RPpocket: An RNA-Protein Intuitive Database with RNA Pocket Topology Resources.
RNA–protein interaction
interaction mechanism
pocket database
Journal
International journal of molecular sciences
ISSN: 1422-0067
Titre abrégé: Int J Mol Sci
Pays: Switzerland
ID NLM: 101092791
Informations de publication
Date de publication:
21 Jun 2022
21 Jun 2022
Historique:
received:
24
05
2022
revised:
13
06
2022
accepted:
20
06
2022
entrez:
9
7
2022
pubmed:
10
7
2022
medline:
14
7
2022
Statut:
epublish
Résumé
RNA-protein complexes regulate a variety of biological functions. Thus, it is essential to explore and visualize RNA-protein structural interaction features, especially pocket interactions. In this work, we develop an easy-to-use bioinformatics resource: RPpocket. This database provides RNA-protein complex interactions based on sequence, secondary structure, and pocket topology analysis. We extracted 793 pockets from 74 non-redundant RNA-protein structures. Then, we calculated the binding- and non-binding pocket topological properties and analyzed the binding mechanism of the RNA-protein complex. The results showed that the binding pockets were more extended than the non-binding pockets. We also found that long-range forces were the main interaction for RNA-protein recognition, while short-range forces strengthened and optimized the binding. RPpocket could facilitate RNA-protein engineering for biological or medical applications.
Identifiants
pubmed: 35805909
pii: ijms23136903
doi: 10.3390/ijms23136903
pmc: PMC9266927
pii:
doi:
Substances chimiques
Ligands
0
Proteins
0
RNA
63231-63-0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : National Natural Science Foundation of China
ID : 12175081
Références
Genes Dev. 2002 Oct 15;16(20):2583-92
pubmed: 12381658
RSC Adv. 2020 Jan 10;10(4):2004-2015
pubmed: 35494619
Cell Res. 2022 Jan;32(1):9-23
pubmed: 34737357
BMC Bioinformatics. 2019 Oct 15;20(1):497
pubmed: 31615418
Wiley Interdiscip Rev RNA. 2017 Jan;8(1):
pubmed: 27324829
Nucleic Acids Res. 2017 Jan 4;45(D1):D408-D414
pubmed: 27794551
BMC Bioinformatics. 2006 Jun 21;7:312
pubmed: 16790052
BMC Bioinformatics. 2021 Sep 8;22(1):428
pubmed: 34496744
Nucleic Acids Res. 2019 Jan 8;47(D1):D601-D606
pubmed: 30445601
RNA. 2013 Dec;19(12):1605-16
pubmed: 24145824
Bioinformatics. 2012 Dec 1;28(23):3150-2
pubmed: 23060610
FEBS J. 2007 Dec;274(24):6378-91
pubmed: 18005254
J Mol Biol. 1971 Feb 14;55(3):379-400
pubmed: 5551392
Bioinformatics. 2006 Jul 1;22(13):1658-9
pubmed: 16731699
Nucleic Acids Res. 2017 Jul 3;45(W1):W337-W343
pubmed: 28472372
Nucleic Acids Res. 2015 Feb 18;43(3):1370-9
pubmed: 25609700
Bioinformatics. 2018 Sep 15;34(18):3131-3136
pubmed: 29718097
Nucleic Acids Res. 2015 Jul 1;43(W1):W258-63
pubmed: 25990735
Pac Symp Biocomput. 2010;:293-301
pubmed: 19908381
Nucleic Acids Res. 2014 Jan;42(Database issue):D114-22
pubmed: 24185695
BMC Bioinformatics. 2014;15 Suppl 15:S5
pubmed: 25474259
Nucleic Acids Res. 2000 Jan 1;28(1):235-42
pubmed: 10592235
Trends Biochem Sci. 2017 May;42(5):369-382
pubmed: 28268044
Nucleic Acids Res. 2017 Jul 3;45(W1):W365-W373
pubmed: 28521030
Nucleic Acids Res. 2015 Jan;43(Database issue):D36-42
pubmed: 25355515
Nat Rev Genet. 2013 Apr;14(4):275-87
pubmed: 23478349
BMC Bioinformatics. 2010 May 06;11:231
pubmed: 20459631
RNA Biol. 2011 Mar-Apr;8(2):305-15
pubmed: 21505273
Annu Rev Biophys Bioeng. 1977;6:151-76
pubmed: 326146
Bioinformatics. 2012 Aug 1;28(15):2074-5
pubmed: 22628523
Nucleic Acids Res. 2019 Jan 8;47(D1):D529-D541
pubmed: 30476227
Nat Biotechnol. 2006 Dec;24(12):1565-7
pubmed: 17160063
Proteins. 2012 Jul;80(7):1872-82
pubmed: 22488990
J Comput Chem. 2013 Feb 5;34(4):311-8
pubmed: 23047523
Protein Eng. 1995 Feb;8(2):127-34
pubmed: 7630882
Nucleic Acids Res. 2015 Jul 1;43(W1):W425-30
pubmed: 25977296
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W555-62
pubmed: 20478824
J Chem Inf Model. 2011 Oct 24;51(10):2778-86
pubmed: 21919503
Nucleic Acids Res. 2013 Jan;41(Database issue):D841-4
pubmed: 23193266
BMC Bioinformatics. 2019 Nov 29;20(1):617
pubmed: 31783725
Semin Cell Dev Biol. 2011 Jun;22(4):359-65
pubmed: 21333748
Nucleic Acids Res. 2020 Jan 8;48(D1):D160-D165
pubmed: 31670377
Nucleic Acids Res. 2018 Jan 4;46(D1):D194-D201
pubmed: 29040625
Bioinformatics. 2015 Oct 15;31(20):3377-9
pubmed: 26099263
Proteins. 2017 Feb;85(2):256-267
pubmed: 27862282
Nucleic Acids Res. 2020 Jan 8;48(D1):D189-D197
pubmed: 31906603
Comput Biol Chem. 2019 Dec;83:107088
pubmed: 31330489
Annu Rev Biochem. 1979;48:719-54
pubmed: 382996