Distal mutation V486M disrupts the catalytic activity of DPP4 by affecting the flap of the propeller domain

Abstract

Dipeptidyl peptidase-4 (DPP4) plays a crucial role in regulating the bioactivity of glucagon-like peptide-1 (GLP-1) that enhances insulin secretion and pancreatic β-cell proliferation, making it a therapeutic target for type 2 diabetes. Although the crystal structure of DPP4 has been determined, its structure-function mechanism is largely unknown. Here, we examined the biochemical properties of sporadic human DPP4 mutations distal from its catalytic site, among which V486M ablates DPP4 dimerization and causes loss of enzymatic activity. Unbiased molecular dynamics simulations revealed that the distal V486M mutation induces a local conformational collapse in a β-propeller loop (residues 234-260, defined as the flap) and disrupts the dimerization of DPP4. The "open/closed" conformational transitions of the flap whereby capping the active site, are involved in the enzymatic activity of DPP4. Further site-directed mutagenesis guided by theoretical predictions verified the importance of the conformational dynamics of the flap for the enzymatic activity of DPP4. Therefore, the current studies that combined theoretical modeling and experimental identification, provide important insights into the biological function of DPP4 and allow for the evaluation of directed DPP4 genetic mutations before initiating clinical applications and drug development.

Keywords: DPP4; distal mutation; enzymatic activity; molecular dynamics simulation; structure-function mechanism.

Fig. 1. Overview of DPP4 mutant sites and kinetic curves of mutants.

a The structure of DPP4 (PDB ID: 2QT9). Mutant sites were shown in spheres. The catalytic triad (S630, D708 and H740) was shown in sticks. The propeller loop (P234-G260, defined as flap in below text) was colored in marine. b, c Dipeptidyl peptidase activity of WT and mutants was determined with GlyPro-AMC as a substrate in the enzymatic activity assay. K_m curve of DPP4 mutation (b) and means and standard deviations of kinetic constants are plotted (c).

Fig. 2. Biochemical properties of DPP4-WT and DPP4-V486M.

a Stability comparison of WT and V486M. ∆T_m is indicated the difference between mean value of WT and V486M. Mean ± SD values are shown. Inhibitors binding activity comparison of WT (b) and V486M (c) in the absence or presence of DPP4 inhibitor omargliptin. ∆T_m is indicated the difference between mean value of DMSO control and Omarigliptin group. Mean ± SD values are shown. d, e Coomassie blue-stained reducing SDS-PAGE and nonreducing SDS-PAGE (10%) of WT and V486M. e The dimer percent statistics of WT and V486M. The percent 40.8% and 22.7%, indicates dimer percent of WT and V486M, respectively. R, NR, D, M, presents reducing SDS-PAGE, nonreducing SDS-PAGE, dimer, and monomer.

Fig. 3. Analysis of the conformational changes of DPP4-WT and DPP4-V486M.

a The mass center distance between the tip of flap (D243-L246) and catalytic triad (Flap-Core distance) was calculated to evaluate the conformational changes of the flap. The conformations with Flap-Core distance less than 27.5 Å refer to “close” state, and the conformations with Flap-Core distance greater than 28.4 Å refer to “open” state. b Representative structures of the “close” and “open” states.

Fig. 4. Analysis of the conformational changes of DPP4-WT and other seven mutants.

The mass center distance between the tip of flap (D243-L246) and catalytic triad (Flap-Core distance) was calculated to evaluate the conformational changes of the flap. The conformations with Flap-Core distance less than 27.5 Å refer to “close” state, and the conformations with Flap-Core distance greater than 28.4 Å refer to “open” state.

Fig. 5. Biochemical properties of flap mutation.

a Structural analysis of “close” states (blue domain) and “open” states (orange domain). The hydrogen bonds were labeled in red dotted line. Enzymatic activity analysis of Flap mutations. K_m curve of flap mutation (b) and means and standard deviations of kinetic constants are plotted (c). d Analysis of dimerization of flap mutation by nonreducing SDS-PAGE. Coomassie blue-stained reduced SDS-PAGE and nonreduced SDS-PAGE (10%) of flap mutations. R, NR, D, M indicates reducing SDS-PAGE, nonreducing SDS-PAGE, dimer, and monomer.

Fig. 6. Analysis of the conformational changes of DPP4-WT and DPP4-S664P.

a The mass center distance between the tip of flap (D243-L246) and catalytic triad (Flap-Core distance) was calculated to evaluate the conformational changes of the flap. b Representative structures of the DPP4-WT and DPP4-S664P, the hydrogen bonds were shown as yellow dotted line. c Thermal stability of S664P mutant in DMSO. The T_m of S664P mutant was 45.12 °C, and T_m of wild type control was 70.06 °C in the front data.