Modelling viral RNA with SAXS Grzegorz Chojnowski EMBL Hamburg - PowerPoint PPT Presentation

Modelling viral RNA with SAXS Grzegorz Chojnowski EMBL Hamburg Solution Scattering from Biological Macromolecules May 5 — June 2, 2020

The central dogma of molecular biology ? DNA RNA PROTEIN In eukaryotes only a fraction of RNA is translated to proteins

Crystal structure models available for many ncRNAs

crystallography cryo-EM Small Angle Scattering

Functional structures in hepatitis C viral genomic RNA Ángel Cantero-Camacho et al. RNA 2017

Adenovirus virus-associated RNA kinase dsRBM dsRBM Dzananovic, Patel, Chojnowski et al JSB 2014

Crystal structure of adenovirus virus-associated RNA Hood, Iris V., et al. Nature Comm. 10.1 (2019): 1-12. (PDB: 6ol3)

Crystal structure of adenovirus virus-associated RNA Hood, Iris V., et al. Nature Comm. 10.1 (2019): 1-12. (PDB: 6ol3)

SAXS data may be used to select models from a set of decoys validation! Boniecki et al NAR 44, e63, 2015 https://genesilico.pl/SimRNAweb/

RNA is a modular biomolecule Chojnowski et al NAR 42, D123-D131, 2014

RNA molecules are stabilized by tertiary interactions

http://genesilico.pl/rnabricks2 Chojnowski et al NAR 42, D123-D131, 2014

RNA molecules share structural motifs Flavin and cobalamin riboswitches share a t-loop contact motif

RNA is a modular biomolecule

Fragment assembly with PyRy3d Joanna M. Kasprzak et al http:// http://genesilico.pl/pyry3d/

Fragment assembly with RNABricks and PyRy3d Fragments may be taken from existing models or RNA structure prediction programs; validation! SimRNA • ROSETTA/FARFAR • MC-Fold/MC-Sym •

Fragment assembly with RNABricks and PyRy3d Dzananovic, Patel, Chojnowski et al JSB, 185, 48-57, 2014

Adenovirus virus-associated RNA kinase dsRBM dsRBM Dzananovic, Patel, Chojnowski et al JSB 2014

1 3 2 4 5 6 validation! Patel, Chojnowski et al Methods 2017

Fragment assembly with RNABricks and PyRy3d Model based on the ab initio reconstructions of protein (cyan) and RNA (orange) components. Dzananovic, Patel, Chojnowski et al JSB, 185, 48-57, 2014

http://genesilico.pl/rnabricks2 Brickworx RNA Masonry jamais vu

RNA Masonry – RNA fragment assembly Model is optimized in a replica exchange Monte-Carlo Scoring function combines SimRNA statistical potential and SAXS curve goodness-of-fit

RNA Masonry geometry refinement The use of SimRNA force field makes the selection of motif combinations plausible

RNA Masonry – RNA fragment assembly Dzananovic, Astha, Chojnowski et al PloS One 12, 2017

RNA fragment assembly Dzananovic, Astha, Chojnowski et al PloS One 12, 2017

Crystal structure model of VA-I

Crystal structure model of VA-I

Quality control and model validation Fragment assembly • reduces ambiguity • lowers the risk of overfitting • generates models with plausible local geometry … and is relatively fast http://molprobity.biochem.duke.edu/ Patel, T. R., Chojnowski, et al. Methods , 118 , 146-162, 2017

Quality control and model validation Patel, T. R., Chojnowski, et al. Methods , 118 , 146-162, 2017

RNA Masonry availability Webservice coming soon, drop me a line if you want to test it now.

Acknowledgements IIMCB Warsaw University of Manitoba Janusz Bujnicki Sean A. McKenna Rafał Zaborowski Evan P Booy Marcin Magnus Edis Dzananovic Tomek Waleń (ClaRNA) University of Alberta Michał Boniecki (SimRNA) Trushar R. Patel Astha Joshi