Gillian Air  /  Sanjay Bidichandani  /  Robert Broyles
Paul DeAngelis  /  Jay Hanas  /  Martin Levine
Guangpu Li  /  Jialing Lin  /  Hiroyuki Matsumoto  / Blaine Mooers /  Ann Louise Olson 

Karla Rodgers  /  Robert Steinberg  /  Leon Unger  /  Paul Weigel   

Christopher West  /  Adam Zlotnick

Structure and function studies of proteins that catalyze DNA recombination. Biophysical investigations of DNA-binding and zinc metalloproteins.

V(D)J recombination is a fundamental process in the development of the immune system, as it leads to diversity of the antigen-binding regions of T cell receptors and immunoglobulins. In the V(D)J recombination reaction, gene segments are selected and fused to produce the DNA sequence that encodes for the variable regions of the antigen-binding receptors. This is a site-specific recombination reaction where each gene segment is flanked by a conserved recombination signal sequence (RSS). The initial step in the reaction is cleavage at the border between a coding gene segment and its flanking RSS. The macromolecular assembly that carries out this site-specific cleavage is referred to as the V(D)J recombinase, which consists of the lymphoid-specific factors RAG1 and RAG2, proteins encoded by the recombination-activating genes.

The enzymatically-active macromolecular assembly is believed to consist of RAG1 and RAG2 bound to two RSS signals forming a synaptic complex, which is followed by coupled cleavage at the border of each RSS. As the two RSS sites may be separated by up to 10⁶ bases in the genome, the topology of such an assembly may be particularly intriguing. Examination of RAG1 and RAG2 and their association in the V(D)J recombinase assembly will provide insight into the molecular mechanism of V(D)J recombination, as well as further our understanding of the fundamental principles of protein-protein and protein-DNA interactions. Current evidence shows that RAG1 and RAG2 are multi-domain proteins. We have identified a novel zinc-binding dimerization domain from residues 265-380 in the 1040 residue murine RAG1 protein. This domain was characterized using a combination of biophysical techniques, including X-ray crystallography. In addition, RAG1 contains a catalytic 'core' region from residues 384-1008. A core region of RAG2 has also been identified from residues 1-387 of the 527 residue full-length murine protein.

Current research in my laboratory is to continue characterization of domains in RAG1, as well as to determine the fundamental protein-protein, protein-metal, and protein-DNA interactions involved in formation of the V(D)J recombination assembly. To accomplish these investigations a combination of biophysical techniques are being used to quantify macromolecular associations, study metal-binding properties, and determine overall structural characteristics of the proteins and complexes in solution. X-ray crystallographic studies will continue to be used to gain information at atomic resolution.

Recent Publications:
Godderz, L.J., Peak, M.M., and Rodgers, K.K. (2005) Analysis of biological macromolecular assemblies using static light scattering methods. Curr. Orig. Chem. 9:  899-908.

Godderz, L.J., and Rodgers, K.K. (2004) RAG1 oligomerization states and secondary structural properties: an initial characterization of V(D)J recombinase complex formation.  Spectrosc. - Int. J. 18:  311-322. 

De, P., and Rodgers, K.K. (2004) DNA cleavage activity of the V(D)J recombination protein RAG1 is autoregulated.  Mol. Cell. Biol. 24: 6850-6860

De, P., and Rodgers, K.K. (2004) Putting the pieces together: Identification and characterization of structural domain in the V(D)J recombination protein RAG1. Immunol. Rev. 200: 70-82. 

Peak, M.M., Arbuckle, J.L., Rodgers, K.K., (2003) The central domain of core RAG1 preferentially recognizes single-stranded RSS heptamer. J. Biol. Chem. 278: 18235-18240.

Godderz, L.J., Rahman, N.S., Risinger, G.M., Arbuckle, J.L., Rodgers, K.K., (2003) Self-association and conformational properties of RAG1: Implications for formation of the V(D)J recombinase. Nucl. Acids Res. 31: 2014-2023.

Arbuckle, J.L., Fauss, L.J., Simpson, R., Ptaszek, L.M., Rodgers, K.K., (2001) Identification of two topologically independent domains in RAG1 and their role in macromolecular interactions relevant to V(D)J recombination. J. Biol. Chem. 276: 37093-37101.

Rodgers, K.K., Villey, I.J., Ptaszek, L., Corbett, E., Schatz, D.G., and Coleman, J.E., (1999) A dimer of the lymphoid protein RAG1 recognizes the recombination signal sequence and the complex stably incorporates the high mobility group protein HMG2. Nucleic Acids Res. 27:2938-2946.

Junker, M., Rodgers, K.K., and Coleman, J.E., (1998) Zinc as a structural and folding element of proteins which interact with DNA. Inorg. Chem. Acta. 275-276:481-492

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