Professor
Department of Chemistry
Krieger School of Arts & Sciences

draper@jhu.edu

154 Remsen Hall
3400 N. Charles Street
Baltimore, MD 21218

Office: 410-516-7448
Lab: 410-516-7447

'RNA folding' has become a vigorous area of research as many unexpected and important functional roles have been discovered for RNA molecules. My lab is using a variety of physical techniques to ask questions about the energetics of RNA folding- what factors account for the stability of an RNA tertiary structure under physiological conditions? Do RNAs use different strategies to achieve the same stability?

Much of our work in recent years has been 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 Mg2+ is more effective than monovalent ions at reducing the electrostatic free energy of RNA tertiary structures.  Part of the challenge in thinking about ions and RNA is that the ions may explore a wide range of environments, from 'diffuse' ions that remain fully hydrated ions and sense only long-range coulombic forces from the RNA, to partially dehydrated ions at the RNA surface and 'chelated' ions that occupy pockets within the RNA  structure.  Our strategy has been to design experiments that measure so-called 'preferential interaction coefficients' between ions and RNA; these thermodynamic parameters sum the contributions from ions in all environments.  By examining RNAs with very different architectures and using theoretical and computational approaches to interpret the interaction coefficients, we are beginning to discern the different ways ions may stabilize an RNA.  In many RNAs, diffuse ions account for all or most of the Mg2+-induced stabilization, but in RNAs that are intrinsically difficult to fold, a small number of chelated Mg2+ ions also provide a substantial favorable free energy.  Although monovalent ions are not as strongly stabilizing as Mg2+, many RNAs form stable tertiary structures in physiological concentrations of K+, and some have evolved chelation sites specific for K+.

A theme that recurs in our work is that ion interactions with unfolded RNAs are already very strong, and in most cases those interactions are only incrementally strengthened when the RNA folds to the native state.  The precise nature of the unfolded RNA- how extended or compact it is, how it responds to changes in ion concentration- therefore becomes an important problem. Interesting examples are provided by 'riboswitch' RNAs, which adopt specific tertiary structures in response to the binding of small molecule ligands. We find natural selection has tuned their stability by affecting both the extension of the unfolded state and the architecture of the native state.

Another major area of interest is the dependence of RNA stability on osmolytes, small organic molecules that cells use (along with ions) to regulate their water content in response to changes in the composition of the external medium. Virtually all osmolytes destabilize RNA secondary structure but some strongly stabilize RNA tertiary structure. Part of the motivation for these studies is our interest in the in vivo stabilities of functional RNAs, but we also find that osmolytes can be useful tools for probing the interactions of RNAs with water and ions.

Selected Publications
Lambert, D., D. Leipply, R. Shiman, and D.E. Draper. (2009) The influence of monovalent cation size on the stability of RNA tertiary structures. J. Mol. Biol. 390:791-804.

Chen, A.A., D.E. Draper, and R.V. Pappu. (2009) Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop. J. Mol. Biol. 390: 805-819.

Grilley, D., A.M. Soto, and D.E. Draper. (2009) Direct quantitation of Mg2+ - RNA interactions by use of a fluorescent dye. Meth. Enzymol. 455:71-94.

Draper, D.E. (2008) RNA folding: thermodynamic and molecular descriptions of the roles of ions. Biophys. J. 95:5489-5495.

Iben, J.R., and D.E. Draper. (2008) Specific interactions of the L10(L12)4 ribosomal protein complex with mRNA, rRNA, and L11. Biochemistry 47:2721-31.

Grilley, D., V. Misra, G. Caliskan, and D.E. Draper. (2007) The importance of partially unfolded conformations for Mg(2+)-induced folding of RNA tertiary structure: structural models and free energies of Mg(2+) interactions. Biochemistry 46-10266-10278.

Lambert, D., and D.E. Draper. (2007) Effects of osmolytes on RNA secondary and tertiary structure stabilities and RNA-Mg(2+) interactions. J. Mol. Biol. 370:993-1005.

Soto, A.M., V. Misra, and D.E. Draper. (2007) Tertiary structure of an RNA pseudoknot is stabilized by "diffuse" Mg(2+) ions. Biochemistry 46:2973-2983.

Lee, D., J.D. Walsh, P. Yu, M.A. Markus, T. Choli-Papadopoulou, C.D. Schwieters, S. Krueger, D.E. Draper, and Y.X. Wang. (2007) The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes. J. Mol. Biol. 36:1007-1022.

Grilley, D., A.M. Soto, and D.E. Draper. (2006) Mg2+ - RNA interaction free energies and their relation to the folding of RNA tertiary structures. Proc. Natl. Acad. Sci. USA 103:14003-14008.

Maeder, C., and D.E. Draper. (2006) Optimization of a ribosomal structural domain by natural selection. Biochemistry 45:6635-6643.

Maeder, C., and D.E. Draper. (2005) A small protein unique to bacteria organizes rRNA tertiary structure over an extensive region of the 50S ribosomal subunit. J. Mol. Biol. 354:436-446.

Draper, D.E., D. Grilley and A.M. Soto. (2005) Ions and RNA folding. Annu. Rev. Biophys. Biomol. Struct. 34:221-43.

Draper, D.E. (2004) A guide to ions and RNA structure. RNA 10:335-343.

Misra, V.K., R. Shiman and D.E. Draper. (2003) A thermodynamic framework for the magnesium-dependent folding of RNA. Biopolymers 69:118-136.

García-García, C., and D.E. Draper. (2003) Electrostatic interactions in a peptide-RNA complex. J. Mol. Biol. 311:75-88.

Conn, G. L., A.G. Gittis, E.E. Lattman, V. Misra and D.E. Draper. (2002) A compact RNA tertiary structure contains a buried backbone - K+ complex. J. Mol. Biol. 318:963-973.

Misra, V., and D.E. Draper. (2002) The linkage between magnesium binding and RNA folding. J. Mol. Biol. 317:509-523.