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For: Pham VV, Salguero C, Khan SN, Meagher JL, Brown WC, Humbert N, de Rocquigny H, Smith JL, D'Souza VM. HIV-1 Tat interactions with cellular 7SK and viral TAR RNAs identifies dual structural mimicry. Nat Commun 2018;9:4266. [PMID: 30323330 PMCID: PMC6189040 DOI: 10.1038/s41467-018-06591-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 09/11/2018] [Indexed: 01/05/2023]  Open
Number Cited by Other Article(s)
1
Gibaut QM, Li C, Cheng A, Moranguinho I, Mori LP, Valente ST. FUBP3 enhances HIV-1 transcriptional activity and regulates immune response pathways in T cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2025;36:102525. [PMID: 40248217 PMCID: PMC12005928 DOI: 10.1016/j.omtn.2025.102525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2024] [Accepted: 03/21/2025] [Indexed: 04/19/2025]
2
Kicker E, Kouros A, Zatloukal K, Harant H. The Virus Entry Pathway Determines Sensitivity to the Antiviral Peptide TAT-I24. Viruses 2025;17:458. [PMID: 40284901 PMCID: PMC12031635 DOI: 10.3390/v17040458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2025] [Accepted: 03/19/2025] [Indexed: 04/29/2025]  Open
3
Bou-Nader C, Link KA, Suddala KC, Knutson JR, Zhang J. Structures of complete HIV-1 TAR RNA portray a dynamic platform poised for protein binding and structural remodeling. Nat Commun 2025;16:2252. [PMID: 40050622 PMCID: PMC11885821 DOI: 10.1038/s41467-025-57519-w] [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: 10/01/2024] [Accepted: 02/25/2025] [Indexed: 03/09/2025]  Open
4
D'Orso I. The HIV-1 Transcriptional Program: From Initiation to Elongation Control. J Mol Biol 2025;437:168690. [PMID: 38936695 PMCID: PMC11994015 DOI: 10.1016/j.jmb.2024.168690] [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: 04/01/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
5
Yang Y, Murrali MG, Wang Y, Galvan S, Ajjampore N, Feigon J. HEXIM1 homodimer binds two sites on 7SK RNA to release autoinhibition for P-TEFb inactivation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.10.617642. [PMID: 39416148 PMCID: PMC11482958 DOI: 10.1101/2024.10.10.617642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
6
Henninger JE, Young RA. An RNA-centric view of transcription and genome organization. Mol Cell 2024;84:3627-3643. [PMID: 39366351 PMCID: PMC11495847 DOI: 10.1016/j.molcel.2024.08.021] [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: 05/07/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 10/06/2024]
7
Ziu T, Sambur E, Ruzsics Z, Hengel H, Grabherr R, Höfinger S, Harant H. In Vitro Profiling of the Antiviral Peptide TAT-I24. Int J Mol Sci 2024;25:10463. [PMID: 39408791 PMCID: PMC11477294 DOI: 10.3390/ijms251910463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Revised: 09/26/2024] [Accepted: 09/26/2024] [Indexed: 10/20/2024]  Open
8
Schynkel T, Snippenberg WV, Verniers K, Jang GM, Krogan NJ, Mestdagh P, Vandekerckhove L, Trypsteen W. Interactome of the HIV-1 proteome and human host RNA. EMBO Rep 2024;25:4078-4090. [PMID: 39122863 PMCID: PMC11387401 DOI: 10.1038/s44319-024-00222-6] [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: 11/09/2023] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024]  Open
9
Chakraborty A, Samant D, Sarkar R, Sangeet S, Prusty S, Roy S. RNA's Dynamic Conformational Selection and Entropic Allosteric Mechanism in Controlling Cascade Protein Binding Events. J Phys Chem Lett 2024;15:6115-6125. [PMID: 38830201 DOI: 10.1021/acs.jpclett.4c00740] [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: 06/05/2024]
10
Jin L, Zhang S, Song Z, Heng X, Chen SJ. Kinetic pathway of HIV-1 TAR cotranscriptional folding. Nucleic Acids Res 2024;52:6066-6078. [PMID: 38738640 PMCID: PMC11162800 DOI: 10.1093/nar/gkae362] [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] [Received: 01/16/2024] [Revised: 04/09/2024] [Accepted: 04/24/2024] [Indexed: 05/14/2024]  Open
11
Ward S, Childs A, Staley C, Waugh C, Watts JA, Kotowska AM, Bhosale R, Borkar AN. Integrating cryo-OrbiSIMS with computational modelling and metadynamics simulations enhances RNA structure prediction at atomic resolution. Nat Commun 2024;15:4367. [PMID: 38777820 PMCID: PMC11111741 DOI: 10.1038/s41467-024-48694-3] [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: 09/18/2023] [Accepted: 05/05/2024] [Indexed: 05/25/2024]  Open
12
Mbonye U, Karn J. The cell biology of HIV-1 latency and rebound. Retrovirology 2024;21:6. [PMID: 38580979 PMCID: PMC10996279 DOI: 10.1186/s12977-024-00639-w] [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] [Indexed: 04/07/2024]  Open
13
Li Y, Liu X, Fujinaga K, Gross JD, Frankel AD. Enhanced NF-κB activation via HIV-1 Tat-TRAF6 cross-talk. SCIENCE ADVANCES 2024;10:eadi4162. [PMID: 38241362 PMCID: PMC10798561 DOI: 10.1126/sciadv.adi4162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 12/21/2023] [Indexed: 01/21/2024]
14
Abasi M, Ranjbari J, Ghanbarian H. 7SK small nuclear RNA (Rn7SK) induces apoptosis through intrinsic and extrinsic pathways in human embryonic kidney cell line. Mol Biol Rep 2024;51:96. [PMID: 38193993 DOI: 10.1007/s11033-023-08934-z] [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: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 01/10/2024]
15
Levintov L, Vashisth H. Structural and computational studies of HIV-1 RNA. RNA Biol 2024;21:1-32. [PMID: 38100535 PMCID: PMC10730233 DOI: 10.1080/15476286.2023.2289709] [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] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]  Open
16
Khatkar P, Mensah G, Ning S, Cowen M, Kim Y, Williams A, Abulwerdi FA, Zhao Y, Zeng C, Le Grice SFJ, Kashanchi F. HIV-1 Transcription Inhibition Using Small RNA-Binding Molecules. Pharmaceuticals (Basel) 2023;17:33. [PMID: 38256867 PMCID: PMC10819208 DOI: 10.3390/ph17010033] [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: 09/30/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024]  Open
17
Haslecker R, Pham VV, Glänzer D, Kreutz C, Dayie TK, D'Souza VM. Extending the toolbox for RNA biology with SegModTeX: a polymerase-driven method for site-specific and segmental labeling of RNA. Nat Commun 2023;14:8422. [PMID: 38110450 PMCID: PMC10728113 DOI: 10.1038/s41467-023-44254-3] [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: 04/25/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]  Open
18
Roy R, Geng A, Shi H, Merriman DK, Dethoff EA, Salmon L, Al-Hashimi HM. Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble. J Am Chem Soc 2023;145:22964-22978. [PMID: 37831584 DOI: 10.1021/jacs.3c04614] [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] [Indexed: 10/15/2023]
19
Mathez G, Cagno V. Small Molecules Targeting Viral RNA. Int J Mol Sci 2023;24:13500. [PMID: 37686306 PMCID: PMC10487773 DOI: 10.3390/ijms241713500] [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: 08/02/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]  Open
20
Oksuz O, Henninger JE, Warneford-Thomson R, Zheng MM, Erb H, Vancura A, Overholt KJ, Hawken SW, Banani SF, Lauman R, Reich LN, Robertson AL, Hannett NM, Lee TI, Zon LI, Bonasio R, Young RA. Transcription factors interact with RNA to regulate genes. Mol Cell 2023;83:2449-2463.e13. [PMID: 37402367 PMCID: PMC10529847 DOI: 10.1016/j.molcel.2023.06.012] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/16/2023] [Accepted: 06/06/2023] [Indexed: 07/06/2023]
21
Ken ML, Roy R, Geng A, Ganser LR, Manghrani A, Cullen BR, Schulze-Gahmen U, Herschlag D, Al-Hashimi HM. RNA conformational propensities determine cellular activity. Nature 2023;617:835-841. [PMID: 37198487 PMCID: PMC10429349 DOI: 10.1038/s41586-023-06080-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 04/12/2023] [Indexed: 05/19/2023]
22
Camara MB, Sobeh AM, Eichhorn CD. Progress in 7SK ribonucleoprotein structural biology. Front Mol Biosci 2023;10:1154622. [PMID: 37051324 PMCID: PMC10083321 DOI: 10.3389/fmolb.2023.1154622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]  Open
23
Ghanam RH, Eastep GN, Saad JS. Structural Insights into the Mechanism of HIV-1 Tat Secretion from the Plasma Membrane. J Mol Biol 2023;435:167880. [PMID: 36370804 PMCID: PMC9822876 DOI: 10.1016/j.jmb.2022.167880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
24
Mbonye U, Kizito F, Karn J. New insights into transcription elongation control of HIV-1 latency and rebound. Trends Immunol 2023;44:60-71. [PMID: 36503686 PMCID: PMC11932764 DOI: 10.1016/j.it.2022.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022]
25
Rocchi C, Louvat C, Miele AE, Batisse J, Guillon C, Ballut L, Lener D, Negroni M, Ruff M, Gouet P, Fiorini F. The HIV-1 Integrase C-Terminal Domain Induces TAR RNA Structural Changes Promoting Tat Binding. Int J Mol Sci 2022;23:13742. [PMID: 36430221 PMCID: PMC9692563 DOI: 10.3390/ijms232213742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 11/10/2022]  Open
26
Valyaeva AA, Tikhomirova MA, Potashnikova DM, Bogomazova AN, Snigiryova GP, Penin AA, Logacheva MD, Arifulin EA, Shmakova AA, Germini D, Kachalova AI, Saidova AA, Zharikova AA, Musinova YR, Mironov AA, Vassetzky YS, Sheval EV. Ectopic expression of HIV-1 Tat modifies gene expression in cultured B cells: implications for the development of B-cell lymphomas in HIV-1-infected patients. PeerJ 2022;10:e13986. [PMID: 36275462 PMCID: PMC9586123 DOI: 10.7717/peerj.13986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/11/2022] [Indexed: 01/19/2023]  Open
27
Kognole AA, Hazel A, MacKerell AD. SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules. J Chem Theory Comput 2022;18:5672-5691. [PMID: 35913731 PMCID: PMC9474704 DOI: 10.1021/acs.jctc.2c00381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
28
Pham VV, Gao M, Meagher JL, Smith JL, D'Souza VM. A structure-based mechanism for displacement of the HEXIM adapter from 7SK small nuclear RNA. Commun Biol 2022;5:819. [PMID: 35970937 PMCID: PMC9378691 DOI: 10.1038/s42003-022-03734-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/19/2022] [Indexed: 11/09/2022]  Open
29
Chen YL, He W, Kirmizialtin S, Pollack L. Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations. CELL REPORTS. PHYSICAL SCIENCE 2022;3:100971. [PMID: 35936555 PMCID: PMC9351628 DOI: 10.1016/j.xcrp.2022.100971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
30
Ning S, Wang H, Zeng C, Zhao Y. Prediction of allosteric druggable pockets of cyclin-dependent kinases. Brief Bioinform 2022;23:6643454. [PMID: 35830869 DOI: 10.1093/bib/bbac290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/07/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022]  Open
31
Rocchi C, Gouet P, Parissi V, Fiorini F. The C-Terminal Domain of HIV-1 Integrase: A Swiss Army Knife for the Virus? Viruses 2022;14:v14071397. [PMID: 35891378 PMCID: PMC9316232 DOI: 10.3390/v14071397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/22/2022] [Indexed: 12/31/2022]  Open
32
Van Damme R, Li K, Zhang M, Bai J, Lee WH, Yesselman JD, Lu Z, Velema WA. Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells. Nat Commun 2022;13:911. [PMID: 35177610 PMCID: PMC8854666 DOI: 10.1038/s41467-022-28602-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 01/19/2022] [Indexed: 02/06/2023]  Open
33
Kotar A, Ma S, Keane SC. pH dependence of C•A, G•A and A•A mismatches in the stem of precursor microRNA-31. Biophys Chem 2022;283:106763. [DOI: 10.1016/j.bpc.2022.106763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 12/22/2022]
34
Ning S, Zeng C, Zeng C, Zhao Y. The TAR binding dynamics and its implication in Tat degradation mechanism. Biophys J 2021;120:5158-5168. [PMID: 34762866 PMCID: PMC8715215 DOI: 10.1016/j.bpj.2021.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/25/2021] [Accepted: 11/03/2021] [Indexed: 10/19/2022]  Open
35
Kognole AA, Lee J, Park SJ, Jo S, Chatterjee P, Lemkul JA, Huang J, MacKerell AD, Im W. CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. J Comput Chem 2021;43:359-375. [PMID: 34874077 DOI: 10.1002/jcc.26795] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/10/2021] [Accepted: 11/25/2021] [Indexed: 12/18/2022]
36
Chavali SS, Mali SM, Bonn R, Saseendran A, Bennett RP, Smith HC, Fasan R, Wedekind JE. Cyclic peptides with a distinct arginine-fork motif recognize the HIV trans-activation response RNA in vitro and in cells. J Biol Chem 2021;297:101390. [PMID: 34767799 DOI: 10.1016/j.jbc.2021.101390] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 12/21/2022]  Open
37
Covelo-Molares H, Obrdlik A, Poštulková I, Dohnálková M, Gregorová P, Ganji R, Potěšil D, Gawriyski L, Varjosalo M, Vaňáčová Š. The comprehensive interactomes of human adenosine RNA methyltransferases and demethylases reveal distinct functional and regulatory features. Nucleic Acids Res 2021;49:10895-10910. [PMID: 34634806 PMCID: PMC8565353 DOI: 10.1093/nar/gkab900] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 12/26/2022]  Open
38
Molecular coevolution of nuclear and nucleolar localization signals inside basic domain of HIV-1 Tat. J Virol 2021;96:e0150521. [PMID: 34613791 DOI: 10.1128/jvi.01505-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
39
Liu Y, Kotar A, Hodges TL, Abdallah K, Taleb MH, Bitterman BA, Jaime S, Schaubroeck KJ, Mathew E, Morgenstern NW, Lohmeier A, Page JL, Ratanapanichkich M, Arhin G, Johnson BL, Cherepanov S, Moss SC, Zuniga G, Tilson NJ, Yeoh ZC, Johnson BA, Keane SC. NMR chemical shift assignments of RNA oligonucleotides to expand the RNA chemical shift database. BIOMOLECULAR NMR ASSIGNMENTS 2021;15:479-490. [PMID: 34449019 DOI: 10.1007/s12104-021-10049-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 08/22/2021] [Indexed: 06/13/2023]
40
TAR RNA Mediated Folding of a Single-Arginine-Mutant HIV-1 Tat Protein within HeLa Cells Experiencing Intracellular Crowding. Int J Mol Sci 2021;22:ijms22189998. [PMID: 34576162 PMCID: PMC8468913 DOI: 10.3390/ijms22189998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 09/03/2021] [Accepted: 09/11/2021] [Indexed: 11/17/2022]  Open
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Interplay between Host tRNAs and HIV-1: A Structural Perspective. Viruses 2021;13:v13091819. [PMID: 34578400 PMCID: PMC8473020 DOI: 10.3390/v13091819] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 12/23/2022]  Open
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Chen R, Zhang Y, Chen P, Pang Y, Li H, Chen Z, Zhang X, Zhang H, Li W. [7SK truncation at 128-179 nt suppresses embryonic stem cell proliferation in vitro by downregulating CDC6]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021;41:1125-1130. [PMID: 34549701 DOI: 10.12122/j.issn.1673-4254.2021.08.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Levintov L, Vashisth H. Role of conformational heterogeneity in ligand recognition by viral RNA molecules. Phys Chem Chem Phys 2021;23:11211-11223. [PMID: 34010381 DOI: 10.1039/d1cp00679g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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The Peptide TAT-I24 with Antiviral Activity against DNA Viruses Binds Double-Stranded DNA with High Affinity. Biologics 2021. [DOI: 10.3390/biologics1010003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Dixit U, Bhutoria S, Wu X, Qiu L, Spira M, Mathew S, Harris R, Adams LJ, Cahill S, Pathak R, Rajesh Kumar P, Nguyen M, Acharya SA, Brenowitz M, Almo SC, Zou X, Steven AC, Cowburn D, Girvin M, Kalpana GV. INI1/SMARCB1 Rpt1 domain mimics TAR RNA in binding to integrase to facilitate HIV-1 replication. Nat Commun 2021;12:2743. [PMID: 33980829 PMCID: PMC8115288 DOI: 10.1038/s41467-021-22733-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/24/2021] [Indexed: 11/09/2022]  Open
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Ganser LR, Chu CC, Bogerd HP, Kelly ML, Cullen BR, Al-Hashimi HM. Probing RNA Conformational Equilibria within the Functional Cellular Context. Cell Rep 2021;30:2472-2480.e4. [PMID: 32101729 DOI: 10.1016/j.celrep.2020.02.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/24/2019] [Accepted: 01/31/2020] [Indexed: 12/17/2022]  Open
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Luo L, Chiu LY, Sugarman A, Gupta P, Rouskin S, Tolbert BS. HnRNP A1/A2 Proteins Assemble onto 7SK snRNA via Context Dependent Interactions. J Mol Biol 2021;433:166885. [PMID: 33684393 DOI: 10.1016/j.jmb.2021.166885] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 02/08/2023]
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Chavali SS, Mali SM, Jenkins JL, Fasan R, Wedekind JE. Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors. J Biol Chem 2020;295:16470-16486. [PMID: 33051202 PMCID: PMC7864049 DOI: 10.1074/jbc.ra120.015444] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/24/2020] [Indexed: 01/28/2023]  Open
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Depicting HIV-1 Transcriptional Mechanisms: A Summary of What We Know. Viruses 2020;12:v12121385. [PMID: 33287435 PMCID: PMC7761857 DOI: 10.3390/v12121385] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 12/19/2022]  Open
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Chavali SS, Cavender CE, Mathews DH, Wedekind JE. Arginine Forks Are a Widespread Motif to Recognize Phosphate Backbones and Guanine Nucleobases in the RNA Major Groove. J Am Chem Soc 2020;142:19835-19839. [PMID: 33170672 DOI: 10.1021/jacs.0c09689] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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