RNA polymerase (RNAP) is the enzyme that catalyzes the first step in gene expression--the transcription of genetic information into messenger RNA. As such it is the principal target for factors regulating gene expression and its basic functions and structural features are highly conserved evolutionarily. The broad goal of this project is the understanding of the molecular mechanism of RNAP function and regulation. In collaboration with X-ray crystallographers, Dr. Goldfarb would like to understand RNAP structure in relation to its interactions with DNA, with nucleotide substrates, and with its RNA product. Single amino acid substitutions will be generated in the cloned genes, rpoB and rpoC, which specify the two largest subunits of RNAP holoenzyme. The mutations will be characterized using a variety of in vitro assays to determine which discrete activities of the enzyme are affected. In addition, the PI proposes to develop a series of engineered nucleic acid model ligands that bind stably to RNAP to form complexes analogous to those formed during transcription elongation; these ligands will be used for co-crystallization with the enzyme to refine the structural models and ascertain differences in conformations assumed by the enzyme at discrete steps in the transcription elongation reaction.
| Mustaev, Arkady; Malik, Muhammad; Zhao, Xilin et al. (2014) Fluoroquinolone-gyrase-DNA complexes: two modes of drug binding. J Biol Chem 289:12300-12 |
| Kurepina, N; Kreiswirth, B N; Mustaev, A (2013) Growth-inhibitory activity of natural and synthetic isothiocyanates against representative human microbial pathogens. J Appl Microbiol 115:943-54 |
| Wirpsza, Laura; Krasnoperov, Lev; Mustaev, Arkady (2013) New quinolone-based thiol-reactive lanthanide luminescent probes. J Photochem Photobiol A Chem 251:30-37 |
| Sosunova, Ekaterina; Sosunov, Vasily; Epshtein, Vitaly et al. (2013) Control of transcriptional fidelity by active center tuning as derived from RNA polymerase endonuclease reaction. J Biol Chem 288:6688-703 |
| Pillai, Shyamala; Krasnoperov, Lev; Mustaev, Arkady (2013) Simple no-chromatography procedure for amine-reactive Eu(3+) luminescent chelates optimal for bioconjugation. J Photochem Photobiol A Chem 255:16-23 |
| Kozlov, Maxim; Nudler, Eugeny; Nikiforov, Vadim et al. (2013) Reactive rifampicin derivative able to damage transcription complex. Bioconjug Chem 24:443-7 |
| Pratt, Ayiasha; Garcia-Effron, Guillermo; Zhao, Yanan et al. (2013) Evaluation of fungal-specific fluorescent labeled echinocandin probes as diagnostic adjuncts. Med Mycol 51:103-7 |
| Pillai, Shyamala; Kozlov, Maxim; Marras, Salvatore A E et al. (2012) New cross-linking quinoline and quinolone derivatives for sensitive fluorescent labeling. J Fluoresc 22:1021-32 |
| Wirpsza, Laura; Pillai, Shyamala; Batish, Mona et al. (2012) Highly bright avidin-based affinity probes carrying multiple lanthanide chelates. J Photochem Photobiol B 116:22-9 |
| Malik, Muhammad; Marks, Kevin R; Mustaev, Arkady et al. (2011) Fluoroquinolone and quinazolinedione activities against wild-type and gyrase mutant strains of Mycobacterium smegmatis. Antimicrob Agents Chemother 55:2335-43 |
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