Fig. 2: Structural proteomics reveals isoform differences upon progesterone response element (PRE) binding.

A Consolidated HDX-MS data, run in triplicate, showing the differential analysis between unbound PR vs. PRE-bound, where the top is PR-B, and the bottom is PR-A. Domains are labeled as follows: N-terminal Domain (NTD), DNA-binding domain (DBD), Hinge region (Hinge), and Ligand-binding domain (LBD). Exchange data is representative of a full seven-timepoint differential HDX experiment with sample injection after 10, 30, 60, 300, 900, and 3600 s of deuterium exchange. B Trimmed AlphaFold 3.0 model (residues 375–769) of PR-A homodimer with unbound PR-A vs. PR-A:PRE HDX overlays. Highlighted regions are the PR dimerization domain (residues 885–922 within LBD) and the DBD C-terminal extension (right, residues 633–670). Residue labeling corresponds to the PR-B numbering. Cooler colors indicate comparative reductions in deuterium exchange. C XiView images of differential PR-A ± PRE experiments, where all validated crosslinks are shown. Selected N-terminal crosslinks not identified in PR-A:PRE XL-MS experiments are highlighted in red, with crosslinks mapped onto PR-B numbering, with the gray region representing the 164 amino acids not expressed in PR-A. Results representative of triplicate experiments, with validation in Skyline. D XiView of differential PR-B ± PRE experiments, where all validated crosslinks are shown. Selected N-terminal crosslinks not identified in PR-B:PRE XL-MS experiments are shown in red.