Past exam of the biochemistry course of the University of Cambridge / 2025 / Paper 5 / Section 2 / 2 / b / Solution

The main diagonal contains relatively dark blocks separated by much paler off-diagonal regions. This supports a modular protein with internally more confidently predicted regions but uncertain relative packing. In particular, the broad early region ending near residue 650 and the later region are poorly positioned relative to one another. Smaller blocks within these regions suggest further domain subdivision.

Thus the compact-looking arrangement in the ribbon drawing should not be treated as a uniquely established structure of the whole enzyme. The matrix can suggest protein domain boundaries and flexible inter-domain relationships; it neither proves domain independence experimentally nor establishes that uncertainty is caused by a particular motion.