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

Abstract 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 CHARMM36m force fields. The increase in temperature from 28 °C to 37 °C doubled the conformational space explored at neutral pH and weakened both dimers through the 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.