ENZYMES. Serine Proteases Chymotrypsin, Trypsin, Elastase, Subtisisin. Principle of Enzyme Catalysis

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1 ENZYMES Serine Proteases Chymotrypsin, Trypsin, Elastase, Subtisisin Principle of Enzyme Catalysis Linus Pauling (1946) formulated the first basic principle of enzyme catalysis Enzyme increase the rate of a chemical reaction by binding tighter and stabilizing the transition state of its specific substrate more than the ground state Therefore, higher affinity of the enzyme for the transition state plays an major role in determining substrate specificity 1

2 Enzymes decrease the activation energy of chemical reactions Enzymes decrease the activation energy of chemical reactions 2

3 Michaelis-Menten Steady-State Kinetic Model Leonard Michaelis and Maud Menten (1913) Catalytic reaction is divided into two processes Formation of the enzyme substrate complex via non-covalent interactions (rapid and reversible, no chemical changes ) Conversion of substrate to product (Chemical reaction) Michaelis-Menten Steady-State Approximation The concentration of the enzyme-substrate complex is constant Michaelis-Menten Steady-State Kinetic Model Michaelis-Menten steady-state approximation is a good approximation if the rate measured are restricted to a short time interval over which the concentration of the substrate does not greatly change concentration of enzyme is negligible compared to concentration of substrate initial rate measured Pre-steady state: concentration of intermediates build up to their steady state Steady-state: reaction rate changes relatively slowly with time rates of enzymatic reactions are traditionally measured during this period 3

4 Michaelis-Menten Steady-State Kinetic Model The use of pre-steady state kinetics is superior as a means of analyzing the chemical mechanisms of enzyme catalysis Steady state kinetics is more important for the understanding of metabolism since it measures the catalytic activity in the steady state conditions of the cell Michaelis-Menten Equation 1 cat E + S ES E + P dp = k dt [ ES] d dt [ ES] [ ES] [ E][ S] k [ ES] k [ ES] [ E][ S] [ E] = [ E] + [ ES] T [ ES] k = k = k k v = K cat k k -1 cat = k + k [ E] + k k [ E] T [ S] + [ S] M cat cat T cat + k [ S] = K [ E] T [ S] + [ S] M = 4

5 Michaelis-Menten Equation At high concentration of substrate Rate is directly proportional to concentration of enzyme Rate follows saturation kinetics with respect to concentration of substrate At sufficiently low [S] rate increases linearly with [S] [ S] v = V >>> K max M kcat = K [ E] T [ S] + [ S] M k [ E] T At very low concentration of substrate K M >>>> [ S] kcat [ E] T [ S] kcat [ E] T [ S] Vmax[ S] v = = = K + [ S] K K M M cat M Proteinases/ Proteases Functions In viruses: Cleave presursor molecules of the coat proteins Bacteria produce many different extracellular proteinases to degrade proteins in their surrondings Higher organisms use proteases for Food digestion Cleavage of signal peptides Control of blood pressure, clotting In vivo, the activity of many proteases is controlled by endogenous protein inhibitors 5

6 Proteinases/ Proteases Four functional families Serine proteases Cysteine proteases Aspartic proteases Metallo proteases Classification based on functional criterion: The nature of the most prominent functional group in active site Protease Reaction 6

7 Serine Protease Reaction All serine proteases use a Catalytic Triad to hydrolyze peptide bonds Serine Histidine Aspartic acid Serine Protease Reaction 7

8 Serine Protease Reaction Structural Requirement for Catalytic Action A general base (His) that can accept a proton from the hydroxyl group of the reactive serine Tight binding and stabilization of the tetrahedral transition state Oxyanion hole-provision of groups that can form hydrogen bonds to the negatively charged oxygen Positive charge on histidine Non specific binding of the main chain: Serine proteases have no absolute substrate specificity Main chain forms a short anti parallel beta sheet with a loop region of the enzyme One of the H-bond in enzyme-substrate complexes (3.6A) H-bond in complexes mimics of transition state is shorter Nonspecific binding contribute to stabilization of the transition state 8

9 Structural Requirement for Catalytic Action Structural Preference for particular side chain before the scissile bond Specificity pocket must accommodate the side chain in terms of interactions and size Specificity Pocket of Chymotrypsin James at al., J. Mol. Biol. 144:43-88, 1980 In vivo, chymotrypsin is a proteolytic enzyme acting in the digestive systems of mammals and other organisms. Inhibitor: Ac-Pro-Ala-Pro-Tyr-CooH 9

10 Specificity Pocket of trypsin C.S. Craik et al., Science 228: , 1985 Mutant (Ala216, Ala226)+ Lys Mutant + benzamide Chymotrypsin: two antiparallel β-barrel domains Three polypeptide chains 10

11 Chymotrypsin: two antiparallel β-barrel domains Trypsin 11

12 Bacterial Protease: Subtilisin a protease secreted by a soil bacillus Alpha/beta structure Added to detergents in washing powder to facilitate removal of proteinaceous stains Catalytic triad Red:polypeptide inhibitor Purple: oxyanion hole Orange; non-specific binding Active Site of Subtilisin Red: bound polypeptide inhibitor (eglin) Catalytic triad: Ser221, His64, Asp32 Oxyanion hole: Asn155 Specificity pocket Non-specific binding of peptide 12

13 Chymotrypsin Subtilisin Probing the Role of the Specificity Pocket What would happen if Gly226 and Gly216 in trypsin were mutated to Ala? Model building shows that Arg and Lys-containing substrate should be accomodated. Ala226 expected to accommodate Lys better than Arg. With Ala216 the opposite is true Would k cat, Km and the specificity constant (kcat/km) change? How? Why? 13

14 Engineered mutants in the substrate specificity pocket change the rate of catalysis Engineered mutants in the substrate specificity pocket change the rate of catalysis Mutants were designed to change specificity But, the largest change occurred in the catalytic rates Interpretation Mutations affect the structure of the enzyme in additional ways, possibly causing conformational changes outside the specificity pocket These conformational changes reduce the stabilization of the transition state and the activation energy of the reaction 14

15 Lesson/THM Critical amino acid residues can have multiple roles in determining a protein s structure and therefore its function 15