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Pérez Socas LB, Ambroggio EE. The influence of myristoylation, liposome surface charge and nucleic acid interaction in the partition properties of HIV-1 Gag-N-terminal peptides to membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183421. [PMID: 32710855 DOI: 10.1016/j.bbamem.2020.183421] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/25/2020] [Accepted: 07/07/2020] [Indexed: 01/10/2023]
Abstract
The group-specific antigen (GAG) polyprotein of HIV-1 is the main coordinator of the virus assembly process at the plasma membrane (PM) and is directed by its N-terminal matrix domain (MA). MA is myristoylated and possess a highly basic region (HBR) responsible for the interaction with the negative lipids of the PM, especially with PIP2. In addition, MA binds RNA molecules proposed as a regulatory step of the assembly process. Here we study the interaction of a synthetic peptide (N-terminal 21 amino acids of MA) and liposomes of different compositions using a variety of biophysical techniques. Particularly, we use the fluorescence properties of the single tryptophan of the peptide to analyze its partition to membranes, where we harness for first time the analytical ability of spectral phasors method to study this interaction. We found that electrostatic interactions play an important role for peptide partition to membranes and myristoylation reduces the free energy of the process. Interestingly, we observe that while the presence of PIP2 does not cause measurable changes on the peptide-membrane interaction, the interaction is favored by cholesterol. Additionally, we found that the partition process goes through a transition state involving peptide disaggregation and changes in the peptide secondary structure. On the other hand, we found that the presence of oligonucleotides competes with the interaction with lipids by increasing peptide solubility. In summary, we think that our results, in context of the current knowledge of the role of HIV-1 MA, contribute to a better molecular understanding of the membrane association process.
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Affiliation(s)
- Luis Benito Pérez Socas
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica-Ranwel Caputto, Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina; CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina
| | - Ernesto Esteban Ambroggio
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica-Ranwel Caputto, Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina; CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Haya de la Torre y Medina Allende s/n, Córdoba X5000HUA, Argentina.
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2
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HIV-1 matrix mutations that alter gag membrane binding modulate mature core formation and post-entry events. Virology 2019; 532:97-107. [PMID: 31055063 DOI: 10.1016/j.virol.2019.04.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 11/21/2022]
Abstract
The matrix (MA) domain of HIV-1 Gag directs membrane binding of the Gag precursor polyprotein during the late events of virus replication. However, the effects of alteration in Gag membrane binding early post-infection are not well understood. To investigate impacts of MA mutations that alter Gag membrane binding on the phenotypes of newly produced virus particles, we extensively characterized two MA mutants by virological, biochemical, and morphological approaches. The V6R mutation, which decreases Gag membrane binding, modified Gag processing and core morphogenesis and impaired core uncoating, reverse transcription, and viral DNA integration. On the other hand, the L20K mutation, which increases Gag membrane binding, primarily decreased integrated DNA levels without affecting the viral components and morphology. These data suggest that HIV-1 MA plays roles in functional core formation and the following post-entry steps of the virus replication cycle. (140/150 words).
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3
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Olson ED, Musier-Forsyth K. Retroviral Gag protein-RNA interactions: Implications for specific genomic RNA packaging and virion assembly. Semin Cell Dev Biol 2018; 86:129-139. [PMID: 29580971 DOI: 10.1016/j.semcdb.2018.03.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/09/2018] [Accepted: 03/22/2018] [Indexed: 02/04/2023]
Abstract
Retroviral Gag proteins are responsible for coordinating many aspects of virion assembly. Gag possesses two distinct nucleic acid binding domains, matrix (MA) and nucleocapsid (NC). One of the critical functions of Gag is to specifically recognize, bind, and package the retroviral genomic RNA (gRNA) into assembling virions. Gag interactions with cellular RNAs have also been shown to regulate aspects of assembly. Recent results have shed light on the role of MA and NC domain interactions with nucleic acids, and how they jointly function to ensure packaging of the retroviral gRNA. Here, we will review the literature regarding RNA interactions with NC, MA, as well as overall mechanisms employed by Gag to interact with RNA. The discussion focuses on human immunodeficiency virus type-1, but other retroviruses will also be discussed. A model is presented combining all of the available data summarizing the various factors and layers of selection Gag employs to ensure specific gRNA packaging and correct virion assembly.
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Affiliation(s)
- Erik D Olson
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, Ohio State University, Columbus, OH, 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, and Center for Retrovirus Research, Ohio State University, Columbus, OH, 43210, USA.
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4
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Abstract
Viruses are the most abundant biological entities on earth and show remarkable diversity of genome sequences, replication and expression strategies, and virion structures. Evolutionary genomics of viruses revealed many unexpected connections but the general scenario(s) for the evolution of the virosphere remains a matter of intense debate among proponents of the cellular regression, escaped genes, and primordial virus world hypotheses. A comprehensive sequence and structure analysis of major virion proteins indicates that they evolved on about 20 independent occasions, and in some of these cases likely ancestors are identifiable among the proteins of cellular organisms. Virus genomes typically consist of distinct structural and replication modules that recombine frequently and can have different evolutionary trajectories. The present analysis suggests that, although the replication modules of at least some classes of viruses might descend from primordial selfish genetic elements, bona fide viruses evolved on multiple, independent occasions throughout the course of evolution by the recruitment of diverse host proteins that became major virion components.
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5
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Li Y, Frederick KM, Haverland NA, Ciborowski P, Belshan M. Investigation of the HIV-1 matrix interactome during virus replication. Proteomics Clin Appl 2015; 10:156-63. [PMID: 26360636 DOI: 10.1002/prca.201400189] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 07/15/2015] [Accepted: 09/07/2015] [Indexed: 12/18/2022]
Abstract
PURPOSE Like all viruses, human immunodeficiency virus type 1 (HIV-1) requires host cellular factors for productive replication. Identification of these factors may lead to the development of novel cell-based inhibitors. EXPERIMENTAL DESIGN A Strep-tag was inserted into the C-terminus of the matrix (MA) region of the HIV-1 gag gene. The resultant virus was replication competent and used to infect Jurkat T-cells. MA complexes were affinity purified with Strep-Tactin agarose. Protein quantification was performed using sequential window acquisition of all theoretical fragment ion spectra (SWATH) MS, data were log2 -transformed, and Student t-tests with Bonferroni correction used to determine statistical significance. Several candidate proteins were validated by immunoblot and investigated for their role in virus infection by siRNA knockdown assays. RESULTS A total of 17 proteins were found to be statistically different between the infected versus uninfected and untagged control samples. X-ray repair cross-complementing protein 6 (Ku70), X-ray repair cross-complementing protein 5 (Ku80), and Y-box binding protein 1 (YB-1) were confirmed to interact with MA by immunoblot. Knockdown of two candidates, EZRIN and Y-box binding protein 1, enhanced HIV infection in vitro. CONCLUSIONS AND CLINICAL RELEVANCE The Strep-tag allowed for the capture of viral protein complexes in the context of virus replication. Several previously described factors were identified and at least two candidate proteins were found to play a role in HIV-1 infection. These data further increase our understanding of HIV host -cell interactions.
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Affiliation(s)
- Yan Li
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, USA
| | - Kristin M Frederick
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Nicole A Haverland
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Pawel Ciborowski
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA.,The Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
| | - Michael Belshan
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, USA.,The Nebraska Center for Virology, University of Nebraska, Lincoln, NE, USA
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6
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Deshmukh L, Ghirlando R, Clore GM. Conformation and dynamics of the Gag polyprotein of the human immunodeficiency virus 1 studied by NMR spectroscopy. Proc Natl Acad Sci U S A 2015; 112:3374-9. [PMID: 25713345 PMCID: PMC4371905 DOI: 10.1073/pnas.1501985112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Assembly and maturation of the human immunodeficiency virus type 1 (HIV-1) are governed by the Gag polyprotein. Here we study the conformation and dynamics of a large HIV-1 Gag fragment comprising the matrix, capsid, spacer peptide 1 and nucleocapsid domains (referred to as ΔGag) by heteronuclear multidimensional NMR spectroscopy. In solution, ΔGag exists in a dynamic equilibrium between monomeric and dimeric states. In the presence of nucleic acids and at low ionic strength ΔGag assembles into immature virus-like particles. The structured domains of ΔGag (matrix, the N- and C-terminal domains of capsid, and the N- and C-terminal zinc knuckles of nucleocapsid) retain their fold and reorient semi-independently of one another; the linkers connecting the structural domains, including spacer peptide 1 that connects capsid to nucleocapsid, are intrinsically disordered. Structural changes in ΔGag upon proteolytic processing by HIV-1 protease, monitored by NMR in real-time, demonstrate that the conformational transition of the N-terminal 13 residues of capsid from an intrinsically disordered coil to a β-hairpin upon cleavage at the matrix|capsid junction occurs five times faster than cleavage at the capsid|spacer peptide 1 junction. Finally, nucleic acids interact with both nucleocapsid and matrix domains, and proteolytic processing at the spacer peptide 1|nucleocapsid junction by HIV-1 protease is accelerated in the presence of single-stranded DNA.
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Affiliation(s)
| | - Rodolfo Ghirlando
- Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
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7
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Olety B, Ono A. Roles played by acidic lipids in HIV-1 Gag membrane binding. Virus Res 2014; 193:108-15. [PMID: 24998886 PMCID: PMC4252750 DOI: 10.1016/j.virusres.2014.06.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 06/18/2014] [Accepted: 06/23/2014] [Indexed: 10/25/2022]
Abstract
The MA domain mediates plasma membrane (PM) targeting of HIV-1 Gag, leading to particle assembly at the PM. The interaction between MA and acidic phospholipids, in addition to N-terminal myristoyl moiety, promotes Gag binding to lipid membranes. Among acidic phospholipids, PI(4,5)P2, a PM-specific phosphoinositide, is essential for proper HIV-1 Gag localization to the PM and efficient virus particle production. Recent studies further revealed that MA-bound RNA negatively regulates HIV-1 Gag membrane binding and that PI(4,5)P2 is necessary to overcome this RNA-imposed block. In this review, we will summarize the current understanding of Gag-membrane interactions and discuss potential roles played by acidic phospholipids.
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Affiliation(s)
- Balaji Olety
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Akira Ono
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
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8
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Alfadhli A, Barklis E. The roles of lipids and nucleic acids in HIV-1 assembly. Front Microbiol 2014; 5:253. [PMID: 24917853 PMCID: PMC4042026 DOI: 10.3389/fmicb.2014.00253] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 05/08/2014] [Indexed: 11/23/2022] Open
Abstract
During HIV-1 assembly, precursor Gag (PrGag) proteins are delivered to plasma membrane (PM) assembly sites, where they are triggered to oligomerize and bud from cells as immature virus particles. The delivery and triggering processes are coordinated by the PrGag matrix (MA) and nucleocapsid (NC) domains. Targeting of PrGag proteins to membranes enriched in cholesterol and phosphatidylinositol-4,5-bisphosphate (PI[4,5]P2) is mediated by the MA domain, which also has been shown to bind both RNA and DNA. Evidence suggests that the nucleic-acid-binding function of MA serves to inhibit PrGag binding to inappropriate intracellular membranes, prior to delivery to the PM. At the PM, MA domains putatively trade RNA ligands for PI(4,5)P2 ligands, fostering high-affinity membrane binding. Triggering of oligomerization, budding, and virus particle release results when NC domains on adjacent PrGag proteins bind to viral RNA, leading to capsid (CA) domain oligomerization. This process leads to the assembly of immature virus shells in which hexamers of membrane-bound MA trimers appear to organize above interlinked CA hexamers. Here, we review the functions of retroviral MA proteins, with an emphasis on the nucleic-acid-binding capability of the HIV-1 MA protein, and its effects on membrane binding.
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Affiliation(s)
- Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University Portland, OR, USA
| | - Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University Portland, OR, USA
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Kuzembayeva M, Dilley K, Sardo L, Hu WS. Life of psi: how full-length HIV-1 RNAs become packaged genomes in the viral particles. Virology 2014; 454-455:362-70. [PMID: 24530126 DOI: 10.1016/j.virol.2014.01.019] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 01/03/2014] [Accepted: 01/24/2014] [Indexed: 12/27/2022]
Abstract
As a member of the retrovirus family, HIV-1 packages its RNA genome into particles and replicates through a DNA intermediate that integrates into the host cellular genome. The multiple genes encoded by HIV-1 are expressed from the same promoter and their expression is regulated by splicing and ribosomal frameshift. The full-length HIV-1 RNA plays a central role in viral replication as it serves as the genome in the progeny virus and is used as the template for Gag and GagPol translation. In this review, we summarize findings that contribute to our current understanding of how full-length RNA is expressed and transported, cis- and trans-acting elements important for RNA packaging, the locations and timing of RNA:RNA and RNA:Gag interactions, and the processes required for this RNA to be packaged into viral particles.
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Affiliation(s)
- Malika Kuzembayeva
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Kari Dilley
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Luca Sardo
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA.
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10
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[Membrane Binding of Retroviral Gag Proteins]. Uirusu 2014; 64:155-64. [PMID: 26437838 DOI: 10.2222/jsv.64.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Location of virus assembly in infected cells has major influences on efficiencies of virus assembly and release and on post-assembly processes including cell-to-cell transmission. Therefore, for better understanding of virus spread and for developing new antiviral strategies, it is important to elucidate mechanisms by which the subcellular site of virus particle assembly is determined. Retrovirus particle assembly is driven by viral structural protein Gag. In the case of HIV-1, Gag binds to the plasma membrane (PM) via the N-terminal MA domain and forms nascent particles at this location. Recent studies reveled that PM-specific phospholipid PI(4,5)P2 plays an important role in directing Gag to the PM through its interaction with MA. In this review, I will summarize our current understanding of relationships between retroviral MA domains and phospholipids in cellular membranes and discuss possible mechanisms by which lipids and other factors regulate membrane binding and subcellular localization of retroviral Gag proteins.
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11
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Qualley DF, Lackey CM, Paterson JP. Inositol phosphates compete with nucleic acids for binding to bovine leukemia virus matrix protein: implications for deltaretroviral assembly. Proteins 2013; 81:1377-85. [PMID: 23504872 DOI: 10.1002/prot.24281] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 02/15/2013] [Accepted: 02/26/2013] [Indexed: 12/23/2022]
Abstract
The matrix (MA) domain of retroviral Gag proteins plays a crucial role in virion assembly. In human immunodeficiency virus type 1 (HIV-1), a lentivirus, the presence of phosphatidylinositol-(4,5)-bisphosphate triggers a conformational change allowing the MA domain to bind the plasma membrane (PM). In this study, the MA protein from bovine leukemia virus (BLV) was used to investigate the mechanism of viral Gag binding to the membrane during replication of a deltaretrovirus. Fluorescence spectroscopy was used to measure the binding affinity of MA for two RNA constructs derived from the BLV genome as well as for single-stranded DNA (ssDNA). The importance of electrostatic interactions and the ability of inositol hexakisphosphate (IP6) to compete with nucleic acids for binding to MA were also investigated. Our data show that IP6 effectively competes with RNA and DNA for BLV MA binding, while [NaCl] of greater than 100 mM is required to produce any observable effect on DNA-MA binding. These results suggest that BLV assembly may be highly dependent on the specific interaction of the MA domain with components of the PM, as observed previously with HIV-1. The mode of MA binding to nucleic acids and the implications for BLV assembly are discussed.
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Affiliation(s)
- Dominic F Qualley
- Department of Chemistry, Berry College, Mt. Berry, Georgia 30149-5016, USA.
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12
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Neira JL. Nuclear magnetic resonance spectroscopy to study virus structure. Subcell Biochem 2013; 68:145-76. [PMID: 23737051 DOI: 10.1007/978-94-007-6552-8_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) is a spectroscopic technique based in the absorption of radiofrequency radiation by atomic nuclei in the presence of an external magnetic field. NMR has followed a "bottom-up" approach to solve the structures of isolated domains of viral proteins, including capsid protein subunits. NMR has been instrumental to describe conformational changes in viral proteins and nucleic acids, showing the presence of dynamic equilibria which are thought to be important at different stages of the virus life cycle; in this sense, NMR is also the only technique currently available to describe, in atomic detail, the conformational preferences of natively unfolded viral proteins. NMR has also complemented X-ray crystallography and has been combined with electron microscopy to obtain pseudo-atomic models of entire virus capsids. Finally, the joint use of liquid and solid-state NMR has allowed the identification of conformational changes in intact viral capsids on insertion in host membranes.
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Affiliation(s)
- José L Neira
- Instituto de Biología Molecular y Celular, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain,
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13
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Alfadhli A, McNett H, Eccles J, Tsagli S, Noviello C, Sloan R, López CS, Peyton DH, Barklis E. Analysis of small molecule ligands targeting the HIV-1 matrix protein-RNA binding site. J Biol Chem 2012; 288:666-76. [PMID: 23135280 DOI: 10.1074/jbc.m112.399865] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The matrix domain (MA) of the HIV-1 precursor Gag (PrGag) protein directs PrGag proteins to assembly sites at the plasma membrane by virtue of its affinity to the phospholipid, phosphatidylinositol-4,5-bisphosphate (PI(4,5)P(2)). MA also binds to RNA at a site that overlaps its PI(4,5)P(2) site, suggesting that RNA binding may protect MA from associating with inappropriate cellular membranes prior to PrGag delivery to the PM. Based on this, we have developed an assay in which small molecule competitors to MA-RNA binding can be characterized, with the assumption that such compounds might interfere with essential MA functions and help elucidate additional features of MA binding. Following this approach, we have identified four compounds, including three thiadiazolanes, that compete with RNA for MA binding. We also have identified MA residues involved in thiadiazolane binding and found that they overlap the MA PI(4,5)P(2) and RNA sites. Cell culture studies demonstrated that thiadiazolanes inhibit HIV-1 replication but are associated with significant levels of toxicity. Nevertheless, these observations provide new insights into MA binding and pave the way for the development of antivirals that target the HIV-1 matrix domain.
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Affiliation(s)
- Ayna Alfadhli
- Vollum Institute and Department of Microbiology, Oregon Health and Science University, Portland, Oregon 97201-3098, USA
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14
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Taylor JEN, Chow JYH, Jeffries CM, Kwan AH, Duff AP, Hamilton WA, Trewhella J. Calmodulin binds a highly extended HIV-1 MA protein that refolds upon its release. Biophys J 2012; 103:541-549. [PMID: 22947870 PMCID: PMC3414894 DOI: 10.1016/j.bpj.2012.06.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 06/15/2012] [Accepted: 06/28/2012] [Indexed: 10/28/2022] Open
Abstract
Calmodulin (CaM) expression is upregulated upon HIV-1 infection and interacts with proteins involved in viral processing, including the multifunctional HIV-1 MA protein. We present here the results of studies utilizing small-angle neutron scattering with contrast variation that, when considered in the light of earlier fluorescence and NMR data, show CaM binds MA in an extended open-clamp conformation via interactions with two tryptophans that are widely spaced in sequence and space. The interaction requires a disruption of the MA tertiary fold such that MA becomes highly extended in a long snakelike conformation. The CaM-MA interface is extensive, covering ~70% of the length of the MA such that regions known to be important in MA interactions with critical binding partners would be impacted. The CaM conformation is semiextended and as such is distinct from the classical CaM-collapse about short α-helical targets. NMR data show that upon dissociation of the CaM-MA complex, either by the removal of Ca(2+) or increasing ionic strength, MA reforms its native tertiary contacts. Thus, we observe a high level of structural plasticity in MA that may facilitate regulation of its activities via intracellular Ca(2+)-signaling during viral processing.
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Affiliation(s)
- James E N Taylor
- Bragg Institute, Australian Nuclear Science and Technology Organisation, New South Wales, Australia; School of Molecular Bioscience, The University of Sydney, New South Wales, Australia
| | - John Y H Chow
- School of Molecular Bioscience, The University of Sydney, New South Wales, Australia
| | - Cy M Jeffries
- School of Molecular Bioscience, The University of Sydney, New South Wales, Australia
| | - Ann H Kwan
- School of Molecular Bioscience, The University of Sydney, New South Wales, Australia
| | - Anthony P Duff
- Bragg Institute, Australian Nuclear Science and Technology Organisation, New South Wales, Australia
| | - William A Hamilton
- Bragg Institute, Australian Nuclear Science and Technology Organisation, New South Wales, Australia
| | - Jill Trewhella
- School of Molecular Bioscience, The University of Sydney, New South Wales, Australia.
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15
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Xue B, Mizianty MJ, Kurgan L, Uversky VN. Protein intrinsic disorder as a flexible armor and a weapon of HIV-1. Cell Mol Life Sci 2012; 69:1211-59. [PMID: 22033837 PMCID: PMC11114566 DOI: 10.1007/s00018-011-0859-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 09/28/2011] [Accepted: 10/03/2011] [Indexed: 01/19/2023]
Abstract
Many proteins and protein regions are disordered in their native, biologically active states. These proteins/regions are abundant in different organisms and carry out important biological functions that complement the functional repertoire of ordered proteins. Viruses, with their highly compact genomes, small proteomes, and high adaptability for fast change in their biological and physical environment utilize many of the advantages of intrinsic disorder. In fact, viral proteins are generally rich in intrinsic disorder, and intrinsically disordered regions are commonly used by viruses to invade the host organisms, to hijack various host systems, and to help viruses in accommodation to their hostile habitats and to manage their economic usage of genetic material. In this review, we focus on the structural peculiarities of HIV-1 proteins, on the abundance of intrinsic disorder in viral proteins, and on the role of intrinsic disorder in their functions.
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Affiliation(s)
- Bin Xue
- Department of Molecular Medicine, University of South Florida, College of Medicine, 12901 Bruce B. Downs Blvd, MDC07, Tampa, FL 33612 USA
| | - Marcin J. Mizianty
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2V4 Canada
| | - Lukasz Kurgan
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB T6G 2V4 Canada
| | - Vladimir N. Uversky
- Department of Molecular Medicine, University of South Florida, College of Medicine, 12901 Bruce B. Downs Blvd, MDC07, Tampa, FL 33612 USA
- Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region Russia
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16
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Ghanam RH, Samal AB, Fernandez TF, Saad JS. Role of the HIV-1 Matrix Protein in Gag Intracellular Trafficking and Targeting to the Plasma Membrane for Virus Assembly. Front Microbiol 2012; 3:55. [PMID: 22363329 PMCID: PMC3281212 DOI: 10.3389/fmicb.2012.00055] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 02/01/2012] [Indexed: 11/13/2022] Open
Abstract
Human immunodeficiency virus type-1 (HIV-1) encodes a polypeptide called Gag that is able to form virus-like particles in vitro in the absence of any cellular or viral constituents. During the late phase of the HIV-1 infection, Gag polyproteins are transported to the plasma membrane (PM) for assembly. In the past two decades, in vivo, in vitro, and structural studies have shown that Gag trafficking and targeting to the PM are orchestrated events that are dependent on multiple factors including cellular proteins and specific membrane lipids. The matrix (MA) domain of Gag has been the focus of these studies as it appears to be engaged in multiple intracellular interactions that are suggested to be critical for virus assembly and replication. The interaction between Gag and the PM is perhaps the most understood. It is now established that the ultimate localization of Gag on punctate sites on the PM is mediated by specific interactions between the MA domain of Gag and phosphatidylinositol-4,5-bisphosphate [PI(4,5)P(2)], a minor lipid localized on the inner leaflet of the PM. Structure-based studies revealed that binding of PI(4,5)P(2) to MA induces minor conformational changes, leading to exposure of the myristyl (myr) group. Exposure of the myr group is also triggered by binding of calmodulin, enhanced by factors that promote protein self-association like the capsid domain of Gag, and is modulated by pH. Despite the steady progress in defining both the viral and cellular determinants of retroviral assembly and release, Gag's intracellular interactions and trafficking to its assembly sites in the infected cell are poorly understood. In this review, we summarize the current understanding of the structural and functional role of MA in HIV replication.
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Affiliation(s)
- Ruba H Ghanam
- Department of Microbiology, University of Alabama at Birmingham Birmingham, AL, USA
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Huang Y, Cai M, Clore GM, Craigie R. No interaction of barrier-to-autointegration factor (BAF) with HIV-1 MA, cone-rod homeobox (Crx) or MAN1-C in absence of DNA. PLoS One 2011; 6:e25123. [PMID: 21966431 PMCID: PMC3178605 DOI: 10.1371/journal.pone.0025123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 08/25/2011] [Indexed: 11/18/2022] Open
Abstract
Barrier-to-autointegration factor is a cellular protein that protects retroviral DNA from autointegration. Its cellular role is not well understood, but genetic studies show that it is essential and depletion or knockout results in lethal nuclear defects. In addition to binding DNA, BAF interacts with the LEM domain, a domain shared among a family of lamin-associated polypeptides. BAF has also been reported to interact with several other viral and cellular proteins suggesting that these interactions may be functionally relevant. We find that, contrary to previous reports, BAF does not interact with HIV-1 MA, cone-rod homeobox (Crx) or MAN1-C. The reported interactions can be explained by indirect association through DNA binding and are unlikely to be biologically relevant. A mutation that causes a premature aging syndrome lies on the previously reported MAN1-C binding surface of BAF. The absence of direct binding of BAF to MAN1-C eliminates disruption of this interaction as the cause of the premature aging phenotype.
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Affiliation(s)
- Ying Huang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mengli Cai
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Robert Craigie
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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Lu K, Heng X, Summers MF. Structural determinants and mechanism of HIV-1 genome packaging. J Mol Biol 2011; 410:609-33. [PMID: 21762803 DOI: 10.1016/j.jmb.2011.04.029] [Citation(s) in RCA: 185] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 04/11/2011] [Accepted: 04/11/2011] [Indexed: 11/30/2022]
Abstract
Like all retroviruses, the human immunodeficiency virus selectively packages two copies of its unspliced RNA genome, both of which are utilized for strand-transfer-mediated recombination during reverse transcription-a process that enables rapid evolution under environmental and chemotherapeutic pressures. The viral RNA appears to be selected for packaging as a dimer, and there is evidence that dimerization and packaging are mechanistically coupled. Both processes are mediated by interactions between the nucleocapsid domains of a small number of assembling viral Gag polyproteins and RNA elements within the 5'-untranslated region of the genome. A number of secondary structures have been predicted for regions of the genome that are responsible for packaging, and high-resolution structures have been determined for a few small RNA fragments and protein-RNA complexes. However, major questions regarding the RNA structures (and potentially the structural changes) that are responsible for dimeric genome selection remain unanswered. Here, we review efforts that have been made to identify the molecular determinants and mechanism of human immunodeficiency virus type 1 genome packaging.
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Affiliation(s)
- Kun Lu
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
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Alfadhli A, McNett H, Tsagli S, Bächinger HP, Peyton DH, Barklis E. HIV-1 matrix protein binding to RNA. J Mol Biol 2011; 410:653-66. [PMID: 21762806 DOI: 10.1016/j.jmb.2011.04.063] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Revised: 04/22/2011] [Accepted: 04/25/2011] [Indexed: 11/26/2022]
Abstract
The matrix (MA) domain of the human immunodeficiency virus type 1 (HIV-1) precursor Gag (PrGag) protein plays multiple roles in the viral replication cycle. One essential role is to target PrGag proteins to their lipid raft-associated phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P(2)] assembly sites at the plasma membranes of infected cells. In addition to this role, several reports have implicated nucleic acid binding properties to retroviral MAs. Evidence indicates that RNA binding enhances the binding specificity of MA to PI(4,5)P(2)-containing membranes and supports a hypothesis in which RNA binding to MA acts as a chaperone that protects MA from associating with inappropriate cellular membranes prior to PrGag delivery to plasma membrane assembly sites. To gain a better understanding of HIV-1 MA-RNA interactions, we have analyzed the interaction of HIV MA with RNA ligands that were selected previously for their high affinities to MA. Binding interactions were characterized via bead binding, fluorescence anisotropy, gel shift, and analytical ultracentrifugation methods. Moreover, MA residues that are involved in RNA binding were identified from NMR chemical shift data. Our results indicate that the MA RNA and PI(4,5)P(2) binding sites overlap and suggest models for Gag-membrane and Gag-RNA interactions and for the HIV assembly pathway.
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Affiliation(s)
- Ayna Alfadhli
- Vollum Institute and Department of Microbiology, Oregon Health and Science University, Portland, OR 97201-3098, USA.
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