Computational modeling of protein-RNA complex structures.

Irina Tuszynska, Dorota Matelska, Marcin Magnus, Grzegorz Chojnowski, Joanna M Kasprzak, Lukasz P Kozlowski, Stanislaw Dunin-Horkawicz, Janusz M Bujnicki

Journal: Methods (San Diego, Calif.) 2014;65(3):310-9

PMID: 24083976

Full Text on Elsevier Science View on PubMed

Abstract

Protein-RNA interactions play fundamental roles in many biological processes, such as regulation of gene expression, RNA splicing, and protein synthesis. The understanding of these processes improves as new structures of protein-RNA complexes are solved and the molecular details of interactions analyzed. However, experimental determination of protein-RNA complex structures by high-resolution methods is tedious and difficult. Therefore, studies on protein-RNA recognition and complex formation present major technical challenges for macromolecular structural biology. Alternatively, protein-RNA interactions can be predicted by computational methods. Although less accurate than experimental measurements, theoretical models of macromolecular structures can be sufficiently accurate to prompt functional hypotheses and guide e.g. identification of important amino acid or nucleotide residues. In this article we present an overview of strategies and methods for computational modeling of protein-RNA complexes, including software developed in our laboratory, and illustrate it with practical examples of structural predictions.

Address: Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland. Electronic address: [email protected].; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland. Electronic address: [email protected].; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland. Electronic address: [email protected].; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland. Electronic address: [email protected].; Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614 Poznan, Poland. Electronic address: [email protected].; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland. Electronic address: [email protected].; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland. Electronic address: [email protected].; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland; Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, PL-61-614 Poznan, Poland. Electronic address: [email protected].

DOI: 10.1016/j.ymeth.2013.09.014

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MeSH Terms: Bacillus subtilis, Binding Sites, Computational Biology, Databases, Protein, Escherichia coli, Escherichia coli Proteins, Molecular Conformation, Molecular Docking Simulation, Protein Binding, RNA, Ribosomal, 16S, RNA-Binding Proteins, Riboswitch, Software, Thermoanaerobacter