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However, its role in cancer, particularly luminal bladder cancer, remains debated. The overexpression and activation of PPAR\u03b3 are implicated in tumorigenesis. Specific gain-of-function mutations (M280I, I290M, and T475M) within the ligand-binding domain of PPAR\u03b3 are associated with bladder cancer and receptor activation. The underlying molecular pathways prompted by these mutations remain unclear. We employed a dual-basin structure-based model (db-SBM) to explore the conformational dynamics between the inactive and active states of PPAR\u03b3 and examined the effects of the M280I, I290M, and T475M mutations. Our findings, consistent with the existing literature, reveal heightened ligand-independent transcriptional activity in the I290M and T475M mutants. Both mutants showed enhanced stabilization of the active state compared to the wild-type receptor, with the I290M mutation promoting a specific transition route, making it a prime candidate for further study. Electrostatic analysis identified residues K303 and E488 as pivotal in the I290M activation cascade. Biophysical assays confirmed that disrupting the K303\u2013E488 interaction reduced the thermal stabilization characteristic of the I290M mutation. Our study demonstrates the predictive capabilities of combining simulation and cheminformatics methods, validated by biochemical experiments, to gain insights into molecular activation mechanisms and identify target residues for protein modulation.<\/jats:p>","DOI":"10.1063\/5.0232041","type":"journal-article","created":{"date-parts":[[2024,10,23]],"date-time":"2024-10-23T10:17:14Z","timestamp":1729678634000},"update-policy":"https:\/\/doi.org\/10.1063\/aip-crossmark-policy-page","source":"Crossref","is-referenced-by-count":0,"title":["Exploring the molecular pathways of the activation process in PPAR<i>\u03b3<\/i> recurrent bladder cancer mutants"],"prefix":"10.1063","volume":"161","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0927-3825","authenticated-orcid":false,"given":"Vin\u00edcius M.","family":"de Oliveira","sequence":"first","affiliation":[{"name":"Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, LNBio\/CNPEM 1 , Campinas, SP,","place":["Brazil"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1741-1362","authenticated-orcid":false,"given":"Caique C.","family":"Malospirito","sequence":"additional","affiliation":[{"name":"Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, LNBio\/CNPEM 1 , Campinas, SP,","place":["Brazil"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0285-8700","authenticated-orcid":false,"given":"Fernando B.","family":"da Silva","sequence":"additional","affiliation":[{"name":"Centre of New Technologies, University of Warsaw 2 , Warsaw,","place":["Poland"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4184-8046","authenticated-orcid":false,"given":"Nat\u00e1lia B.","family":"Videira","sequence":"additional","affiliation":[{"name":"Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, LNBio\/CNPEM 1 , Campinas, SP,","place":["Brazil"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0246-8884","authenticated-orcid":false,"given":"Marieli M. 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