دورية أكاديمية
High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs.
| العنوان: | High-resolution view of HIV-1 reverse transcriptase initiation complexes and inhibition by NNRTI drugs. |
|---|---|
| المؤلفون: | Ha B; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA., Larsen KP; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.; Program in Biophysics, Stanford University, Stanford, CA, USA.; Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA., Zhang J; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA., Fu Z; Department of Chemistry and Molecular Biophysics, Columbia University, New York, NY, USA.; Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, Howard Hughes Medical Institute, New York, NY, USA., Montabana E; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA., Jackson LN; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA., Chen DH; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA., Puglisi EV; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. epuglisi@stanford.edu. |
| المصدر: | Nature communications [Nat Commun] 2021 May 04; Vol. 12 (1), pp. 2500. Date of Electronic Publication: 2021 May 04. |
| نوع المنشور: | Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S. |
| اللغة: | English |
| بيانات الدورية: | Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101528555 Publication Model: Electronic Cited Medium: Internet ISSN: 2041-1723 (Electronic) Linking ISSN: 20411723 NLM ISO Abbreviation: Nat Commun Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: [London] : Nature Pub. Group |
| مواضيع طبية MeSH: | HIV Reverse Transcriptase/*chemistry , HIV-1/*drug effects , RNA, Transfer, Lys/*chemistry , RNA, Viral/*chemistry , Reverse Transcriptase Inhibitors/*chemistry, Alkynes/chemistry ; Alkynes/pharmacology ; Benzoxazines/chemistry ; Benzoxazines/pharmacology ; Catalytic Domain ; Cryoelectron Microscopy ; Cyclopropanes/chemistry ; Cyclopropanes/pharmacology ; HIV Reverse Transcriptase/genetics ; HIV Reverse Transcriptase/metabolism ; HIV-1/enzymology ; HIV-1/genetics ; HIV-1/metabolism ; Models, Molecular ; Nevirapine/chemistry ; Nevirapine/pharmacology ; Nucleic Acid Conformation/drug effects ; RNA, Transfer, Lys/genetics ; RNA, Viral/genetics ; Reverse Transcriptase Inhibitors/pharmacology |
| مستخلص: | Reverse transcription of the HIV-1 viral RNA genome (vRNA) is an integral step in virus replication. Upon viral entry, HIV-1 reverse transcriptase (RT) initiates from a host tRNA Lys |
| References: | Hu, W.-S. & Hughes, S. H. HIV-1 reverse transcription. Cold Spring Harb. Perspect. Med. 2, a006882–a006882 (2012). (PMID: 23028129347539510.1101/cshperspect.a006882) Lanchy, J. M. et al. Contacts between reverse transcriptase and the primer strand govern the transition from initiation to elongation of HIV-1 reverse transcription. J. Biol. Chem. 273, 24425–24432 (1998). (PMID: 973373310.1074/jbc.273.38.24425) Lanchy, J. M., Ehresmann, C., Le Grice, S. F., Ehresmann, B. & Marquet, R. Binding and kinetic properties of HIV-1 reverse transcriptase markedly differ during initiation and elongation of reverse transcription. EMBO J. 15, 7178–7187 (1996). (PMID: 900379345254510.1002/j.1460-2075.1996.tb01109.x) Isel, C. et al. Specific initiation and switch to elongation of human immunodeficiency virus type 1 reverse transcription require the post-transcriptional modifications of primer tRNA3Lys. EMBO J. 15, 917–924 (1996). (PMID: 863131245028910.1002/j.1460-2075.1996.tb00426.x) Larsen, K. P., Choi, J., Prabhakar, A., Puglisi, E. V. & Puglisi, J. D. Relating structure and dynamics in RNA biology. Cold Spring Harb. Perspect. Biol. 11, a032474 (2019). (PMID: 3126294810.1101/cshperspect.a0324746601459) Isel, C., Ehresmann, C. & Marquet, R. Initiation of HIV reverse transcription. Viruses 2, 213–243 (2010). (PMID: 21994608318555010.3390/v2010213) Sarafianos, S. G. et al. Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition. J. Mol. Biol. 385, 693–713 (2009). (PMID: 1902226210.1016/j.jmb.2008.10.071) Beerens, N. & Berkhout, B. The tRNA primer activation signal in the human immunodeficiency virus type 1 genome is important for initiation and processive elongation of reverse transcription. J. Virol. 76, 2329–2339 (2002). (PMID: 1183641115380410.1128/jvi.76.5.2329-2339.2002) Beerens, N., Groot, F. & Berkhout, B. Initiation of HIV-1 reverse transcription is regulated by a primer activation signal. J. Biol. Chem. 276, 31247–31256 (2001). (PMID: 1138497610.1074/jbc.M102441200) Goldschmidt, V., Ehresmann, C., Ehresmann, B. & Marquet, R. Does the HIV-1 primer activation signal interact with tRNA3 Lys during the initiation of reverse transcription? Nucleic Acids Res. 31, 850–859 (2003). (PMID: 1256048014920710.1093/nar/gkg187) Iwatani, Y., Rosen, A. E., Guo, J., Musier-Forsyth, K. & Levin, J. G. Efficient initiation of HIV-1 reverse transcription in vitro. Requirement for RNA sequences downstream of the primer binding site abrogated by nucleocapsid protein-dependent primer-template interactions. J. Biol. Chem. 278, 14185–14195 (2003). (PMID: 1256032710.1074/jbc.M211618200) Larsen, K. P. et al. Architecture of an HIV-1 reverse transcriptase initiation complex. Nature 557, 118–122 (2018). (PMID: 29695867593429410.1038/s41586-018-0055-9) Larsen, K. P. et al. Distinct conformational states underlie pausing during initiation of HIV-1 reverse transcription. J. Mol. Biol. 432, 4499–4522 (2020). (PMID: 3251200510.1016/j.jmb.2020.06.0037387199) Das, K., Martinez, S. E., DeStefano, J. J. & Arnold, E. Structure of HIV-1 RT/dsRNA initiation complex prior to nucleotide incorporation. Proc. Natl Acad. Sci. USA 116, 7308–7313 (2019). (PMID: 3090289510.1073/pnas.18141701166462067) Das, K., Martinez, S. E., Bauman, J. D. & Arnold, E. HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism. Nat. Struct. Mol. Biol. 19, 253–259 (2012). (PMID: 22266819335913210.1038/nsmb.2223) Lapkouski, M., Tian, L., Miller, J. T., Le Grice, S. F. J. & Yang, W. Complexes of HIV-1 RT, NNRTI and RNA/DNA hybrid reveal a structure compatible with RNA degradation. Nat. Struct. Mol. Biol. 20, 230–236 (2013). (PMID: 23314251397318210.1038/nsmb.2485) Rittinger, K., Divita, G. & Goody, R. S. Human immunodeficiency virus reverse transcriptase substrate-induced conformational changes and the mechanism of inhibition by nonnucleoside inhibitors. Proc. Natl Acad. Sci. USA 92, 8046–8049 (1995). (PMID: 754401310.1073/pnas.92.17.804641283) Spence, R. A., Kati, W. M., Anderson, K. S. & Johnson, K. A. Mechanism of inhibition of HIV-1 reverse transcriptase by nonnucleoside inhibitors. Science 267, 988–993 (1995). (PMID: 7532321752674710.1126/science.7532321) Hooker, C. W., Lott, W. B. & Harrich, D. Inhibitors of human immunodeficiency virus type 1 reverse transcriptase target distinct phases of early reverse transcription. J. Virol. 75, 3095–3104 (2001). (PMID: 1123883611410310.1128/JVI.75.7.3095-3104.2001) Huang, H., Chopra, R., Verdine, G. L. & Harrison, S. C. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 282, 1669–1675 (1998). (PMID: 983155110.1126/science.282.5394.1669) Tian, L., Kim, M. S., Li, H., Wang, J. & Yang, W. Structure of HIV-1 reverse transcriptase cleaving RNA in an RNA/DNA hybrid. Proc. Natl Acad. Sci. USA 115, 507–512 (2018). (PMID: 2929593910.1073/pnas.17197461155777007) Ren, J. et al. Structural basis for the resilience of efavirenz (DMP-266) to drug resistance mutations in HIV-1 reverse transcriptase. Structure 8, 1089–1094 (2000). (PMID: 1108063010.1016/S0969-2126(00)00513-X) Kohlstaedt, L. A., Wang, J., Friedman, J. M., Rice, P. A. & Steitz, T. A. Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 256, 1783–1790 (1992). (PMID: 137740310.1126/science.1377403) Ren, J. et al. High resolution structures of HIV-1 RT from four RT-inhibitor complexes. Nat. Struct. Biol. 2, 293–302 (1995). (PMID: 754093410.1038/nsb0495-293) Xavier Ruiz, F. & Arnold, E. Evolving understanding of HIV-1 reverse transcriptase structure, function, inhibition, and resistance. Curr. Opin. Struct. Biol. 61, 113–123 (2020). (PMID: 31935541759692410.1016/j.sbi.2019.11.011) Hughes, S. H. Reverse transcription of retroviruses and LTR retrotransposons. Microbiol Spectr. 3, MDNA3-0027-2014 (2015). (PMID: 2610470410.1128/microbiolspec.MDNA3-0027-2014) Julias, J. G., McWilliams, M. J., Sarafianos, S. G., Arnold, E. & Hughes, S. H. Mutations in the RNase H domain of HIV-1 reverse transcriptase affect the initiation of DNA synthesis and the specificity of RNase H cleavage in vivo. Proc. Natl Acad. Sci. USA 99, 9515–9520 (2002). (PMID: 1209390810.1073/pnas.142123199123172) Liu, S., Abbondanzieri, E. A., Rausch, J. W., Le Grice, S. F. & Zhuang, X. Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates. Science 322, 1092–1097 (2008). (PMID: 19008444271704310.1126/science.1163108) Coey, A., Larsen, K., Puglisi, J. D. & Viani Puglisi, E. Heterogeneous structures formed by conserved RNA sequences within the HIV reverse transcription initiation site. RNA 22, 1689–1698 (2016). (PMID: 27613581506662110.1261/rna.056804.116) Puglisi, E. V. & Puglisi, J. D. Secondary structure of the HIV reverse transcription initiation complex by NMR. J. Mol. Biol. 410, 863–874 (2011). (PMID: 21763492371011910.1016/j.jmb.2011.04.024) Götte, M. et al. HIV-1 reverse transcriptase-associated RNase H cleaves RNA/RNA in arrested complexes: implications for the mechanism by which RNase H discriminates between RNA/RNA and RNA/DNA. EMBO J. 14, 833–841 (1995). (PMID: 753372539815010.1002/j.1460-2075.1995.tb07061.x) Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005). (PMID: 1618256310.1016/j.jsb.2005.07.007) Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016). (PMID: 26592709471134310.1016/j.jsb.2015.11.003) Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017). (PMID: 28250466549403810.1038/nmeth.4193) Scheres, S. H. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J. Struct. Biol. 180, 519–530 (2012). (PMID: 23000701369053010.1016/j.jsb.2012.09.006) Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018). (PMID: 30412051625042510.7554/eLife.42166) Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017). (PMID: 2816547310.1038/nmeth.4169) Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D. Biol. Crystallogr. 66, 213–221 (2010). (PMID: 20124702281567010.1107/S0907444909052925) Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Crystallogr. D. Struct. Biol. 74, 531–544 (2018). (PMID: 29872004609649210.1107/S2059798318006551) Williams, C. J. et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci. 27, 293–315 (2018). (PMID: 2906776610.1002/pro.3330) Barad, B. A. et al. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nat. Methods 12, 943–946 (2015). (PMID: 26280328458948110.1038/nmeth.3541) Lu, X. J., Bussemaker, H. J. & Olson, W. K. DSSR: an integrated software tool for dissecting the spatial structure of RNA. Nucleic Acids Res. 43, e142 (2015). (PMID: 261848744666379) Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D. Biol. Crystallogr. 66, 486–501 (2010). (PMID: 20383002285231310.1107/S0907444910007493) Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018). |
| معلومات مُعتمدة: | P50 AI150464 United States AI NIAID NIH HHS; T32 GM008294 United States GM NIGMS NIH HHS; R01 GM129325 United States GM NIGMS NIH HHS; T32 HG000044 United States HG NHGRI NIH HHS |
| المشرفين على المادة: | 0 (Alkynes) 0 (Benzoxazines) 0 (Cyclopropanes) 0 (RNA, Transfer, Lys) 0 (RNA, Viral) 0 (Reverse Transcriptase Inhibitors) 99DK7FVK1H (Nevirapine) EC 2.7.7.- (reverse transcriptase, Human immunodeficiency virus 1) EC 2.7.7.49 (HIV Reverse Transcriptase) JE6H2O27P8 (efavirenz) |
| تواريخ الأحداث: | Date Created: 20210505 Date Completed: 20210524 Latest Revision: 20230131 |
| رمز التحديث: | 20230201 |
| مُعرف محوري في PubMed: | PMC8096811 |
| DOI: | 10.1038/s41467-021-22628-9 |
| PMID: | 33947853 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 2041-1723 |
|---|---|
| DOI: | 10.1038/s41467-021-22628-9 |