Here is a representation of the inhibitor APF from the RCSB 'Ligand' link.

Chymotrypsin tries to bind to this because it has some similarity to its natural substrate - think back!

Which one of the following best describes what portion of this molecule 'looks' chemically similar to something that chymotrypsin could naturally bind to?

Question

Here is a representation of the inhibitor APF from the RCSB 'Ligand' link.

Chymotrypsin tries to bind to this because it has some similarity to its natural substrate - think back!

Which one of the following best describes what portion of this molecule 'looks' chemically similar to something that chymotrypsin could naturally bind to?

BlackTom AI · Accepted Answer

To approach this question, we first note the context: chymotrypsin is a protease that recognizes peptide bonds adjacent to bulky hydrophobic/aromatic side chains, particularly phenylalanine (Phe), tyrosine (Tyr), or tryptophan (Trp). The inhibitor APF is drawn in a way that features a segment resembling a peptide bond with an adjacent aromatic side chain, mimicking the protease’s natural substrate recognition.
Option 1: 'Part of this molecule approximates a polypeptide C-terminal end with a Trp R-group next to it' — This would imply a structural motif representing a C-terminal end of a peptide with a Trp side chain nearby. Chymotrypsin binding typically involves recognition of internal peptide bonds and specific residues at the scissile (bonded) position, not specifically a C-terminal motif. Therefore this description does not best capture the classic substrate-like feature that chymotrypsin would bind.
Option 2: 'Part of this molecule approximates a polypeptide N-terminal end with a Tyr R-group next to it' — Similarly, an N-terminal motif with Tyr is not the classic mimicry of the scissile bond that chymotrypsin recognizes. The protease interacts with residues around the cleavage site, and while Tyr is aromatic, the description emphasizes an N-terminal end rather than a bond-centered mimicry, making this option less accurate.
Option 3: 'Part of this molecule approximates a peptide bond with a Phe R-group next to it' — This directly reflects the fundamental idea: a peptide bond-like feature (the bond between amino acid–like units) with an adjacent phenylalanine (Phe) side chain. This mirrors the key interaction chymotrypsin has with substrates—recognition of a peptide bond adjacent to a bulky hydrophobic aromatic side chain such as Phe. Thus, this option most accurately describes the substrate-like region that chymotrypsin would bind to, aligning with the enzyme’s specificity.
In sum, the substance of the correct choice is that the molecule contains a motif resembling a peptide bond with a Phe-type aromatic side chain next to it, which is precisely the kind of chemical feature chymotrypsin recognizes in its natural substrates. The other options describe ends or motifs that are not the classic substrate mimicry leveraged by chymotrypsin binding.

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