The C‑terminal Region of D‑DT Regulates Molecular Recognition for Protein–Ligand Complexes

Systematic
analysis of molecular recognition is critical for understanding
the biological function of macromolecules. For the immunomodulatory
protein D-dopachrome tautomerase (D-DT), the mechanism of protein–ligand
interactions is poorly understood. Here, 17 carefully designed protein
variants and wild type (WT) D-DT were interrogated with an array of
complementary techniques to elucidate the structural basis of ligand
recognition. Utilization of a substrate and two selective inhibitors
with distinct binding profiles offered previously unseen mechanistic
insights into D-DT–ligand interactions. Our results demonstrate
that the C-terminal region serves a key role in molecular recognition
via regulation of the active site opening, protein–ligand interactions,
and conformational flexibility of the pocket’s environment.
While our study is the first comprehensive analysis of molecular recognition
for D-DT, the findings reported herein promote the understanding of
protein functionality and enable the design of new structure-based
drug discovery projects.