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David E. Draper
Physical Biochemistry Johns Hopkins University Phone: 410.516.7448 PhD - University of Oregon "RNA folding" has become a vigorous area of research as many unexpected and important functional roles have been discovered for RNA molecules. Re search in my lab is concerned with two related questions about RNA: What are the energetics of folding compact RNA tertiary structures? How do pro teins recognize specific RNA sites and carry out specific tasks? A variety of physical, biochemical, and genetic techniques are being used to expl ore 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 RN A folding. Most of our current efforts in this area concern two highly co nserved regions of the ribosome that bind elongation factor G (EF-G), whi ch catalyzes GTP hydrolysis and translocation of the ribosome along the m essenger RNA. Each region consists of a ribosomal RNA fragment and severa l ribosomal proteins; assembly of these complexes and their interactions with EF-G are being studied by physical methods. Mutations whose properti es are known from the in vitro studies are being introduced into ribosome s 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, which, in conjunction wit h solution thermodynamic studies, has yielded considerable insight into p rotein - RNA recognition mechanisms and unexpected features of RNA tertia ry folding. Our crystallographic efforts are being carried out in collabo ration with Prof. Ed Lattman's laboratory in the Biophysics Department. In the last few years we have been particularly concerned with electrost atic aspects of RNA. Folding of an RNA tertiary structure is opposed by t he unfavorable free energy needed to bring negatively charged phosphates into proximity, and it has long been known that Mg(2+) is much more effec tive than monovalent ions at reducing the electrostatic free energy of RN A 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 experiment al measurements of Mg(2+) - RNA interactions to further test our predicti ons. In other work, we are examining the electrostatic component of prote in - RNA binding, and again are making measurements in simple peptide - RNA complexes to test our theoretical predictions quantitatively. |
