RNA-Puzzles round IV: 3D Structure predictions of four ribozymes and two aptamers

Zhichao Miao, Ryszard W. Adamiak, Maciej Antczak, Michał J. Boniecki, Janusz Bujnicki, Shi Jie Chen, Clarence Yu Cheng, Yi Cheng, Fang Chieh Chou, Rhiju Das, Nikolay V. Dokholyan, Feng Ding, Caleb Geniesse, Yangwei Jiang, Astha Joshi, Andrey Krokhotin, Marcin Magnus, Olivier Mailhot, Francois Major, Thomas H. MannPaweł Piątkowski, Radoslaw Pluta, Mariusz Popenda, Joanna Sarzynska, Lizhen Sun, Marta Szachniuk, Siqi Tian, Jian Wang, Jun Wang, Andrew M. Watkins, Jakub Wiedemann, Yi Xiao, Xiaojun Xu, Joseph D. Yesselman, Dong Zhang, Yi Zhang, Zhenzhen Zhang, Chenhan Zhao, Peinan Zhao, Yuanzhe Zhou, Tomasz Zok, Adriana Żyła, Aiming Ren, Robert T. Batey, Barbara L. Golden, Lin Huang, David M. Lilley, Yijin Liu, Dinshaw J. Patel, Eric Westhof

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

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 a) the comparison between the automated web servers 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. We show that correct prediction of coaxial stacking and tertiary contacts is essential for the prediction of RNA architecture, while ligand binding modes can be only 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.

Original languageEnglish (US)
JournalRNA
Volume26
Issue number8
DOIs
StatePublished - Aug 2020

All Science Journal Classification (ASJC) codes

  • Molecular Biology

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