Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, 02-109 Warsaw, and Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland; email: iamb@genesilico.pl
In addition to mRNAs, whose primary function is transmission of genetic information from DNA to proteins, numerous other classes of RNA molecules exist, which are involved in a variety of functions, such as catalyzing biochemical reactions or performing regulatory roles. In analogy to proteins, the function of these RNAs often depends on 3D structure and dynamics, which are largely determined by the ribonucleotide sequence. Experimental determination of high-resolution RNA structures is both laborious and difficult, and therefore the majority of known RNAs remain structurally uncharacterized. To address this problem, computational structure prediction methods were developed. All computational methods suffer from various limitations that make them generally unreliable for structure prediction of long RNA sequences. However, in many cases the limitations of computational and experimental methods can be overcome by combining these two complementary approaches with each other.
I will present computational methods for prediction of RNA 3D structures and RNA-protein complexes developed in my group, with emphasis on software that can utilize restraints derived from experimental analyzes (SimRNA and PyRy3D). I will also present a method for structure-based RNA sequence design.
References:
- Rother et al. (2011) RNA and protein 3D structure modeling: similarities and differences. J Mol Model, 17, 2325-2336.
- Tuszynska and Bujnicki (2011) DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking. BMC Bioinformatics, 12, 348.
Rother et al. (2011) ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Res, 39, 4007-4022.
- Chojnowski et al. (2012) RIBER/DIBER: a software suite for crystal content analysis in the studies of protein-nucleic acid complexes. Bioinformatics, 28, 880-881.
- Pietal et al. (2012) RNAmap2D - calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures. BMC Bioinformatics, 13, 333.
- Matelska et al. (2013) S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA. RNA 19(10):1341-8.
- Tuszynska et al. (2013) Computational modeling of protein-RNA complex structures. Methods 2014 Feb;65(3):310-9
- Chojnowski et al. (2014) RNA Bricks - a database of RNA 3D motifs and their interactions Nucleic Acids Res 42(1):D123-31.
- Smietanski et al. (2014) Structural analysis of human 2′-O-ribose methyltransferases involved in mRNA cap structure formation Nature Commun 5:3004, doi:10.1038/ncomms4004
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- Głów et al. (2015) Sequence-specific cleavage of dsRNA by Mini-III RNase. Nucleic Acids Res. 2015 Jan 29. pii: gkv009.