Protein-nucleic acid interactions lie at the heart of many biological processes, including transcription, replication, and cellular maintenance. To date, however, there have been very few published X-ray and NMR structures of these types of complexes. Photochemical crosslinking of these complexes is an attractive method for analyzing these types of interactions. Photons are """"""""zero-length"""""""" crosslinkers, which means they induce covalent bonds between reactive species without a molecular bridge. We have direct experimental evidence that crosslinked peptide-nucleotide species can be fully characterized by mass spectrometry. We have been successful in using mass spectrometry to analyze the protein- oligonucleotide complex formed between pol beta and oligonucleotide d(ATATATA), as well as that of peptide-oligonucleotide complexes arising from a tryptic digest. We have also had success in confirming recent NMR results regarding the protein-binding site. We are actively pursuing using nanosecond-pulsed laser UV crosslinking, which could, in principle, explore specific interactions at the microsecond and millisecond time scale. It is at this point where the facilities at the Computer Graphics Lab are of most use. As the solution structure of this protein-oligonucleotide system has been solved, we can complement the NMR data by providing insight to the molecular dynamics and the topology of such systems. We hope to use molecular dynamics studies of this recently-solved complex to explore specific interactions at the nanosecond time scale, and use the information in conjunction with our crosslinking results, as well as the solution structure, to provide a more complete picture of the complex series of events that take place with these types of systems.
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