RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme

Zhichao Miao, Ryszard W. Adamiak, Maciej Antczak, Robert T. Batey, Alexander J. Becka, Marcin Biesiada, Michał J. Boniecki, Janusz M. Bujnicki, Shi Jie Chen, Clarence Yu Cheng, Fang Chieh Chou, Adrian R. Ferré-D'Amaré, Rhiju Das, Wayne K. Dawson, Feng Ding, Nikolay Dokholyan, Stanisław Dunin-Horkawicz, Caleb Geniesse, Kalli Kappel, Wipapat KladwangAndrey Krokhotin, Grzegorz E. Łach, François Major, Thomas H. Mann, Marcin Magnus, Katarzyna Pachulska-Wieczorek, Dinshaw J. Patel, Joseph A. Piccirilli, Mariusz Popenda, Katarzyna J. Purzycka, Aiming Ren, Greggory M. Rice, John Santalucia, Joanna Sarzynska, Marta Szachniuk, Arpit Tandon, Jeremiah J. Trausch, Siqi Tian, Jian Wang, Kevin M. Weeks, Benfeard Williams, Yi Xiao, Xiaojun Xu, Dong Zhang, Tomasz Zok, Eric Westhof

Research output: Contribution to journalArticle

49 Citations (Scopus)

Abstract

RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homologyderived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.ustrasbg.fr/rnapuzzles/.

Original languageEnglish (US)
Pages (from-to)655-672
Number of pages18
JournalRNA
Volume23
Issue number5
DOIs
StatePublished - May 1 2017

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Riboswitch
Catalytic RNA
RNA
Ligands
Glutamine
Methionine
Binding Sites

All Science Journal Classification (ASJC) codes

  • Molecular Biology

Cite this

Miao, Z., Adamiak, R. W., Antczak, M., Batey, R. T., Becka, A. J., Biesiada, M., ... Westhof, E. (2017). RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA, 23(5), 655-672. https://doi.org/10.1261/rna.060368.116
Miao, Zhichao ; Adamiak, Ryszard W. ; Antczak, Maciej ; Batey, Robert T. ; Becka, Alexander J. ; Biesiada, Marcin ; Boniecki, Michał J. ; Bujnicki, Janusz M. ; Chen, Shi Jie ; Cheng, Clarence Yu ; Chou, Fang Chieh ; Ferré-D'Amaré, Adrian R. ; Das, Rhiju ; Dawson, Wayne K. ; Ding, Feng ; Dokholyan, Nikolay ; Dunin-Horkawicz, Stanisław ; Geniesse, Caleb ; Kappel, Kalli ; Kladwang, Wipapat ; Krokhotin, Andrey ; Łach, Grzegorz E. ; Major, François ; Mann, Thomas H. ; Magnus, Marcin ; Pachulska-Wieczorek, Katarzyna ; Patel, Dinshaw J. ; Piccirilli, Joseph A. ; Popenda, Mariusz ; Purzycka, Katarzyna J. ; Ren, Aiming ; Rice, Greggory M. ; Santalucia, John ; Sarzynska, Joanna ; Szachniuk, Marta ; Tandon, Arpit ; Trausch, Jeremiah J. ; Tian, Siqi ; Wang, Jian ; Weeks, Kevin M. ; Williams, Benfeard ; Xiao, Yi ; Xu, Xiaojun ; Zhang, Dong ; Zok, Tomasz ; Westhof, Eric. / RNA-Puzzles Round III : 3D RNA structure prediction of five riboswitches and one ribozyme. In: RNA. 2017 ; Vol. 23, No. 5. pp. 655-672.
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abstract = "RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homologyderived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.ustrasbg.fr/rnapuzzles/.",
author = "Zhichao Miao and Adamiak, {Ryszard W.} and Maciej Antczak and Batey, {Robert T.} and Becka, {Alexander J.} and Marcin Biesiada and Boniecki, {Michał J.} and Bujnicki, {Janusz M.} and Chen, {Shi Jie} and Cheng, {Clarence Yu} and Chou, {Fang Chieh} and Ferr{\'e}-D'Amar{\'e}, {Adrian R.} and Rhiju Das and Dawson, {Wayne K.} and Feng Ding and Nikolay Dokholyan and Stanisław Dunin-Horkawicz and Caleb Geniesse and Kalli Kappel and Wipapat Kladwang and Andrey Krokhotin and Łach, {Grzegorz E.} and Fran{\cc}ois Major and Mann, {Thomas H.} and Marcin Magnus and Katarzyna Pachulska-Wieczorek and Patel, {Dinshaw J.} and Piccirilli, {Joseph A.} and Mariusz Popenda and Purzycka, {Katarzyna J.} and Aiming Ren and Rice, {Greggory M.} and John Santalucia and Joanna Sarzynska and Marta Szachniuk and Arpit Tandon and Trausch, {Jeremiah J.} and Siqi Tian and Jian Wang and Weeks, {Kevin M.} and Benfeard Williams and Yi Xiao and Xiaojun Xu and Dong Zhang and Tomasz Zok and Eric Westhof",
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Miao, Z, Adamiak, RW, Antczak, M, Batey, RT, Becka, AJ, Biesiada, M, Boniecki, MJ, Bujnicki, JM, Chen, SJ, Cheng, CY, Chou, FC, Ferré-D'Amaré, AR, Das, R, Dawson, WK, Ding, F, Dokholyan, N, Dunin-Horkawicz, S, Geniesse, C, Kappel, K, Kladwang, W, Krokhotin, A, Łach, GE, Major, F, Mann, TH, Magnus, M, Pachulska-Wieczorek, K, Patel, DJ, Piccirilli, JA, Popenda, M, Purzycka, KJ, Ren, A, Rice, GM, Santalucia, J, Sarzynska, J, Szachniuk, M, Tandon, A, Trausch, JJ, Tian, S, Wang, J, Weeks, KM, Williams, B, Xiao, Y, Xu, X, Zhang, D, Zok, T & Westhof, E 2017, 'RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme', RNA, vol. 23, no. 5, pp. 655-672. https://doi.org/10.1261/rna.060368.116

RNA-Puzzles Round III : 3D RNA structure prediction of five riboswitches and one ribozyme. / Miao, Zhichao; Adamiak, Ryszard W.; Antczak, Maciej; Batey, Robert T.; Becka, Alexander J.; Biesiada, Marcin; Boniecki, Michał J.; Bujnicki, Janusz M.; Chen, Shi Jie; Cheng, Clarence Yu; Chou, Fang Chieh; Ferré-D'Amaré, Adrian R.; Das, Rhiju; Dawson, Wayne K.; Ding, Feng; Dokholyan, Nikolay; Dunin-Horkawicz, Stanisław; Geniesse, Caleb; Kappel, Kalli; Kladwang, Wipapat; Krokhotin, Andrey; Łach, Grzegorz E.; Major, François; Mann, Thomas H.; Magnus, Marcin; Pachulska-Wieczorek, Katarzyna; Patel, Dinshaw J.; Piccirilli, Joseph A.; Popenda, Mariusz; Purzycka, Katarzyna J.; Ren, Aiming; Rice, Greggory M.; Santalucia, John; Sarzynska, Joanna; Szachniuk, Marta; Tandon, Arpit; Trausch, Jeremiah J.; Tian, Siqi; Wang, Jian; Weeks, Kevin M.; Williams, Benfeard; Xiao, Yi; Xu, Xiaojun; Zhang, Dong; Zok, Tomasz; Westhof, Eric.

In: RNA, Vol. 23, No. 5, 01.05.2017, p. 655-672.

Research output: Contribution to journalArticle

TY - JOUR

T1 - RNA-Puzzles Round III

T2 - 3D RNA structure prediction of five riboswitches and one ribozyme

AU - Miao, Zhichao

AU - Adamiak, Ryszard W.

AU - Antczak, Maciej

AU - Batey, Robert T.

AU - Becka, Alexander J.

AU - Biesiada, Marcin

AU - Boniecki, Michał J.

AU - Bujnicki, Janusz M.

AU - Chen, Shi Jie

AU - Cheng, Clarence Yu

AU - Chou, Fang Chieh

AU - Ferré-D'Amaré, Adrian R.

AU - Das, Rhiju

AU - Dawson, Wayne K.

AU - Ding, Feng

AU - Dokholyan, Nikolay

AU - Dunin-Horkawicz, Stanisław

AU - Geniesse, Caleb

AU - Kappel, Kalli

AU - Kladwang, Wipapat

AU - Krokhotin, Andrey

AU - Łach, Grzegorz E.

AU - Major, François

AU - Mann, Thomas H.

AU - Magnus, Marcin

AU - Pachulska-Wieczorek, Katarzyna

AU - Patel, Dinshaw J.

AU - Piccirilli, Joseph A.

AU - Popenda, Mariusz

AU - Purzycka, Katarzyna J.

AU - Ren, Aiming

AU - Rice, Greggory M.

AU - Santalucia, John

AU - Sarzynska, Joanna

AU - Szachniuk, Marta

AU - Tandon, Arpit

AU - Trausch, Jeremiah J.

AU - Tian, Siqi

AU - Wang, Jian

AU - Weeks, Kevin M.

AU - Williams, Benfeard

AU - Xiao, Yi

AU - Xu, Xiaojun

AU - Zhang, Dong

AU - Zok, Tomasz

AU - Westhof, Eric

PY - 2017/5/1

Y1 - 2017/5/1

N2 - RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homologyderived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.ustrasbg.fr/rnapuzzles/.

AB - RNA-Puzzles is a collective experiment in blind 3D RNA structure prediction. We report here a third round of RNA-Puzzles. Five puzzles, 4, 8, 12, 13, 14, all structures of riboswitch aptamers and puzzle 7, a ribozyme structure, are included in this round of the experiment. The riboswitch structures include biological binding sites for small molecules (S-adenosyl methionine, cyclic diadenosine monophosphate, 5-amino 4-imidazole carboxamide riboside 5'-triphosphate, glutamine) and proteins (YbxF), and one set describes large conformational changes between ligand-free and ligand-bound states. The Varkud satellite ribozyme is the most recently solved structure of a known large ribozyme. All puzzles have established biological functions and require structural understanding to appreciate their molecular mechanisms. Through the use of fast-track experimental data, including multidimensional chemical mapping, and accurate prediction of RNA secondary structure, a large portion of the contacts in 3D have been predicted correctly leading to similar topologies for the top ranking predictions. Template-based and homologyderived predictions could predict structures to particularly high accuracies. However, achieving biological insights from de novo prediction of RNA 3D structures still depends on the size and complexity of the RNA. Blind computational predictions of RNA structures already appear to provide useful structural information in many cases. Similar to the previous RNA-Puzzles Round II experiment, the prediction of non-Watson-Crick interactions and the observed high atomic clash scores reveal a notable need for an algorithm of improvement. All prediction models and assessment results are available at http://ahsoka.ustrasbg.fr/rnapuzzles/.

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Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M et al. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA. 2017 May 1;23(5):655-672. https://doi.org/10.1261/rna.060368.116