Structure-Function of DNA Binding Proteins
Viruses such as human Parvo B19 cause outbreaks of infection in humans, and in some cases severe side effects including the possible triggering of autoimmune disorders in genetically predisposed individuals. We study the viral proteins in order to understand their roles in viral replication, their ability in some cases to transactivate cellular genes, for rational drug design against the viruses, and finally to engineer them for new uses in biomedical research. We also study the interactions between the viral proteins and human cells to understand the connection between viral infection and the triggering of autoimmune disease.
We have unexpectedly discovered the presence of domain swapping (where a region of a protein from molecule swaps places with the same domain in a second copy of the protein) in a sequence specific endonuclease from Streptomyces griseus. The domain swapping stabilizes a tetrameric form of the nuclease, which may be responsible for the unusual properties of this enzyme: after cleavage of its target site in DNA, it will cleave additional different (secondary) sequences. The enzyme is stimulated to cleave these secondary sites at least 10 fold. The secondary sites would not be protected in the organism, hence cleavage of the secondary sites could result in severe DNA damage and consequently cell death. We have also discovered that the enzyme has a propensity to form large polymers when bound to DNA, which may serve to sequester activated enzymes away from the host genome. We have recently solved and published the 8.6 Å cryo-electron microscopy structure of this polymer: Allosteric Regulation of DNA Cleavage and Sequence-Specificity through Run-On Oligomerization, Lyumikis D., Talley, H., Stewart, A., Shah, S., Park, C.K., Tama, F., Potter, C.S., Carragher, B., Horton, N.C. (2013), Structure, 21, 1848-1858.
Direct Readout of DNA sequences by proteins involves hydrogen bonding and van der Waals contacts between the protein and the base edges of DNA in the major groove, where the location and types of groups are distinguishable among the different DNA bases. Indirect readout involves all forms of recognition excluding direct readout. Since direct readout is visible using structural studies and point mutations, it has been much better characterized. Indirect readout is less obvious, and inferred by the presence of specificity without direct readout contacts. It may involve water mediated hydrogen bonds or distortions in DNA that distiguish sequences energetically. Follow the link HERE to read more about our studies of indirect readout of DNA sequence.