RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers

Zhichao Miao (Lead / Corresponding author), Ryszard W. Adamiak, Maciej Antczak, Michal J. Boniecki, Janusz M. 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. MannPawel Piatkowski, 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 Zyla, Aiming Ren, Robert T. Batey, Barbara L. Golden, Lin Huang, David M. Lilley, Yijin Liu, Dinshaw J. Patel, Eric Westhof

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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.

Original languageEnglish
Number of pages36
JournalRNA: a Publication of the RNA Society
Early online date5 May 2020
DOIs
Publication statusE-pub ahead of print - 5 May 2020

Keywords

  • RNA structure
  • aptamer
  • modeing
  • prediction
  • ribozyme

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    Miao, Z., Adamiak, R. W., Antczak, M., Boniecki, M. J., Bujnicki, J. M., Chen, S-J., Cheng, C. Y., Cheng, Y., Chou, F-C., Das, R., Dokholyan, N. V., Ding, F., Geniesse, C., Jiang, Y., Joshi, A., Krokhotin, A., Magnus, M., Mailhot, O., Major, F., ... Westhof, E. (2020). RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. RNA: a Publication of the RNA Society. https://doi.org/10.1261/rna.075341.120