Multiscale Simulations and Cryo-Electron Microscopy Reveal the Transition Pathway of Dengue Virus-like Particle Nanoassembly

TL;DR

This study uses cryo-EM and simulations to reveal how dengue virus-like particles assemble, providing insights for vaccine development.

Contribution

The work provides the first cryo-EM structure of immature DENV-2 VLPs and identifies a steric pathway for their maturation.

Findings

Immature DENV-2 VLPs have prM–E spikes on a T = 1 shell, distinct from the T = 3 lattice of virions.

Multiscale simulations reveal a sliding-rotating rearrangement pathway for prM–E spikes during maturation.

Lipid core mobility and localized protrusion events are linked to protein rearrangements during maturation.

Abstract

Dengue virus (DENV) continues to impose a global health
burden,
and virus-like particles (VLPs) are promising vaccine candidates,
owing to their ability to elicit broadly neutralizing antibodies.
However, the lack of nanoscale structural insights into the VLP maturation
process has limited rational engineering. Here, we report the cryo-electron
microscopy (cryo-EM) structure of immature DENV serotype 2 VLPs, revealing
prM–E spikes arrayed on a T = 1 shell, consistent
with mature DENV-2 VLPs and distinct from the virion, which exhibits
a T = 3 icosahedral lattice. To connect the experimentally
determined immature and mature endpoint structures, we employed a
multiscale molecular dynamics (MD) framework to assess sterically
feasible transition pathways. The simulations support the steric feasibility
of a sliding-rotating rearrangement in which trimeric prM–E
spikes reorganize into flat E dimers (E–E) without clashes.
In virions, trimers reorganize into extended rafts of three parallel
E dimers, whereas in VLPs, which lack the long-range symmetry and
geometric constraints of the T = 3 lattice, maturation
proceeds via a less extensive rearrangement in which neighboring monomers
form small triangular clusters of three dimers. In addition, the simulations
reveal pronounced lipid core mobility during maturation, including
transient and spatially localized lipid protrusion events that preferentially
occur near regions undergoing protein rearrangement, consistent with
a potential role for dynamic membrane remodeling in accommodating
maturation-associated structural changes. We also established a stable
Chinese hamster ovary (CHO-K1) producer cell line, enabling efficient
production of immature DENV serotype 2 VLPs. Together, this work defines
a structure-dynamics framework that links steric feasibility, membrane
composition, and particle stability and outlines process-relevant,
testable hypotheses to inform future engineering of dengue VLPs that
may ultimately guide vaccine design.

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