Khiewdee C.Ounjai P.Pipatpolkai T.Mahidol University2025-07-162025-07-162025-01-01Journal of Chemical Information and Modeling (2025)15499596https://repository.li.mahidol.ac.th/handle/123456789/111224Intracellular cholesterol homeostasis is regulated by the sterol response element-binding protein (SREBP) pathway through the SREBP cleavage-activating protein (SCAP) and the insulin-induced gene protein (INSIG). Previous studies highlighted that high concentrations of cholesterol mediated the dimerization between INSIG and SCAP, which led to an inhibition of cholesterol uptake and biogenesis. However, the molecular understanding of the SCAP-INSIG and cholesterol interactions remains elusive. Here, we used coarse-grained (CG) and atomistic (AT) molecular dynamics (MD) simulation to determine interactions between INSIG, SCAP, and cholesterol. Our work highlighted the novel binding pocket in the luminal domain at atomistic resolution. Using a combination of the AlphaFold3 model and Go̅-martini force field, we showed that loop 7 dynamics are crucial for cholesterol binding and are able to highlight conserved residues, which lead to INSIG-SCAP dimerization. Together, our work highlights novel mechanisms of cholesterol sensor pathways and will benefit the development of novel therapeutic strategies for diseases, such as neuroinflammatory disease, caused by irregular cholesterol homeostasis.Chemical EngineeringChemistryComputer ScienceSocial SciencesArticleSCOPUS10.1021/acs.jcim.5c001312-s2.0-1050099009661549960X