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 (Lead / Corresponding author)

    Research output: Contribution to journalArticlepeer-review

    78 Citations (Scopus)
    77 Downloads (Pure)

    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.

    Original languageEnglish
    Pages (from-to)982-995
    Number of pages14
    JournalRNA: a Publication of the RNA Society
    Volume26
    Issue number8
    Early online date5 May 2020
    DOIs
    Publication statusPublished - 1 Aug 2020

    Keywords

    • RNA structure
    • aptamer
    • modeling
    • prediction
    • ribozyme

    ASJC Scopus subject areas

    • Molecular Biology

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