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Kinetoplastid RNA editing ligases 1 and 2 exhibit different electrostatic properties

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Abstract

Kinetoplastid RNA editing ligases 1 and 2 (KREL1 and KREL2) share a significant degree of sequence homology. However, biochemical experiments have reported that KREL1 and KREL2 differ in their functional roles during the RNA editing process. In this study, we hypothesize that dissimilar roles for KREL1 and KREL2 proteins arise from their different physicochemical characteristics. To test our hypothesis at sequence level, we plotted theoretical titration curves for KREL1, KREL2 and their binding partner proteins. The plots showed a lower isoelectric point for KREL1 compared to that for KREL2 as well as more relative alkalinity and acidity for binding partner proteins of KREL1 and KREL2 at net charge zero, respectively. At structure level, based on the available high resolution structure of KREL1 N-terminal domain and strong sequence similarity between KRELs and other ligases, we built the homology model of KREL2 N-terminal domain. Using Poisson-Boltzmann continuum approach, we calculated the electrostatic potential isosurfaces of KREL1 structure and KREL2 model. KREL1 and KREL2 coordinates differed in their electrostatic isopotential patterns. A wider negative patch on the surface of KREL1 suggests differential affinity for another protein compared to KREL2. In contrast, a larger positive patch on the KREL2 surface predicts its differential affinity and/or specificity for its RNA substrate. Subsequently, we employed in silico mutational scanning and identified the surface-exposed residues contributing to the long-range electrostatic energy of KRELs. We predict that two structurally conserved loops of KRELs, not previously reported in the literature, also recognize their RNA substrates. Our results provide important information about the physicochemical properties of RNA editing ligases that could contribute to the ligation step of RNA editing.

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Acknowledgements

We thank the members of the Salavati laboratory for their discussion and critical reading of the manuscript. We also thank Prof. Enrico O. Purisima (National Research Council of Canada) for valuable comments. Research at the Institute of Parasitology is supported by the Centre for Host-Parasite Interactions and Le Fonds québécois de la recherche sur la nature et les technologies (FQRNT), Quebec. This research is supported by the National Sciences and Engineering Research Council of Canada (NSERC) grant #328186 and Leaders Opportunity Fund (LOF) grant #12573 to R.S.

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  1. Institute of Parasitology, McGill Centre for Bioinformatics, 21–111 Lakeshore Road, Ste. Anne de Bellevue, Quebec, H9X 3V9, Canada

    Alireza Shaneh & Reza Salavati

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  1. Alireza Shaneh
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  2. Reza Salavati
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Correspondence to Reza Salavati.

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Supplementary Figure

The electrostatic potential dendeogram (epogram) of the modeled TbREL2 and the crystal structure of TbREL1 (PDB:1XDN). The clusters are bound in red boxes. The best model is labeled as “TbREL2 N-terminal model” (DOC 32 kb).

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Shaneh, A., Salavati, R. Kinetoplastid RNA editing ligases 1 and 2 exhibit different electrostatic properties. J Mol Model 16, 61–76 (2010). https://doi.org/10.1007/s00894-009-0506-1

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