Single-Cell Biophysics: Measurement, Modulation, and Modeling

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Single-Cell Biophysics: Measurement, Modulation, and Modeling Poster Abstracts
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34-POS Board 17
Integrative Models of Complete Viruses – Combining Structure, Genomics and Modeling
Roland G. Huber1, Jan K. Marzinek1,2, Daniel Holdbrook 1, Ana de Suoto Martins3, Ivo
Martins3, Yue Wan4, Peter J. Bond 1,2 .
1A*STAR Bioinformatics Institute (BII), Singapore, Singapore, 2NUS Department of Biological
Sciences (DBS), Singapore, Singapore, 4A*STAR Genome Institute Singapore (GIS), Singapore,
Singapore.3Instituto de Medicina Molecular, Lisboa, Portugal,
Dengue and Zika viruses belong to the Flavivirus family of mosquito-borne infections prevalent
in tropical and subtropical regions. They are enveloped, single-stranded positive-sense RNA
viruses with a genome of approximately 11kb and form virions of ~45 nm in diameter. In recent
years, near-atomistic cryo-EM structures have become available. While these structures reveal
the precise organization of the protein envelope, they are not able to resolve either the lipid
membrane or the viral core in detail.
To probe deeper into the viral particle, we created detailed models of the viral envelope
including the lipid vesicle circumscribed by the envelope proteins. These models reveal a
tensioned membrane structure that follows the icosahedral pattern given by the symmetry of the
surrounding proteins. We show how anionic lipids within the lipid vesicle anchor the membrane
to the protein coat. We propose that this tension within the deformed lipid vesicle may store
energy that is used to overcome the activation barrier for fusion with the late endosomal
membrane and subsequent release of the viral genome.
Within the envelope, the viral genome interacts with a highly charged capsid protein. Cryo-EM
structures do not show a simple geometric capsid as commonly found in non-enveloped viruses.
In order to determine interaction sites of this capsid protein with the viral genome we performed
a nuclease digestion assay: protein-bound segments are better protected from digestion and can
be sequenced. Subsequent alignment against the full genome reveals the location of these
protected fragments.
Integrating structural, biochemical, genomic, and computational methods thus allowed us to
create a near-atomistic, dynamic model of the mature virion. We are currently modeling the
fusion of these particles with endosomal membrane models, which may allow us to identify
novel targets for therapeutics against these and other Flaviviruses.