(Modeling proteins) (Chymotrypsin Mechanism: Step 1, Step 2, Step 3, Step 4, Step 5, Step 6)

Step 4: Chymotrypsin Mechanism - After scission of the peptide bond

Although the tetrahedral intermediate in the chymotrypsin catalyzes hydrolysis of a peptide bond is a local minimum on the Potential Energy Surface, it should only be regarded as metastable: the peptide C - N bond, at 1.64 Ångstroms, is highly stretched compared to the ~1.38 Ångstroms in a normal peptide bond.  At the carbonyl end of the peptide bond is the tetrahedral intermediate, at the other end is a cationic nitrogen atom; together these two structures form a Zwitterion.  This highly charged bond can easily break to form an amine and an ester. In the system being modeled here, scission of the peptide bond has occurred, resulting in a tryptophan esterified to Ser195 and an isolated methylamine molecule.  (PDB file) (ARC file)

Interesting features

(A) The Zwitterionic labile peptide bond has been broken, giving rise to a simple amine here, representing the protein fragment resulting from scission, and an ester.

(B) There is a water molecule positioned 4.4 Ångstroms from the ester group.  This will be used in hydrolyzing the ester group.

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Interesting parts:
His57 Asp102 Ser189 Gly193 Asp194
Ser195 Ser214 Ser214 Gly216 Ser217
Gly226 Gly250 Ala251 Trp252 Thr253
H2O

Catalytic triad:
His57 Asp102 Ser195

Substrate:
Gly250 Ala251 Trp252 Thr253


Oxyanion hole plus substrate:
Gly193 Asp194 Ser195 Gly250 Ala251
Trp252 Thr253

Tetrahedral intermediate:
Gly193 Asp194 Ser195 Trp252 Thr253

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:
Ser189 Gly216 Ser217 Gly226 Gly250
Ala251 Trp252

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