Jack A. Dunkle, Ph.D. - US grants

This award is supported by the Major Research Instrumentation and the Chemistry Research Instrumentation programs. Professor Elizabeth Papish from University of Alabama Tuscaloosa and colleagues Kevin Shaughnessy, Paul Rupar, Jack Dunkle and Jared Allred have acquired a dual source single crystal diffractometer equipped with a high resolution detector. In general, an X-ray diffractometer allows accurate and precise measurements of the full three-dimensional structure of a molecule, including bond distances and angles, and provides accurate information about the spatial arrangement of a molecule relative to neighboring molecules. The studies described here impact many areas, including organic and inorganic chemistry, materials chemistry and biochemistry. This instrument is an integral part of teaching as well as research and research training of graduate and undergraduate students in chemistry and biochemistry at this institution. Students are involved in chemical and protein research. The resource is also utilized by several neighboring primarily undergraduate institutions and historically black colleges and universities (HBCUs).

The award of the diffractometer is aimed at enhancing research and education at all levels. It especially impacts the characterization of solid materials and new polymers to harness solar energy and studies of diffuse X-ray scattering to determine how local changes in structure lead to macroscopic properties. The instrumentation is also used for studies following the syntheses of monodisperse small nanomolecules and the design of catalysts for carbon dioxide reduction and cross-coupling. The diffractometer benefits studies of biological macromolecules to understand gene expression and antibiotic resistance.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Project Summary/Abstract RNA modification enzymes are ubiquitous among the three domains of life and necessary for the proper function of many cellular RNAs. RNA substrates may be unstructured or highly base-paired as in tRNA or rRNA. Direct inspection of the sequence of highly base-paired RNAs is challenging because of the deep and narrow major groove of the RNA helix. How RNA modification enzymes achieve specificity for highly base- paired substrates is an open question. Two mechanisms feature prominently: protein promoted melting of base pairs to form interactions between the protein and the Watson-Crick faces of nucleotides or protein recognition of a specific three-dimensional RNA shape indirectly driven by RNA sequence. It is previously unknown how general these mechanisms are among RNA modification enzymes and if a few paradigms exist which can explain the specificity mechanisms of many classes of RNA modification enzymes. This proposal will use characterization of the structure and mechanism of the erythromycin resistance methyltransferase enzyme family to address the problem of RNA modification enzyme specificity, moving toward the goal of identifying common mechanistic strategies used for specific modification of highly base-paired RNA substrates. Erythromycin resistance methyltransferase enzymes methylate a specific adenosine residue of rRNA adjacent to the peptidyl transferase center of the ribosome sterically occluding the binding of multiple antibiotics that target the ribosome. The enzymes contribute to the significant public health problem of antibiotic resistance and also are an excellent model system for basic science. In Aims 1 and 2, steady-state and pre-steady state kinetics assays will be performed to understand how protein structure and RNA sequence and structure drive specificity. Wild type protein and rRNA substrates will be used along with site-directed mutants of both enzyme and rRNA towards the goal of building a kinetic mechanism for RNA methylation and understanding how specific protein-RNA interactions contribute to the mechanism. Aim 3 encompasses experiments using small- angle x-ray scattering to build a three-dimensional model of enzyme interaction with rRNA. Throughout the Aims we will assay two evolutionarily distinct members of the erythromycin resistance methyltransferase family to determine if there is an idiosyncratic or conserved mechanism for this enzyme family.

Project Summary CRISPR (clustered regularly interspaced short palindromic repeats) and CRISPR-associated (Cas) proteins are a group of diverse crRNA guided nucleases providing prokaryotes adaptive immunity to foreign genetic elements. Cas10-Csm is an approximately 300 kDa multiprotein complex that upon detecting foreign RNA transcripts initiates a DNA and RNA degradation response. Distinct CRISPR-Cas types use the information in crRNA to detect either double-stranded DNA or single-stranded RNA. While much is known concerning the specificity mechanisms of dsDNA detection by Type I (Cascade) and Type II (Cas9) systems, little is known concerning the specificity mechanisms of ssRNA detection by Type III (Cas10) systems. This is significant because evidence exists that the mechanisms for enforcing specificity during dsDNA detection and ssRNA detection are fundamentally different: competition between rehybridization of the non-base paired DNA strand to re-form dsDNA or binding to a Cas protein is essential to the dsDNA detecting specificity mechanism. This mechanism is not possible during specific detection of ssRNA. The hypothesis will be tested that in the Cas10- Csm system mismatches in specific, sensitive locations within the crRNA-target RNA duplex disrupt interference. Cas10-Csm structural models suggest the Csm2 component of Cas10-Csm directly contacts bound target RNA. We will test the hypothesis that Csm2 plays an integral role in detecting cognate RNA binding to Cas10-Csm and relays this signal to Cas10 via structural changes. We will use cryo-EM to determine the `structural mechanism' for Cas10 activation. The research proposed will impact several emerging biotechnologies such as the deployment of Cas10 as a point-of-care RNA virus diagnostic.