In the article about the 6GCH chymotrypsin record (Brady et al. 1990), the authors mentioned that there are two possible versions of the APF inhibitor in 3D. Remember that they sometimes referred to the inhibitor in three parts as Ac-Phe-CF3.

They said "Although the enzyme was treated with a racemic mixture of Ac-D,L-Phe-CF3 ... only the isomers with the L configuration at phenylalanine are observed on the enzyme."

As needed, refresh yourself what it means for an amino acid to have a D vs. L configuration, e.g. here
Links to an external site.
.

Referring to the figure below, which one of the following best describes why chymotrypsin was only able to bind to 50% of the inhibitor that was provided to it?

Question

In the article about the 6GCH chymotrypsin record (Brady et al. 1990), the authors mentioned that there are two possible versions of the APF inhibitor in 3D. Remember that they sometimes referred to the inhibitor in three parts as Ac-Phe-CF3.

They said "Although the enzyme was treated with a racemic mixture of Ac-D,L-Phe-CF3 ... only the isomers with the L configuration at phenylalanine are observed on the enzyme."

As needed, refresh yourself what it means for an amino acid to have a D vs. L configuration, e.g. here
Links to an external site.
.

Referring to the figure below, which one of the following best describes why chymotrypsin was only able to bind to 50% of the inhibitor that was provided to it?

BlackTom AI · Accepted Answer

Question restatement: You’re asked to pick the description that best explains why chymotrypsin could bind only 50% of the provided APF inhibitor, given that only L-phenylalanine containing isomers are observed on the enzyme.
Option A: The regions would have bound in an inverted manner, with the Phe being attacked by the Ser and the peptide bond in the specificity pocket. This would imply an inverted catalytic arrangement, which is not consistent with how chymotrypsin’s Ser/His/Asp catalytic triad engages substrates. The protease’s mechanism requires the scissile bond to line up with the catalytic serine; an inverted attack would violate the established catalytic geometry and is not a plausible description for how binding would yield partial occupancy.
Option B: The regions would have bound in a rotated manner, with the Phe in the oxyanion hole and the CF3 in the specificity pocket. In chymotrypsin, the oxyanion hole stabilizes the transition state rather than accommodating the phenylalanine side chain itself as a primary binding element. Putting Phe into the oxyanion hole contradicts the known substrate orientation: the Phe side chain binds in the specificity pocket, not in the oxyanion hole, and CF3 is not the primary determinant of positioning in the pocket. Thus this rotation scenario misrepresents how substrate recognition works and would not neatly account for 50% binding.
Option C: Proteins have 50% L-amino acids, so chymotrypsin always binds to 50% of the peptide bonds that it encounters. This is a misconception: enzyme specificity is not determined by a random 50/50 distribution of L vs D amino acids in a bulk context. Enzymes do have stereospecificity and preferentially bind L-amino acids, but the claim that it always binds half of all encountered peptide bonds is an oversimplification and ignores the precise stereochemical and conformational requirements of binding, orientation, and catalysis. In this scenario, the 50% binding outcome is better explained by stereochemical compatibility rather than a blanket 50% availability of bonds.
Option D: The Phe may have been able to find the specificity pocket, but the peptide bond would have been mis-aligned relative to the Ser attacker. This description aligns with the known mechanism: chymotrypsin requires proper alignment of the scissile peptide bond with the catalytic serine in the active site. If only the L isomer is observed, but the inhibitor is supplied as a racemate, half of the molecules would place the Phe into the specificity pocket correctly while the corresponding peptide bond could be misaligned with the attacking serine, preventing catalysis. Hence, only half of the inhibitor would achieve the productive orientation needed for binding and catalysis, leading to observed 50% binding.
Note: Other options either misstate fundamental enzymology (e.g., inverted binding or unnatural localization of the substrate components) or rely on incorrect generalizations about amino acid composition in proteins. The most consistent explanation with the described stereochemical constraints and the active-site geometry is the misalignment of the scissile bond relative to the Ser nucleophile while the Phe occupies the specificity pocket.

BIOL3612.MERGED.202610 Activity Questions from the Literature 3B: Quickly breaking specific peptide bonds

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