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For: Andreou AZ, Klostermeier D. Conformational changes of DEAD-box helicases monitored by single molecule fluorescence resonance energy transfer. Methods Enzymol 2012;511:75-109. [PMID: 22713316 DOI: 10.1016/b978-0-12-396546-2.00004-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Number Cited by Other Article(s)
1
Krause L, Willing F, Andreou AZ, Klostermeier D. The domains of yeast eIF4G, eIF4E and the cap fine-tune eIF4A activities through an intricate network of stimulatory and inhibitory effects. Nucleic Acids Res 2022;50:6497-6510. [PMID: 35689631 PMCID: PMC9226541 DOI: 10.1093/nar/gkac437] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/19/2022] [Accepted: 05/23/2022] [Indexed: 12/13/2022]  Open
2
Venus S, Jankowsky E. Measuring the impact of cofactors on RNA helicase activities. Methods 2022;204:376-385. [PMID: 35429628 PMCID: PMC9306305 DOI: 10.1016/j.ymeth.2022.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/03/2022] [Accepted: 04/12/2022] [Indexed: 12/25/2022]  Open
3
Chakraborty A, Krause L, Klostermeier D. Determination of rate constants for conformational changes of RNA helicases by single-molecule FRET TIRF microscopy. Methods 2022;204:428-441. [PMID: 35304246 DOI: 10.1016/j.ymeth.2022.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/10/2022] [Accepted: 03/13/2022] [Indexed: 12/18/2022]  Open
4
Analysis of the conformational space and dynamics of RNA helicases by single-molecule FRET in solution and on surfaces. Methods Enzymol 2022;673:251-310. [DOI: 10.1016/bs.mie.2022.03.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
5
DEAD-box RNA Helicase DDX3: Functional Properties and Development of DDX3 Inhibitors as Antiviral and Anticancer Drugs. Molecules 2020;25:molecules25041015. [PMID: 32102413 PMCID: PMC7070539 DOI: 10.3390/molecules25041015] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/05/2020] [Accepted: 02/21/2020] [Indexed: 12/11/2022]  Open
6
Licatalosi DD, Ye X, Jankowsky E. Approaches for measuring the dynamics of RNA-protein interactions. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020;11:e1565. [PMID: 31429211 PMCID: PMC7006490 DOI: 10.1002/wrna.1565] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 07/20/2019] [Accepted: 07/25/2019] [Indexed: 12/17/2022]
7
Andreou AZ, Harms U, Klostermeier D. Single-stranded regions modulate conformational dynamics and ATPase activity of eIF4A to optimize 5'-UTR unwinding. Nucleic Acids Res 2019;47:5260-5275. [PMID: 30997503 PMCID: PMC6547412 DOI: 10.1093/nar/gkz254] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/26/2019] [Accepted: 03/29/2019] [Indexed: 01/14/2023]  Open
8
Jiang C, Tang Y, Ding L, Tan R, Li X, Lu J, Jiang J, Cui Z, Tang Z, Li W, Cao Z, Schneider-Poetsch T, Jiang W, Luo C, Ding Y, Liu J, Dang Y. Targeting the N Terminus of eIF4AI for Inhibition of Its Catalytic Recycling. Cell Chem Biol 2019;26:1417-1426.e5. [DOI: 10.1016/j.chembiol.2019.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 05/26/2019] [Accepted: 07/23/2019] [Indexed: 12/12/2022]
9
Hashemi V, Masjedi A, Hazhir-Karzar B, Tanomand A, Shotorbani SS, Hojjat-Farsangi M, Ghalamfarsa G, Azizi G, Anvari E, Baradaran B, Jadidi-Niaragh F. The role of DEAD-box RNA helicase p68 (DDX5) in the development and treatment of breast cancer. J Cell Physiol 2018;234:5478-5487. [PMID: 30417346 DOI: 10.1002/jcp.26912] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/13/2018] [Indexed: 12/13/2022]
10
Samatanga B, Andreou AZ, Klostermeier D. Allosteric regulation of helicase core activities of the DEAD-box helicase YxiN by RNA binding to its RNA recognition motif. Nucleic Acids Res 2017;45:1994-2006. [PMID: 28115633 PMCID: PMC5389509 DOI: 10.1093/nar/gkx014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/08/2016] [Accepted: 01/04/2017] [Indexed: 11/30/2022]  Open
11
Andreou AZ, Harms U, Klostermeier D. eIF4B stimulates eIF4A ATPase and unwinding activities by direct interaction through its 7-repeats region. RNA Biol 2016;14:113-123. [PMID: 27858515 DOI: 10.1080/15476286.2016.1259782] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]  Open
12
Gubaev A, Weidlich D, Klostermeier D. DNA gyrase with a single catalytic tyrosine can catalyze DNA supercoiling by a nicking-closing mechanism. Nucleic Acids Res 2016;44:10354-10366. [PMID: 27557712 PMCID: PMC5137430 DOI: 10.1093/nar/gkw740] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/20/2016] [Accepted: 08/12/2016] [Indexed: 01/10/2023]  Open
13
Gyimesi M, Harami GM, Kocsis ZS, Kovács M. Recent adaptations of fluorescence techniques for the determination of mechanistic parameters of helicases and translocases. Methods 2016;108:24-39. [PMID: 27133766 DOI: 10.1016/j.ymeth.2016.04.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/22/2016] [Accepted: 04/25/2016] [Indexed: 01/11/2023]  Open
14
Comparative Evolution of Duplicated Ddx3 Genes in Teleosts: Insights from Japanese Flounder, Paralichthys olivaceus. G3-GENES GENOMES GENETICS 2015;5:1765-73. [PMID: 26109358 PMCID: PMC4528332 DOI: 10.1534/g3.115.018911] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
15
Fluorescence methods in the investigation of the DEAD-box helicase mechanism. ACTA ACUST UNITED AC 2014;105:161-92. [PMID: 25095995 DOI: 10.1007/978-3-0348-0856-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
16
Dai TY, Cao L, Yang ZC, Li YS, Tan L, Ran XZ, Shi CM. P68 RNA helicase as a molecular target for cancer therapy. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2014;33:64. [PMID: 25150365 PMCID: PMC4431487 DOI: 10.1186/s13046-014-0064-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/16/2014] [Indexed: 12/23/2022]
17
Samatanga B, Klostermeier D. DEAD-box RNA helicase domains exhibit a continuum between complete functional independence and high thermodynamic coupling in nucleotide and RNA duplex recognition. Nucleic Acids Res 2014;42:10644-54. [PMID: 25123660 PMCID: PMC4176333 DOI: 10.1093/nar/gku747] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
18
Lulchev P, Klostermeier D. Reverse gyrase--recent advances and current mechanistic understanding of positive DNA supercoiling. Nucleic Acids Res 2014;42:8200-13. [PMID: 25013168 PMCID: PMC4117796 DOI: 10.1093/nar/gku589] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
19
Gubaev A, Klostermeier D. Reprint of "The mechanism of negative DNA supercoiling: a cascade of DNA-induced conformational changes prepares gyrase for strand passage". DNA Repair (Amst) 2014;20:130-141. [PMID: 24974097 DOI: 10.1016/j.dnarep.2014.06.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 01/03/2014] [Accepted: 01/13/2014] [Indexed: 01/04/2023]
20
Sun Y, Atas E, Lindqvist LM, Sonenberg N, Pelletier J, Meller A. Single-molecule kinetics of the eukaryotic initiation factor 4AI upon RNA unwinding. Structure 2014;22:941-8. [PMID: 24909782 DOI: 10.1016/j.str.2014.04.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/06/2014] [Accepted: 04/24/2014] [Indexed: 11/30/2022]
21
Gubaev A, Klostermeier D. The mechanism of negative DNA supercoiling: a cascade of DNA-induced conformational changes prepares gyrase for strand passage. DNA Repair (Amst) 2014;16:23-34. [PMID: 24674625 DOI: 10.1016/j.dnarep.2014.01.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 01/03/2014] [Accepted: 01/13/2014] [Indexed: 11/29/2022]
22
Lanz MA, Farhat M, Klostermeier D. The acidic C-terminal tail of the GyrA subunit moderates the DNA supercoiling activity of Bacillus subtilis gyrase. J Biol Chem 2014;289:12275-85. [PMID: 24563461 DOI: 10.1074/jbc.m114.547745] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
23
Molecular dynamics simulation of the allosteric regulation of eIF4A protein from the open to closed state, induced by ATP and RNA substrates. PLoS One 2014;9:e86104. [PMID: 24465900 PMCID: PMC3900488 DOI: 10.1371/journal.pone.0086104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/05/2013] [Indexed: 11/19/2022]  Open
24
Andreou AZ, Klostermeier D. eIF4B and eIF4G jointly stimulate eIF4A ATPase and unwinding activities by modulation of the eIF4A conformational cycle. J Mol Biol 2013;426:51-61. [PMID: 24080224 DOI: 10.1016/j.jmb.2013.09.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 08/22/2013] [Accepted: 09/23/2013] [Indexed: 01/07/2023]
25
Geißler V, Altmeyer S, Stein B, Uhlmann-Schiffler H, Stahl H. The RNA helicase Ddx5/p68 binds to hUpf3 and enhances NMD of Ddx17/p72 and Smg5 mRNA. Nucleic Acids Res 2013;41:7875-88. [PMID: 23788676 PMCID: PMC3763533 DOI: 10.1093/nar/gkt538] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
26
Putnam AA, Jankowsky E. DEAD-box helicases as integrators of RNA, nucleotide and protein binding. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013;1829:884-93. [PMID: 23416748 DOI: 10.1016/j.bbagrm.2013.02.002] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 02/04/2013] [Accepted: 02/06/2013] [Indexed: 01/10/2023]
27
König SLB, Liyanage PS, Sigel RKO, Rueda D. Helicase-mediated changes in RNA structure at the single-molecule level. RNA Biol 2013;10:133-48. [PMID: 23353571 DOI: 10.4161/rna.23507] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
28
Andreou AZ, Klostermeier D. The DEAD-box helicase eIF4A: paradigm or the odd one out? RNA Biol 2012;10:19-32. [PMID: 22995829 DOI: 10.4161/rna.21966] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
29
Lanz MA, Klostermeier D. The GyrA-box determines the geometry of DNA bound to gyrase and couples DNA binding to the nucleotide cycle. Nucleic Acids Res 2012;40:10893-903. [PMID: 22977179 PMCID: PMC3510516 DOI: 10.1093/nar/gks852] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
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