Imaging Science Seminar: Using X-ray Photons to Study RNA editing in Trypanosomes and Tools to ease the use of PyMOL

Imaging Science Seminar
Using X-ray Photons to Study RNA editing in Trypanosomes and Tools to ease the use of PyMOL

Dr. Blaine Mooers
Associate Professor
University of Oklahoma Health Sciences Center

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Abstract:

Uridine (U) insertion/deletion editing in trypanosomes corrects the coding sequence of most mitochondrial mRNAs. This editing is required for the subsequent expression of several mitochondrial proteins. The editing reactions are directed by hundreds of different guide RNAs. 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 study fragments of the RNA editing substrates.We use both in-house and synchrotron radiation X-ray sources. I will share the details of doing biology experiments at billion dollar physics facilities. To visualize the resulting molecular structures, we use PyMOL, a popular molecular graphics program. It is easy to make beautiful overview figures of biomacromolecules with PyMOL, but it is not so easy to other structural analysis tasks. I will present a set of tools that we developed to ease the use of PyMOL.

Bio:
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.

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