[PMID]: | 28138060 |
[Au] Autor: | 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 NV; Dunin-Horkawicz S; Geniesse C; Kappel K; Kladwang W; Krokhotin A; Lach 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 |
[Ad] Endereço: | Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 67000 Strasbourg, France; z.miao@ibmc-cnrs.unistra.fr e.westhof@ibmc-cnrs.unistra.fr. |
[Ti] Título: | RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. |
[So] Source: | RNA;23(5):655-672, 2017 May. |
[Is] ISSN: | 1469-9001 |
[Cp] País de publicação: | United States |
[La] Idioma: | eng |
[Ab] Resumo: | 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 ( -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 homology-derived 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.u-strasbg.fr/rnapuzzles/. |
[Mh] Termos MeSH primário: |
RNA Catalítico/química Riboswitch
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[Mh] Termos MeSH secundário: |
Aminoimidazol Carboxamida/química Aminoimidazol Carboxamida/metabolismo Aptâmeros de Nucleotídeos/química Aptâmeros de Nucleotídeos/metabolismo Fosfatos de Dinucleosídeos/metabolismo Endorribonucleases/química Endorribonucleases/metabolismo Glutamina/química Glutamina/metabolismo Ligantes Modelos Moleculares Conformação de Ácido Nucleico RNA Catalítico/metabolismo Ribonucleotídeos/química Ribonucleotídeos/metabolismo S-Adenosilmetionina/química S-Adenosilmetionina/metabolismo
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[Pt] Tipo de publicação: | JOURNAL ARTICLE |
[Nm] Nome de substância:
| 0 (Aptamers, Nucleotide); 0 (Dinucleoside Phosphates); 0 (Ligands); 0 (RNA, Catalytic); 0 (Ribonucleotides); 0 (Riboswitch); 0 (cyclic diadenosine phosphate); 0RH81L854J (Glutamine); 360-97-4 (Aminoimidazole Carboxamide); 7LP2MPO46S (S-Adenosylmethionine); 82989-82-0 (5-aminoimidazole-4-carboxamide-1-ribofuranosyl triphosphate); EC 3.1.- (Endoribonucleases); EC 3.1.27.- (varkud satellite ribozyme) |
[Em] Mês de entrada: | 1706 |
[Cu] Atualização por classe: | 170609 |
[Lr] Data última revisão:
| 170609 |
[Sb] Subgrupo de revista: | IM |
[Da] Data de entrada para processamento: | 170201 |
[St] Status: | MEDLINE |
[do] DOI: | 10.1261/rna.060368.116 |
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