4-3 (P i) Alkaline phosphatase: M 2 dependent Bugg, pp Phosphatases: General acid-base mechanism

13 Phosphatases: Covalent mechanism 2 mechanism 163 Glucose 6-phosphatase: covalent catalysis Fructose 1,6-bisphosphatase: General acid-base catalysis

14 Associative vs dissociative mechanism: Chiral phosphate Use three isotopes of oxygen, 16, 17, 18 1 P 2 1 _ 2 P -or- _ P 2 _ P 2 _ P -or- P _ Does the observation of stereochemically defined products (retention or inversion of stereochemistry) rule out the dissociative mechanism involving metaphosphate ion? 165 Tyrosine phosphatase conserved aspartate, cysteine, and arginine Tyr Asp _ P _ Csy _ Arg 2 Tyr P 4-3 (P i )

15 Phosphodiesterase: ibonuclease (ase): catalyzes the hydrolysis of the phosphodiester bond of A. Catalytic groups are is-12 and is-119 is P - B B is ase Bell shaped p vs. rate profile: max rate at p ~ 6.0 indicative of general acid-general base catalysis. Mechanism requires both an imidazole and imdiazolium for catalysis is P - - B is B Bugg, pp pk a3 of histidine is ~ P P Thiamin Diphosphate P P - - a a FAD P P 2 = AD = -P 3 2 ADP Folic Acid 2 ome Cofactors Biotin 2 P 2 Fe eme Pyridoxal Phophates Glutathione FM P P P P Coenzyme A (CoA) C Co - P Vitamin B12 Lipoic Acid