Scientific Report 2006

Molecular Biology

Design and Informatics in Structural Virology

V.S. Reddy, S. Kumar, M. Tripp, P. Singh, R. Mannige, I. Borelli, J. Loo, C.L. Brooks III, J.E. Johnson, M. Manchester, G. Nemerow, A. Schneemann

We are interested in understanding the structural underpinnings and requirements for formation and function 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 into uniform capsids, binding to host cells, and delivery of the genome to the targeted cells. Simple viruses, such as nonenveloped viruses, form closed protein shells 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.

In collaboration of with G.R. Nemerow, Department of Immunology, we are using x-ray crystallographic methods to determine the structure of the entire human adenovirus particle, currently at about 9-Å resolution. We are continuing to collect diffraction data at higher resolution. We continue to maintain and expand the virus structure database, namely VIPERdb (http://viperdb.scripps.edu), where the coordinates of the characterized spherical capsid structures are stored and organized in terms of viral taxonomy and capsid architecture. We are developing structural analysis tools to “mine” the capsid structures in terms of protein-protein interactions, contacting residue pairs, association energies, contributions of individual residues, and surface characteristics. VIPERdb is being developed as part of the Multiscale Modeling Tools for Structural Biology, a National Institutes of Health research resource headed by C.L. Brooks, Department of Molecular Biology. In addition, on the basis of 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.

We are generating decoys of pathogenic molecules on the surfaces of viral capsids that can be used as vaccines against cytotoxins such as ricin. Currently, tomato bushy stunt virus–like capsids are our 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 external P-domain with the proteins of interest rather than inserting them in a loop.

Publications

Hsu, C., Singh, P., Ochoa, W., Manayani, D.J., Manchester, M., Schneemann, A., Reddy, V.S. Characterization of polymorphism displayed by the coat protein mutants of tomato bushy stunt virus. Virology 349:222, 2006.

Natarajan, P., Lander, G.C., Shepherd, C.M., Reddy, V.S., Brooks, C.L. III, Johnson, J.E. Exploring icosahedral virus structures with VIPER. Nat. Rev. Microbiol. 3:809, 2005.

Shepherd, C.M., Borelli, I.A., Lander, G., Natarajan, P., Siddavanahalli, V., Bajaj, C., Johnson, J.E., Brooks, C.L. III, Reddy, V.S. VIPERdb: a relational database for structural virology. Nucleic Acids Res. 34(Database Issue):D386, 2006.

Taylor, D.J., Speir, J.A., Reddy, V., Cingolani, G., Pringle, F.M., Ball, L.A., Johnson, J.E. Preliminary x-ray characterization of authentic providence virus and attempts to express its coat protein gene in recombinant baculovirus. Arch. Virol. 151:155, 2006.