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.
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Acknowledgements
This work was supported by the National Natural Science Foundation of China (No. 92057116), the National Science and Technology Major Project (2018ZX09711002-018), the Strategic Priority Research Program of Chinese Academy of Sciences grant (XDA12040204), the Shanghai Commission of Science and Technology (18431900900), and National Key R&D Program of China (2016YFA0502301 and 2017YFB0202601). The molecular dynamics simulations were partially run at the TianHe 1 supercomputer in Tianjin and TianHe 2 supercomputer in Guangzhou.
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JYL and WLZ put forward to conception and contributed to research design. TTL planned and carried out the biochemistry experiments and analyzed the data. MBS participated in the enzymatic experiments. CP performed molecular dynamics simulations and analyzed the data. ZJX participated in the molecular dynamics simulations experimental design. JQW contributed clinical flowing-up data of DPP4-V486M carrier and project discussion. JL contributed reagents and analytic tools. TTL and CP contributed to writing the paper, and JYL and WLZ reviewed/edited the paper.
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Li, Tt., Peng, C., Wang, Jq. et al. Distal mutation V486M disrupts the catalytic activity of DPP4 by affecting the flap of the propeller domain. Acta Pharmacol Sin 43, 2147–2155 (2022). https://doi.org/10.1038/s41401-021-00818-x
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DOI: https://doi.org/10.1038/s41401-021-00818-x
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