(Modeling proteins) (Chymotrypsin Mechanism: Step 1, Step 2, Step 3, Step 4, Step 5, Step 6)
A postulated stationary point in the reaction of Ser195 with the peptide bond to form the Zwitterionic tetrahedral intermediate involves the migration of the hydroxyl proton to His57 to form a histidinium or imidazolium cation. This is predicted to be a stationary point, and examination of the predicted structure does in fact show the expected features: Asp102 is anionic, His57 is cationic, and Trp252 is anionic. (PDB file) (ARC file)
(A) Most important, the carbonyl carbon of Trp252 now has a tetrahedral coordination. The carbonyl oxygen now has a formal negative charge.
(B) Both hydrogen bonds from Gly193 and Ser195 of the oxyanion hole to the anionic carbonyl oxygen of Trp252 are now stronger, the Gly193 bond shortening from 1.81Å to 1.77Å, and the Ser195 bond shortening from 2.02Å to 1.88Å.
(C) A hydrogen bond now exists between Ser195 and His57, although it is quite long, at 2.31Å.
(D) The C-N bond involving the tetrahedral carbon has increased in length only slightly from the normal 1.36Å in the starting model to 1.47Å, suggesting a slight weakening of the peptide bond.
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Toggle display all Toggle center picture Fit to screen Interesting parts:
Catalytic triad:
Substrate:
Oxyanion hole plus substrate:
Tetrahedral intermediate:
Ser195 forms two bonds with Trp252, first, the ester bond between the hydroxyl oxygen and the carbonyl carbon of Trp252, forming the tetrahedral intermediate, carbon atom 3485, and second, the hydrogen bond between Ser195 peptide hydrogen and Trp252's carbonyl oxygen. Gly193 forms a similar hydrogen bond. Between Gly 193 and Ser195 is the ionized Asp194, which forms a salt bridge with Ile16. Substrate in Hydrophobic pocket:
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