Graduate Study in - Chemistry - Johns Hopkins University

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David E. Draper Physical Biochemistry draper@jhu.edu “ RNA folding” has become a vigorous area of research as many unexpected and important functional roles have been discovered for RNA molecules. Research in my lab is concerned with two related questions about RNA: What are the energetics of folding compact RNA tertiary structures How do proteins recognize specific RNA sites and carry out specific tasks A variety of physical, biochemical, and genetic techniques are being used to explore several RNA systems. For a number of years, we have used ribosomal protein - RNA complexes as systems to explore different aspects of protein - RNA recognition and RNA folding. Most of our current efforts in this area concern two highly conserved regions of the ribosome that bind elongation factor G (EF-G), which catalyzes GTP hydrolysis and translocation of the ribosome along the messenger RNA. Each region consists of a ribosomal RNA fragment and several ribosomal proteins; assembly of these complexes and their interactions with EF-G are being studied by physical methods. Mutations whose properties are known from the in vitro studies are being introduced into ribosomes in vivo, to probe the functional significance of the complexes that are being prepared. Initial work in this area resulted in the first crystal structure of a ribosomal protein - RNA complex (Conn et al., 1999), which, in conjunction with solution thermodynamic studies, has yielded considerable insight into protein - RNA recognition mechanisms and unexpected features of RNA tertiary folding. Our crystallographic efforts are being carried out in collaboration with Prof. Ed Lattman’s laboratory in the Biophysics Department. In the last few years we have been particularly concerned with electrostatic aspects of RNA. Folding of an RNA tertiary structure is opposed by the unfavorable free energy needed to bring negatively charged phosphates into proximity, and it has long been known that Mg 2+ is much more effective than monovalent ions at reducing the electrostatic free energy of RNA tertiary folds. We have recently developed a theoretical framework for describing cation interactions with RNA. The model successfully accounts for the special properties of Mg 2+ , and we are making direct experimental measurements of Mg 2+ - RNA interactions to further test our predictions. In other work, we are examining the electrostatic component of protein - RNA binding, and again are making measurements in simple peptide - RNA complexes to test our theoretical predictions quantitatively. Ph.D., University of Oregon Postdoctoral, University of Colorado NIH Career Development Award NIH MERIT Award Selected publications include: Conn, G. L., Gittis, A. G., Minod, V., Lattman, E. E. & Draper, D. E. (2002). A compact RNA tertiary structure contains a buried backbone - K + complex. J. Mol. Biol., 318, 963-973. Misra, V. K. & Draper, D. E. (2001). A thermodynamic framework for Mg 2+ binding to RNA. Proc. Natl. Acad. Sci. U S A 98, 12456- 12461. Misra, V. K. & Draper, D. E. (2002). The linkage between magnesium binding and RNA folding. J. Mol. Biol., 317, 507-521. Gerstner, R. B., Pak, Y. & Draper, D. E. (2002). Recognition of 16S rRna by ribosomal protein S4 from Baccillus stearothermophilus. Biochemistry 40, 7165-7133. Shiman, R. & Draper, D. E. (2000). Stabilization of RNA tertiary structure by monovalent cations. J. Mol. Biol., 302, 79-91. Draper, D. E. (1999). Themes in RNA-protein recognition. J. Mol. Biol., 293, 255-270. Conn, G. L., Draper, D. E., Lattman, E. E. & Gittis, A. G. (1999). Crystal structure of a conserved ribosomal protein - RNA complex. Science, 284, 1171-1174. Graduate Study in Chemistry at The Johns Hopkins University 9
D. Howard Fairbrother Ph.D., Northwestern University Postdoctoral, University of California, Berkeley NSF CAREER Award Experimental Surface Chemistry Reactions at Polymer and Environmental Interfaces Materials Processing howardf@jhu.edu Dr. Fairbrother’s research program is focused on elucidating the mechanisms of chemical reactions that occur on surfaces and in thin films as well as their impact on material properties. This interest is motivated by the wide range of technologically significant processes that are mediated by surface reactions including catalysis, materials processing as well as adhesion and friction. The modification of polymer surfaces in vacuum environments is important in a number of different situations including plasma processing, polymer metallization and for vehicles in low earth orbits. We are exploring the microscopic surface events that accompany polymer surface processing (Figure 1) and their impact on interfacial properties. For example, we have explored the modification of fluorinated organic films during X-ray irradiation and metallization as well as the reactions of oxygen free radicals with self assembled monolayers. Surface reactions are also responsible for a wide range of environmental processes including atmospheric chemistry on ice and aerosol particles and the elementary reaction steps in Fe-based organohalide remediation in groundwater. Using an electrochemical cell coupled to a surface analysis chamber we are studying the liquid/solid interface, specifically the effect of surface composition on the rate and product partitioning associated with Fe-based organohalide remediation. In related studies we are also studying the mechanisms associated with electron beam and plasma remediation of chlorocarbons in aqueous solutions (Figure 2). Our studies utilize a wide variety of modern surface analytical tools including X-ray Photoelectron Spectroscopy (XPS), Infrared Spectroscopy, Mass Spectrometry and Atomic Force Microscopy (AFM). A number of our projects are highly collaborative in nature, involving interactions with the Department of Geography and Environmental Engineering and the Department of Materials Science and Engineering. Selected Publications: “Electron-Stimulated Chemical Reactions in Carbon Tetrachloride/Water (Ice) Films” A. J. Wagner, C. Vecitis, D. H. Fairbrother, J. Phys. Chem. B. 102 (2002) 4432. “Effect of X-ray Irradiation on the Chemical and Physical Properties of Semifluorinated Self- Assembled Monolayer”, A. J. Wagner, S. R. Carlo, C. Vecitis, D. H. Fairbrother, Langmuir 18 (2002) 1542. “Self-Assembled Monolayers as Models for Polymeric Interfaces,” C. C. Perry, S. R. Carlo, A. J. Wagner, C. Vecitis, J. Torres, K. Kolegraf, D. H. Fairbrother (ACS Symposium Series on “Solid Surfaces and Thin Films”) “Radical Reactions with Organic Thin Films: Chemical Interaction of Atomic Oxygen with an X-ray Modified Self-Assembled Monolayer” J. Torres, C.C. Perry, S.J. Bransfield, D.H. Fairbrother, J. Phys. Chem. B., 106 (2002) 6265. Figure 1: AFM image of a PTFE (Teflon) surface during Ti Deposition Figure 2: Mass Spectrum of Volatile Species Produced during Electron Beam Irradiation of Ice (bottom) and a 13 CCl 4 /Ice Film (top) 10 Graduate Study in Chemistry at The Johns Hopkins University
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