Ribozymes are ideal model systems for the vast number of non-protein coding RNAs found in all domains of life, since they have an easily detectable biological function - catalysis. They also are of high biological and biotechnological relevance in their own right for their roles in the processing and regulation of genetic information. Yet, a quarter century after their discovery, our understanding of catalysis by ribozymes still pales compared to that of catalysis by protein enzymes. Over the last two funding cycles, the PI's group has made substantial contributions to our understanding of the folding and mechanism of the class of small ribozymes. All five members of this class were investigated to varying degrees, with particular focus on the hammerhead and hepatitis delta virus (HDV) ribozymes. Several important discoveries were also made on the hairpin ribozyme as a particularly intriguing model system, on which we will follow up during the current funding period, bringing to bear our signature integration of biophysical and biochemical tools.
In Specific Aim 1, we will test the hypothesis that the persistent folding heterogeneity of the hairpin ribozyme, observed at the single molecule level, is caused by slow repuckering of specific nucleotide sugars. Similar folding heterogeneity of chemically identical isomers has been observed for a number of RNAs when (re)folded in vitro, but still lacks a molecular explanation. We have recently succeeded in avoiding this heterogeneity when natively purifying the RNA directly from an in vitro transcription reaction, paving the way for investigating the molecular basis of folding heterogeneity in the hairpin ribozyme by a combination of single molecule fluorescence resonance energy transfer (smFRET), footprinting, and molecular dynamics (MD) simulations.
In Specific Aim 2, in collaboration with Jiri Sponer, a computational scientist and long-standing collaborator, and Joseph Wedekind, an X-ray crystallographer, we will test the hypothesis that a network of global molecular motions in the hairpin ribozyme has an impact on those local molecular motions that lead to catalysis. Such a linkage has been suggested for protein enzymes, but has not been rigorously tested for any ribozyme. To this end, we will introduce site-specific modifications into the hairpin ribozyme and probe, using a combination of enzymology, smFRET, X-ray crystallography, and MD simulation, the impact of each of these modifications on local and global structure, dynamics, and function.
In Specific Aim 3, we will test a set of specific mechanistic proposals for the role of A38 and water in catalysis of the hairpin ribozyme.
This aim follows up on our previous observation that a judiciously placed A38 residue is flanked in the solvent- protected catalytic core by several tightly bound water molecules. We will pursue a broadly sampled QM/MM treatment of the catalytic reaction in collaboration with Jiri Sponer and Joseph Wedekind, as well as quantum chemist Michal Otyepka. We anticipate that results from these three Specific Aims will significantly deepen our understanding of the biological function of non-coding RNAs in general.
Ribozymes are ideal model systems for the vast number of non-protein coding RNAs found in all domains of life, since they have an easily detectable biological function - catalysis. They also are of high biological and biotechnological relevance in their own right for their roles in the processing and regulation of genetic information. In this project renewal, three enigmatic hallmarks of a small model ribozyme, the hairpin ribozyme, will be mechanistically dissected to deepen our understanding of biologically relevant non-coding RNAs in general.
|Mlýnský, Vojt?ch; Walter, Nils G; Šponer, Ji?í et al. (2015) The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations. Phys Chem Chem Phys 17:670-9|
|Widom, Julia R; Dhakal, Soma; Heinicke, Laurie A et al. (2014) Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update. Arch Toxicol 88:1965-85|
|Sripathi, Kamali N; Tay, Wendy W; Banáš, Pavel et al. (2014) Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape. RNA 20:1112-28|
|Todd, Gabrielle C; Walter, Nils G (2013) Secondary structure of bacteriophage T4 gene 60 mRNA: implications for translational bypassing. RNA 19:685-700|
|Pitchiaya, Sethuramasundaram; Krishnan, Vishalakshi; Custer, Thomas C et al. (2013) Dissecting non-coding RNA mechanisms in cellulo by Single-molecule High-Resolution Localization and Counting. Methods 63:188-99|
|Marek, Matthew S; Johnson-Buck, Alexander; Walter, Nils G (2011) The shape-shifting quasispecies of RNA: one sequence, many functional folds. Phys Chem Chem Phys 13:11524-37|
|Mlynsky, Vojtech; Banas, Pavel; Walter, Nils G et al. (2011) QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms. J Phys Chem B 115:13911-24|
|Spano, Meredith Newby; Walter, Nils G (2011) Solution structure of an alternate conformation of helix27 from Escherichia coli16S rRNA. Biopolymers 95:653-68|
|Johnson-Buck, Alexander E; McDowell, Sarah E; Walter, Nils G (2011) Metal ions: supporting actors in the playbook of small ribozymes. Met Ions Life Sci 9:175-96|
|Blanco, Mario; Walter, Nils G (2010) Analysis of complex single-molecule FRET time trajectories. Methods Enzymol 472:153-78|
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