Bio 100 Serine Proteases 9/26/11

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1 Assigned Reading: 4th ed The Chymotrypsin Mechanism Involves Acylation And Deacylation Of A Ser Residue p. 213 BOX 20-1 Penicillin and β-lactamase p Some Enzymes Are Regulated By Proteolytic Cleavage Of An Enzyme Precursor p th ed The Chymotrypsin Mechanism Involves Acylation And Deacylation Of A Ser Residue p An Understanding of Enzyme Mechanism Drives Important Advances in Medicine p Some Enzymes Are Regulated By Proteolytic Cleavage Of An Enzyme Precursor p. 226 The Serine Proteases are an evolutionarily-related Family of Enzymes A study of chymotrypsin exemplifies the following general principles of enzyme structure/function: Transition state stabilization (Oxyanion Pocket) Acid-Base Catalysis (Catalytic Triad) Covalent Catalysis (Ser 195 acyl intermediate) Proximity Effect (H 2 O positioned relative to acyl intermediate) Regulation by post-translational modification (specific cleavage by trypsin) 1 of 6

2 CHYMOTRYPSIN MECHANISM the polypeptide substrate at the top of the diagram on p. 216/208 is shown in the reverse of the standard N-C orientation the catalytic cycle of chymotrypsin uses the same rx. mechanism twice with minor variations; i.e. 2 similar transition state structures the key role of His 57 in the "catalytic triad" relies on the presence of 2 nitrogens in the imidazole ring, one acting as H + acceptor from Ser 195 and the other as partial H + donor by formation of a "low barrier hydrogen bond" with Asp 102 the removal of the proton from Ser 195 via the triad increases the δ - on the oxygen, making it a stronger nucleophile which then can attack the carbonyl carbon in substrate as the attack proceeds towards transition its transition state, additional negative charge develops on the substrate carbonyl oxygen and at the same time the carbon morphs from a planar trigonal to a tetrahedral configuration the incipient charge on the substrate carbonyl oxygen would hinder achieving transition state were it not diluted by the formation of H-bonds to the amide nitrogens of Gly 193 and ser 195 in the "oxyanion pocket" This is permitted by the tetrahedral configuration and contributes to transition state stabilization. the proton abstracted from Ser 195, now on His 57, establishes H-bonding with the amide nitrogen of the peptide bond undergoing cleavage, further stabilizing the transition state the H acquired by His 57 from Ser 195 takes the electron pair of the peptide bond at this point the peptide bond has been cleaved and the amino fragment is released from the enzyme leaving the acyl fragment covalently bonded to Ser 195 the two H- bonds in the oxyanion pocket are lost as the carbon becomes trigonal again a water molecule enters the active site and, by H-bonding to His 57 is oriented to facilitate nucleophilic attack of the oxygen on the carbonyl carbon (proximity effect) as the hydroxyl group of water goes on the carbon, its other hydrogen is abstracted by His 57 and forms a H-bond to Ser the second transition state is analogous to the first, being stabilized by the same two H bonds in the oxyanion pocket reformation of the carbonyl restores the catalytic triad to its original configuration acyl fragment released 2 of 6

3 Bio 100 Serine Proteases 9/26/11 Consider the fate of the hydrogen originally shared by His57 and Ser195 in the triad: it ends up on the nitrogen of the amino fragment and is replaced by one of the hydrogens of the water molecule. How cleavage of chymotrypsinogen activates the catalytic triad An Understanding of Enzyme Mechanism Drives Important Advances in Medicine p. 216 We are not covering HIV Protease The β-lactam ring is an analog of the D-alanyl-D-alanyl end group of the peptidoglycan precursor. 3 of 6

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6 TRY THIS MATCHING EXERCISE: The left-hand column there is a list of amino acids that are important functional players in chymotrypsin. Match them up with the specific functional descriptions in the right-hand column. Descriptions may be used more than once. Ser 195 A. Part of Catalytic Triad His 57 B. Accepts H + from Ser (Base catalysis) Asp 102 C. Donates H + to the amino leaving group. Gly 193 D. Nucleophilic attack on substrate carbonyl carbon. Ile 16 E. Stabilization of tetrahedral intermediate by H-bonding to -O -. Asp 194 F. Forms low barrier H bond to a His. G. Participates in a salt bridge (ionic interaction) that converts inactive zymogen to active enzyme. The solution is posted on the web site. This diagram of transition state stabilization is nice in some ways, but I think there is something misleading about it. What do you think? 6 of 6