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For: Chang YP, Xu M, Machado ACD, Yu XJ, Rohs R, Chen XS. Mechanism of origin DNA recognition and assembly of an initiator-helicase complex by SV40 large tumor antigen. Cell Rep 2013;3:1117-27. [PMID: 23545501 DOI: 10.1016/j.celrep.2013.03.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 01/10/2013] [Accepted: 03/01/2013] [Indexed: 10/27/2022]  Open
Number Cited by Other Article(s)
1
Shahid T, Danazumi AU, Tehseen M, Alhudhali L, Clark AR, Savva CG, Hamdan SM, De Biasio A. Structural dynamics of DNA unwinding by a replicative helicase. Nature 2025;641:240-249. [PMID: 40108462 PMCID: PMC12043514 DOI: 10.1038/s41586-025-08766-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 02/10/2025] [Indexed: 03/22/2025]
2
Shin J, Meinke G, Bohm AA, Bullock PA. A model for polyomavirus helicase activity derived in part from the AlphaFold2 structure of SV40 T-antigen. J Virol 2024;98:e0111924. [PMID: 39311578 PMCID: PMC11494911 DOI: 10.1128/jvi.01119-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 08/11/2024] [Indexed: 09/27/2024]  Open
3
Sun JW, Thomas JS, Monkovic JM, Gibson H, Nagapurkar A, Frezzo JA, Katyal P, Punia K, Mahmoudinobar F, Renfrew PD, Montclare JK. Supercharged coiled-coil protein with N-terminal decahistidine tag boosts siRNA complexation and delivery efficiency of a lipoproteoplex. J Pept Sci 2024;30:e3594. [PMID: 38499991 DOI: 10.1002/psc.3594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
4
Sangeeta, Mishra SK, Bhattacherjee A. Role of Shape Deformation of DNA-Binding Sites in Regulating the Efficiency and Specificity in Their Recognition by DNA-Binding Proteins. JACS AU 2024;4:2640-2655. [PMID: 39055163 PMCID: PMC11267559 DOI: 10.1021/jacsau.4c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 07/27/2024]
5
Durairaj J, Follonier OM, Leuzinger K, Alexander LT, Wilhelm M, Pereira J, Hillenbrand CA, Weissbach FH, Schwede T, Hirsch HH. Structural implications of BK polyomavirus sequence variations in the major viral capsid protein Vp1 and large T-antigen: a computational study. mSphere 2024;9:e0079923. [PMID: 38501831 PMCID: PMC11036806 DOI: 10.1128/msphere.00799-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/21/2024] [Indexed: 03/20/2024]  Open
6
Jiang Y, Chiu TP, Mitra R, Rohs R. Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding. Biophys J 2024;123:248-259. [PMID: 38130056 PMCID: PMC10808038 DOI: 10.1016/j.bpj.2023.12.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/22/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]  Open
7
Shao Z, Su S, Yang J, Zhang W, Gao Y, Zhao X, Zhang Y, Shao Q, Cao C, Li H, Liu H, Zhang J, Lin J, Ma J, Gan J. Structures and implications of the C962R protein of African swine fever virus. Nucleic Acids Res 2023;51:9475-9490. [PMID: 37587714 PMCID: PMC10516667 DOI: 10.1093/nar/gkad677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/01/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023]  Open
8
Wan L, Toland S, Robinson-McCarthy LR, Lee N, Schaich MA, Hengel SR, Li X, Bernstein KA, Van Houten B, Chang Y, Moore PS. Unlicensed origin DNA melting by MCV and SV40 polyomavirus LT proteins is independent of ATP-dependent helicase activity. Proc Natl Acad Sci U S A 2023;120:e2308010120. [PMID: 37459531 PMCID: PMC10372695 DOI: 10.1073/pnas.2308010120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 06/21/2023] [Indexed: 07/20/2023]  Open
9
Pajenda S, Hevesi Z, Eder M, Gerges D, Aiad M, Koldyka O, Winnicki W, Wagner L, Eskandary F, Schmidt A. Lessons from Polyomavirus Immunofluorescence Staining of Urinary Decoy Cells. Life (Basel) 2023;13:1526. [PMID: 37511901 PMCID: PMC10381542 DOI: 10.3390/life13071526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]  Open
10
SV40 T-antigen uses a DNA shearing mechanism to initiate origin unwinding. Proc Natl Acad Sci U S A 2022;119:e2216240119. [PMID: 36442086 PMCID: PMC9894130 DOI: 10.1073/pnas.2216240119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
11
Yeager C, Carter G, Gohara DW, Yennawar NH, Enemark E, Arnold J, Cameron CE. Enteroviral 2C protein is an RNA-stimulated ATPase and uses a two-step mechanism for binding to RNA and ATP. Nucleic Acids Res 2022;50:11775-11798. [PMID: 36399514 PMCID: PMC9723501 DOI: 10.1093/nar/gkac1054] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/16/2022] [Accepted: 10/26/2022] [Indexed: 11/19/2022]  Open
12
Onwubiko NO, Scheffel F, Tessmer I, Nasheuer HP. SV40 T antigen helicase domain regions responsible for oligomerisation regulate Okazaki fragment synthesis initiation. FEBS Open Bio 2022;12:649-663. [PMID: 35073603 PMCID: PMC8886539 DOI: 10.1002/2211-5463.13373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/21/2021] [Accepted: 01/21/2022] [Indexed: 11/11/2022]  Open
13
Jessop M, Felix J, Gutsche I. AAA+ ATPases: structural insertions under the magnifying glass. Curr Opin Struct Biol 2021;66:119-128. [PMID: 33246198 PMCID: PMC7973254 DOI: 10.1016/j.sbi.2020.10.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/19/2020] [Accepted: 10/27/2020] [Indexed: 11/29/2022]
14
Lara-Gonzalez S, Dantas Machado AC, Rao S, Napoli AA, Birktoft J, Di Felice R, Rohs R, Lawson CL. The RNA Polymerase α Subunit Recognizes the DNA Shape of the Upstream Promoter Element. Biochemistry 2020;59:4523-4532. [PMID: 33205945 DOI: 10.1021/acs.biochem.0c00571] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
15
Schnepf M, von Reutern M, Ludwig C, Jung C, Gaul U. Transcription Factor Binding Affinities and DNA Shape Readout. iScience 2020;23:101694. [PMID: 33163946 PMCID: PMC7607496 DOI: 10.1016/j.isci.2020.101694] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/30/2020] [Accepted: 10/13/2020] [Indexed: 12/16/2022]  Open
16
Onwubiko NO, Borst A, Diaz SA, Passkowski K, Scheffel F, Tessmer I, Nasheuer HP. SV40 T antigen interactions with ssDNA and replication protein A: a regulatory role of T antigen monomers in lagging strand DNA replication. Nucleic Acids Res 2020;48:3657-3677. [PMID: 32128579 PMCID: PMC7144908 DOI: 10.1093/nar/gkaa138] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/14/2020] [Accepted: 02/26/2020] [Indexed: 01/08/2023]  Open
17
Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria. Proc Natl Acad Sci U S A 2020;117:14322-14330. [PMID: 32518115 DOI: 10.1073/pnas.2002933117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]  Open
18
The Ubiquitin-Specific Protease Usp7, a Novel Merkel Cell Polyomavirus Large T-Antigen Interaction Partner, Modulates Viral DNA Replication. J Virol 2020;94:JVI.01638-19. [PMID: 31801860 DOI: 10.1128/jvi.01638-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/01/2019] [Indexed: 02/06/2023]  Open
19
Perera HM, Behrmann MS, Hoang JM, Griffin WC, Trakselis MA. Contacts and context that regulate DNA helicase unwinding and replisome progression. Enzymes 2019;45:183-223. [PMID: 31627877 DOI: 10.1016/bs.enz.2019.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
20
Azad RN, Zafiropoulos D, Ober D, Jiang Y, Chiu TP, Sagendorf JM, Rohs R, Tullius TD. Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations. Nucleic Acids Res 2019;46:2636-2647. [PMID: 29390080 PMCID: PMC5946862 DOI: 10.1093/nar/gky033] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 01/15/2018] [Indexed: 12/22/2022]  Open
21
Laponogov I, Pan XS, Veselkov DA, Skamrova GB, Umrekar TR, Fisher LM, Sanderson MR. Trapping of the transport-segment DNA by the ATPase domains of a type II topoisomerase. Nat Commun 2018;9:2579. [PMID: 29968711 PMCID: PMC6030046 DOI: 10.1038/s41467-018-05005-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 05/25/2018] [Indexed: 11/09/2022]  Open
22
Structural Insights into the CRTC2–CREB Complex Assembly on CRE. J Mol Biol 2018;430:1926-1939. [DOI: 10.1016/j.jmb.2018.04.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 04/19/2018] [Accepted: 04/25/2018] [Indexed: 11/18/2022]
23
Li J, Sagendorf JM, Chiu TP, Pasi M, Perez A, Rohs R. Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding. Nucleic Acids Res 2018;45:12877-12887. [PMID: 29165643 PMCID: PMC5728407 DOI: 10.1093/nar/gkx1145] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]  Open
24
Chiu TP, Rao S, Mann RS, Honig B, Rohs R. Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein-DNA binding. Nucleic Acids Res 2017;45:12565-12576. [PMID: 29040720 PMCID: PMC5716191 DOI: 10.1093/nar/gkx915] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 09/28/2017] [Indexed: 12/16/2022]  Open
25
Baez CF, Brandão Varella R, Villani S, Delbue S. Human Polyomaviruses: The Battle of Large and Small Tumor Antigens. Virology (Auckl) 2017;8:1178122X17744785. [PMID: 29238174 PMCID: PMC5721967 DOI: 10.1177/1178122x17744785] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/30/2017] [Indexed: 12/17/2022]  Open
26
Chang CW, Lee S, Tsai FTF. Structural Elements Regulating AAA+ Protein Quality Control Machines. Front Mol Biosci 2017;4:27. [PMID: 28523272 PMCID: PMC5415569 DOI: 10.3389/fmolb.2017.00027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 04/13/2017] [Indexed: 11/13/2022]  Open
27
Origin DNA Melting-An Essential Process with Divergent Mechanisms. Genes (Basel) 2017;8:genes8010026. [PMID: 28085061 PMCID: PMC5295021 DOI: 10.3390/genes8010026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/27/2016] [Accepted: 01/03/2017] [Indexed: 02/07/2023]  Open
28
Gai D, Wang D, Li SX, Chen XS. The structure of SV40 large T hexameric helicase in complex with AT-rich origin DNA. eLife 2016;5. [PMID: 27921994 PMCID: PMC5140265 DOI: 10.7554/elife.18129] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 11/03/2016] [Indexed: 12/12/2022]  Open
29
Buck CB, Van Doorslaer K, Peretti A, Geoghegan EM, Tisza MJ, An P, Katz JP, Pipas JM, McBride AA, Camus AC, McDermott AJ, Dill JA, Delwart E, Ng TFF, Farkas K, Austin C, Kraberger S, Davison W, Pastrana DV, Varsani A. The Ancient Evolutionary History of Polyomaviruses. PLoS Pathog 2016;12:e1005574. [PMID: 27093155 PMCID: PMC4836724 DOI: 10.1371/journal.ppat.1005574] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/23/2016] [Indexed: 12/21/2022]  Open
30
Trakselis MA. Structural Mechanisms of Hexameric Helicase Loading, Assembly, and Unwinding. F1000Res 2016;5. [PMID: 26918187 PMCID: PMC4755419 DOI: 10.12688/f1000research.7509.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/25/2016] [Indexed: 11/20/2022]  Open
31
Meinke G, Phelan PJ, Shin J, Gagnon D, Archambault J, Bohm A, Bullock PA. Structural Based Analyses of the JC Virus T-Antigen F258L Mutant Provides Evidence for DNA Dependent Conformational Changes in the C-Termini of Polyomavirus Origin Binding Domains. PLoS Pathog 2016;12:e1005362. [PMID: 26735515 PMCID: PMC4703215 DOI: 10.1371/journal.ppat.1005362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/04/2015] [Indexed: 11/21/2022]  Open
32
Musayev FN, Zarate-Perez F, Bardelli M, Bishop C, Saniev EF, Linden RM, Henckaerts E, Escalante CR. Structural Studies of AAV2 Rep68 Reveal a Partially Structured Linker and Compact Domain Conformation. Biochemistry 2015;54:5907-19. [PMID: 26314310 PMCID: PMC4636433 DOI: 10.1021/acs.biochem.5b00610] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
33
Musayev FN, Zarate-Perez F, Bishop C, Burgner JW, Escalante CR. Structural Insights into the Assembly of the Adeno-associated Virus Type 2 Rep68 Protein on the Integration Site AAVS1. J Biol Chem 2015;290:27487-99. [PMID: 26370092 DOI: 10.1074/jbc.m115.669960] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Indexed: 11/06/2022]  Open
34
Deng Z, Wang Q, Liu Z, Zhang M, Machado ACD, Chiu TP, Feng C, Zhang Q, Yu L, Qi L, Zheng J, Wang X, Huo X, Qi X, Li X, Wu W, Rohs R, Li Y, Chen Z. Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator. Nat Commun 2015;6:7642. [PMID: 26134419 PMCID: PMC4506495 DOI: 10.1038/ncomms8642] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 05/27/2015] [Indexed: 01/21/2023]  Open
35
Abe N, Dror I, Yang L, Slattery M, Zhou T, Bussemaker HJ, Rohs R, Mann RS. Deconvolving the recognition of DNA shape from sequence. Cell 2015;161:307-18. [PMID: 25843630 DOI: 10.1016/j.cell.2015.02.008] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 12/08/2014] [Accepted: 01/26/2015] [Indexed: 01/25/2023]
36
Quantitative modeling of transcription factor binding specificities using DNA shape. Proc Natl Acad Sci U S A 2015;112:4654-9. [PMID: 25775564 DOI: 10.1073/pnas.1422023112] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
37
Chiu TP, Yang L, Zhou T, Main BJ, Parker SCJ, Nuzhdin SV, Tullius TD, Rohs R. GBshape: a genome browser database for DNA shape annotations. Nucleic Acids Res 2014;43:D103-9. [PMID: 25326329 PMCID: PMC4384032 DOI: 10.1093/nar/gku977] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]  Open
38
Shin J, Phelan PJ, Chhum P, Bashkenova N, Yim S, Parker R, Gagnon D, Gjoerup O, Archambault J, Bullock PA. Analysis of JC virus DNA replication using a quantitative and high-throughput assay. Virology 2014;468-470:113-125. [PMID: 25155200 DOI: 10.1016/j.virol.2014.07.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/09/2014] [Accepted: 07/21/2014] [Indexed: 12/17/2022]
39
Slattery M, Zhou T, Yang L, Dantas Machado AC, Gordân R, Rohs R. Absence of a simple code: how transcription factors read the genome. Trends Biochem Sci 2014;39:381-99. [PMID: 25129887 DOI: 10.1016/j.tibs.2014.07.002] [Citation(s) in RCA: 366] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 12/21/2022]
40
O'Shea VL, Berger JM. Loading strategies of ring-shaped nucleic acid translocases and helicases. Curr Opin Struct Biol 2014;25:16-24. [PMID: 24878340 PMCID: PMC4040187 DOI: 10.1016/j.sbi.2013.11.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 12/16/2022]
41
Meinke G, Phelan PJ, Kalekar R, Shin J, Archambault J, Bohm A, Bullock PA. Insights into the initiation of JC virus DNA replication derived from the crystal structure of the T-antigen origin binding domain. PLoS Pathog 2014;10:e1003966. [PMID: 24586168 PMCID: PMC3930596 DOI: 10.1371/journal.ppat.1003966] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/16/2014] [Indexed: 01/07/2023]  Open
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Siggers T, Gordân R. Protein-DNA binding: complexities and multi-protein codes. Nucleic Acids Res 2013;42:2099-111. [PMID: 24243859 PMCID: PMC3936734 DOI: 10.1093/nar/gkt1112] [Citation(s) in RCA: 162] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
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Yang L, Zhou T, Dror I, Mathelier A, Wasserman WW, Gordân R, Rohs R. TFBSshape: a motif database for DNA shape features of transcription factor binding sites. Nucleic Acids Res 2013;42:D148-55. [PMID: 24214955 PMCID: PMC3964943 DOI: 10.1093/nar/gkt1087] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
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Polyomavirus large T antigen binds symmetrical repeats at the viral origin in an asymmetrical manner. J Virol 2013;87:13751-9. [PMID: 24109229 DOI: 10.1128/jvi.01740-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]  Open
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Dror I, Zhou T, Mandel-Gutfreund Y, Rohs R. Covariation between homeodomain transcription factors and the shape of their DNA binding sites. Nucleic Acids Res 2013;42:430-41. [PMID: 24078250 PMCID: PMC3874178 DOI: 10.1093/nar/gkt862] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
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Zhou T, Yang L, Lu Y, Dror I, Dantas Machado AC, Ghane T, Di Felice R, Rohs R. DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale. Nucleic Acids Res 2013;41:W56-62. [PMID: 23703209 PMCID: PMC3692085 DOI: 10.1093/nar/gkt437] [Citation(s) in RCA: 230] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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