Apolipoprotein E (APOE) 4 is a well-established genetic risk factor for Alzheimer's Disease (AD). Mutations V236E and R251G reduce AD risk, but their molecular mechanisms remain unclear. This study employs molecular dynamics (MD) simulations to analyze how these mutations alter APOE4 structure and dynamics, particularly in lipidation and oligomerization regions. MD simulations of APOE2, APOE3, APOE4, and the APOE4 variants V236E and R251G were conducted over 1000 ns. Results show that both mutations reduce the flexibility of the overlapping lipidation-oligomerization region, making it comparable to APOE2 and APOE3. Additionally, V236E and R251G decrease the surface area of these regions but through distinct mechanisms. V236E predominantly alters hydrophilic regions, inducing more turns and bends. R251G affects both hydrophilic and hydrophobic areas, increasing random coil formations. These structural changes suggest that the protective effects of V236E and R251G stem from reduced flexibility in key functional domains of APOE4, offering insights into potential AD therapies.
