RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers
- Zhichao Miao1,2,3,
- Ryszard W. Adamiak4,5,
- Maciej Antczak4,5,
- Michał J. Boniecki6,
- Janusz Bujnicki6,
- Shi-Jie Chen7,
- Clarence Yu Cheng8,
- Yi Cheng7,
- Fang-Chieh Chou8,
- Rhiju Das8,
- Nikolay V. Dokholyan9,10,
- Feng Ding11,
- Caleb Geniesse8,
- Yangwei Jiang7,
- Astha Joshi6,24,
- Andrey Krokhotin12,13,
- Marcin Magnus6,25,
- Olivier Mailhot14,
- Francois Major14,
- Thomas H. Mann8,26,
- Paweł Piątkowski6,
- Radoslaw Pluta6,27,
- Mariusz Popenda4,
- Joanna Sarzynska4,
- Lizhen Sun7,
- Marta Szachniuk4,5,
- Siqi Tian8,
- Jian Wang9,
- Jun Wang15,
- Andrew M. Watkins8,
- Jakub Wiedemann4,5,
- Yi Xiao15,
- Xiaojun Xu7,
- Joseph D. Yesselman8,28,
- Dong Zhang7,
- Yi Zhang15,
- Zhenzhen Zhang11,
- Chenhan Zhao7,
- Peinan Zhao7,
- Yuanzhe Zhou7,
- Tomasz Zok5,
- Adriana Żyła6,29,
- Aiming Ren16,
- Robert T. Batey17,
- Barbara L. Golden18,
- Lin Huang19,20,21,
- David M. Lilley21,
- Yijin Liu21,
- Dinshaw J. Patel22 and
- Eric Westhof23
- 1Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China;
- 2European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, CB10 1SD, United Kingdom;
- 3Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, United Kingdom;
- 4Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland;
- 5Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland;
- 6International Institute of Molecular and Cell Biology in Warsaw, Księcia Trojdena 4, 02-109 Warsaw, Poland;
- 7Department of Physics and Astronomy, Department of Biochemistry, MU Institute for Data Science and Informatics, University of Missouri-Columbia, Missouri 65211, USA;
- 8Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA;
- 9Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, 17033, USA;
- 10Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, Pennsylvania, 17033, USA;
- 11Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA;
- 12Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA;
- 13Departments of Pathology, Genetics and Developmental Biology, Howard Hughes Medical Institute, Stanford Medical School, Palo Alto, California, 94305, USA;
- 14Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Operations Research, Université de Montréal, Montréal, Québec, H3C 3J7, Canada;
- 15School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China;
- 16Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China;
- 17Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, Colorado 80309-0596, USA;
- 18Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA;
- 19Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P. R. China;
- 20RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, P. R. China;
- 21Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom;
- 22Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA;
- 23Arch et Reactivite de l'ARN, Univ de Strasbourg, Inst de Biol Mol et Cell du CNRS, 67084 Strasbourg, France
- Corresponding authors: zmiao{at}ebi.ac.uk, e.westhof{at}ibmc-cnrs.unistra.fr
Abstract
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA 3D structure prediction. With agreement from crystallographers, the RNA structures are predicted by various groups before the publication of the crystal structures. We now report the prediction of 3D structures for six RNA sequences: four nucleolytic ribozymes and two riboswitches. Systematic protocols for comparing models and crystal structures are described and analyzed. In these six puzzles, we discuss (i) the comparison between the automated web servers and human experts; (ii) the prediction of coaxial stacking; (iii) the prediction of structural details and ligand binding; (iv) the development of novel prediction methods; and (v) the potential improvements to be made. We show that correct prediction of coaxial stacking and tertiary contacts is essential for the prediction of RNA architecture, while ligand binding modes can only be predicted with low resolution and simultaneous prediction of RNA structure with accurate ligand binding still remains out of reach. All the predicted models are available for the future development of force field parameters and the improvement of comparison and assessment tools.
Keywords
Footnotes
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Article is online at http://www.rnajournal.org/cgi/doi/10.1261/rna.075341.120.
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Freely available online through the RNA Open Access option.
- Received March 12, 2020.
- Accepted April 3, 2020.
This article, published in RNA, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
