Influence of an antiviral compound on the temperature dependence of viral protein flexibility and packing: a molecular dynamics study.

The antiviral activity of compounds that bind an internal pocket of picornaviruses is due in part to stabilization of the protein capsid and inhibition of the uncoating process required for virus replication. Information on the basis for this structural stabilization of the virus capsid is important to elucidate the mechanism of antiviral action and provide insights into the disassembly process. It has been proposed that this stabilization is entropically based, since binding the nonpolar antiviral compound increases the compressibility, and thus the conformational flexibility, of the virus. Such a proposal predicts a difference in the temperature dependence of the atomic positional fluctuations for free virus and drug-bound virus; nonpolar interactions are weaker and less directional, and would give rise to greater conformational disorder at low temperature. Further, the transition that has been observed in globular proteins to a state resembling a frozen liquid, in which the protein is considered "trapped" in potential energy wells, is predicted to occur at lower temperature when the antiviral compound is bound. Results described here from computer simulations of rhinovirus over a range in temperature show these predicted changes in conformational disorder and the temperature of the transition in mobility. In addition to providing independent support for the above proposal for antiviral activity, these results indicate that the mobility transition of a protein can be controlled by the binding of an appropriate ligand, an effect not previously reported.