Biomedical and Chemical Engineering Research Seminar Series

Dr. Blaine Mooers

"Structural Studies of RNA editing in Trypanosomes and Tools to ease the use of PyMOL"

Abstract:
Uridine (U) insertion/deletion editing in trypanosomes is an extensive post-transcriptional process that corrects the coding sequence of most mitochondrial mRNAs. This editing is required for the subsequent expression of several mitochondrial proteins. The number of Us that are inserted far exceeds that number that is deleted; there is a net increase in the number of codons after editing. Enzyme cascades do the editing in the mitochondrion. The editing reactions are directed by hundreds of different guide RNAs. Each guide RNA has the sequence complement of a fragment of the final edited mRNA sequence. Consequently, much of the genetic information for the final RNA transcript comes from both its corresponding gene and the genes for the set of guide RNAs that direct its editing. In other words, the genetic information flows from DNA to RNA along multiple parallel pathways. Our goal is to obtain a rigorous description of the structural biology of this type of RNA editing to improve our understanding of its evolutionary basis, clarify the relationship between this type of RNA editing and other types of RNA editing, and provide a structural basis of the design of better drugs to fight infections with trypanosomes which threaten 600 million people worldwide. We have been using X-crystallography and small angle X-ray scattering to the study fragments of the RNA editing substrates. To visualize the resulting structures, we use PyMOL, a molecular graphics program is popular for making images for publication. It is easy to make beautiful overview figures of biomacromolecules with PyMOL, but it is not so easy to do other structural analysis tasks. I will present tools that we developed to ease the use of PyMOL.

Biography:
Blaine Mooers is an Associate Professor of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. He is also a member of the Stephenson Cancer Center, serves as director of the Laboratory of Biomolecular Structure and Function, academic director of the Biomolecular Structure Core of Oklahoma COBRE in Structural Biology, and two-time chair of the Stanford Synchrotron Radiation LightSource Users' Executive Committee, which represents 2200 laboratories. He earned a Ph.D. in Biochemistry and Biophysics with P. Shing Ho at Oregon State University. He was a Howard Hughes Medical Institute fellow with Brian Matthews at the University of Oregon. As a post-doc, he worked on problems in protein structure and design and RNA structure. His research interests include the role of RNA structure in the RNA editing system in trypanosomes. His lab uses X-ray crystallography, small-angle X-ray scattering, structure-based drug design, and molecular dynamics simulations. He also collaborates with OUHSC colleagues on crystallographic studies to develop better anti-cancer compounds. He has been using Python and Jupyter to aid the analysis of his data for the past ten years. His research interests include developing software to improve computational workflows in structural biology. A Warren L. DeLano Memorial PyMOL Open-Source Fellowship funded some of his earlier work. The National Institutes of Health currently funds his research.

Faculty/Lab Website: Mooers, Blaine H.M. PhD - OUHSC Department of Biochemistry & Molecular Biology

For more information, please contact the faculty lead, Dr. Cristian A. Linte.