Antibiotics such as aminoglycosides function through binding to the decoding region aminoacyl site (A site) of 16S rRNA and inhibit protein synthesis. My project is focused on studies of aminoglycoside analogues and rRNA interactions through biophysical approaches. Acrylamide quenching studies were carried out to monitor the aminoglycoside-induced conformational changes in the A site via fluorescent measurements. MS-ESI (mass spectrometry electrospray ionization) is used to screen small molecules containing the neamine sugar moiety that target the ribosomal acyltransfer site. These small molecules are useful to determine the important contributions from each functional group on the sugar moiety. Further, we use SPR (surface plasmon resonance) to study the kinetics of aminoglycosides binding to the A site. Supported by NIH AI 055496 (PI:Shahriar Mobashery).
Figure 1: A) The secondary structure of 16S rRNA and the location of decoding region A site. (1) B) Acrylamide quenching studies. C) MS spectra of the A-site model titrated with paromomycin. D) SPR sensorgram of paromomycin binding to the A site.
1) Woese, C. R.; Winker, S.; Gutell, R. R. Proceedings of the National Academy of Sciences of the United States of America1990, 87, 8467.