# Molecular Mechanism of pH-Induced Protrusion Configuration Switching in Piscine Betanodavirus Implies a Novel Antiviral Strategy

## TL;DR

This study reveals how the structure of a fish virus changes in acidic environments, offering new insights for developing antiviral treatments.

## Contribution

The paper identifies a novel pH-dependent conformational switch in the virus's protrusions and potential drug targets.

## Key findings

- Protrusions of NNV compact and rest under acidic conditions, as revealed by cryo-EM and NMR.
- A flexible loop in the P-domain converts to a β-strand under low pH, enabling trimerization.
- A low-pH-favored conformation in the P-domain linker contributes to protrusion resting.

## Abstract

Many viruses contain
surface spikes or protrusions that
are essential
for virus entry. These surface structures can thereby be targeted
by antiviral drugs to treat viral infections. Nervous necrosis virus
(NNV), a simple nonenveloped virus in the genus of betanodavirus,
infects fish and damages aquaculture worldwide. NNV has 60 conspicuous
surface protrusions, each comprising three protrusion domains (P-domain)
of its capsid protein. NNV uses protrusions to bind to common receptors
of sialic acids on the host cell surface to initiate its entry via
the endocytic pathway. However, structural alterations of NNV in response
to acidic conditions encountered during this pathway remain unknown,
while detailed interactions of protrusions with receptors are unclear.
Here, we used cryo-EM to discover that Grouper NNV protrusions undergo
low-pH-induced compaction and resting. NMR and molecular dynamics
(MD) simulations were employed to probe the atomic details. A solution
structure of the P-domain at pH 7.0 revealed a long flexible loop
(amino acids 311–330) and a pocket outlined by this loop. Molecular
docking analysis showed that the N-terminal moiety of sialic acid
inserted into this pocket to interact with conserved residues inside.
MD simulations demonstrated that part of this loop converted to a
β-strand under acidic conditions, allowing for P-domain trimerization
and compaction. Additionally, a low-pH-favored conformation is attained
for the linker connecting the P-domain to the NNV shell, conferring
resting protrusions. Our findings uncover novel pH-dependent conformational
switching mechanisms underlying NNV protrusion dynamics potentially
utilized for facilitating NNV entry, providing new structural insights
into complex NNV-host interactions with the identification of putative
druggable hotspots on the protrusion.