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Chagas BCA, Zhou X, Guerrero M, Ilina TV, Ishima R. Interplay between protease and reverse transcriptase dimerization in a model HIV-1 polyprotein. Protein Sci 2024; 33:e5080. [PMID: 38896002 PMCID: PMC11187873 DOI: 10.1002/pro.5080] [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: 02/12/2024] [Revised: 05/01/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024]
Abstract
The Gag-Pol polyprotein in human immunodeficiency virus type I (HIV-1) encodes enzymes that are essential for virus replication: protease (PR), reverse transcriptase (RT), and integrase (IN). The mature forms of PR, RT and IN are homodimer, heterodimer and tetramer, respectively. The precise mechanism underlying the formation of dimer or tetramer is not yet understood. Here, to gain insight into the dimerization of PR and RT in the precursor, we prepared a model precursor, PR-RT, incorporating an inactivating mutation at the PR active site, D25A, and including two residues in the p6* region, fused to a SUMO-tag, at the N-terminus of the PR region. We also prepared two mutants of PR-RT containing a dimer dissociation mutation either in the PR region, PR(T26A)-RT, or in the RT region, PR-RT(W401A). Size exclusion chromatography showed both monomer and dimer fractions in PR-RT and PR(T26A)-RT, but only monomer in PR-RT(W401A). SEC experiments of PR-RT in the presence of protease inhibitor, darunavir, significantly enhanced the dimerization. Additionally, SEC results suggest an estimated PR-RT dimer dissociation constant that is higher than that of the mature RT heterodimer, p66/p51, but slightly lower than the premature RT homodimer, p66/p66. Reverse transcriptase assays and RT maturation assays were performed as tools to assess the effects of the PR dimer-interface on these functions. Our results consistently indicate that the RT dimer-interface plays a crucial role in the dimerization in PR-RT, whereas the PR dimer-interface has a lesser role.
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Affiliation(s)
| | - Xiaohong Zhou
- Department of Structural BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Michel Guerrero
- Department of Structural BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Tatiana V. Ilina
- Department of Structural BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
| | - Rieko Ishima
- Department of Structural BiologyUniversity of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
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2
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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: 5] [Impact Index Per Article: 1.7] [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
Abstract
The cellular metabolism of host tRNAs and life cycle of HIV-1 cross paths at several key virus-host interfaces. Emerging data suggest a multi-faceted interplay between host tRNAs and HIV-1 that plays essential roles, both structural and regulatory, in viral genome replication, genome packaging, and virion biogenesis. HIV-1 not only hijacks host tRNAs and transforms them into obligatory reverse transcription primers but further commandeers tRNAs to regulate the localization of its major structural protein, Gag, via a specific interface. This review highlights recent advances in understanding tRNA-HIV-1 interactions, primarily from a structural perspective, which start to elucidate their underlying molecular mechanisms, intrinsic specificities, and biological significances. Such understanding may provide new avenues toward developing HIV/AIDS treatments and therapeutics including small molecules and RNA biologics that target these host-virus interfaces.
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3
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Large Multidomain Protein NMR: HIV-1 Reverse Transcriptase Precursor in Solution. Int J Mol Sci 2020; 21:ijms21249545. [PMID: 33333923 PMCID: PMC7765405 DOI: 10.3390/ijms21249545] [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: 11/22/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 11/17/2022] Open
Abstract
NMR studies of large proteins, over 100 kDa, in solution are technically challenging and, therefore, of considerable interest in the biophysics field. The challenge arises because the molecular tumbling of a protein in solution considerably slows as molecular mass increases, reducing the ability to detect resonances. In fact, the typical 1H-13C or 1H-15N correlation spectrum of a large protein, using a 13C- or 15N-uniformly labeled protein, shows severe line-broadening and signal overlap. Selective isotope labeling of methyl groups is a useful strategy to reduce these issues, however, the reduction in the number of signals that goes hand-in-hand with such a strategy is, in turn, disadvantageous for characterizing the overall features of the protein. When domain motion exists in large proteins, the domain motion differently affects backbone amide signals and methyl groups. Thus, the use of multiple NMR probes, such as 1H, 19F, 13C, and 15N, is ideal to gain overall structural or dynamical information for large proteins. We discuss the utility of observing different NMR nuclei when characterizing a large protein, namely, the 66 kDa multi-domain HIV-1 reverse transcriptase that forms a homodimer in solution. Importantly, we present a biophysical approach, complemented by biochemical assays, to understand not only the homodimer, p66/p66, but also the conformational changes that contribute to its maturation to a heterodimer, p66/p51, upon HIV-1 protease cleavage.
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Ilina T, Slack RL, Guerrero M, Ishima R. Effect of Lysyl-tRNA Synthetase on the Maturation of HIV-1 Reverse Transcriptase. ACS OMEGA 2020; 5:16619-16627. [PMID: 32685828 PMCID: PMC7364630 DOI: 10.1021/acsomega.0c01449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
In human immunodeficiency virus-1 (HIV-1), reverse transcriptase (RT) is encoded as a 66 kDa protein, p66, in the Gag-Pol polyprotein. This protein is proteolytically cleaved by HIV-1 protease (PR) to finally generate a mature RT that is a heterodimer, composed of a p66 subunit and a p66-derived 51 kDa subunit, p51. In our prior work, we demonstrated that tRNALys3 binding to p66/p66 facilitates efficient cleavage of p66 to p51 by PR. However, tRNALys3 is known to be recruited to the virus by forming a complex with lysyl-tRNA synthetase (LysRS). Herein, we tested whether LysRS can have an effect on RT maturation in vitro. Importantly, our data show no significant differences in RT maturation in the presence of LysRS. Furthermore, no apparent p66/66 interaction with LysRS was observed. Although PR cleaved LysRS, it did not immediately release tRNALys3 from LysRS. Thus, we conclude that a free fraction of tRNALys3, which is in equilibrium with a LysRS-bound form, interacts with p66/p66 without any additional mechanism involving release of tRNALys3 from LysRS. Given that only transient tRNALys3-p66/p66 interaction is needed for efficient RT maturation, a small amount of free tRNA may be sufficient for this process. These studies reveal molecular level insights into RT maturation and will be useful for the design of cellular/viral experiments to better understand the role of tRNA in HIV-1 replication.
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Nguyen PDM, Zheng J, Gremminger TJ, Qiu L, Zhang D, Tuske S, Lange MJ, Griffin PR, Arnold E, Chen SJ, Zou X, Heng X, Burke DH. Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase. Nucleic Acids Res 2020; 48:2709-2722. [PMID: 31943114 PMCID: PMC7049723 DOI: 10.1093/nar/gkz1224] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/17/2019] [Accepted: 01/03/2020] [Indexed: 12/31/2022] Open
Abstract
RNA aptamers that bind HIV-1 reverse transcriptase (RT) inhibit RT in enzymatic and viral replication assays. Some aptamers inhibit RT from only a few viral clades, while others show broad-spectrum inhibition. Biophysical determinants of recognition specificity are poorly understood. We investigated the interface between HIV-1 RT and a broad–spectrum UCAA-family aptamer. SAR and hydroxyl radical probing identified aptamer structural elements critical for inhibition and established the role of signature UCAA bulge motif in RT-aptamer interaction. HDX footprinting on RT ± aptamer shows strong contacts with both subunits, especially near the C-terminus of p51. Alanine scanning revealed decreased inhibition by the aptamer for mutants P420A, L422A and K424A. 2D proton nuclear magnetic resonance and SAXS data provided constraints on the solution structure of the aptamer and enable computational modeling of the docked complex with RT. Surprisingly, the aptamer enhanced proteolytic cleavage of precursor p66/p66 by HIV-1 protease, suggesting that it stabilizes the productive conformation to allow maturation. These results illuminate features at the RT-aptamer interface that govern recognition specificity by a broad-spectrum antiviral aptamer, and they open new possibilities for accelerating RT maturation and interfering with viral replication.
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Affiliation(s)
- Phuong D M Nguyen
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University Missouri, Columbia, MO 65211, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Liming Qiu
- Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA
| | - Dong Zhang
- Department of Physics and Astronomy, University Missouri, Columbia, MO 65211, USA
| | - Steve Tuske
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Margaret J Lange
- Department of Molecular Microbiology & Immunology, University Missouri, Columbia, MO 65211, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology & Medicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Shi-Jie Chen
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Department of Physics and Astronomy, University Missouri, Columbia, MO 65211, USA.,MU Institute for Data Science and Informatics, University Missouri, Columbia, MO 65211, USA
| | - Xiaoqin Zou
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Dalton Cardiovascular Research Center, University Missouri, Columbia, MO 65211, USA.,Department of Physics and Astronomy, University Missouri, Columbia, MO 65211, USA.,MU Institute for Data Science and Informatics, University Missouri, Columbia, MO 65211, USA
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Donald H Burke
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University Missouri, Columbia, MO 65211, USA.,Department of Molecular Microbiology & Immunology, University Missouri, Columbia, MO 65211, USA
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6
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Xavier Ruiz F, Arnold E. Evolving understanding of HIV-1 reverse transcriptase structure, function, inhibition, and resistance. Curr Opin Struct Biol 2020; 61:113-123. [PMID: 31935541 DOI: 10.1016/j.sbi.2019.11.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 11/28/2019] [Indexed: 10/25/2022]
Abstract
The essential role of reverse transcription in the HIV life cycle is illustrated by the fact that half of the ∼30 FDA-approved drugs for HIV treatment target HIV-1 reverse transcriptase (RT). Even though more than 160 structures of RT deposited in the Protein Data Bank (PDB) have revealed the molecular architecture of RT in great detail, some key states of RT function and inhibition remain still unknown. Recent structures of RT initiation complexes, RT poised for RNA hydrolysis, and RT with approved drugs and investigational compounds have provided a deeper understanding of RT function and inhibition, suggesting novel avenues for targeting this central enzyme of HIV.
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Affiliation(s)
- Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, 08854, NJ, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, 08854, NJ, USA.
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7
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Slack RL, Ilina TV, Xi Z, Giacobbi NS, Kawai G, Parniak MA, Sarafianos SG, Sluis Cremer N, Ishima R. Conformational Changes in HIV-1 Reverse Transcriptase that Facilitate Its Maturation. Structure 2019; 27:1581-1593.e3. [PMID: 31471129 DOI: 10.1016/j.str.2019.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/10/2019] [Accepted: 08/09/2019] [Indexed: 01/18/2023]
Abstract
HIV-1 reverse transcriptase (RT) is translated as part of the Gag-Pol polyprotein that is proteolytically processed by HIV-1 protease (PR) to finally become a mature heterodimer, composed of a p66 and a p66-derived 51-kDa subunit, p51. Our previous work suggested that tRNALys3 binding to p66/p66 introduces conformational changes in the ribonuclease (RNH) domain of RT that facilitate efficient cleavage of p66 to p51 by PR. In this study, we characterized the conformational changes in the RNH domain of p66/p66 imparted by tRNALys3 using NMR. Moreover, the importance of tRNALys3 in RT maturation was confirmed in cellulo by modulating the levels of Lys-tRNA synthetase, which affects recruitment of tRNALys3 to the virus. We also employed nonnucleoside RT inhibitors, to modulate the p66 dimer-monomer equilibrium and monitor the resulting structural changes. Taken together, our data provide unique insights into the conformational changes in p66/p66 that drive PR cleavage.
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Affiliation(s)
- Ryan L Slack
- Department of Structural Biology, University of Pittsburgh School of Medicine, Room 1037, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Tatiana V Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, Room 1037, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Zhaoyong Xi
- Department of Structural Biology, University of Pittsburgh School of Medicine, Room 1037, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Nicholas S Giacobbi
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Gota Kawai
- Department of Life and Environmental Sciences, Chiba Institute of Technology, Chiba, Japan
| | - Michael A Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicolas Sluis Cremer
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Room 1037, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA.
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8
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London RE. HIV-1 Reverse Transcriptase: A Metamorphic Protein with Three Stable States. Structure 2019; 27:420-426. [PMID: 30639227 DOI: 10.1016/j.str.2018.11.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/31/2018] [Accepted: 11/27/2018] [Indexed: 11/18/2022]
Abstract
There has been a steadily increasing appreciation of the fact that the relationship between protein sequence and structure is often sufficiently ambiguous to allow a single sequence to adopt alternative, stable folds. Living organisms have been able to utilize such metamorphic proteins in remarkable and unanticipated ways. HIV-1 reverse transcriptase is among the earliest such proteins identified and remains a unique example in which a functional heterodimer contains two, alternatively folded polymerase domains. Structural characterization of the p66 precursor protein combined with NMR spectroscopic and molecular modeling studies have provided insights into the factors underlying the metamorphic transition and the subunit-specific programmed unfolding step required to expose the protease cleavage site within the ribonuclease H domain, supporting the conversion of the p66/p66' precursor into the mature p66/p51 heterodimer.
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Affiliation(s)
- Robert E London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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