Finding and using local symmetry in identifying lower domain movements in hexon subunits of the herpes simplex virus type 1 B capsid

A characteristic of virus assembly is the use of symmetry to construct a co mplex capsid from a limited number of different proteins. Many spherical vi ruses display not only icosahedral symmetry, but also local symmetries, whi ch further increase the redundancy of their structural proteins. We have de veloped a computational procedure for evaluating the quality of these local symmetries that allows us to probe the extent of local structural variatio ns among subunits. This type of analysis can also provide orientation param eters for carrying out non-icosahedral averaging of quasi-equivalent subuni ts during three-dimensional structural determination. We have used this pro cedure to analyze the three types of hexon (P, E and C) in the 8.5 Angstrom resolution map of the herpes simplex virus type 1 (HSV-1) B capsid, determ ined by electron cryomicroscopy. The comparison of the three herons showed that they have good overall 6-fold symmetry and are almost identical throug hout most of their lengths. The largest difference among the three Lies nea r the inner surface in a region of about 34 Angstrom in thickness. In this region, the P hexon displays slightly lower 6-fold symmetry than the C and E herons. More detailed analysis showed that parts of two of the P hexon su bunits are displaced counterclockwise with respect to their expected 6-fold positions. The most highly displaced subunit interacts with a subunit from an adjacent P hexon (P'). Using the local 6-fold symmetry axis of the P he xon as a rotation axis, we examined the geometrical relationships among the local symmetry axes of the surrounding capsomeres. Deviations from exact s ymmetry are also found among these local symmetry axes. The relevance of th ese findings to the process of capsid assembly is considered. (C) 2001 Acad emic Press.