Molecular Recognition in Biological Systems and Bioinformatics

Model of the conserved domains of the ScV RdRp compared to the known structure of the Norwalk Virus RdRp

Protein structure and function; RNA-protein interactions; Evolution of viruses

Molecular virology: This lab has worked on the molecular virology of small dsRNA viruses for over 25 years. Currently we are exploring the nature of the RNA-protein interaction that results in packaging of the viral plus strand. We have explored the RNA recognition site via PCR amplification techniques and defined the site as a small (20 base) region with a specific secondary structure. Similarly, the region of the large protein (over 1500 amino acids) that recognizes this sequence has been delimited to about 150 amino acids. We are now in the process of mutating each of these residues one at a time to map the contact residues.

Virmatics LLC virtual cloning suite; Structure-dependent motif search

Saccharomyces cerevisiae

RNA-dependent RNA polymerase, viral capsid polypeptides

All the usual molecular biology techniques, as well as viral purification techniques

Bruenn, J. (2008). The Ustilago maydis viruses. Encyclopedia of Virology, in press

Duax, W. L., V. Pletnev, A. Addlagatta, J. Bruenn, and C. M. Weeks. 2003. Rational Proteomics I. Fingerprint Identification and Cofactor Specificity in the Short-Chain Oxidoreductase (SCOR) Enzyme Family. Proteins 53:931-943.

Lopinski, John D., Dinman, Jonathan D., and Bruenn, Jeremy A. (2000). Kinetics of ribosomal pausing during programmed -1 translational frameshifting. Molec. Cell. Biol. 20, 1095-1103

Li, N., Erman, M., Pangborn, W., Duax, W.L., Park, C.-M Bruenn, J.A., and Ghosh, D. (1999). Structure of Ustilago maydis killer toxin KP6 α-subunit: a multimeric assembly with a central pore. J. Biol. Chem. 274, 20425-20431

Yao, W., Adelman, K., and Bruenn, J.A. (1997). In vitro selection of packaging sites in a double-stranded RNA virus. J. Virol. 71, 2157-2162.