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For: Cilley CD, Williamson JR. Structural mimicry in the phage phi21 N peptide-boxB RNA complex. RNA 2003;9:663-676. [PMID: 12756325 PMCID: PMC1370434 DOI: 10.1261/rna.2189203] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2002] [Accepted: 02/14/2003] [Indexed: 05/24/2023]
Number Cited by Other Article(s)
1
RPflex: A Coarse-Grained Network Model for RNA Pocket Flexibility Study. Int J Mol Sci 2023;24:ijms24065497. [PMID: 36982570 PMCID: PMC10058308 DOI: 10.3390/ijms24065497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/18/2023]  Open
2
Early antitermination in the atypical coliphage mEp021 mediated by the Gp17 protein. Arch Virol 2023;168:92. [PMID: 36795170 DOI: 10.1007/s00705-023-05721-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/09/2023] [Indexed: 02/17/2023]
3
Raad NG, Ghattas IR, Amano R, Watanabe N, Sakamoto T, Smith CA. Altered‐specificity mutants of the HIV Rev arginine‐rich motif‐RRE IIB interaction. J Mol Recognit 2020;33:e2833. [DOI: 10.1002/jmr.2833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 12/08/2019] [Accepted: 12/20/2019] [Indexed: 11/10/2022]
4
Parsonnet NV, Lammer NC, Holmes ZE, Batey RT, Wuttke DS. The glucocorticoid receptor DNA-binding domain recognizes RNA hairpin structures with high affinity. Nucleic Acids Res 2019;47:8180-8192. [PMID: 31147715 DOI: 10.1093/nar/gkz486] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/17/2019] [Accepted: 05/21/2019] [Indexed: 01/04/2023]  Open
5
Krepl M, Vögele J, Kruse H, Duchardt-Ferner E, Wöhnert J, Sponer J. An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch. Nucleic Acids Res 2018;46:6528-6543. [PMID: 29893898 PMCID: PMC6061696 DOI: 10.1093/nar/gky490] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/23/2018] [Indexed: 01/04/2023]  Open
6
Goodson JR, Klupt S, Zhang C, Straight P, Winkler WC. LoaP is a broadly conserved antiterminator protein that regulates antibiotic gene clusters in Bacillus amyloliquefaciens. Nat Microbiol 2017;2:17003. [PMID: 28191883 DOI: 10.1038/nmicrobiol.2017.3] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/04/2017] [Indexed: 01/22/2023]
7
HK022 Nun Requires Arginine-Rich Motif Residues Distinct from λ N. J Bacteriol 2015;197:3573-82. [PMID: 26350130 DOI: 10.1128/jb.00466-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/24/2015] [Indexed: 11/20/2022]  Open
8
Simon B, Masiewicz P, Ephrussi A, Carlomagno T. The structure of the SOLE element of oskar mRNA. RNA (NEW YORK, N.Y.) 2015;21:1444-53. [PMID: 26089324 PMCID: PMC4509934 DOI: 10.1261/rna.049601.115] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/29/2015] [Indexed: 05/23/2023]
9
Simon B, Masiewicz P, Ephrussi A, Carlomagno T. The structure of the SOLE element of oskar mRNA. RNA (NEW YORK, N.Y.) 2015;21:1444-1453. [PMID: 26089324 DOI: 10.1261/rna.049601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/29/2015] [Indexed: 05/23/2023]
10
Possik EJ, Bou Sleiman MS, Ghattas IR, Smith CA. Randomized codon mutagenesis reveals that the HIV Rev arginine-rich motif is robust to substitutions and that double substitution of two critical residues alters specificity. J Mol Recognit 2013;26:286-96. [PMID: 23595810 DOI: 10.1002/jmr.2272] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Revised: 02/09/2013] [Accepted: 02/10/2013] [Indexed: 02/05/2023]
11
Harris RC, Bredenberg JH, Silalahi ARJ, Boschitsch AH, Fenley MO. Understanding the physical basis of the salt dependence of the electrostatic binding free energy of mutated charged ligand-nucleic acid complexes. Biophys Chem 2011;156:79-87. [PMID: 21458909 DOI: 10.1016/j.bpc.2011.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 02/08/2011] [Accepted: 02/21/2011] [Indexed: 12/01/2022]
12
Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FHT. Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011;58:1-61. [PMID: 21241883 DOI: 10.1016/j.pnmrs.2010.10.001] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 04/24/2010] [Indexed: 05/30/2023]
13
Zhang X, Lee SW, Zhao L, Xia T, Qin PZ. Conformational distributions at the N-peptide/boxB RNA interface studied using site-directed spin labeling. RNA (NEW YORK, N.Y.) 2010;16:2474-2483. [PMID: 20980674 PMCID: PMC2995408 DOI: 10.1261/rna.2360610] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 09/11/2010] [Indexed: 05/30/2023]
14
Bahadur RP, Kannan S, Zacharias M. Binding of the bacteriophage P22 N-peptide to the boxB RNA motif studied by molecular dynamics simulations. Biophys J 2010;97:3139-49. [PMID: 20006951 DOI: 10.1016/j.bpj.2009.09.035] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 08/28/2009] [Accepted: 09/01/2009] [Indexed: 11/30/2022]  Open
15
Horiya S, Inaba M, Koh CS, Uehara H, Masui N, Mizuguchi M, Ishibashi M, Matsufuji S, Harada K. Replacement of the λ boxB RNA-N peptide with heterologous RNA-peptide interactions relaxes the strict spatial requirements for the formation of a transcription anti-termination complex. Mol Microbiol 2009;74:85-97. [DOI: 10.1111/j.1365-2958.2009.06852.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
16
Michael LA, Chenault JA, Miller BR, Knolhoff AM, Nagan MC. Water, Shape Recognition, Salt Bridges, and Cation–Pi Interactions Differentiate Peptide Recognition of the HIV Rev-Responsive Element. J Mol Biol 2009;392:774-86. [DOI: 10.1016/j.jmb.2009.07.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 07/06/2009] [Accepted: 07/16/2009] [Indexed: 10/20/2022]
17
The RNA-binding domain of bacteriophage P22 N protein is highly mutable, and a single mutation relaxes specificity toward lambda. J Bacteriol 2008;190:7699-708. [PMID: 18820025 DOI: 10.1128/jb.00997-08] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
18
Kawakami J, Okabe S, Tanabe Y, Sugimoto N. Recognition of a flipped base in a hairpinloop DNA by a small peptide. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008;27:292-308. [PMID: 18260012 DOI: 10.1080/15257770701845261] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
19
Bacteriophage P22 antitermination boxB sequence requirements are complex and overlap with those of lambda. J Bacteriol 2008;190:4263-71. [PMID: 18424516 DOI: 10.1128/jb.00059-08] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
20
Epshtein V, Cardinale CJ, Ruckenstein AE, Borukhov S, Nudler E. An allosteric path to transcription termination. Mol Cell 2008;28:991-1001. [PMID: 18158897 DOI: 10.1016/j.molcel.2007.10.011] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2007] [Revised: 07/18/2007] [Accepted: 10/10/2007] [Indexed: 01/22/2023]
21
dos Santos G, Simmonds AJ, Krause HM. A stem-loop structure in the wingless transcript defines a consensus motif for apical RNA transport. Development 2007;135:133-43. [PMID: 18045835 DOI: 10.1242/dev.014068] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
22
Kawakami J, Sugimoto N, Tokitoh H, Tanabe Y. A novel stable RNA pentaloop that interacts specifically with a motif peptide of lambda-N protein. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2006;25:397-416. [PMID: 16838834 DOI: 10.1080/15257770600684027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
23
Franklin NC. Morphing molecular specificities between Arm-peptide and NUT-RNA in the antitermination complexes of bacteriophages lambda and P22. Mol Microbiol 2004;52:815-22. [PMID: 15101986 DOI: 10.1111/j.1365-2958.2004.04018.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
24
Das C, Frankel AD. Sequence and structure space of RNA-binding peptides. Biopolymers 2003;70:80-5. [PMID: 12925994 DOI: 10.1002/bip.10429] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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