Structure of TraI Protein: First Structural Evidence of Negative Cooperativity of DNA Binding

1. Structure of TraI Protein: First Structural Evidence of Negative Cooperativity of DNA Binding Dan Neumann, National Institute of Standards and Technology, DMR 0944772 TraI is a protein that is essential for the transfer of DNA between bacteria. Such transfer plays a key role in the spread of genes responsible for an increased abundance of pathogenic or antibiotic resistant bacteria creating serious public health hazards. SANS results, obtained using the CHRNS-supported SANS instrument and all-atom ensemble modeling techniques, have been used to model the family of solution structures for the N-terminal portions of the TraI protein. Our first finding indicates that the region between the two DNA binding domains is only partially ordered, therefore provides a way that this large protein can traverse through 20 Ångstrombacterial pores. Our second finding indicates that the two DNA binding domains, that have been shown to exhibit negative cooperativity, are close in space. This work provides the basis for further study to elucidate the structural factors of DNA transfer that could potentially enable the development of drugs that stop transfer of antibiotic resistance in bacteria. Study of TraI 1-569. Distribution of Rg values from ensemble modeling Volumetric plot indicating that the nickase domain (red) is close in space to ssDNA domain (blue) Representative single structure. This is the first structural evidence that these two domains may have correlated functional roles in the binding of DNA. Sample structures from the ensembles that fit the SANS data for TraI 1-381. This confirms that this region is flexible and allow for the TraI protein to pass through bacterial pores. Dan Neumann, NIST, DMR 0944772 N. Wright et al, Proteins Struct. Funct. Bioninf. 80, 2250-2261 (2012). NIGMS RO1 GM61017