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Modelling viral RNA with SAXS
Grzegorz Chojnowski EMBL Hamburg
Solution Scattering from Biological Macromolecules May 5 — June 2, 2020
Modelling viral RNA with SAXS Grzegorz Chojnowski EMBL Hamburg - - PowerPoint PPT Presentation
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
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Crystal structure models available for many ncRNAs
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crystallography cryo-EM Small Angle Scattering
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Functional structures in hepatitis C viral genomic RNA
Ángel Cantero-Camacho et al. RNA 2017
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Adenovirus virus-associated RNA
kinase dsRBM dsRBM Dzananovic, Patel, Chojnowski et al JSB 2014
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Crystal structure of adenovirus virus-associated RNA
Hood, Iris V., et al. Nature Comm. 10.1 (2019): 1-12. (PDB: 6ol3)
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Crystal structure of adenovirus virus-associated RNA
Hood, Iris V., et al. Nature Comm. 10.1 (2019): 1-12. (PDB: 6ol3)
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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/
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RNA is a modular biomolecule
Chojnowski et al NAR 42, D123-D131, 2014
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RNA molecules are stabilized by tertiary interactions
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http://genesilico.pl/rnabricks2 Chojnowski et al NAR 42, D123-D131, 2014
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Flavin and cobalamin riboswitches share a t-loop contact motif
RNA molecules share structural motifs
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RNA is a modular biomolecule
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Fragment assembly with PyRy3d
Joanna M. Kasprzak et al http:// http://genesilico.pl/pyry3d/
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validation!
Fragment assembly with RNABricks and PyRy3d
Fragments may be taken from existing models
- r RNA structure prediction programs;
- SimRNA
- ROSETTA/FARFAR
- MC-Fold/MC-Sym
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Fragment assembly with RNABricks and PyRy3d
Dzananovic, Patel, Chojnowski et al JSB, 185, 48-57, 2014
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Adenovirus virus-associated RNA
kinase dsRBM dsRBM Dzananovic, Patel, Chojnowski et al JSB 2014
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Patel, Chojnowski et al Methods 2017
validation!
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Model based on the ab initio reconstructions of protein (cyan) and RNA (orange) components.
Fragment assembly with RNABricks and PyRy3d
Dzananovic, Patel, Chojnowski et al JSB, 185, 48-57, 2014
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Brickworx RNA Masonry jamais vu
http://genesilico.pl/rnabricks2
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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
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RNA Masonry geometry refinement
The use of SimRNA force field makes the selection of motif combinations plausible
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RNA Masonry – RNA fragment assembly
Dzananovic, Astha, Chojnowski et al PloS One 12, 2017
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RNA fragment assembly
Dzananovic, Astha, Chojnowski et al PloS One 12, 2017
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Crystal structure model of VA-I
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Crystal structure model of VA-I
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Patel, T. R., Chojnowski, et al. Methods, 118, 146-162, 2017
Quality control and model validation
http://molprobity.biochem.duke.edu/
Fragment assembly
- reduces ambiguity
- lowers the risk of overfitting
- generates models with plausible local geometry
… and is relatively fast
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Patel, T. R., Chojnowski, et al. Methods, 118, 146-162, 2017
Quality control and model validation
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RNA Masonry availability
Webservice coming soon, drop me a line if you want to test it now.
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