Synergistic Effects of pH and Temperature on Dengue Virus Envelope Dimers: Insights from Microsecond Molecular Dynamics Simulations

Dengue pathogenesis depends on a conformational rearrangement of the envelope (E) glycoprotein induced by low pH; however, how pH and temperature cooperate to destabilize its prefusion dimeric state, a fundamental step that enables the formation of the fusion-active trimer, remains unclear. Here, we investigate this synergy for Dengue serotypes of greatest medical relevance, DENV-2 and DENV-3. All-atom molecular dynamics simulations were performed on the microsecond scale at 28°C, 37°C, and 40°C under pH 5-7 using the CHARMM36m force field. The increase in temperature from 28°C to 37°C doubled the conformational space explored at neutral pH and weakened both dimers through reduction or loss of the interaction network along the dimeric interface. Acidification amplified this effect in a serotype-specific manner: DENV-2 required pH 5, while DENV-3 responded at pH 6. Distance and principal component analyses revealed an asymmetric dissociation route, termed the "compensatory embrace", in which retraction of Domains I and III in one monomer is balanced by advancement of its partner on the opposite side, temporarily preserving the number of inter-subunit contacts. Structural analyses highlighted the difference in histidine distribution between the serotypes. These results outline hierarchical physicochemical triggers that convert the dimer into fusion-competent monomers. Targeting the interfacial interaction network or reinforcing the compensatory embrace to prevent completion of dissociation offers new perspectives for broad-spectrum antivirals and immunogen design, underscoring the value of long-timescale molecular dynamics in drug discovery.