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 glycoprotein (pE) induced by low pH. However, how pH and temperature cooperate to destabilize the dimeric form of the pE, 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, 6, and 7 using CHARMM36m force fields and complemented by extended coarse-grained molecular dynamics simulations for the DENV-2 system at 37 °C and pH 5, and for the DENV-3 system at 28 °C and pH 5, and at 37 °C and pH 7. Our simulations suggest that increasing the temperature from 28 to 37 °C tends to expand the conformational space at neutral pH, potentially weakening dimer integrity through modulation of the interfacial interaction network. Acidification appears to amplify this effect in a serotype–specific manner: in our simulations DENV-2 required pH 5, while DENV-3 responded at pH 6. Additionally, distance and principal component analyses revealed an asymmetric dissociation pathway, termed the “compensatory embrace”, observed in both all-atom and coarse-grained models. Structural analyses further highlighted the differences in histidine distribution between the serotypes. Moreover, interaction mapping at 37 °C identified candidate interfacial contacts that may act as pH-sensitive latches, maintaining stability at pH 7 but breaking upon acidification. Collectively, these results suggest a potential hierarchy of physicochemical triggers that may contribute to the conversion of dimer into fusion-competent monomers. These interfacial hotspots and the “compensatory embrace” constitute structurally informed targets that, pending validation under native virion conditions, may guide the rational design of antivirals and immunogens, underscoring the value of long-time scale molecular dynamics simulations as a hypothesis-generating tool in drug discovery.