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HIV-1 Uncoating and Reverse Transcription Require eEF1A Binding to Surface-Exposed Acidic Residues of the Reverse Transcriptase Thumb Domain. mBio 2018; 9:mBio.00316-18. [PMID: 29588400 PMCID: PMC5874916 DOI: 10.1128/mbio.00316-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Once HIV-1 enters a cell, the viral core is uncoated by a poorly understood mechanism and the HIV-1 genomic RNA is reverse transcribed into DNA. Host cell factors are essential for these processes, although very few reverse transcription complex binding host cell factors have been convincingly shown to affect uncoating or reverse transcription. We previously reported that cellular eukaryotic translation elongation factor 1A (eEF1A) interacts tightly and directly with HIV-1 reverse transcriptase (RT) for more efficient reverse transcription. Here we report that the surface-exposed acidic residues in the HIV-1 RT thumb domain alpha-J helix and flanking regions are important for interaction with eEF1A. Mutation of surface-exposed acidic thumb domain residues D250, E297, E298, and E300 to arginine resulted in various levels of impairment of the interaction between RT and eEF1A. This indicates that this negatively charged region in the RT thumb domain is important for interaction with the positively charged eEF1A protein. The impairment of RT and eEF1A interaction by the RT mutations correlated with the efficiency of reverse transcription, uncoating, and infectivity. The best example of this is the strictly conserved E300 residue, where mutation significantly impaired the interaction of RT with eEF1A and virus replication in CD4+ T cells without affecting in vitro RT catalytic activity, RT heterodimerization, or RNase H activity. This study demonstrated that the interaction between surface-exposed acidic residues of the RT thumb domain and eEF1A is important for HIV-1 uncoating, reverse transcription, and replication. HIV-1, like all viruses, requires host cell proteins for its replication. Understanding the mechanisms behind virus-host interactions can lay the foundation for future novel therapeutic developments. Our lab has identified eEF1A as a key HIV-1 RT binding host protein that is important for the reverse transcription of HIV-1 genomic RNA into DNA. Here we identify the first surface-exposed RT residues that underpin interactions with eEF1A. Mutation of one strictly conserved RT residue (E300R) delayed reverse transcription and viral core uncoating and strongly inhibited HIV-1 replication in CD4+ T cells. This study advances the structural and mechanistic detail of the key RT-eEF1A interaction in HIV-1 infection and indicates its importance in uncoating for the first time. This provides a further basis for the development of an RT-eEF1A interaction-inhibiting anti-HIV-1 drug and suggests that the surface-exposed acidic patch of the RT thumb domain may be an attractive drug target.
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Structural Maturation of HIV-1 Reverse Transcriptase-A Metamorphic Solution to Genomic Instability. Viruses 2016; 8:v8100260. [PMID: 27690082 PMCID: PMC5086598 DOI: 10.3390/v8100260] [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: 07/01/2016] [Accepted: 09/12/2016] [Indexed: 12/13/2022] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT)—a critical enzyme of the viral life cycle—undergoes a complex maturation process, required so that a pair of p66 precursor proteins can develop conformationally along different pathways, one evolving to form active polymerase and ribonuclease H (RH) domains, while the second forms a non-functional polymerase and a proteolyzed RH domain. These parallel maturation pathways rely on the structural ambiguity of a metamorphic polymerase domain, for which the sequence–structure relationship is not unique. Recent nuclear magnetic resonance (NMR) studies utilizing selective labeling techniques, and structural characterization of the p66 monomer precursor have provided important insights into the details of this maturation pathway, revealing many aspects of the three major steps involved: (1) domain rearrangement; (2) dimerization; and (3) subunit-selective RH domain proteolysis. This review summarizes the major structural changes that occur during the maturation process. We also highlight how mutations, often viewed within the context of the mature RT heterodimer, can exert a major influence on maturation and dimerization. It is further suggested that several steps in the RT maturation pathway may provide attractive targets for drug development.
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Eyckerman S, Titeca K, Van Quickelberghe E, Cloots E, Verhee A, Samyn N, De Ceuninck L, Timmerman E, De Sutter D, Lievens S, Van Calenbergh S, Gevaert K, Tavernier J. Trapping mammalian protein complexes in viral particles. Nat Commun 2016; 7:11416. [PMID: 27122307 PMCID: PMC4853472 DOI: 10.1038/ncomms11416] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 03/22/2016] [Indexed: 01/22/2023] Open
Abstract
Cell lysis is an inevitable step in classical mass spectrometry–based strategies to analyse protein complexes. Complementary lysis conditions, in situ cross-linking strategies and proximal labelling techniques are currently used to reduce lysis effects on the protein complex. We have developed Virotrap, a viral particle sorting approach that obviates the need for cell homogenization and preserves the protein complexes during purification. By fusing a bait protein to the HIV-1 GAG protein, we show that interaction partners become trapped within virus-like particles (VLPs) that bud from mammalian cells. Using an efficient VLP enrichment protocol, Virotrap allows the detection of known binary interactions and MS-based identification of novel protein partners as well. In addition, we show the identification of stimulus-dependent interactions and demonstrate trapping of protein partners for small molecules. Virotrap constitutes an elegant complementary approach to the arsenal of methods to study protein complexes. A large portion of the proteome carries out its cellular function as part of macromolecular complexes. Here the authors describe Virotrap, a novel lysis-free approach for the isolation and identification of biologically relevant protein-protein and small molecule-protein interactions.
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Affiliation(s)
- Sven Eyckerman
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Kevin Titeca
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Emmy Van Quickelberghe
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Eva Cloots
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Annick Verhee
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Noortje Samyn
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Leentje De Ceuninck
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Evy Timmerman
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Delphine De Sutter
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Sam Lievens
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, Ghent B-9000, Belgium
| | - Kris Gevaert
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
| | - Jan Tavernier
- VIB Medical Biotechnology Center, VIB, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium.,Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, Ghent B-9000, Belgium
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Li D, Wei T, Rawle DJ, Qin F, Wang R, Soares DC, Jin H, Sivakumaran H, Lin MH, Spann K, Abbott CM, Harrich D. Specific Interaction between eEF1A and HIV RT Is Critical for HIV-1 Reverse Transcription and a Potential Anti-HIV Target. PLoS Pathog 2015; 11:e1005289. [PMID: 26624286 PMCID: PMC4666417 DOI: 10.1371/journal.ppat.1005289] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/30/2015] [Indexed: 11/19/2022] Open
Abstract
Reverse transcription is the central defining feature of HIV-1 replication. We previously reported that the cellular eukaryotic elongation factor 1 (eEF1) complex associates with the HIV-1 reverse transcription complex (RTC) and the association is important for late steps of reverse transcription. Here we show that association between the eEF1 and RTC complexes occurs by a strong and direct interaction between the subunit eEF1A and reverse transcriptase (RT). Using biolayer interferometry and co-immunoprecipitation (co-IP) assays, we show that association between the eEF1 and RTC complexes occurs by a strong (KD ~3–4 nM) and direct interaction between eEF1A and reverse transcriptase (RT). Biolayer interferometry analysis of cell lysates with titrated levels of eEF1A indicates it is a predominant cellular RT binding protein. Both the RT thumb and connection domains are required for interaction with eEF1A. A single amino acid mutation, W252A, within the thumb domain impaired co-IP between eEF1A and RT, and also significantly reduced the efficiency of late reverse transcription and virus replication when incorporated into infectious HIV-1. Molecular modeling analysis indicated that interaction between W252 and L303 are important for RT structure, and their mutation to alanine did not impair heterodimerisation, but negatively impacted interaction with eEF1A. Didemnin B, which specifically binds eEF1A, potently inhibited HIV-1 reverse transcription by greater than 2 logs at subnanomolar concentrations, especially affecting reverse transcription late DNA synthesis. Analysis showed reduced levels of RTCs from HIV-1-infected HEK293T treated with didemnin B compared to untreated cells. Interestingly, HIV-1 with a W252A RT mutation was resistant to didemnin B negative effects showing that didemnin B affects HIV-1 by targeting the RT-eEF1A interaction. The combined evidence indicates a direct interaction between eEF1A and RT is crucial for HIV reverse transcription and replication, and the RT-eEF1A interaction is a potential drug target. After infecting a target cell, HIV-1 like all retroviruses converts the viral single strand RNA genome into double strand DNA by the process called reverse transcription. Host proteins are known to be important for reverse transcription yet a direct role for any host protein has not been demonstrated. In this paper, we show that a eukaryotic translation elongation factor (eEF1A), an abundant cellular protein, directly and strongly binds to the viral enzyme reverse transcriptase (RT). The biological relevance of the association is supported by mutational analysis of RT and by treating cells with the small molecule didemnin B that specifically binds eEF1A. Mutation of RT or treatment of cells with didemnin B resulted in significantly decreased efficiency of reverse transcription. Didemnin B treatment of cells disrupted HIV-1’s ability to maintain the viral machinery necessary for reverse transcription. However, an HIV-1 mutant, which does not interact with eEF1A, was resistant to didemnin B negative effects on early viral replication, showing that didemnin B affects HIV-1 by targeting the RT-eEF1A interaction. Altogether, this study demonstrates that eEF1A is an integral component of the viral reverse transcription complex and that the RT-eEF1A interaction is a possible new drug target to inhibit HIV-1 replication.
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Affiliation(s)
- Dongsheng Li
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Ting Wei
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Daniel J. Rawle
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Fangyun Qin
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Rui Wang
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Dinesh C. Soares
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom
| | - Hongping Jin
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Haran Sivakumaran
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Min-Hsuan Lin
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Kirsten Spann
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, Australia
- School of Biomedical Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Catherine M. Abbott
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom
| | - David Harrich
- Department of Cell and Molecular Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
- * E-mail:
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5
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Lemmens I, Lievens S, Tavernier J. MAPPIT, a mammalian two-hybrid method for in-cell detection of protein-protein interactions. Methods Mol Biol 2015; 1278:447-55. [PMID: 25859968 DOI: 10.1007/978-1-4939-2425-7_29] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
MAPPIT (MAmmalian Protein-Protein Interaction Trap) is a two-hybrid technology that facilitates the detection and analysis of interactions between proteins in living mammalian cells. The system is based on type 1 cytokine receptor signaling. The bait protein of interest is fused to a chimeric signaling-deficient cytokine receptor, the signaling competence of which is restored upon recruitment of a prey protein that is coupled to a functional cytokine receptor domain. MAPPIT exhibits an excellent signal-to-noise ratio, detects a wide variety of protein-protein interactions (PPIs) including transient and indirect interactions, and has been shown to be highly complementary to other two-hybrid methods with respect to the interactions it can detect. Variants of the method were developed to allow large-scale PPI screening, mapping of protein interaction interfaces, PPI inhibitor screening and drug profiling. This chapter describes a basic 4-day MAPPIT protocol for the analysis of interaction between two designated proteins.
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Affiliation(s)
- Irma Lemmens
- Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, 9000, Ghent, Belgium
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6
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Lievens S, Gerlo S, Lemmens I, De Clercq DJH, Risseeuw MDP, Vanderroost N, De Smet AS, Ruyssinck E, Chevet E, Van Calenbergh S, Tavernier J. Kinase Substrate Sensor (KISS), a mammalian in situ protein interaction sensor. Mol Cell Proteomics 2014; 13:3332-42. [PMID: 25154561 DOI: 10.1074/mcp.m114.041087] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Probably every cellular process is governed by protein-protein interaction (PPIs), which are often highly dynamic in nature being modulated by in- or external stimuli. Here we present KISS, for KInase Substrate Sensor, a mammalian two-hybrid approach designed to map intracellular PPIs and some of the dynamic features they exhibit. Benchmarking experiments indicate that in terms of sensitivity and specificity KISS is on par with other binary protein interaction technologies while being complementary with regard to the subset of PPIs it is able to detect. We used KISS to evaluate interactions between different types of proteins, including transmembrane proteins, expressed at their native subcellular location. In situ analysis of endoplasmic reticulum stress-induced clustering of the endoplasmic reticulum stress sensor ERN1 and ligand-dependent β-arrestin recruitment to GPCRs illustrated the method's potential to study functional PPI modulation in complex cellular processes. Exploring its use as a tool for in cell evaluation of pharmacological interference with PPIs, we showed that reported effects of known GPCR antagonists and PPI inhibitors are properly recapitulated. In a three-hybrid setup, KISS was able to map interactions between small molecules and proteins. Taken together, we established KISS as a sensitive approach for in situ analysis of protein interactions and their modulation in a changing cellular context or in response to pharmacological challenges.
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Affiliation(s)
- Sam Lievens
- From the ‡ Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, 9000 Ghent, Belgium ; §Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Sarah Gerlo
- From the ‡ Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, 9000 Ghent, Belgium ; §Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Irma Lemmens
- From the ‡ Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, 9000 Ghent, Belgium ; §Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Dries J H De Clercq
- ¶Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Martijn D P Risseeuw
- ¶Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Nele Vanderroost
- From the ‡ Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, 9000 Ghent, Belgium ; §Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Anne-Sophie De Smet
- From the ‡ Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, 9000 Ghent, Belgium ; §Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Elien Ruyssinck
- From the ‡ Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, 9000 Ghent, Belgium ; §Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, 9000 Ghent, Belgium
| | - Eric Chevet
- ‖French National Institute for Health and Medical Research (INSERM) U1053, University of Bordeaux Segalen, 146 Rue Leo Saignat, 33000 Bordeaux, France
| | - Serge Van Calenbergh
- ¶Laboratory for Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium
| | - Jan Tavernier
- From the ‡ Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, 9000 Ghent, Belgium ; §Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, A. Baertsoenkaai 3, 9000 Ghent, Belgium;
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Lievens S, Caligiuri M, Kley N, Tavernier J. The use of mammalian two-hybrid technologies for high-throughput drug screening. Methods 2012; 58:335-42. [PMID: 22917772 DOI: 10.1016/j.ymeth.2012.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Revised: 05/03/2012] [Accepted: 08/07/2012] [Indexed: 11/19/2022] Open
Abstract
Developing agents that target protein-protein interactions (PPIs) is an emerging field in drug discovery. Although this target class has hitherto remained underexplored, it holds exceptional promise related to the large amount of potential PPI targets compared to single protein targets and it offers important opportunities to increase the specificity of therapeutic molecules. While several PPI modulating therapeutics have recently been reported and a number of these are in clinical trial, progress in the field has been hampered by the lack of efficient screening systems. Recently, a number of cellular approaches have been developed that complement classical in vitro screening methods and which exhibit a number of important assets related to the physiological context they provide. Here we discuss the utility of two-hybrid technologies towards high-throughput screening for PPI inhibitors, in particular those that operate in a mammalian cellular background. We review a number of cases where mammalian two-hybrids have been successfully applied to identify small molecule disruptors of PPIs and zoom in further on the MAPPIT (Mammalian Protein-Protein Interaction Trap) technology platform. The value of this approach for drug discovery is illustrated by recent data from MAPPIT-based screening projects.
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Affiliation(s)
- Sam Lievens
- Department of Medical Protein Research, VIB, Ghent, Belgium
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Van Schoubroeck B, Van Acker K, Dams G, Jochmans D, Clayton R, Berke JM, Lievens S, Van der Heyden J, Tavernier J. MAPPIT as a high-throughput screening assay for modulators of protein-protein interactions in HIV and HCV. Methods Mol Biol 2012; 812:295-307. [PMID: 22218868 DOI: 10.1007/978-1-61779-455-1_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The discovery of novel antivirals for HIV and HCV has been a focus of intensive research for many years. Where the inhibition of critical viral enzymes by small molecules has proven effective for many viruses, there is considerable merit in pursuing protein-protein interactions (PPIs) as targets for therapeutic intervention. The mammalian protein-protein interaction trap (MAPPIT) is a two-hybrid system used for the study of PPIs. The bait and prey proteins are linked to deficient cytokine receptor chimeras, where the bait and prey interaction and subsequent ligand stimulation restores JAK-STAT signaling, resulting in reporter gene expression controlled by a STAT3-responsive promoter. We report the use of MAPPIT as a high-throughput screening assay for the discovery of inhibitors or stimulators of the Vif-APOBEC3G interaction and the reverse transcriptase heterodimerization (RTp66-RTp51) for HIV and the NS4A-NS3 interaction for HCV.
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Bovijn C, Ulrichts P, De Smet AS, Catteeuw D, Beyaert R, Tavernier J, Peelman F. Identification of interaction sites for dimerization and adapter recruitment in Toll/interleukin-1 receptor (TIR) domain of Toll-like receptor 4. J Biol Chem 2011; 287:4088-98. [PMID: 22139835 DOI: 10.1074/jbc.m111.282350] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Toll-like receptor signaling requires interactions of the Toll/IL-1 receptor (TIR) domains of the receptor and adapter proteins. Using the mammalian protein-protein interaction trap strategy, homology modeling, and site-directed mutagenesis, we identify the interaction surfaces in the TLR4 TIR domain for the TLR4-TLR4, TLR4-MyD88 adapter-like (MAL), and TLR4-TRIF-related adapter molecule (TRAM) interaction. Two binding sites are equally important for TLR4 dimerization and adapter recruitment. In a model based on the crystal structure of the dimeric TLR10 TIR domain, the first binding site mediates TLR4-TLR4 TIR-TIR interaction. Upon dimerization, two identical second binding sites of the TLR4 TIR domain are juxtaposed and form an extended binding platform for both MAL and TRAM. In our mammalian protein-protein interaction trap assay, MAL and TRAM compete for binding to this platform. Our data suggest that adapter binding can stabilize the TLR4 TIR dimerization.
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Affiliation(s)
- Celia Bovijn
- Department of Medical Protein Research, Unit of Molecular Signal Transduction in Inflammation, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9000 Ghent, Belgium
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MAPPIT: a protein interaction toolbox built on insights in cytokine receptor signaling. Cytokine Growth Factor Rev 2011; 22:321-9. [PMID: 22119007 DOI: 10.1016/j.cytogfr.2011.11.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
MAPPIT (mammalian protein-protein interaction trap) is a two-hybrid interaction mapping technique based on functional complementation of a type I cytokine receptor signaling pathway. Over the last decade, the technology has been extended into a platform of complementary assays for the detection of interactions among proteins and between chemical compounds and proteins, and for the identification of small molecules that interfere with protein-protein interactions. Additionally, several screening approaches have been developed to broaden the utility of the platform. In this review we provide an overview of the different components of the MAPPIT toolbox and highlight a number of applications in interactomics, drug screening and compound target profiling.
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11
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Interactive proteomics research technologies: recent applications and advances. Curr Opin Biotechnol 2011; 22:50-8. [DOI: 10.1016/j.copbio.2010.09.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 09/01/2010] [Accepted: 09/01/2010] [Indexed: 12/25/2022]
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Jochmans D, Anders M, Keuleers I, Smeulders L, Kräusslich HG, Kraus G, Müller B. Selective killing of human immunodeficiency virus infected cells by non-nucleoside reverse transcriptase inhibitor-induced activation of HIV protease. Retrovirology 2010; 7:89. [PMID: 20950436 PMCID: PMC2974656 DOI: 10.1186/1742-4690-7-89] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 10/15/2010] [Indexed: 12/03/2022] Open
Abstract
Background Current antiretroviral therapy against human immunodeficiency virus (HIV-1) reduces viral load and thereby prevents viral spread, but it cannot eradicate proviral genomes from infected cells. Cells in immunological sanctuaries as well as cells producing low levels of virus apparently contribute to a reservoir that maintains HIV persistence in the presence of highly active antiretroviral therapy. Thus, accelerated elimination of virus producing cells may represent a complementary strategy to control HIV infection. Here we sought to exploit HIV protease (PR) related cytotoxicity in order to develop a strategy for drug induced killing of HIV producing cells. PR processes the viral Gag and Gag-Pol polyproteins during virus maturation, but is also implicated in killing of virus producing cells through off-target cleavage of host proteins. It has been observed previously that micromolar concentrations of certain non-nucleoside reverse transcriptase inhibitors (NNRTIs) can stimulate intracellular PR activity, presumably by enhancing Gag-Pol dimerization. Results Using a newly developed cell-based assay we compared the degree of PR activation displayed by various NNRTIs. We identified inhibitors showing higher potency with respect to PR activation than previously described for NNRTIs, with the most potent compounds resulting in ~2-fold increase of the Gag processing signal at 250 nM. The degree of enhancement of intracellular Gag processing correlated with the compound's ability to enhance RT dimerization in a mammalian two-hybrid assay. Compounds were analyzed for their potential to mediate specific killing of chronically infected MT-4 cells. Levels of cytotoxicity on HIV infected cells determined for the different NNRTIs corresponded to the relative degree of drug induced intracellular PR activation, with CC50 values ranging from ~0.3 μM to above the tested concentration range (10 μM). Specific cytotoxicity was reverted by addition of PR inhibitors. Two of the most active compounds, VRX-480773 and GW-678248, were also tested in primary human cells and mediated cytotoxicity on HIV-1 infected peripheral blood mononuclear cells. Conclusion These data present proof of concept for targeted drug induced elimination of HIV producing cells. While NNRTIs themselves may not be sufficiently potent for therapeutic application, the results provide a basis for the development of drugs exploiting this mechanism of action.
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Affiliation(s)
- Dirk Jochmans
- Department of Infectious Diseases, Virology, University of Heidelberg, Germany
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Lavens D, Peelman F, Van der Heyden J, Uyttendaele I, Catteeuw D, Verhee A, Van Schoubroeck B, Kurth J, Hallenberger S, Clayton R, Tavernier J. Definition of the interacting interfaces of Apobec3G and HIV-1 Vif using MAPPIT mutagenesis analysis. Nucleic Acids Res 2009; 38:1902-12. [PMID: 20015971 PMCID: PMC2847223 DOI: 10.1093/nar/gkp1154] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The host restriction factor Apobec3G is a cytidine deaminase that incorporates into HIV-1 virions and interferes with viral replication. The HIV-1 accessory protein Vif subverts Apobec3G by targeting it for proteasomal degradation. We propose a model in which Apobec3G N-terminal domains symmetrically interact via a head-to-head interface containing residues 122 RLYYFW 127. To validate this model and to characterize the Apobec3G–Apobec3G and the Apobec3G–Vif interactions, the mammalian protein–protein interaction trap two-hybrid technique was used. Mutations in the head-to-head interface abrogate the Apobec3G–Apobec3G interaction. All mutations that inhibit Apobec3G–Apobec3G binding also inhibit the Apobec3G–Vif interaction, indicating that the head-to head interface plays an important role in the interaction with Vif. Only the D128K, P129A and T32Q mutations specifically affect the Apobec3G–Vif association. In our model, D128, P129 and T32 cluster at the edge of the head-to-head interface, possibly forming a Vif binding site composed of two Apobec3G molecules. We propose that Vif either binds at the Apobec3G head-to-head interface or associates with an RNA-stabilized Apobec3G oligomer.
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Affiliation(s)
- Delphine Lavens
- Department of Medical Protein Research, VIB, Department of Biochemistry, Ghent University, A. Baertsoenkaai 3, 9000 Ghent
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Lievens S, Lemmens I, Tavernier J. Mammalian two-hybrids come of age. Trends Biochem Sci 2009; 34:579-88. [PMID: 19786350 DOI: 10.1016/j.tibs.2009.06.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 06/12/2009] [Accepted: 06/12/2009] [Indexed: 12/22/2022]
Abstract
A diverse series of mammalian two-hybrid technologies for the detection of protein-protein interactions have emerged in the past few years, complementing the established yeast two-hybrid approach. Given the mammalian background in which they operate, these assays open new avenues to study the dynamics of mammalian protein interaction networks, i.e. the temporal, spatial and functional modulation of protein-protein associations. In addition, novel assay formats are available that enable high-throughput mammalian two-hybrid applications, facilitating their use in large-scale interactome mapping projects. Finally, as they can be applied in drug discovery and development programs, these techniques also offer exciting new opportunities for biomedical research.
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Affiliation(s)
- Sam Lievens
- Department of Medical Protein Research, VIB, A. Baertsoenkaai 3, 9000 Ghent, Belgium
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