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For: Patel N, Dykeman EC, Coutts RH, Lomonossoff GP, Rowlands DJ, Phillips SE, Ranson N, Twarock R, Tuma R, Stockley PG. Revealing the density of encoded functions in a viral RNA. Proc Natl Acad Sci U S A 2015;112:2227-32. [PMID: 25646435 DOI: 10.1073/pnas.1420812112] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
Number Cited by Other Article(s)
1
Peyret H, Shah SN, Meshcheriakova Y, Saunders K, Lomonossoff GP. How do RNA viruses select which RNA to package? The plant virus experience. Virology 2025;604:110435. [PMID: 39893746 DOI: 10.1016/j.virol.2025.110435] [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: 12/03/2024] [Revised: 01/13/2025] [Accepted: 01/23/2025] [Indexed: 02/04/2025]
2
Paine AW, Hagan MF, Manoharan VN. Disassembly of Virus-Like Particles and the Stabilizing Role of the Nucleic Acid Cargo. J Phys Chem B 2025;129:1516-1528. [PMID: 39841546 PMCID: PMC11822259 DOI: 10.1021/acs.jpcb.4c07215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2025]
3
Bugea T, Suss R, Gargowitsch L, Truong C, Perronet K, Tresset G. Probing Single-Molecule Dynamics in Self-Assembling Viral Nucleocapsids. NANO LETTERS 2024;24:14821-14828. [PMID: 39504127 DOI: 10.1021/acs.nanolett.4c04458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2024]
4
Wroblewski E, Patel N, Javed A, Mata CP, Chandler-Bostock R, Lekshmi BG, Ulamec SM, Clark S, Phillips SEV, Ranson NA, Twarock R, Stockley PG. Visualizing Viral RNA Packaging Signals in Action. J Mol Biol 2024;436:168765. [PMID: 39214281 DOI: 10.1016/j.jmb.2024.168765] [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: 08/01/2024] [Revised: 08/20/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
5
Tresset G, Li S, Gargowitsch L, Matthews L, Pérez J, Zandi R. Glass-like Relaxation Dynamics during the Disorder-to-Order Transition of Viral Nucleocapsids. J Phys Chem Lett 2024;15:10210-10218. [PMID: 39356145 DOI: 10.1021/acs.jpclett.4c02158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
6
Bukina V, Božič A. Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA. Biophys J 2024;123:3397-3407. [PMID: 39118324 PMCID: PMC11480767 DOI: 10.1016/j.bpj.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/17/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]  Open
7
Luque A, Reguera D. Theoretical Studies on Assembly, Physical Stability, and Dynamics of Viruses. Subcell Biochem 2024;105:693-741. [PMID: 39738961 DOI: 10.1007/978-3-031-65187-8_19] [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] [Indexed: 01/02/2025]
8
Asor R, Singaram SW, Levi-Kalisman Y, Hagan MF, Raviv U. Effect of ionic strength on the assembly of simian vacuolating virus capsid protein around poly(styrene sulfonate). THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023;46:107. [PMID: 37917241 PMCID: PMC11827716 DOI: 10.1140/epje/s10189-023-00363-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/09/2023] [Indexed: 11/04/2023]
9
Mizrahi I, Bruinsma R, Rudnick J. Spanning tree model and the assembly kinetics of RNA viruses. Phys Rev E 2022;106:044405. [PMID: 36397584 DOI: 10.1103/physreve.106.044405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 05/17/2022] [Indexed: 06/16/2023]
10
Li S, Zandi R. Biophysical Modeling of SARS-CoV-2 Assembly: Genome Condensation and Budding. Viruses 2022;14:2089. [PMID: 36298645 PMCID: PMC9611094 DOI: 10.3390/v14102089] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 11/18/2022]  Open
11
Tsidilkovski L, Mohajerani F, Hagan MF. Microcompartment assembly around multicomponent fluid cargoes. J Chem Phys 2022;156:245104. [PMID: 35778087 PMCID: PMC9249432 DOI: 10.1063/5.0089556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]  Open
12
Feser CJ, Lees CJ, Lammers DT, Riddle MJ, Bingham JR, Eckert MJ, Tolar J, Osborn MJ. Engineering CRISPR/Cas9 for Multiplexed Recombinant Coagulation Factor Production. Int J Mol Sci 2022;23:ijms23095090. [PMID: 35563479 PMCID: PMC9100926 DOI: 10.3390/ijms23095090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 11/16/2022]  Open
13
Patel N, Clark S, Weiß EU, Mata CP, Bohon J, Farquhar ER, Maskell DP, Ranson NA, Twarock R, Stockley PG. In vitro functional analysis of gRNA sites regulating assembly of hepatitis B virus. Commun Biol 2021;4:1407. [PMID: 34916604 PMCID: PMC8677749 DOI: 10.1038/s42003-021-02897-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 11/16/2021] [Indexed: 11/16/2022]  Open
14
Hill SR, Twarock R, Dykeman EC. The impact of local assembly rules on RNA packaging in a T = 1 satellite plant virus. PLoS Comput Biol 2021;17:e1009306. [PMID: 34428224 PMCID: PMC8384211 DOI: 10.1371/journal.pcbi.1009306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/26/2021] [Indexed: 02/05/2023]  Open
15
Dechant PP, He YH. Machine-learning a virus assembly fitness landscape. PLoS One 2021;16:e0250227. [PMID: 33951035 PMCID: PMC8099058 DOI: 10.1371/journal.pone.0250227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 04/01/2021] [Indexed: 02/05/2023]  Open
16
Mohajerani F, Sayer E, Neil C, Inlow K, Hagan MF. Mechanisms of Scaffold-Mediated Microcompartment Assembly and Size Control. ACS NANO 2021;15:4197-4212. [PMID: 33683101 PMCID: PMC8058603 DOI: 10.1021/acsnano.0c05715] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
17
Chandler-Bostock R, Mata CP, Bingham RJ, Dykeman EC, Meng B, Tuthill TJ, Rowlands DJ, Ranson NA, Twarock R, Stockley PG. Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts. PLoS Pathog 2020;16:e1009146. [PMID: 33370422 PMCID: PMC7793301 DOI: 10.1371/journal.ppat.1009146] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 01/08/2021] [Accepted: 11/11/2020] [Indexed: 02/04/2023]  Open
18
Dong Y, Li S, Zandi R. Effect of the charge distribution of virus coat proteins on the length of packaged RNAs. Phys Rev E 2020;102:062423. [PMID: 33466113 DOI: 10.1103/physreve.102.062423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/17/2020] [Indexed: 01/20/2023]
19
San Emeterio J, Pollack L. Visualizing a viral genome with contrast variation small angle X-ray scattering. J Biol Chem 2020;295:15923-15932. [PMID: 32913117 PMCID: PMC7681021 DOI: 10.1074/jbc.ra120.013961] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/04/2020] [Indexed: 01/14/2023]  Open
20
Martín-Bravo M, Gomez Llorente JM, Hernández-Rojas J. A minimal coarse-grained model for the low-frequency normal mode analysis of icosahedral viral capsids. SOFT MATTER 2020;16:3443-3455. [PMID: 32196061 DOI: 10.1039/d0sm00299b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
21
Buzón P, Maity S, Roos WH. Physical virology: From virus self-assembly to particle mechanics. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020;12:e1613. [PMID: 31960585 PMCID: PMC7317356 DOI: 10.1002/wnan.1613] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/01/2019] [Accepted: 12/11/2019] [Indexed: 12/19/2022]
22
Martínez-Turiño S, García JA. Potyviral coat protein and genomic RNA: A striking partnership leading virion assembly and more. Adv Virus Res 2020;108:165-211. [PMID: 33837716 DOI: 10.1016/bs.aivir.2020.09.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
23
Twarock R, Stockley PG. RNA-Mediated Virus Assembly: Mechanisms and Consequences for Viral Evolution and Therapy. Annu Rev Biophys 2019;48:495-514. [PMID: 30951648 PMCID: PMC7612295 DOI: 10.1146/annurev-biophys-052118-115611] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
24
Kotta-Loizou I, Peyret H, Saunders K, Coutts RHA, Lomonossoff GP. Investigating the Biological Relevance of In Vitro-Identified Putative Packaging Signals at the 5' Terminus of Satellite Tobacco Necrosis Virus 1 Genomic RNA. J Virol 2019;93:e02106-18. [PMID: 30814279 PMCID: PMC6475782 DOI: 10.1128/jvi.02106-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/06/2019] [Indexed: 12/14/2022]  Open
25
Nonequilibrium self-assembly dynamics of icosahedral viral capsids packaging genome or polyelectrolyte. Nat Commun 2018;9:3071. [PMID: 30082710 PMCID: PMC6078970 DOI: 10.1038/s41467-018-05426-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 07/05/2018] [Indexed: 11/20/2022]  Open
26
Twarock R, Bingham RJ, Dykeman EC, Stockley PG. A modelling paradigm for RNA virus assembly. Curr Opin Virol 2018;31:74-81. [PMID: 30078702 PMCID: PMC6281560 DOI: 10.1016/j.coviro.2018.07.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 07/04/2018] [Indexed: 12/14/2022]
27
Bieniasz P, Telesnitsky A. Multiple, Switchable Protein:RNA Interactions Regulate Human Immunodeficiency Virus Type 1 Assembly. Annu Rev Virol 2018;5:165-183. [PMID: 30048218 DOI: 10.1146/annurev-virology-092917-043448] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
28
Shrestha N, Weber PH, Burke SV, Wysocki WP, Duvall MR, Bujarski JJ. Next generation sequencing reveals packaging of host RNAs by brome mosaic virus. Virus Res 2018;252:82-90. [PMID: 29753892 DOI: 10.1016/j.virusres.2018.05.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/05/2018] [Accepted: 05/09/2018] [Indexed: 12/28/2022]
29
Twarock R, Leonov G, Stockley PG. Hamiltonian path analysis of viral genomes. Nat Commun 2018;9:2021. [PMID: 29789600 PMCID: PMC5964074 DOI: 10.1038/s41467-018-03713-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/02/2018] [Indexed: 12/25/2022]  Open
30
Lomonossoff GP. So What Have Plant Viruses Ever Done for Virology and Molecular Biology? Adv Virus Res 2018;100:145-162. [PMID: 29551134 DOI: 10.1016/bs.aivir.2017.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
31
Li S, Erdemci-Tandogan G, van der Schoot P, Zandi R. The effect of RNA stiffness on the self-assembly of virus particles. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018;30:044002. [PMID: 29235442 PMCID: PMC7104906 DOI: 10.1088/1361-648x/aaa159] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/06/2017] [Accepted: 12/13/2017] [Indexed: 05/21/2023]
32
Bingham RJ, Dykeman EC, Twarock R. RNA Virus Evolution via a Quasispecies-Based Model Reveals a Drug Target with a High Barrier to Resistance. Viruses 2017;9:E347. [PMID: 29149077 PMCID: PMC5707554 DOI: 10.3390/v9110347] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/14/2017] [Accepted: 11/16/2017] [Indexed: 12/26/2022]  Open
33
Patel N, Wroblewski E, Leonov G, Phillips SEV, Tuma R, Twarock R, Stockley PG. Rewriting nature's assembly manual for a ssRNA virus. Proc Natl Acad Sci U S A 2017;114:12255-12260. [PMID: 29087310 PMCID: PMC5699041 DOI: 10.1073/pnas.1706951114] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
34
Song Y, Gorbatsevych O, Liu Y, Mugavero J, Shen SH, Ward CB, Asare E, Jiang P, Paul AV, Mueller S, Wimmer E. Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes. Proc Natl Acad Sci U S A 2017;114:E8731-E8740. [PMID: 28973853 PMCID: PMC5642728 DOI: 10.1073/pnas.1714385114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
35
Dykeman EC. A Model for Viral Assembly around an Explicit RNA Sequence Generates an Implicit Fitness Landscape. Biophys J 2017;113:506-516. [PMID: 28793206 DOI: 10.1016/j.bpj.2017.06.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/11/2017] [Accepted: 06/19/2017] [Indexed: 12/15/2022]  Open
36
Beren C, Dreesens LL, Liu KN, Knobler CM, Gelbart WM. The Effect of RNA Secondary Structure on the Self-Assembly of Viral Capsids. Biophys J 2017;113:339-347. [PMID: 28711172 DOI: 10.1016/j.bpj.2017.06.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/31/2017] [Accepted: 06/20/2017] [Indexed: 12/31/2022]  Open
37
Poudel L, Twarock R, Steinmetz NF, Podgornik R, Ching WY. Impact of Hydrogen Bonding in the Binding Site between Capsid Protein and MS2 Bacteriophage ssRNA. J Phys Chem B 2017;121:6321-6330. [PMID: 28581757 DOI: 10.1021/acs.jpcb.7b02569] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
38
Patel N, White SJ, Thompson RF, Bingham R, Weiß EU, Maskell DP, Zlotnick A, Dykeman E, Tuma R, Twarock R, Ranson NA, Stockley PG. HBV RNA pre-genome encodes specific motifs that mediate interactions with the viral core protein that promote nucleocapsid assembly. Nat Microbiol 2017;2:17098. [PMID: 28628133 PMCID: PMC5495169 DOI: 10.1038/nmicrobiol.2017.98] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 05/17/2017] [Indexed: 12/20/2022]
39
Subcellular Localization of HIV-1 gag-pol mRNAs Regulates Sites of Virion Assembly. J Virol 2017;91:JVI.02315-16. [PMID: 28053097 DOI: 10.1128/jvi.02315-16] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 12/23/2016] [Indexed: 02/07/2023]  Open
40
Shakeel S, Dykeman EC, White SJ, Ora A, Cockburn JJB, Butcher SJ, Stockley PG, Twarock R. Genomic RNA folding mediates assembly of human parechovirus. Nat Commun 2017;8:5. [PMID: 28232749 PMCID: PMC5431903 DOI: 10.1038/s41467-016-0011-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/16/2016] [Indexed: 01/04/2023]  Open
41
Le MT, Kasprzak WK, Kim T, Gao F, Young MYL, Yuan X, Shapiro BA, Seog J, Simon AE. Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch. eLife 2017;6:e22883. [PMID: 28186489 PMCID: PMC5336357 DOI: 10.7554/elife.22883] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/07/2017] [Indexed: 11/29/2022]  Open
42
In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus. Nature 2016;541:112-116. [PMID: 27992877 PMCID: PMC5701785 DOI: 10.1038/nature20589] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/26/2016] [Indexed: 12/11/2022]
43
Borodavka A, Singaram SW, Stockley PG, Gelbart WM, Ben-Shaul A, Tuma R. Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures. Biophys J 2016;111:2077-2085. [PMID: 27851933 PMCID: PMC5113152 DOI: 10.1016/j.bpj.2016.10.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 09/25/2016] [Accepted: 10/11/2016] [Indexed: 12/26/2022]  Open
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Erdemci-Tandogan G, Wagner J, van der Schoot P, Podgornik R, Zandi R. Effects of RNA branching on the electrostatic stabilization of viruses. Phys Rev E 2016;94:022408. [PMID: 27627336 DOI: 10.1103/physreve.94.022408] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Indexed: 11/07/2022]
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Perlmutter JD, Mohajerani F, Hagan MF. Many-molecule encapsulation by an icosahedral shell. eLife 2016;5. [PMID: 27166515 PMCID: PMC4947392 DOI: 10.7554/elife.14078] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 05/10/2016] [Indexed: 12/31/2022]  Open
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Stewart H, Bingham R, White SJ, Dykeman EC, Zothner C, Tuplin AK, Stockley PG, Twarock R, Harris M. Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging. Sci Rep 2016;6:22952. [PMID: 26972799 PMCID: PMC4789732 DOI: 10.1038/srep22952] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 02/19/2016] [Indexed: 12/11/2022]  Open
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Rolfsson Ó, Middleton S, Manfield IW, White SJ, Fan B, Vaughan R, Ranson NA, Dykeman E, Twarock R, Ford J, Kao CC, Stockley PG. Direct Evidence for Packaging Signal-Mediated Assembly of Bacteriophage MS2. J Mol Biol 2016;428:431-48. [PMID: 26608810 PMCID: PMC4751978 DOI: 10.1016/j.jmb.2015.11.014] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/06/2015] [Accepted: 11/08/2015] [Indexed: 01/20/2023]
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Stockley PG, White SJ, Dykeman E, Manfield I, Rolfsson O, Patel N, Bingham R, Barker A, Wroblewski E, Chandler-Bostock R, Weiß EU, Ranson NA, Tuma R, Twarock R. Bacteriophage MS2 genomic RNA encodes an assembly instruction manual for its capsid. BACTERIOPHAGE 2016;6:e1157666. [PMID: 27144089 PMCID: PMC4836477 DOI: 10.1080/21597081.2016.1157666] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 12/11/2022]
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Prevelige PE. Follow the Yellow Brick Road: A Paradigm Shift in Virus Assembly. J Mol Biol 2015;428:416-8. [PMID: 26707196 DOI: 10.1016/j.jmb.2015.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Krupovic M, Kuhn JH, Fischer MG. A classification system for virophages and satellite viruses. Arch Virol 2015;161:233-47. [PMID: 26446887 DOI: 10.1007/s00705-015-2622-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/21/2015] [Indexed: 11/28/2022]
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