PROBING THE POTENTIAL GLYCOPROTEIN BINDING-SITE OF SINDBIS VIRUS CAPSID PROTEIN WITH DIOXANE AND MODEL-BUILDING

Alphavirus budding from the plasma membrane is initiated by the specif ic interaction of the nucleocapsid with the cytoplasmic domain of the glycoprotein E2. It was proposed (Lee et al., Structure 4:531-541, 199 6) that binding of the capsid protein residues 108 to 110 (the ''N-ter minal arm'' residues) to a hydrophobic pocket on the surface of the ne ighboring capsid protein in the crystal structure mimics the binding o f the E2 C-terminal residues into this pocket. In addition, structural comparisons of wild-type and mutant Sindbis virus capsid protein (SCP ) and Semliki Forest virus capsid protein suggested that budding is as sociated with a switch between two conformations of the hydrophobic po cket. To test the proposed mechanism, SCP(114-264), which is missing t he N-terminal arm, was crystallized to examine the pocket conformation when the pocket is empty. However, the pocket was occupied by dioxane molecules from the crystallization solution. The pocket conformation was the same as that when it was occupied by the N-terminal arm, demon strating that the pocket favors binding ligands of appropriate size an d shape. (C) 1998 Wiley-Liss, Inc.