The protein regulatory system formed by VAMP2/SYNTAXIN1/SNAP25(+)APOE4 may indirectly contribute to the development of Alzheimer’s disease through the in vivo regulation of Alzheimer’s disease patients’ progression, according to a comparison of the simulation results of VAMP2/SYNTAXIN1/SNAP25(+)APOE4 and VAMP2/SYNTAXIN1/SNAP25(+)APOE3. The gene discussed is APOE; the disease is Alzheimer disease.