EMBL EMBL Virus Structure Resource
AVS module description

The problem

A typical challenge to the structural biologist is the two fold problem of understanding a complex structure and of preparing images which are sufficiently clear that they will convey that understanding to colleagues. Often it is necessary to devise visualization tools which are suited to the particular structure being examined. Several examples are shown from work with the enveloped virus Semliki Forest Virus. Semliki Forest virus is an enveloped virus of 700A diameter containing distinct layers of structure. The viral RNA is surrounded by a protein capsid which is enveloped by a lipid bilayer which is penetrated by transmembrane spikes. An important biological question in such a system is the interaction between the different layers of structure. An understanding of such interactions is critical for an understanding of the mechanism of virus assembly and control of disassembly.

User written modules

AVS does not provide ideal tools for examining such spherically concentric structures. A series of very simple modules have been written for cutting out spherical shells (r_crop), wedges of density (w_crop), triangular pyramids of density (w_crop) and cylinders (cyl_crop). A complementary approach to the problem is to convert the density of the structure to polar coordinates so that superposition of layers can be shown directly.

These simple modules can them be combined with standard modules to show the organization in SFV.

Pannel A (tiff representation) shows the use of w_crop to reveal the layers of the virion. A wedge containing the projecting domains of the trimeric spikes, the interlocking skirts above the membrane and the membrane itself is cut away to reveal the capsid within the structure.

Juxtaposition of a central section and a surface view in Panel B (tiff representation) reveals the complexity of the internal structure. The seperation between the two leaflets of the bilayer are seen easilty as is the close apposition of the capsid to the inner leaflet of the bilayer.

Pannel C (tiff representation) shows the result of combining several uses of r_crop with w_crop and multiple instances of isosurface to produce a side view of the different structures around a single spike. By giving each isosurface a seperate color with the geometry viewer, the components can be distinguished easily. The segment of the capsid is shown in green, the two leaflets of the bilayer and the transmembrane domains of the spike proteins are shown in red, the skirt domains which almost cover the membrane in yellow and the projecting domains of the spikes in blue.

The relative positions of the projecting domains and skirts of the spikes and the capsid can be seen in Panel E (tiff representation) which was generated by the network shown in Panel D (tiff representation) . Each of these strutures is shown in a distinct but representaion so their relation is revealed. The network shows the great advantage of the use of user written modules. Adherence to the constraints on writing modules for AVS results in the generation of modules which will be completely consistent with the standard ones so that mixing presents no problem. Of the thirteen distinct modules required to generate, only two (r_crop and w_crop) needed to be developed from scratch.

The module convert_polar allows a different approach to visualizing a multilayer structure. Conversion from Cartesian (x,y,z) to polar (r,theta,phi) coordinates produces a polar map which can be manipulated with the standard AVS modules to display the superposition of spikes and capsid.

Panel F (tiff representation) shows a section close to the two fold axis of the map plotted in r (horizontal) and theta (vertical). Sections of constant r at the level of the capsid ( (Panel G) (tiff representation) ) and the spikes (Panel H) reveal the complementary arrangement of the spikes and capsid. Although the icosahedral symmetry and triangulation number (T=4) are the same for both, the spikes are clustered as trimers and the capsid subunits are clustered as hexamers and pentamers. Hence the spikes i interact with multiple clusters of capsid proteins. For example, each three fold spike interacts with capisd units in both hexamer and pentamer clusters.