This application proposes computational investigations of the properties of picornaviruses associated with antiviral activity and receptor recognition, and of the compressibility and structural: stability of globular proteins. Members of the virus family of Picornaviridae are causative agents of a broad spectrum of human and animal diseases initiated by attachment to cell surface receptors. Considerable effort has focused on the development of antiviral compounds against picornaviruses. The mechanism of antiviral activity, and the physical/chemical basis of receptor recognition will be examined by molecular dynamics simulation studies. Specific issues to be addressed include the long-range dynamic effects of antiviral compounds binding in an internal hydrophobic pocket of human rhinovirus (HRV) on the conformational properties of the virus. Based on previous results, it is proposed that long-range effects of antiviral compounds alter the dynamics of residues at the 5-fold symmetry axis, and that this response contributes to the antiviral activity of WIN compounds. We will explore this question using large-scale simulations. In addition, free-energy methods will be used to probe the basis of intercellular adhesion molecule 1 (ICAM-1) specificity for HRV and coxsackievirus (CV). Recent progress in the determination of structures of the picornavirus-receptor complexes from cryo-electron microscopy reconstruction provide a new opportunity for computational analysis to elucidate receptor recognition. Effects of receptor amino acid mutations on virus capsid binding, which cannot be explained from the structures, will be examined using free energy simulations. Finally, mechanisms of antiviral activity and receptor recognition are associated with fundamental physical properties of proteins, and computational studies based on questions related to stability, compressibility and solvation are also proposed. The detailed information of MD simulations will be exploited to elucidate a newly recognized correspondence between protein compressibility and energetics by defining the basis for stabilization of buried charge in proteins. The compressibility of hydration waters and analysis of protein solution compressibilities will also be probed.
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