TCB Publications - Abstract
Juan R. Perilla and Klaus Schulten. Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations. Nature Communications, 8:15959, 2017. (PMC: PMC5524983)
1,300 proteins
with
altogether 4 million atoms. Although the capsid proteins are all identical,
they
nevertheless arrange themselves into a largely asymmetric structure made
of
hexamers and pentamers. The large number of degrees of freedom and
lack of
symmetry pose a challenge to studying the chemical details of the HIV
capsid.
Simulations of over 64 million atoms for over 1 
allow us to
conduct a
comprehensive study of the chemical–physical properties of an empty HIV-
1
capsid, including its electrostatics, vibrational and acoustic properties, and
the
effects of solvent (ions and water) on the capsid. The simulations reveal
critical
details about the capsid with implications to biological function.
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