Hydrophobic-at-interface regions in viral fusion protein ectodomains

In this chapter we shall describe how to apply the hydrophobicity-at-interf ace scale, as proposed by Wimley and White [Wimley, W. C. and White, S. H. (1996) Nature Struct. Biol. 3:842-848], to the detection of amino acid sequ ences of viral envelope glycoproteins putatively engaged in interactions wi th the target membranes. In addition, a new approach will be briefly introd uced to infer the bilayer location at equilibrium of membrane-partitioning sequences. The use of these new procedures may be important in describing t he molecular mechanism leading to the formation of a fusion pore by viral g lycoproteins.