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X-Ray diffraction data have been obtained for nine related antiviral agents
("WIN compounds") while bound to human rhinovirus 14 (HRV14). These compounds
can inhibit both viral attachment to host cells and uncoating. To calculate
interpretable electron density maps it was necessary to account for (1) the low
(approximately 60%) occupancies of these compounds in the crystal, (2) the large
(up to 7.9 A) conformational changes induced at the attachment site, and (3) the
incomplete diffraction data. Application of a density difference map technique,
which exploits the 20-fold noncrystallographic redundancy in HRV14, resulted in
clear images of the HRV14:WIN complexes. A real-space refinement procedure was
used to fit atomic models to these maps. The binding site of WIN compounds in
HRV14 is a hydrophobic pocket composed mainly from residues that form the
beta-barrel of VP1. Among rhinoviruses, the residues associated with the binding
pocket are far more conserved than external residues and are mostly contained
within regular secondary structural elements. Molecular dynamics simulations of
three HRV14:WIN complexes suggest that portions of the WIN compounds and viral
protein near the entrance of the binding pocket are more flexible than portions
deeper within the beta-barrel.
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