One of the projects that will be used to evaluate the collaboratory's success is an investigation of DNA repair mechanisms being jointly conducted by Dr. Teri Klein of the UCSF Computer Graphics Laboratory and Dr. Arthur Grollman at SUNY Stony Brook.
The structural integrity of DNA is essential to cellular viability, and that integrity is continually threatened by intra- and extra-cellular processes. Damaged DNA is repaired through several distinct and complentary mechanisms. This collaboration focuses on the base excision repair (BER) pathway.
The central theme of the BER investigation is determining the relationship between sequence, molecular structure, and biological function. Using a site-specific approach, structure-to-function relationships are being explored, with the long-term goal of understanding how DNA damage is recognized by repair enzymes. Specifically, a prototype system consisting of DNA containing the mutagen 8-oxoguanine and the E. coli protein FPG is being examined. The collaboration has established that a single zinc finger motif is involved in the binding of FPG protein to DNA duplexes containing 8-oxoguanine. Site-directed mutagenesis of amino acids at critical positions in the helix region of the zinc finger motif is being used to determine possible points of contact with the DNA.
An examination of sequence homologies among FPG proteins from a variety of organisms has revealed an additional conserved motif flanking the helix-hairpin-helix region of the protein. Combining FPG sequence information with structural information from homologous proteins, the entire FPG protein can now be modeled by homology.
The initial models of the FPG zinc finger-DNA complex were created at UCSF. Refinements of these models via molecular dynamics simulations have been and are being performed at SUNY Stony Brook. Data is exchanged via the Internet while discussions are held by electronic mail with occasional telephone conversations.
Problems occur when the modeling and refinement personnel have different conceptions of how the research ought to proceed. Due to inefficient communications, these differences are sometimes not properly conveyed (and are therefore not resolved) which can lead to much wasted time and resources when dynamics simulations thereby have to be recomputed. The use of a CHIMERA-based molecular modeling collaboratory will alleviate many of these problems due to its facility for multi-media interaction between the researchers and because it will allow the collaborators to analyze identical models of zinc finger-DNA complexes.