Scientific Report 2005

Molecular Biology

Design and Informatics in Structural Virology

V.S. Reddy, C.M. Shepherd, C. Hsu, S. Kumar, R. Mannige, I. Borelli, C.L. Brooks III, J.E. Johnson, M. Manchester, A. Schneemann

We are interested in understanding the structural underpinnings and requirements for formation of viral capsids and in designing novel protein shells that polyvalently display molecules of interest. To this end, we use structural, computational, informatics, and genetic methods.

Viruses are highly evolved macromolecular machines that perform a variety of functions during their life cycle, including selective packaging of the genome, self-assembly, binding to host cells, and delivery of the genome to the targeted cells. Simple viruses, such as nonenveloped viruses, form closed protein shells or capsids of uniform size and character by the self-association of structural and functional components: proteins and the nucleic acid genome. Hence, these viruses are useful for structural and functional analyses.

To understand the requirements for formation of the closed protein shell in viral capsids in terms of structure and interactions, we established a repository of structurally characterized viral capsids in a relational database format, namely the Viper Particle Explorer (http://viperdb.scripps.edu). At the database, we use computational methods to analyze these protein shells in terms of protein-protein interactions: contacting residue pairs, association energies, individual residue contributions, and surface characteristics. To facilitate these studies, we are developing structural tools for analysis of viral structures as part of the Multiscale Modeling Tools for Structural Biology, the National Institutes of Health research resource headed by C.L. Brooks, Department of Molecular Biology. The structural and taxonomic data and the derived results are stored in a MySQL database for ease of querying and comparing the properties of interest within and across families of viruses. Furthermore, using the structural similarity that occurs within a virus family, we are building homology models for the uncharacterized members of virus families. These models will be useful for molecular virologists investigating structural and functional relationships in viruses.

To generate novel reagents, such as vaccines and antitoxins against cytotoxins such as ricin and pathogens in general, we are expressing decoys of pathogenic molecules on the surfaces of viral capsids. Currently, tomato bushy stunt virus–like capsids are the display platform of choice; the platform consists of multiple copies of a 2-domain capsid protein subunit with the C-terminal P-domain exposed on the surface. Such a unique subunit structure is useful for attaching peptides or proteins of interest at the end of the C terminus of the capsid protein or for replacing the P-domain with the proteins of interest rather than inserting them in a loop.

Publications

Reddy, V.S., Johnson J.E. Structure-derived insights into virus assembly. Adv. Virus Res. 64C:45, 2005.

Reddy, V.S., Schneemann, A., Johnson, J.E. Nodavirus endopeptidase. In: Handbook of Proteolytic Enzymes, 2nd ed. Barrett, A., Rawlings, N.D., Woessner, J.F. (Eds.). Academic Press, San Diego, 2004, p. 197.

Shepherd, C.M., Reddy, V.S. Extent of protein-protein interactions and quasi-equivalence in viral capsids. Proteins 58:472, 2005.