This video shows the reconstruction and simulation of poliovirus using the
BlueGene/Q supercomputer at the Victorian Life Sciences Computation
Initiative. The poliovirus model is being used as a basis for
understanding antiviral drugs, virus infection and helps us to
learn how to model related viruses such as Enterovirus 71.
Publications
Roberts, J.A., Kuiper, M.J., Thorley, B.R., Smooker P.M., Hung.
A., 2012. Investigation of a predicted N-terminal amphipathic
a-helix using atomistic molecular dynamics simulation of a complete
prototype poliovirus virion. Journal of Molecular Graphics and
Modelling, 38, September: 165-173 Link
Liu, H., Roberts J. A., Moore, D., Anderson, B., Pallansch, M.
A., Pevear, D. C., Collett M. S., Oberste, M. S., Characterization
of Poliovirus Variants Selected for Resistance to the Antiviral
Compound V-073 Antimicrobial Agents and Chemotherapy, 56 (11):
5568-5574. Link
Poliovirus representations
(click thumbnails to view large images)
Cutaway representation of a complete poliovirus virion after a
0.1 microsecond simulation. Image shows the genomic RNA in the
core with associated Magnesium ions (purple). The protein chains
that comprise the surrounding capsid are shown as Blue (VP1),
Red (VP2), Yellow (VP3) and Green (VP4). Simulations totalled
3.7 million atoms and were performed using a BlueGene/Q supercomputer
at VLSCI, Image created using the Tachyon renderer in VMD.
Contact Jason.Roberts@mh.org.au
for further details.
Cutaway representation of a complete poliovirus virion after a
36 nanosecond simulation. Image shows the genomic RNA in the core.
Secondary structure is represented in “new cartoon”
form, with a transparent surface representation coloured by radial
distance from core. Simulations totalled 3.7 million atoms and
were performed using a BlueGene/Q supercomputer at VLSCI,
Image created using the Tachyon renderer in VMD
using a STRIDE representation of secondary structure.
Viewpoint of the poliovirus capsid structure showing the interlocking
protein chains that comprise the surrounding capsid highlighting
the icosahedral symmetry of the virus. Protein chains are shown
as Blue (VP1), Yellow (VP2), Red (VP3) and Green (VP4). This simulation
totalled 3.3 million atoms and was performed using a BlueGene/Q
supercomputer at VLSCI, Image created using the Tachyon renderer
in VMD.
Viewpoint of the poliovirus capsid structure showing the interlocking
protein chains that comprise the surrounding capsid, this representation
is presented using a transparent surface to assist in the visualisation
of the underlying protein and genomic structures. Protein chains
are shown as Blue (VP1), Yellow (VP2), Red (VP3) and Green (VP4).
This simulation totalled 3.3 million atoms and was performed using
a BlueGene/Q supercomputer at VLSCI, Image created using the Tachyon
renderer in VMD.
