Protein Tyrosine Phosphatase 1B (PTP1B) is a validated therapeutic target in obesity, diabetes, and cancer. Its conserved, polar active site challenges selective inhibitor design. We used hydrogen-deuterium exchange mass spectrometry (HDX-MS) and room temperature crystallography to map the structural dynamics of PTP1B variants observed in patients with low recorded BMI. Induced mutations at the allosteric L16 site and targeted small molecule ligands, also characterized by crystallography and HDX, perturb the PTP1B allosteric network in a way that enables us to develop compounds with improved specificity for PTP1B. Ligand-specific HDX patterns revealed distinct modes of allosteric modulation, correlating with varying binding affinities and inhibition profiles. Complementary crystallographic studies of PTP1B L16 mutants provided high-resolution insight into the effects of ligand binding and the conformational changes that lead to allosteric control of the active site. These results highlight the potential of allosteric sites to help solve selective inhibitor development problems for many other protein tyrosine phosphatases.

Mutations have widespread effects on protein dynamics in solution measured by HDX-MS.<br /> (<b>A</b>) Mutant-WT difference HDX values at 300 seconds of labeling for selected high-quality peptides spanning the PTP1B sequence. Several key structural regions of PTP1B are indicated with brackets. <br /> (<b>B</b>-<b>D</b>) Mutant-WT difference HDX values at 300 seconds of labeling at the single-amide level (see Methods) mapped to a crystal structure of WT PTP1B (PDB ID: 1T49 (<i>41</i>)) for (<b>B</b>) I19V, (<b>C</b>) Q78R, and (<b>D</b>) D245G.

Mutations have widespread effects on protein dynamics in solution measured by HDX-MS.
(A) Mutant-WT difference HDX values at 300 seconds of labeling for selected high-quality peptides spanning the PTP1B sequence. Several key structural regions of PTP1B are indicated with brackets.
(B-D) Mutant-WT difference HDX values at 300 seconds of labeling at the single-amide level (see Methods) mapped to a crystal structure of WT PTP1B (PDB ID: 1T49 (41)) for (B) I19V, (C) Q78R, and (D) D245G.

Prof. Daniel Keedy

Assistant Professor, CUNY Advanced Science Research Center

Appearances