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HIV-1 Capsid (.mp4, 14.6M)
All-atom model of the HIV capsid, with multiple colors. Pentamers and hexamers use different color representations.
Construction of a Cylindrical HIV Capsid (.mpg, 73M)
This movie shows a cylinder constructed of HIV capsid "CA" proteins, which is being simulated to help us understand the detailed interactions between the CA proteins. Normally, HIV capsids are cone-shaped structures built from hexameric and pentameric CA protein oligomers, but cylindrical structures like the one shown here, can spontaneously assemble in lab situations. This cylindrical HIV capsid was constructed to match experimental data, and is a first step towards building a realistic atomic model of a "real-life" conical HIV capsid.
Cylindrical HIV Capsid Assembly (.mpg, 11.3M)
HIV capsids are normally asymmetric, cone-shaped assemblies formed out of hexameric and pentameric oligomers of the HIV "CA" protein. However, cylindrical capsid constructs can form from the self-assembly of CA-hexamers in artificial lab situations. These cylindrical capsids are interesting because it is believed that the curvature and interactions of the CA-hexamers is very similar to what is found in real-life capsids, which are harder to study. This movie shows a piece of cylindrical capsid that was constructed to match experimental data. Simulating the cylindrical capsid and observing the characteristics of the CA-hexamers will be the first step towards eventual construction of a realistic cone-shaped HIV capsid.
Simulation of an Empty Viral Capsid (.mpg, 15.4M)
The empty capsid of Satellite Tobacco Mosaic Virus was simulated for 10 ns. Although the complete virus is very stable, the empty capsid collapses: a pronounced instability develops on the surface.
Simulation of the Complete Satellite Tobacco Mosaic Virus (.mpg, 22.1M)
The complete Satellite Tobacco Mosaic Virus was simulated (1 million atoms for 14 ns). The virus is very stable, however its compounds exhibit considerable motion in an asymmetric fashion.
Pushing Down on a Virus Capsid (.mpg, 3.8M)
To understand how viruses break open in and infect the human body, scientists need to investigate the physical/mechanical properties of the virus body (a capsid). The movie shows a pointer (bronze, rounded grid on top) pushing down on a hepatitis B virus capsid (red, green, blue, yellow sphere), with the inside of the capsid shown halfway through the movie.