RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers.
RNA structure
aptamer
modeling
prediction
ribozyme
Journal
RNA (New York, N.Y.)
ISSN: 1469-9001
Titre abrégé: RNA
Pays: United States
ID NLM: 9509184
Informations de publication
Date de publication:
08 2020
08 2020
Historique:
received:
12
03
2020
accepted:
03
04
2020
pubmed:
7
5
2020
medline:
6
10
2020
entrez:
7
5
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 32371455
pii: rna.075341.120
doi: 10.1261/rna.075341.120
pmc: PMC7373991
doi:
Substances chimiques
Aptamers, Nucleotide
0
Ligands
0
RNA, Catalytic
0
Riboswitch
0
RNA
63231-63-0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
982-995Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM134919
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM114015
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM117059
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM073850
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM063732
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM134864
Pays : United States
Organisme : NCATS NIH HHS
ID : UL1 TR002014
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM123247
Pays : United States
Organisme : NCI NIH HHS
ID : R21 CA219847
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA008748
Pays : United States
Organisme : NIGMS NIH HHS
ID : R35 GM122579
Pays : United States
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : NIGMS NIH HHS
ID : R21 GM102716
Pays : United States
Informations de copyright
© 2020 Miao et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.
Références
J Mol Biol. 2013 Oct 23;425(20):3790-8
pubmed: 23711504
Bioinformatics. 2015 Sep 1;31(17):2891-3
pubmed: 25910700
Nature. 1994 Nov 3;372(6501):68-74
pubmed: 7969422
Biochemistry. 2017 Jan 17;56(2):352-358
pubmed: 28001368
Cold Spring Harb Perspect Biol. 2011 Jun 01;3(6):
pubmed: 20943759
PLoS One. 2013 Oct 21;8(10):e74830
pubmed: 24204571
WSEAS Trans Math. 2013 Sep;9(12):941-955
pubmed: 25414570
Nucleic Acids Res. 2020 Jan 24;48(2):576-588
pubmed: 31799609
Protein Sci. 2018 Jan;27(1):293-315
pubmed: 29067766
Trends Biotechnol. 2005 Sep;23(9):450-5
pubmed: 16038997
Nucleic Acids Res. 2012 Aug;40(14):e112
pubmed: 22539264
Nat Methods. 2010 Apr;7(4):291-4
pubmed: 20190761
RNA. 2017 May;23(5):655-672
pubmed: 28138060
Nat Struct Mol Biol. 2009 Dec;16(12):1212-7
pubmed: 19898478
Cell. 1995 Jun 30;81(7):991-1002
pubmed: 7541315
Curr Opin Chem Biol. 2005 Apr;9(2):104-9
pubmed: 15811793
Cell Chem Biol. 2017 Jun 22;24(6):695-702.e2
pubmed: 28529131
Nucleic Acids Res. 2011 May;39(10):4007-22
pubmed: 21300639
Nature. 2004 Nov 18;432(7015):411-5
pubmed: 15549109
Nucleic Acids Res. 2016 Apr 20;44(7):e63
pubmed: 26687716
Annu Rev Biochem. 2000;69:597-615
pubmed: 10966470
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
pubmed: 10592235
RNA. 2008 Jun;14(6):1164-73
pubmed: 18456842
Mol Cell. 2011 Sep 16;43(6):867-79
pubmed: 21925376
Proc Natl Acad Sci U S A. 2004 Apr 27;101(17):6421-6
pubmed: 15096624
RNA. 2017 Sep;23(9):1338-1343
pubmed: 28600356
Sci Rep. 2012;2:734
pubmed: 23071898
Fold Des. 1998;3(6):577-87
pubmed: 9889167
Nature. 2020 Jan;577(7792):706-710
pubmed: 31942072
Proteins. 2014 Feb;82 Suppl 2:1-6
pubmed: 24344053
Mol Cell. 2017 Jan 19;65(2):220-230
pubmed: 27989440
RNA. 2012 Apr;18(4):610-25
pubmed: 22361291
Cold Spring Harb Symp Quant Biol. 2009;74:11-6
pubmed: 19850851
Nat Chem Biol. 2017 May;13(5):508-513
pubmed: 28263963
Nat Methods. 2017 Jan;14(1):45-48
pubmed: 27819659
Biochemistry. 2017 Jan 17;56(2):359-363
pubmed: 28001372
Nucleic Acids Res. 2018 Jan 4;46(D1):D335-D342
pubmed: 29112718
Nature. 1987 Aug 13-19;328(6131):596-600
pubmed: 2441261
Biochemistry. 2010 Nov 2;49(43):9123-31
pubmed: 20931966
Acta Biochim Pol. 2016;63(4):737-744
pubmed: 27741327
Annu Rev Biophys. 2017 May 22;46:483-503
pubmed: 28375730
Nat Chem Biol. 2017 Mar;13(3):295-301
pubmed: 28092358
Nature. 2008 Mar 6;452(7183):51-5
pubmed: 18322526
RNA. 2006 Jan;12(1):83-93
pubmed: 16373494
Nucleic Acids Res. 2016 Jul 8;44(W1):W315-9
pubmed: 27095203
Structure. 2017 Jan 3;25(1):195-202
pubmed: 28017522
Nat Chem Biol. 2015 Aug;11(8):606-10
pubmed: 26167874
Biochemistry. 2016 Feb 2;55(4):633-6
pubmed: 26551631
Nat Chem Biol. 2016 Sep;12(9):702-8
pubmed: 27398999
RNA. 2009 Oct;15(10):1875-85
pubmed: 19710185
RNA. 2015 Jun;21(6):1066-84
pubmed: 25883046
Cell Chem Biol. 2017 Nov 16;24(11):1407-1415.e2
pubmed: 28988949