RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.

Zhichao Miao, Ryszard W Adamiak, Maciej Antczak, Robert T Batey, Alexander J Becka, Marcin Biesiada, Michał J Boniecki, Janusz M Bujnicki, Shi-Jie Chen, Clarence Yu Cheng, Fang-Chieh Chou, Adrian R Ferré-D'Amaré, Rhiju Das, Wayne K Dawson, Feng Ding, Nikolay V Dokholyan, Stanisław Dunin-Horkawicz, Caleb Geniesse, Kalli Kappel, Wipapat Kladwang, Andrey Krokhotin, Grzegorz E Łach, François Major, Thomas H Mann, Marcin Magnus, Katarzyna Pachulska-Wieczorek, Dinshaw J Patel, Joseph A Piccirilli, Mariusz Popenda, Katarzyna J Purzycka, Aiming Ren, Greggory M Rice, John Santalucia, Joanna Sarzynska, Marta Szachniuk, Arpit Tandon, Jeremiah J Trausch, Siqi Tian, Jian Wang, Kevin M Weeks, Benfeard Williams, Yi Xiao, Xiaojun Xu, Dong Zhang, Tomasz Zok, Eric Westhof

Journal: RNA (New York, N.Y.) 2017;23(5):655-672

PMID: 28138060

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Abstract

RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homology-derived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.u-strasbg.fr/rnapuzzles/.

Address: Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67000 Strasbourg, France; [email protected] [email protected].; Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.; Poznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland.; Poznan University of Technology, Institute of Computing Science, 60-965 Poznan, Poland.; Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0596, USA.; Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.; Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland.; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.; Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland.; Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri-Columbia, Columbia, Missouri 65211, USA.; National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA.; Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA.; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.; Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, H3C 3J7, Canada.; Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA.; Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland.; Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA.; Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.; Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.; Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA.; Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA.; DNA Software, Ann Arbor, Michigan 48104, USA.; Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.

DOI: 10.1261/rna.060368.116

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MeSH Terms: Aminoimidazole Carboxamide, Aptamers, Nucleotide, Dinucleoside Phosphates, Endoribonucleases, Glutamine, Ligands, Models, Molecular, Nucleic Acid Conformation, RNA, Catalytic, Ribonucleotides, Riboswitch, S-Adenosylmethionine