Macromolecular complexes formed by the association of
protein with other proteins, protein with nucleic acid
(DNA or RNA), and receptor with ligands as in
neurotransmission are at the heart of all biological
processes. In my lab we are using biochemistry and x-ray
crystallography to understand how these macromolecules
recognize one another in the course of complex
formation.
One such complex that has been well characterized is the
protein-nucleic acid complex found at the ends of
chromosomes in O. nova. During the life-cycle of
these unicellular eukaryotes, a macronucleus is formed
through a fantastic process of DNA cutting, splicing, and
amplification to produce millions of gene-sized
chromosomes, each with precisely defined telomeres
consisting of a 16-nucleotide single strand DNA
complexed with a two-subunit protein, the O. nova
telomere end binding protein.
The crystal structure of this complex solved to 1.86 Å
resolution, reveals interesting structural motifs which
likely contribute to specificity and stability of the
complex. For example, at two locations in the protein-
DNA interface an arginine amino acid sidechain stacks
with a guanisine base, a structure that suggests
recognition through charge-charge interactions, hydrogen
bonding interactions, and packing interactions. By
introducing modifications to the protein or DNA
components of this complex we will test different ideas
of how recognition is achieved. For instance, by
substituting specific amino acid residues or by
synthesizing DNAs with altered nucleotide bases we can
measure the relative contribution of particular hydrogen
bonds or packing interactions towards stability and
specificity of the structure.
Selected Publications
Horvath, M. P. (2007). Single-stranded Nucleic Acid-binding Proteins. In Protein-Nucleic Acid Interactions: Structural biology (Rice, P. A. & Correll, C. C., eds.), pp. (in press). Royal Society of Chemistry, London.
Suzuki, T., McKenzie, M., Ott, E., Ilkun, O. & Horvath, M. P. (2006). DNA binding affinity and sequence permutation preference of the telomere protein from Euplotes crassus. Biochemistry 45, 8628-38.
Buczek, P. & Horvath, M. P. (2006). Structural reorganization and the cooperative binding of single-stranded telomere DNA in Sterkiella nova. J Biol Chem 281, 40124-34.
Buczek, P., Orr, R. S., Pyper, S. R., Shum, M., Kimmel, E., Ota, I., Gerum, S. E. & Horvath, M. P. (2005). Binding linkage in a telomere DNA-protein complex at the ends of Oxytricha nova chromosomes. J Mol Biol 350, 938-52.
Horvath, M. P., Schweiker, V. L., Bevilacqua, J. M., Ruggles, J. A. & Schultz, S. C. (1998). Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA. Cell 95, 963-74.
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