Scientific Report 2003-2004 - Cleveland Clinic Lerner Research ...

Structure, Dynamics, and Function ofRNAs and RibonucleoproteinsWe take a “ribocentric” view of the worldin my laboratory. How do RNAmolecules recognize their specific targetsto affect a myriad of biological processes in thecell, such as protein synthesis, enzyme catalysis,gene regulation, and viral infections? The currentgoal of my research program is to understand, atthe structural molecular level, howRNA molecules recognize theirtargets (such as other RNAs,proteins, and ions) with highaffinity and specificity. Knowledgeof the three-dimensional architectureof biological molecules isfundamental to parsing out thedeterminants of molecularrecognition and possibly toforming the basis for rationaldesign of new drugs. Experimentally,we apply a wide range ofbiochemical and biophysicalmethods but use state-of-the-artnuclear magnetic resonance(NMR) spectroscopy as theprimary structural tool tocharacterize specific modelsystems. Our research interest istherefore focused on two aspects: structureelucidation of biologically important moleculesand methodological developments to study largebiomolecules by NMR spectroscopy.We are presently investigating thestructures of RNAs derived from the catalyticcore of group II introns. These structural studies,coupled with probing the role of metal ions inRNA structure, may shed light on understandingthe catalytic mechanism of self-splicing and thepotential relationship to the mechanisms ofmRNA splicing in vivo.At present, detailed NMR spectroscopicinformation can only be obtained for relativelysmall biomolecules, up to a molecular mass of 20kDa, whereas protein-nucleic acid complexesoften are much larger. One main research effortof the group is therefore to develop newexperimental techniques to alleviate this problem.In the area of methodology development, wefocus on implementing and designing multidimensionalNMR experiments to obtain data onKwaku T. Dayie, Ph.D.large biomolecules. These data will be transformedinto realistic three-dimensional molecularstructures using computer calculations. Inaddition, because many biological processes areundergirded by conformational flexibility, we aredeveloping techniques to probe this phenomenon.These results will provide us with a window onthe impact of dynamics on the structure andfunction of biological molecules.THE DAYIELABORATORYGRADUATE STUDENTHua Li, M.S.TECHNOLOGISTXinxing Wang, M.S.COLLABORATORSRichard A. Padgett, Ph.D. 11Dept. of Molecular Biology,CCFDayie, K.T., and G. Wagner (1997) Carbonyl carbon probe of local mobility in 13 C, 15 N-enriched proteins using high resolution NMR. J. Am. Chem. Soc. 119:7797-7806.Walters, K.J., Dayie, K.T., Reece, R.J., Ptashne, M., and G. Wagner (1997) Structureand mobility of the PUT3 dimer: a DNA pincer. Nat. Struct. Biol. 4:744-750.Zhang, P., Dayie, K.T., and G. Wagner (1997) Unusual lack of internal mobility and fastoverall tumbling in oxidized flavodoxin from Anacystis nidulans. J. Mol. Biol. 272:443-455.Dayie, K.T., Tolbert, T.J., and J.R. Williamson (1998) 3D C(CC)H-TOCSY experimentfor assigning protons and carbons in uniformly 13 C and selectively 2 H-labeled RNA. J.Magn. Reson. 130:97-101.Dr. Dayie is a Staff member in the LRI Departmentof Molecular Biology.Dayie, K.T., Brodsky, A.S., and J.R. Williamson (2002) Base flexibility in HIV-2 TARRNA mapped by solution 15 N, 13 C NMR relaxation. J. Mol. Biol. 317:263-278.Hall, J.D., Dayie, K.E., and D. Fushman (2003) Direct measurement of the 15 N CSA/dipolarrelaxation interference from coupled HSQC spectra. J. Biomol. NMR 26:181-186.175