Is There a Functional Role for the Knotted Topology in Protein UCH-L1?

Knotted proteins are present in nature, but there is
still an open
issue regarding the existence of a universal role for these remarkable
structures. To address this question, we used classical molecular
dynamics (MD) simulations combined with in vitro experiments
to investigate the role of the Gordian knot in the catalytic activity
of UCH-L1. To create an unknotted form of UCH-L1, we modified its
amino acid sequence by truncating several residues from its N-terminus.
Remarkably, we find that deleting the first two N-terminal residues
leads to a partial loss of enzyme activity with conservation of secondary
structural content and knotted topological state. This happens because
the integrity of the N-terminus is critical to ensure the correct
alignment of the catalytic triad. However, the removal of five residues
from the N-terminus, which significantly disrupts the native structure
and the topological state, leads to a complete loss of enzymatic activity.
Overall, our findings indicate that UCH-L1’s catalytic activity
depends critically on the integrity of the N-terminus and the secondary
structure content, with the latter being strongly coupled with the
knotted topological state.