RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers
- Zhichao Miao1,
- Ryszard W. Adamiak2,
- Maciej Antczak3,
- Michal J. Boniecki4,
- Janusz M. Bujnicki4,
- Shi-Jie Chen5,
- Clarence Yu Cheng6,
- Yi Cheng5,
- Fang-Chieh Chou6,
- Rhiju Das6,
- Nikolay V. Dokholyan7,
- Feng Ding8,
- Caleb Geniesse6,
- Yangwei Jiang5,
- Astha Joshi4,
- Andrey Krokhotin9,
- Marcin Magnus10,
- Olivier Mailhot11,
- Francois Major11,
- Thomas H. Mann6,
- Pawel Piatkowski4,
- Radoslaw Pluta4,
- Mariusz Popenda12,
- Joanna Sarzynska12,
- Lizhen Sun5,
- Marta Szachniuk2,
- Siqi Tian6,
- Jian Wang13,
- Jun Wang14,
- Andrew M. Watkins6,
- Jakub Wiedemann2,
- Yi Xiao14,
- Xiaojun Xu5,
- Joseph D. Yesselman15,
- Dong Zhang5,
- Yi Zhang14,
- Zhenzhen Zhang8,
- Chenhan Zhao5,
- Peinan Zhao5,
- Yuanzhe Zhou5,
- Tomasz Zok16,
- Adriana Zyla17,
- Aiming Ren18,
- Robert T. Batey19,
- Barbara L. Golden20,
- Lin Huang21,
- David M. Lilley22,
- Yijin Liu22,
- Dinshaw J. Patel23 and
- Eric Westhof24,25
- 1 Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine; EMBL-EBI; Newcastle University;
- 2 Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland;
- 3 Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland;
- 4 International Institute of Molecular and Cell Biology in Warsaw, Poland;
- 5 Department of Physics and Astronomy, Department of Biochemistry. MU Institute for Data Science and Informatics, University of Missouri-Columbia, USA.;
- 6 Department of Biochemistry, Stanford University School of Medicine, USA;
- 7 Department of Pharmacology, Penn State College of Medicine, Hershey, PA, 17033, USA. Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA.;
- 8 Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States;
- 9 Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Departments of Pathology, Genetics and Developmental Biology, Howard Hughes Medical Institute, S;
- 10 International Institute of Molecular and Cell Biology in Warsaw, Poland Present address: ReMedy-International Research Agenda Unit, Centre of New Technologies, University of Warsaw, Warsaw, Poland;
- 11 Inst for Rsch in Immun and Cancer, Dept of Computer Sci and Op Rsch, Univ de Montreal, Quebec, CA;
- 12 Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland;
- 13 Department of Pharmacology, Penn State College of Medicine, Hershey, PA, 17033, USA.;
- 14 Huazhong University of Science and Technology;
- 15 Department of Biochemistry, Stanford University School of Medicine, USA Present address: Department of Chemistry, University of Nebraska-Lincoln, USA;
- 16 Institute of Computing Science, Poznan University of Technology, 60-965 Poznan, Poland;
- 17 International Institute of Molecular and Cell Biology in Warsaw, Poland Present address: Department of Macromolecular Physics, Faculty of Physics, A. Mickiewicz University, Poznan, Poland;
- 18 Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China;
- 19 Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO 80309-0596, USA;
- 20 Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA;
- 21 Guangdong 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 RNA Biomedical Institute, Sun Yat-Sen Memorial Hospital,;
- 22 Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.;
- 23 Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA;
- 24 Arch et Reactivite de l'ARN, Univ de Strasbourg, Inst de Biol Mol et Cell du CNRS, Strasbourg France
- ↵* Corresponding author; email: 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 six RNA sequences: four structures of nucleolytic ribozymes and two of riboswitches. Systematic protocols for comparing models and crystal structures are described and analyzed. In these six puzzles, we discuss a) the comparison between the automated web server and human experts; b) the prediction of coaxial stacking; c) the prediction of structural details and ligand binding; d) the development of novel prediction methods; and e) the potential improvements to be made. It is illustrated that correct coaxial stacking and tertiary contacts are key for the prediction of RNA architecture, while ligand binding modes can be only predicted with low resolution and accurate ligand binding prediction 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
- Received March 12, 2020.
- Accepted April 3, 2020.
- Published by Cold Spring Harbor Laboratory Press for the RNA Society
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/.
