1
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Heidarnejad F, Namvar A, Sadat SM, Pordanjani PM, Rezaei F, Namdari H, Arjmand S, Bolhassani A. In silico designing of novel epitope-based peptide vaccines against HIV-1. Biotechnol Lett 2024; 46:315-354. [PMID: 38403788 DOI: 10.1007/s10529-023-03464-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 11/16/2023] [Accepted: 12/21/2023] [Indexed: 02/27/2024]
Abstract
The HIV-1 virus has been regarded as a catastrophe for human well-being. The global incidence of HIV-1-infected individuals is increasing. Hence, development of effective immunostimulatory molecules has recently attracted an increasing attention in the field of vaccine design against HIV-1 infection. In this study, we explored the impacts of CD40L and IFN-γ as immunostimulatory adjuvants for our candidate HIV-1 Nef vaccine in human and mouse using immunoinformatics analyses. Overall, 18 IFN-γ-based vaccine constructs (9 constructs in human and 9 constructs in mouse), and 18 CD40L-based vaccine constructs (9 constructs in human and 9 constructs in mouse) were designed. To find immunogenic epitopes, important characteristics of each component (e.g., MHC-I and MHC-II binding, and peptide-MHC-I/MHC-II molecular docking) were determined. Then, the selected epitopes were applied to create multiepitope constructs. Finally, the physicochemical properties, linear and discontinuous B cell epitopes, and molecular interaction between the 3D structure of each construct and CD40, IFN-γ receptor or toll-like receptors (TLRs) were predicted. Our data showed that the full-length CD40L and IFN-γ linked to the N-terminal region of Nef were capable of inducing more effective immune response than multiepitope vaccine constructs. Moreover, molecular docking of the non-allergenic full-length- and epitope-based CD40L and IFN-γ constructs to their cognate receptors, CD40 and IFN-γ receptors, and TLRs 4 and 5 in mouse were more potent than in human. Generally, these findings suggest that the full forms of these adjuvants could be more efficient for improvement of HIV-1 Nef vaccine candidate compared to the designed multiepitope-based constructs.
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Affiliation(s)
| | - Ali Namvar
- Iranian Comprehensive Hemophilia Care Center, Tehran, Iran
| | - Seyed Mehdi Sadat
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | | | - Fatemeh Rezaei
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Haideh Namdari
- Iranian Tissue Bank Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sina Arjmand
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran.
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2
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Heinrich F, Thomas CE, Alvarado JJ, Eells R, Thomas A, Doucet M, Whitlatch KN, Aryal M, Lösche M, Smithgall TE. Neutron Reflectometry and Molecular Simulations Demonstrate HIV-1 Nef Homodimer Formation on Model Lipid Bilayers. J Mol Biol 2023; 435:168009. [PMID: 36773691 PMCID: PMC10079580 DOI: 10.1016/j.jmb.2023.168009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023]
Abstract
The HIV-1 Nef protein plays a critical role in viral infectivity, high-titer replication in vivo, and immune escape of HIV-infected cells. Nef lacks intrinsic biochemical activity, functioning instead through interactions with diverse host cell signaling proteins and intracellular trafficking pathways. Previous studies have established an essential role for Nef homodimer formation at the plasma membrane for most if not all its functions. Here we combined neutron reflectometry of full-length myristoylated Nef bound to model lipid bilayers with molecular simulations based on previous X-ray crystal structures of Nef homodimers. This integrated approach provides direct evidence that Nef associates with the membrane as a homodimer with its structured core region displaced from the membrane for partner protein engagement. Parallel studies of a dimerization-defective mutant, Nef-L112D, demonstrate that the helical dimerization interface present in previous crystal structures stabilizes the membrane-bound dimer. X-ray crystallography of the Nef-L112D mutant in complex with the SH3 domain of the Nef-associated host cell kinase Hck revealed a monomeric 1:1 complex instead of the 2:2 dimer complex formed with wild-type Nef. Importantly, the crystal structure of the Nef-L112D core and SH3 interface are virtually identical to the wild-type complex, indicating that this mutation does not affect the overall Nef fold. These findings support the intrinsic capacity of Nef to homodimerize at lipid bilayers using structural features present in X-ray crystal structures of dimeric complexes.
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Affiliation(s)
- Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, Gaithersburg, MD 20899, USA
| | - Catherine E Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - John J Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Rebecca Eells
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Alyssa Thomas
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Mathieu Doucet
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kindra N Whitlatch
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Manish Aryal
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, Gaithersburg, MD 20899, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
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3
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Firrito C, Bertelli C, Rosa A, Chande A, Ananth S, van Dijk H, Fackler OT, Stoneham C, Singh R, Guatelli J, Pizzato M. A Conserved Acidic Residue in the C-Terminal Flexible Loop of HIV-1 Nef Contributes to the Activity of SERINC5 and CD4 Downregulation. Viruses 2023; 15:652. [PMID: 36992361 PMCID: PMC10057511 DOI: 10.3390/v15030652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/22/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
The host transmembrane protein SERINC5 is incorporated into retrovirus particles and inhibits HIV-1 infectivity. The lentiviral Nef protein counteracts SERINC5 by downregulating it from the cell surface and preventing its incorporation into virions. The ability of Nef to antagonize the host factor varies in magnitude between different HIV-1 isolates. After having identified a subtype H nef allele unable to promote HIV-1 infectivity in the presence of SERINC5, we investigated the molecular determinants responsible for the defective counteraction of the host factor. Chimeric molecules with a subtype C Nef highly active against SERINC5 were constructed to locate Nef residues crucial for the activity against SERINC5. An Asn at the base of the C-terminal loop of the defective nef allele was found in place of a highly conserved acidic residue (D/E 150). The conversion of Asn to Asp restored the ability of the defective Nef to downregulate SERINC5 and promote HIV-1 infectivity. The substitution was also found to be crucial for the ability of Nef to downregulate CD4, but not for Nef activities that do not rely on the internalization of receptors from the cell surface, suggesting a general implication in promoting clathrin-mediated endocytosis. Accordingly, bimolecular fluorescence complementation revealed that the conserved acidic residue contributes to the recruitment of AP2 by Nef. Altogether, our results confirm that Nef downregulates SERINC5 and CD4 by engaging a similar machinery and indicates that, in addition to the di-leucine motif, other residues in the C-terminal flexible loop are important for the ability of the protein to sustain clathrin-mediated endocytosis.
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Affiliation(s)
- Claudia Firrito
- Department of Cellular, Computational and integrative Biology, University of Trento, 38123 Trento, Italy
| | - Cinzia Bertelli
- Department of Cellular, Computational and integrative Biology, University of Trento, 38123 Trento, Italy
| | - Annachiara Rosa
- Department of Cellular, Computational and integrative Biology, University of Trento, 38123 Trento, Italy
| | - Ajit Chande
- Department of Cellular, Computational and integrative Biology, University of Trento, 38123 Trento, Italy
| | - Swetha Ananth
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Hannah van Dijk
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Oliver T. Fackler
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- German Center for Infection Research (DZIF), 69120 Heidelberg, Germany
| | - Charlotte Stoneham
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Rajendra Singh
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - John Guatelli
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- VA San Diego Healthcare System, San Diego, CA 92161, USA
| | - Massimo Pizzato
- Department of Cellular, Computational and integrative Biology, University of Trento, 38123 Trento, Italy
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4
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Kwon Y, Kaake RM, Echeverria I, Suarez M, Karimian Shamsabadi M, Stoneham C, Ramirez PW, Kress J, Singh R, Sali A, Krogan N, Guatelli J, Jia X. Structural basis of CD4 downregulation by HIV-1 Nef. Nat Struct Mol Biol 2020; 27:822-828. [PMID: 32719457 PMCID: PMC7483821 DOI: 10.1038/s41594-020-0463-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/16/2020] [Indexed: 02/06/2023]
Abstract
The HIV-1 Nef protein suppresses multiple immune surveillance mechanisms to promote viral pathogenesis and is an attractive target for the development of novel therapeutics. A key function of Nef is to remove the CD4 receptor from the cell surface by hijacking clathrin- and adaptor protein complex 2 (AP2)-dependent endocytosis. However, exactly how Nef does this has been elusive. Here, we describe the underlying mechanism as revealed by a 3.0-Å crystal structure of a fusion protein comprising Nef and the cytoplasmic domain of CD4 bound to the tetrameric AP2 complex. An intricate combination of conformational changes occurs in both Nef and AP2 to enable CD4 binding and downregulation. A pocket on Nef previously identified as crucial for recruiting class I MHC is also responsible for recruiting CD4, revealing a potential approach to inhibit two of Nef's activities and sensitize the virus to immune clearance.
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Affiliation(s)
- Yonghwa Kwon
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, Dartmouth, MA, USA
| | - Robyn M Kaake
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
| | - Ignacia Echeverria
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Charlotte Stoneham
- The VA San Diego Healthcare System, San Diego, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Peter W Ramirez
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jacob Kress
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, Dartmouth, MA, USA
| | - Rajendra Singh
- The VA San Diego Healthcare System, San Diego, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry and Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Gladstone Institutes, San Francisco, CA, USA
| | - John Guatelli
- The VA San Diego Healthcare System, San Diego, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiaofei Jia
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, Dartmouth, MA, USA.
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Giese S, Lawrence SP, Mazzon M, Nijmeijer BM, Marsh M. The Nef Protein of the Macrophage Tropic HIV-1 Strain AD8 Counteracts Human BST-2/Tetherin. Viruses 2020; 12:E459. [PMID: 32325729 PMCID: PMC7232323 DOI: 10.3390/v12040459] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/15/2020] [Accepted: 04/15/2020] [Indexed: 12/12/2022] Open
Abstract
Bone Marrow Stromal Cell Antigen 2 (BST-2)/tetherin inhibits the release of numerous enveloped viruses by physically tethering nascent particles to infected cells during the process of viral budding from the cell surface. Tetherin also restricts human immunodeficiency virus (HIV), and pandemic main (M) group HIV type 1s (HIV-1s) are thought to rely exclusively on their Vpu proteins to overcome tetherin-mediated restriction of virus release. However, at least one M group HIV-1 strain, the macrophage-tropic primary AD8 isolate, is unable to express Vpu due to a mutation in its translation initiation codon. Here, using primary monocyte-derived macrophages (MDMs), we show that AD8 Nef protein can compensate for the absence of Vpu and restore virus release to wild type levels. We demonstrate that HIV-1 AD8 Nef reduces endogenous cell surface tetherin levels, physically separating it from the site of viral budding, thus preventing HIV retention. Mechanistically, AD8 Nef enhances internalisation of the long isoform of human tetherin, leading to perinuclear accumulation of the restriction factor. Finally, we show that Nef proteins from other HIV strains also display varying degrees of tetherin antagonism. Overall, we show that M group HIV-1s can use an accessory protein other than Vpu to antagonise human tetherin.
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Affiliation(s)
| | | | | | | | - Mark Marsh
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; (S.G.); (S.P.L.); (M.M.); (B.M.N.)
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6
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Wu M, Alvarado JJ, Augelli-Szafran CE, Ptak RG, Smithgall TE. A single β-octyl glucoside molecule induces HIV-1 Nef dimer formation in the absence of partner protein binding. PLoS One 2018; 13:e0192512. [PMID: 29415006 PMCID: PMC5802939 DOI: 10.1371/journal.pone.0192512] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/24/2018] [Indexed: 01/05/2023] Open
Abstract
The HIV-1 Nef accessory protein is essential for viral pathogenicity and AIDS progression. Nef forms complexes with multiple host cell factors to facilitate viral replication and promote immune escape of HIV-infected cells. Previous X-ray crystal structures demonstrate that Nef forms homodimers, the orientation of which are influenced by host cell binding partners. In cell-based fluorescence complementation assays, Nef forms homodimers at the plasma membrane. However, recombinant Nef proteins often exist as monomers in solution, suggesting that membrane interaction may also trigger monomer to dimer transitions. In this study, we show that monomeric Nef core proteins can be induced to form dimers in the presence of low concentrations of the non-ionic surfactant, β-octyl glucoside (βOG). X-ray crystallography revealed that a single βOG molecule is present in the Nef dimer, with the 8-carbon acyl chain of the ligand binding to a hydrophobic pocket formed by the dimer interface. This Nef-βOG dimer interface involves helix αB, as observed in previous dimer structures, as well as a helix formed by N-terminal residues 54-66. Nef dimer formation is stabilized in solution by the addition of βOG, providing biochemical validation for the crystal structure. These observations together suggest that the interaction with host cell lipid mediators or other hydrophobic ligands may play a role in Nef dimerization, which has been previously linked to multiple Nef functions including host cell protein kinase activation, CD4 downregulation, and enhancement of HIV-1 replication.
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Affiliation(s)
- Mousheng Wu
- Department of Chemistry, Drug Discovery Division, Southern Research Institute, Birmingham, AL, United States of America
- * E-mail: (MW); (TES)
| | - John J. Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Corinne E. Augelli-Szafran
- Department of Chemistry, Drug Discovery Division, Southern Research Institute, Birmingham, AL, United States of America
| | - Roger G. Ptak
- Department of Infectious Disease Research, Southern Research Institute, Frederick, MD, United States of America
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
- * E-mail: (MW); (TES)
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7
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Moroco JA, Alvarado JJ, Staudt RP, Shi H, Wales TE, Smithgall TE, Engen JR. Remodeling of HIV-1 Nef Structure by Src-Family Kinase Binding. J Mol Biol 2018; 430:310-321. [PMID: 29258818 PMCID: PMC5801098 DOI: 10.1016/j.jmb.2017.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/07/2017] [Accepted: 12/10/2017] [Indexed: 11/25/2022]
Abstract
The HIV-1 accessory protein Nef controls multiple aspects of the viral life cycle and host immune response, making it an attractive therapeutic target. Previous X-ray crystal structures of Nef in complex with key host cell binding partners have shed light on protein-protein interactions critical to Nef function. Crystal structures of Nef in complex with either the SH3 or tandem SH3-SH2 domains of Src-family kinases reveal distinct dimer conformations of Nef. However, the existence of these Nef dimer complexes in solution has not been established. Here we used hydrogen exchange mass spectrometry (HX MS) to compare the solution conformation of Nef alone and in complexes with the SH3 or the SH3-SH2 domains of the Src-family kinase Hck. HX MS revealed that interaction with the Hck SH3 or tandem SH3-SH2 domains induces protection of the Nef αB-helix from deuterium uptake, consistent with a role for αB in dimer formation. HX MS analysis of a Nef mutant (position Asp123, a site buried in the Nef:SH3 dimer but surface exposed in the Nef:SH3-SH2 complex), showed a Hck-induced conformational change in Nef relative to wild-type Nef. These results support a model in which Src-family kinase binding induces conformational changes in Nef to expose residues critical for interaction with the μ1 subunit of adaptor protein 1 and the major histocompatibility complex-1 tail, and subsequent major histocompatibility complex-1 downregulation and immune escape of HIV-infected cells required for functional interactions with downstream binding partners.
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Affiliation(s)
- Jamie A Moroco
- Department of Chemistry and Chemical Biology, Maildrop 412TF, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
| | - John Jeff Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| | - Ryan P Staudt
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| | - Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Maildrop 412TF, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| | - John R Engen
- Department of Chemistry and Chemical Biology, Maildrop 412TF, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
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Lamers SL, Fogel GB, Liu ES, Barbier AE, Rodriguez CW, Singer EJ, Nolan DJ, Rose R, McGrath MS. Brain-specific HIV Nef identified in multiple patients with neurological disease. J Neurovirol 2017; 24:1-15. [PMID: 29063512 DOI: 10.1007/s13365-017-0586-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 08/28/2017] [Accepted: 10/03/2017] [Indexed: 12/11/2022]
Abstract
HIV-1 Nef is a flexible, multifunctional protein with several cellular targets that is required for pathogenicity of the virus. This protein maintains a high degree of genetic variation among intra- and inter-host isolates. HIV Nef is relevant to HIV-associated neurological diseases (HAND) in patients treated with combined antiretroviral therapy because of the protein's role in promoting survival and migration of infected brain macrophages. In this study, we analyzed 2020 HIV Nef sequences derived from 22 different tissues and 31 subjects using a novel computational approach. This approach combines statistical regression and evolved neural networks (ENNs) to classify brain sequences based on the physical and chemical characteristics of functional Nef domains. Based on training, testing, and validation data, the method successfully classified brain Nef sequences at 84.5% and provided informative features for further examination. These included physicochemical features associated with the Src-homology-3 binding domain, the Nef loop (including the AP-2 Binding region), and a cytokine-binding domain. Non-brain sequences from patients with HIV-associated neurological disease were frequently classified as brain, suggesting that the approach could indicate neurological risk using blood-derived virus or for the development of biomarkers for use in assay systems aimed at drug efficacy studies for the treatment of HIV-associated neurological diseases.
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9
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Navarro Negredo P, Edgar JR, Wrobel AG, Zaccai NR, Antrobus R, Owen DJ, Robinson MS. Contribution of the clathrin adaptor AP-1 subunit µ1 to acidic cluster protein sorting. J Cell Biol 2017; 216:2927-2943. [PMID: 28743825 PMCID: PMC5584140 DOI: 10.1083/jcb.201602058] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/19/2017] [Accepted: 07/07/2017] [Indexed: 11/22/2022] Open
Abstract
Acidic clusters act as sorting signals for packaging cargo into clathrin-coated vesicles (CCVs), and also facilitate down-regulation of MHC-I by HIV-1 Nef. To find acidic cluster sorting machinery, we performed a gene-trap screen and identified the medium subunit (µ1) of the clathrin adaptor AP-1 as a top hit. In µ1 knockout cells, intracellular CCVs still form, but acidic cluster proteins are depleted, although several other CCV components were either unaffected or increased, indicating that cells can compensate for long-term loss of AP-1. In vitro experiments showed that the basic patch on µ1 that interacts with the Nef acidic cluster also contributes to the binding of endogenous acidic cluster proteins. Surprisingly, µ1 mutant proteins lacking the basic patch and/or the tyrosine-based motif binding pocket could rescue the µ1 knockout phenotype completely. In contrast, these mutants failed to rescue Nef-induced down-regulation of MHC class I, suggesting a possible mechanism for attacking the virus while sparing the host cell.
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Affiliation(s)
- Paloma Navarro Negredo
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - Antoni G Wrobel
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - Nathan R Zaccai
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - David J Owen
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
| | - Margaret S Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, England, UK
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10
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Martínez-Bonet M, Palladino C, Briz V, Rudolph JM, Fackler OT, Relloso M, Muñoz-Fernandez MA, Madrid R. A Conserved GPG-Motif in the HIV-1 Nef Core Is Required for Principal Nef-Activities. PLoS One 2015; 10:e0145239. [PMID: 26700863 PMCID: PMC4689412 DOI: 10.1371/journal.pone.0145239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 11/30/2015] [Indexed: 12/26/2022] Open
Abstract
To find out new determinants required for Nef activity we performed a functional alanine scanning analysis along a discrete but highly conserved region at the core of HIV-1 Nef. We identified the GPG-motif, located at the 121–137 region of HIV-1 NL4.3 Nef, as a novel protein signature strictly required for the p56Lck dependent Nef-induced CD4-downregulation in T-cells. Since the Nef-GPG motif was dispensable for CD4-downregulation in HeLa-CD4 cells, Nef/AP-1 interaction and Nef-dependent effects on Tf-R trafficking, the observed effects on CD4 downregulation cannot be attributed to structure constraints or to alterations on general protein trafficking. Besides, we found that the GPG-motif was also required for Nef-dependent inhibition of ring actin re-organization upon TCR triggering and MHCI downregulation, suggesting that the GPG-motif could actively cooperate with the Nef PxxP motif for these HIV-1 Nef-related effects. Finally, we observed that the Nef-GPG motif was required for optimal infectivity of those viruses produced in T-cells. According to these findings, we propose the conserved GPG-motif in HIV-1 Nef as functional region required for HIV-1 infectivity and therefore with a potential interest for the interference of Nef activity during HIV-1 infection.
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Affiliation(s)
- Marta Martínez-Bonet
- Laboratorio de Inmunobiología Molecular, Instituto de Investigación Biomédica Gregorio Marañón (IISGM), 28007 Madrid, Spain
| | - Claudia Palladino
- Laboratorio de Inmunobiología Molecular, Instituto de Investigación Biomédica Gregorio Marañón (IISGM), 28007 Madrid, Spain
| | - Veronica Briz
- Laboratorio de Inmunobiología Molecular, Instituto de Investigación Biomédica Gregorio Marañón (IISGM), 28007 Madrid, Spain
| | - Jochen M. Rudolph
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Oliver T. Fackler
- Department of Infectious Diseases, Integrative Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Miguel Relloso
- Laboratorio de Inmunobiología Molecular, Instituto de Investigación Biomédica Gregorio Marañón (IISGM), 28007 Madrid, Spain
| | - Maria Angeles Muñoz-Fernandez
- Laboratorio de Inmunobiología Molecular, Instituto de Investigación Biomédica Gregorio Marañón (IISGM), 28007 Madrid, Spain
| | - Ricardo Madrid
- Departament of Virology. Centro de Biología Molecular Severo Ochoa, CSIC/UAM, Madrid, Spain
- * E-mail:
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Weiser K, Barton M, Gershoony D, DasGupta R, Cardozo T. HIV's Nef interacts with β-catenin of the Wnt signaling pathway in HEK293 cells. PLoS One 2013; 8:e77865. [PMID: 24130899 PMCID: PMC3795062 DOI: 10.1371/journal.pone.0077865] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 09/13/2013] [Indexed: 11/18/2022] Open
Abstract
The Wnt signaling pathway is implicated in major physiologic cellular functions, such as proliferation, migration, cell fate specification, maintenance of pluripotency and induction of tumorigenicity. Proliferation and migration are important responses of T-cells, which are major cellular targets of HIV infection. Using an informatics screen, we identified a previously unsuspected interaction between HIV’s Nef protein and β-catenin, a key component of the Wnt pathway. A segment in Nef contains identical amino acids at key positions and structurally mimics the β-catenin binding sites on endogenous β-catenin ligands. The interaction between Nef and β-catenin was confirmed in vitro and in a co-immunoprecipitation from HEK293 cells. Moreover, the introduction of Nef into HEK293 cells specifically inhibited a Wnt pathway reporter.
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Affiliation(s)
- Keren Weiser
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Meredith Barton
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Dafna Gershoony
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Ramanuj DasGupta
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Timothy Cardozo
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
- * E-mail:
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12
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Cornall A, Mak J, Greenway A, Tachedjian G. HIV-1 infection of T cells and macrophages are differentially modulated by virion-associated Hck: a Nef-dependent phenomenon. Viruses 2013; 5:2235-52. [PMID: 24051604 PMCID: PMC3798898 DOI: 10.3390/v5092235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 09/01/2013] [Accepted: 09/12/2013] [Indexed: 12/18/2022] Open
Abstract
The proline repeat motif (PxxP) of Nef is required for interaction with the SH3 domains of macrophage-specific Src kinase Hck. However, the implication of this interaction for viral replication and infectivity in macrophages and T lymphocytes remains unclear. Experiments in HIV-1 infected macrophages confirmed the presence of a Nef:Hck complex which was dependent on the Nef proline repeat motif. The proline repeat motif of Nef also enhanced both HIV-1 infection and replication in macrophages, and was required for incorporation of Hck into viral particles. Unexpectedly, wild-type Hck inhibited infection of macrophages, but Hck was shown to enhance infection of primary T lymphocytes. These results indicate that the interaction between Nef and Hck is important for Nef-dependent modulation of viral infectivity. Hck-dependent enhancement of HIV-1 infection of T cells suggests that Nef-Hck interaction may contribute to the spread of HIV-1 infection from macrophages to T cells by modulating events in the producer cell, virion and target cell.
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Affiliation(s)
- Alyssa Cornall
- Centre for Biomedical Research, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne 3004, Victoria, Australia; E-Mails: (A.C.); (A.G.)
- Regional HPV Labnet Reference Laboratory, Department of Microbiology and Infectious Diseases, The Royal Women’s Hospital, Parkville 3052, Victoria, Australia
- Murdoch Children’s Research Institute, Parkville 3052, Victoria, Australia
| | - Johnson Mak
- School of Medicine, Faculty of Health, Deakin University, Geelong 3220, Victoria, Australia; E-Mail:
- Commonwealth Scientific and Industrial Research Organisation, Livestock Industries, Australian Animal Health Laboratory, Geelong 3220, Victoria, Australia
| | - Alison Greenway
- Centre for Biomedical Research, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne 3004, Victoria, Australia; E-Mails: (A.C.); (A.G.)
| | - Gilda Tachedjian
- Centre for Biomedical Research, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne 3004, Victoria, Australia; E-Mails: (A.C.); (A.G.)
- Department of Microbiology, Monash University, Clayton 3168, Victoria, Australia
- Department of Infectious Diseases, Monash University, Melbourne 3004, Victoria, Australia
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +61-3-9282-2256; Fax: +61-3-9282-2100
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13
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Aqil M, Naqvi AR, Bano AS, Jameel S. The HIV-1 Nef protein binds argonaute-2 and functions as a viral suppressor of RNA interference. PLoS One 2013; 8:e74472. [PMID: 24023945 PMCID: PMC3762824 DOI: 10.1371/journal.pone.0074472] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 08/01/2013] [Indexed: 11/21/2022] Open
Abstract
The HIV-1 accessory protein Nef is an important virulence factor. It associates with cellular membranes and modulates the endocytic machinery and signaling pathways. Nef also increases the proliferation of multivesicular bodies (MVBs), which are sites for virus assembly and budding in macrophages. The RNA interference (RNAi) pathway proteins Ago2 and GW182 localize to MVBs, suggesting these to be sites for assembly and turnover of the miRNA-induced silencing complex (miRISC). While RNAi affects HIV replication, it is not clear if the virus encodes a suppressor activity to overcome this innate host response. Here we show that Nef colocalizes with MVBs and binds Ago2 through two highly conserved Glycine-Tryptophan (GW) motifs, mutations in which abolish Nef binding to Ago2 and reduce virus yield and infectivity. Nef also inhibits the slicing activity of Ago2 and disturbs the sorting of GW182 into exosomes resulting in the suppression of miRNA-induced silencing. Thus, besides its other activities, the HIV-1 Nef protein is also proposed to function as a viral suppressor of RNAi (VSR).
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Affiliation(s)
- Madeeha Aqil
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Afsar Raza Naqvi
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Aalia Shahr Bano
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Shahid Jameel
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
- * E-mail:
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14
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Adland E, Carlson JM, Paioni P, Kløverpris H, Shapiro R, Ogwu A, Riddell L, Luzzi G, Chen F, Balachandran T, Heckerman D, Stryhn A, Edwards A, Ndung’u T, Walker BD, Buus S, Goulder P, Matthews PC. Nef-specific CD8+ T cell responses contribute to HIV-1 immune control. PLoS One 2013; 8:e73117. [PMID: 24023819 PMCID: PMC3759414 DOI: 10.1371/journal.pone.0073117] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 07/24/2013] [Indexed: 12/29/2022] Open
Abstract
Recent studies in the SIV-macaque model of HIV infection suggest that Nef-specific CD8+ T-cell responses may mediate highly effective immune control of viraemia. In HIV infection Nef recognition dominates in acute infection, but in large cohort studies of chronically infected subjects, breadth of T cell responses to Nef has not been correlated with significant viraemic control. Improved disease outcomes have instead been associated with targeting Gag and, in some cases, Pol. However analyses of the breadth of Nef-specific T cell responses have been confounded by the extreme immunogenicity and multiple epitope overlap within the central regions of Nef, making discrimination of distinct responses impossible via IFN-gamma ELISPOT assays. Thus an alternative approach to assess Nef as an immune target is needed. Here, we show in a cohort of >700 individuals with chronic C-clade infection that >50% of HLA-B-selected polymorphisms within Nef are associated with a predicted fitness cost to the virus, and that HLA-B alleles that successfully drive selection within Nef are those linked with lower viral loads. Furthermore, the specific CD8+ T cell epitopes that are restricted by protective HLA Class I alleles correspond substantially to effective SIV-specific epitopes in Nef. Distinguishing such individual HIV-specific responses within Nef requires specific peptide-MHC I tetramers. Overall, these data suggest that CD8+ T cell targeting of certain specific Nef epitopes contributes to HIV suppression. These data suggest that a re-evaluation of the potential use of Nef in HIV T-cell vaccine candidates would be justified.
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Affiliation(s)
- Emily Adland
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Jonathan M. Carlson
- Microsoft Research, eScience Group, Los Angeles, California, United States of America
| | - Paolo Paioni
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
| | - Henrik Kløverpris
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- KwaZulu-Natal Research Institute for Tuberculosis & HIV, K-RITH, Nelson R Mandela School of Medicine, University of KwaZuluNatal, Durban, South Africa
| | - Roger Shapiro
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Anthony Ogwu
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Lynn Riddell
- Department of Genitourinary Medicine, Northamptonshire Healthcare NHS Trust,Northampton General Hospital, Northampton, United Kingdom
| | - Graz Luzzi
- Department of Genitourinary Medicine, Wycombe Hospital, High Wycombe, Bucks, United Kingdom
| | - Fabian Chen
- Department of Sexual Health, Royal Berkshire Hospital, Reading, United Kingdom
| | - Thambiah Balachandran
- Department of Genitourinary Medicine, Luton and Dunstable Hospital, Luton, United Kingdom
| | - David Heckerman
- Microsoft Research, eScience Group, Los Angeles, California, United States of America
| | - Anette Stryhn
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne Edwards
- The Oxford Department of Genitourinary Medicine, the Churchill Hospital, Oxford, United Kingdom
| | - Thumbi Ndung’u
- HIV Pathogenesis Programme, the Doris Duke Medical Research Institute, University of KwaZuluNatal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Bruce D. Walker
- HIV Pathogenesis Programme, the Doris Duke Medical Research Institute, University of KwaZuluNatal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Søren Buus
- Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Philip Goulder
- Department of Paediatrics, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
- HIV Pathogenesis Programme, the Doris Duke Medical Research Institute, University of KwaZuluNatal, Durban, South Africa
- Ragon Institute of Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Philippa C. Matthews
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, United Kingdom
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15
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Perrone R, Nadai M, Poe JA, Frasson I, Palumbo M, Palù G, Smithgall TE, Richter SN. Formation of a unique cluster of G-quadruplex structures in the HIV-1 Nef coding region: implications for antiviral activity. PLoS One 2013; 8:e73121. [PMID: 24015290 PMCID: PMC3754912 DOI: 10.1371/journal.pone.0073121] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/24/2013] [Indexed: 01/10/2023] Open
Abstract
G-quadruplexes are tetraplex structures of nucleic acids that can form in G-rich sequences. Their presence and functional role have been established in telomeres, oncogene promoters and coding regions of the human chromosome. In particular, they have been proposed to be directly involved in gene regulation at the level of transcription. Because the HIV-1 Nef protein is a fundamental factor for efficient viral replication, infectivity and pathogenesis in vitro and in vivo, we investigated G-quadruplex formation in the HIV-1 nef gene to assess the potential for viral inhibition through G-quadruplex stabilization. A comprehensive computational analysis of the nef coding region of available strains showed the presence of three conserved sequences that were uniquely clustered. Biophysical testing proved that G-quadruplex conformations were efficiently stabilized or induced by G-quadruplex ligands in all three sequences. Upon incubation with a G-quadruplex ligand, Nef expression was reduced in a reporter gene assay and Nef-dependent enhancement of HIV-1 infectivity was significantly repressed in an antiviral assay. These data constitute the first evidence of the possibility to regulate HIV-1 gene expression and infectivity through G-quadruplex targeting and therefore open a new avenue for viral treatment.
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Affiliation(s)
- Rosalba Perrone
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Jerrod A. Poe
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Manlio Palumbo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Sara N. Richter
- Department of Molecular Medicine, University of Padua, Padua, Italy
- * E-mail:
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16
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Kumar B, Tripathi C, Kanchan RK, Tripathi JK, Ghosh JK, Ramachandran R, Bhadauria S, Tripathi RK. Dynamics of physical interaction between HIV-1 Nef and ASK1: identifying the interacting motif(s). PLoS One 2013; 8:e67586. [PMID: 23799149 PMCID: PMC3683068 DOI: 10.1371/journal.pone.0067586] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 05/20/2013] [Indexed: 11/18/2022] Open
Abstract
FasL mediated preferential apoptosis of bystander CTLs while protection of infected CD4(+)T cells remains one of the hallmarks of immune evasion during HIV infection. The property of infected host cells to evade cell-autonomous apoptosis emanates from ability of HIV-1Nef-protein to physically interact with ASK-1 and thereby inhibit its enzymatic activity. The specific domains of HIV-1Nef through which it may interact with ASK1 and thereby impair the ASK1 activity remain unidentified so far and represent a major challenge towards developing clear understanding about the dynamics of this interaction. Using mammalian two hybrid screen in association with site directed mutagenesis and competitive inhibitor peptides, we identified constituent minimal essential domain (152 DEVGEANN 159) through which HIV-1Nef interacts with ASK1 and inhibits its function. Furthermore our study also unravels a novel alternate mechanism underlying HIV-1 Nef mediated ASK1 functional modulation, wherein by potentiating the inhibitory ser(967) phosphorylation of ASK1, HIV-1Nef negatively modulated ASK1 function.
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Affiliation(s)
- Balawant Kumar
- Division of Toxicology, Central Drug Research Institute (Council of Scientific & Industrial Research), BS-10/1, Sector-10 Jankipuram Extension, Uttar Pradesh, India
| | - Chakrapani Tripathi
- Division of Toxicology, Central Drug Research Institute (Council of Scientific & Industrial Research), BS-10/1, Sector-10 Jankipuram Extension, Uttar Pradesh, India
| | - Ranjana K. Kanchan
- Division of Toxicology, Central Drug Research Institute (Council of Scientific & Industrial Research), BS-10/1, Sector-10 Jankipuram Extension, Uttar Pradesh, India
| | - Jitendra Kumar Tripathi
- Division of Molecular and Structural Biology, Central Drug Research Institute (Council of Scientific & Industrial Research), BS-10/1, Sector-10 Jankipuram Extension, Uttar Pradesh, India
| | - Jimut K. Ghosh
- Division of Molecular and Structural Biology, Central Drug Research Institute (Council of Scientific & Industrial Research), BS-10/1, Sector-10 Jankipuram Extension, Uttar Pradesh, India
| | - Ravishankar Ramachandran
- Division of Molecular and Structural Biology, Central Drug Research Institute (Council of Scientific & Industrial Research), BS-10/1, Sector-10 Jankipuram Extension, Uttar Pradesh, India
| | - Smrati Bhadauria
- Division of Toxicology, Central Drug Research Institute (Council of Scientific & Industrial Research), BS-10/1, Sector-10 Jankipuram Extension, Uttar Pradesh, India
- * (SB); (KT)
| | - Raj Kamal Tripathi
- Division of Toxicology, Central Drug Research Institute (Council of Scientific & Industrial Research), BS-10/1, Sector-10 Jankipuram Extension, Uttar Pradesh, India
- * (SB); (KT)
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17
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Mwimanzi P, Markle TJ, Martin E, Ogata Y, Kuang XT, Tokunaga M, Mahiti M, Pereyra F, Miura T, Walker BD, Brumme ZL, Brockman MA, Ueno T. Attenuation of multiple Nef functions in HIV-1 elite controllers. Retrovirology 2013. [PMID: 23289738 DOI: 10.1186/742-4690-10-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Impaired HIV-1 Gag, Pol, and Env function has been described in elite controllers (EC) who spontaneously suppress plasma viremia to < 50 RNA copies/mL; however, activity of the accessory protein Nef remains incompletely characterized. We examined the ability of 91 Nef clones, isolated from plasma of 45 EC and 46 chronic progressors (CP), to down-regulate HLA class I and CD4, up-regulate HLA class II invariant chain (CD74), enhance viral infectivity, and stimulate viral replication in PBMC. RESULTS In general, EC Nef clones were functional; however, all five activities were significantly lower in EC compared to CP. Nef clones from HLA-B*57-expressing EC exhibited poorer CD4 down-regulation function compared to those from non-B*57 EC, and the number of EC-specific B*57-associated Nef polymorphisms correlated inversely with 4 of 5 Nef functions in these individuals. CONCLUSION Results indicate that decreased HIV-1 Nef function, due in part to host immune selection pressures, may be a hallmark of the EC phenotype.
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Affiliation(s)
- Philip Mwimanzi
- Center for AIDS Research, Kumamoto University, 2-2-1 Honjo, Kumamoto 860-0811, Japan
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18
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Buggert M, Norström MM, Czarnecki C, Tupin E, Luo M, Gyllensten K, Sönnerborg A, Lundegaard C, Lund O, Nielsen M, Karlsson AC. Characterization of HIV-specific CD4+ T cell responses against peptides selected with broad population and pathogen coverage. PLoS One 2012; 7:e39874. [PMID: 22792193 PMCID: PMC3390319 DOI: 10.1371/journal.pone.0039874] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Accepted: 05/28/2012] [Indexed: 11/18/2022] Open
Abstract
CD4+ T cells orchestrate immunity against viral infections, but their importance in HIV infection remains controversial. Nevertheless, comprehensive studies have associated increase in breadth and functional characteristics of HIV-specific CD4+ T cells with decreased viral load. A major challenge for the identification of HIV-specific CD4+ T cells targeting broadly reactive epitopes in populations with diverse ethnic background stems from the vast genomic variation of HIV and the diversity of the host cellular immune system. Here, we describe a novel epitope selection strategy, PopCover, that aims to resolve this challenge, and identify a set of potential HLA class II-restricted HIV epitopes that in concert will provide optimal viral and host coverage. Using this selection strategy, we identified 64 putative epitopes (peptides) located in the Gag, Nef, Env, Pol and Tat protein regions of HIV. In total, 73% of the predicted peptides were found to induce HIV-specific CD4+ T cell responses. The Gag and Nef peptides induced most responses. The vast majority of the peptides (93%) had predicted restriction to the patient’s HLA alleles. Interestingly, the viral load in viremic patients was inversely correlated to the number of targeted Gag peptides. In addition, the predicted Gag peptides were found to induce broader polyfunctional CD4+ T cell responses compared to the commonly used Gag-p55 peptide pool. These results demonstrate the power of the PopCover method for the identification of broadly recognized HLA class II-restricted epitopes. All together, selection strategies, such as PopCover, might with success be used for the evaluation of antigen-specific CD4+ T cell responses and design of future vaccines.
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Affiliation(s)
- Marcus Buggert
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Melissa M. Norström
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Chris Czarnecki
- HIV and Human Genetics, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Emmanuel Tupin
- Department of Virology, Swedish Institute for Infectious Disease Control, Stockholm, Sweden
| | - Ma Luo
- HIV and Human Genetics, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Canada
| | - Katarina Gyllensten
- Gay Men’s Health Clinic, Stockholm South General Hospital (Södersjukhuset), Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Claus Lundegaard
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Ole Lund
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Morten Nielsen
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
| | - Annika C. Karlsson
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
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Campbell PE, Isayev O, Ali SA, Roth WW, Huang MB, Powell MD, Leszczynski J, Bond VC. Validation of a novel secretion modification region (SMR) of HIV-1 Nef using cohort sequence analysis and molecular modeling. J Mol Model 2012; 18:4603-13. [PMID: 22643973 DOI: 10.1007/s00894-012-1452-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 04/30/2012] [Indexed: 01/02/2023]
Abstract
The HIV-1 accessory protein Nef plays an active role in the pathogenesis of AIDS by its numerous cellular interactions that facilitate the release of virus particles. This 27 kDa protein is required for maintenance of the viral replication in HIV, and is also known to contribute to immune evasion, blocking of apoptosis in virus-infected cells and enhancement of virus infectivity. Nef has been shown to be secreted and is present on the surface of virus-infected cells. Recent studies from our laboratory have shown that the Nef protein is secreted from nef-transfected and HIV-1-infected cells in small exosome-like vesicles (40-100 nm diam.) that do not contain virions. We have identified three amino-terminal domains of Nef as necessary for secretion: (i) the four arginine residues (17,19,21, 22) comprising the basic region; (ii) the phosphofurin acidic cluster sequence (PACS) composed of four glutamic acid residues (61-64); (iii) a previously unknown motif spanning amino acid residues 65-69 (VGFPV) which we named the secretion modification region (SMR). In this study, we have used population-based phylogeny data and sequence analysis to characterize the conservation of the Nef SMR domain that regulates vesicle secretion. We have performed in silico computational chemistry analysis involving molecular dynamic structure modeling of mutations in the SMR motif. Sequence analysis of Nef from HIV-1-infected patients, including slow progressors (SP), long term progressors (LTP) and long term non-progressors (LTNP) demonstrated 99 % conservation of the Nef SMR motif. Computational analysis including modeling of wild-type HIV-1 Nef and V66A Nef SMR mutant using structural homology and molecular dynamics of ligand-associated interactions indicated significant structural changes in the Nef mutant, thus supporting the importance of the SMR domain for mediating Nef vesicle secretion.
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Affiliation(s)
- Patrick E Campbell
- Department of Microbiology, Immunology and Biochemistry, Morehouse School of Medicine, Atlanta, GA, USA
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20
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Rodríguez AM, Pascutti MF, Maeto C, Falivene J, Holgado MP, Turk G, Gherardi MM. IL-12 and GM-CSF in DNA/MVA immunizations against HIV-1 CRF12_BF Nef induced T-cell responses with an enhanced magnitude, breadth and quality. PLoS One 2012; 7:e37801. [PMID: 22655069 PMCID: PMC3360004 DOI: 10.1371/journal.pone.0037801] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 04/27/2012] [Indexed: 01/12/2023] Open
Abstract
In Argentina, the HIV epidemic is characterized by the co-circulation of subtype B and BF recombinant viral variants. Nef is an HIV protein highly variable among subtypes, making it a good tool to study the impact of HIV variability in the vaccine design setting. We have previously reported a specific cellular response against NefBF with low cross-reactivity to NefB in mice. The aim of this work was to analyze whether the co-administration of IL-12 and GM-CSF, using DNA and MVA vaccine vectors, could improve the final cellular response induced. Mice received three DNA priming doses of a plasmid that express NefBF plus DNAs expressing IL-12 and/or GM-CSF. Afterwards, all the groups were boosted with a MVAnefBF dose. The highest increase in the magnitude of the NefBF response, compared to that induced in the control was found in the IL-12 group. Importantly, a response with higher breadth was detected in groups which received IL-12 or GM-CSF, evidenced as an increased frequency of recognition of homologous (BF) and heterologous (B) Nef peptides, as well as a higher number of other Nef peptide pools representing different viral subtypes. However, these improvements were lost when both DNA cytokines were simultaneously administered, as the response was focused against the immunodominant peptide with a detrimental response towards subdominant epitopes. The pattern of cytokines secreted and the specific-T-cell proliferative capacity were improved in IL-12 and IL-12+GM-CSF groups. Importantly IL-12 generated a significant higher T-cell avidity against a B heterologous peptide. This study indicates that the incorporation of DNA expressing IL-12 in DNA/MVA schemes produced the best results in terms of improvements of T-cell-response key properties such as breadth, cross-reactivity and quality (avidity and pattern of cytokines secreted). These relevant results contribute to the design of strategies aimed to induce T-cell responses against HIV antigens with higher quality.
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Affiliation(s)
| | | | | | | | | | | | - María Magdalena Gherardi
- Centro Nacional de Referencia para el SIDA, Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail:
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21
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Chutiwitoonchai N, Hiyoshi M, Mwimanzi P, Ueno T, Adachi A, Ode H, Sato H, Fackler OT, Okada S, Suzu S. The identification of a small molecule compound that reduces HIV-1 Nef-mediated viral infectivity enhancement. PLoS One 2011; 6:e27696. [PMID: 22110726 PMCID: PMC3217016 DOI: 10.1371/journal.pone.0027696] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 10/22/2011] [Indexed: 12/14/2022] Open
Abstract
Nef is a multifunctional HIV-1 protein that accelerates progression to AIDS, and enhances the infectivity of progeny viruses through a mechanism that is not yet understood. Here, we show that the small molecule compound 2c reduces Nef-mediated viral infectivity enhancement. When added to viral producer cells, 2c did not affect the efficiency of viral production itself. However, the infectivity of the viruses produced in the presence of 2c was significantly lower than that of control viruses. Importantly, an inhibitory effect was observed with Nef(+) wild-type viruses, but not with viruses produced in the absence of Nef or in the presence of proline-rich PxxP motif-disrupted Nef, both of which displayed significantly reduced intrinsic infectivity. Meanwhile, the overexpression of the SH3 domain of the tyrosine kinase Hck, which binds to a PxxP motif in Nef, also reduced viral infectivity. Importantly, 2c inhibited Hck SH3-Nef binding, which was more marked when Nef was pre-incubated with 2c prior to its incubation with Hck, indicating that both Hck SH3 and 2c directly bind to Nef and that their binding sites overlap. These results imply that both 2c and the Hck SH3 domain inhibit the interaction of Nef with an unidentified host protein and thereby reduce Nef-mediated infectivity enhancement. The first inhibitory compound 2c is therefore a valuable chemical probe for revealing the underlying molecular mechanism by which Nef enhances the infectivity of HIV-1.
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Affiliation(s)
| | | | - Philip Mwimanzi
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Takamasa Ueno
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Akio Adachi
- Department of Microbiology, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Hirotaka Ode
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hironori Sato
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Oliver T. Fackler
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Seiji Okada
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Shinya Suzu
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
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22
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Abstract
HIV proteins target host hub proteins for transient binding interactions. The presence of viral proteins in the infected cell results in out-competition of host proteins in their interaction with hub proteins, drastically affecting cell physiology. Functional genomics and interactome datasets can be used to quantify the sequence hotspots on the HIV proteome mediating interactions with host hub proteins. In this study, we used the HIV and human interactome databases to identify HIV targeted host hub proteins and their host binding partners (H2). We developed a high throughput computational procedure utilizing motif discovery algorithms on sets of protein sequences, including sequences of HIV and H2 proteins. We identified as HIV sequence hotspots those linear motifs that are highly conserved on HIV sequences and at the same time have a statistically enriched presence on the sequences of H2 proteins. The HIV protein motifs discovered in this study are expressed by subsets of H2 host proteins potentially outcompeted by HIV proteins. A large subset of these motifs is involved in cleavage, nuclear localization, phosphorylation, and transcription factor binding events. Many such motifs are clustered on an HIV sequence in the form of hotspots. The sequential positions of these hotspots are consistent with the curated literature on phenotype altering residue mutations, as well as with existing binding site data. The hotspot map produced in this study is the first global portrayal of HIV motifs involved in altering the host protein network at highly connected hub nodes.
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MESH Headings
- Amino Acid Motifs/genetics
- Amino Acid Sequence
- Binding Sites/genetics
- CREB-Binding Protein/metabolism
- Calcium-Calmodulin-Dependent Protein Kinases/metabolism
- Calmodulin/metabolism
- Casein Kinase II/metabolism
- Databases, Protein
- Human Immunodeficiency Virus Proteins/chemistry
- Human Immunodeficiency Virus Proteins/genetics
- Human Immunodeficiency Virus Proteins/metabolism
- Humans
- Hydrophobic and Hydrophilic Interactions
- Mitogen-Activated Protein Kinase 1/metabolism
- Models, Molecular
- Protein Binding
- Protein Interaction Mapping/methods
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Proteins/genetics
- Proteins/metabolism
- env Gene Products, Human Immunodeficiency Virus/chemistry
- env Gene Products, Human Immunodeficiency Virus/genetics
- env Gene Products, Human Immunodeficiency Virus/metabolism
- gag Gene Products, Human Immunodeficiency Virus/chemistry
- gag Gene Products, Human Immunodeficiency Virus/genetics
- gag Gene Products, Human Immunodeficiency Virus/metabolism
- nef Gene Products, Human Immunodeficiency Virus/chemistry
- nef Gene Products, Human Immunodeficiency Virus/genetics
- nef Gene Products, Human Immunodeficiency Virus/metabolism
- rev Gene Products, Human Immunodeficiency Virus/chemistry
- rev Gene Products, Human Immunodeficiency Virus/genetics
- rev Gene Products, Human Immunodeficiency Virus/metabolism
- tat Gene Products, Human Immunodeficiency Virus/chemistry
- tat Gene Products, Human Immunodeficiency Virus/genetics
- tat Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Mahdi Sarmady
- Center for Integrated Bioinformatics, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - William Dampier
- Center for Integrated Bioinformatics, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Aydin Tozeren
- Center for Integrated Bioinformatics, Drexel University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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23
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Abstract
The difference between regional rates of HIV-associated dementia (HAD) in patients infected with different subtypes of HIV suggests that genetic determinants exist within HIV that influence the ability of the virus to replicate in the central nervous system (in Uganda, Africa, subtype D HAD rate is 89%, while subtype A HAD rate is 24%). HIV-1 nef is a multifunctional protein with known toxic effects in the brain compartment. The goal of the current study was to identify if specific three-dimensional nef structures may be linked to patients who developed HAD. HIV-1 nef structures were computationally derived for consensus brain and non-brain sequences from a panel of patients infected with subtype B who died due to varied disease pathologies and consensus subtype A and subtype D sequences from Uganda. Site directed mutation analysis identified signatures in brain structures that appear to change binding potentials and could affect folding conformations of brain-associated structures. Despite the large sequence variation between HIV subtypes, structural alignments confirmed that viral structures derived from patients with HAD were more similar to subtype D structures than to structures derived from patient sequences without HAD. Furthermore, structures derived from brain sequences of patients with HAD were more similar to subtype D structures than they were to their own non-brain structures. The potential finding of a brain-specific nef structure indicates that HAD may result from genetic alterations that alter the folding or binding potential of the protein.
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Affiliation(s)
- Susanna L. Lamers
- Polytechnic Institute of New York University, New York, New York, United States of America
- BioInfoExperts, Thibodaux, Louisiana, United States of America
| | - Art F. Y. Poon
- British Columbia Centre for HIV/AIDs Excellence, British Columbia, Canada
| | - Michael S. McGrath
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States of America
- The AIDS and Cancer Specimen Resource (West Coast ACSR), San Francisco, California, United States of America
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24
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Kwak YT, Raney A, Kuo LS, Denial SJ, Temple BRS, Garcia JV, Foster JL. Self-association of the Lentivirus protein, Nef. Retrovirology 2010; 7:77. [PMID: 20863404 PMCID: PMC2955668 DOI: 10.1186/1742-4690-7-77] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 09/23/2010] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The HIV-1 pathogenic factor, Nef, is a multifunctional protein present in the cytosol and on membranes of infected cells. It has been proposed that a spatial and temporal regulation of the conformation of Nef sequentially matches Nef's multiple functions to the process of virion production. Further, it has been suggested that dimerization is required for multiple Nef activities. A dimerization interface has been proposed based on intermolecular contacts between Nefs within hexagonal Nef/FynSH3 crystals. The proposed dimerization interface consists of the hydrophobic B-helix and flanking salt bridges between R105 and D123. Here, we test whether Nef self-association is mediated by this interface and address the overall significance of oligomerization. RESULTS By co-immunoprecipitation assays, we demonstrated that HIV-1Nef exists as monomers and oligomers with about half of the Nef protomers oligomerized. Nef oligomers were found to be present in the cytosol and on membranes. Removal of the myristate did not enhance the oligomerization of soluble Nef. Also, SIVNef oligomerizes despite lacking a dimerization interface functionally homologous to that proposed for HIV-1Nef. Moreover, HIV-1Nef and SIVNef form hetero-oligomers demonstrating the existence of homologous oligomerization interfaces that are distinct from that previously proposed (R105-D123). Intracellular cross-linking by formaldehyde confirmed that SF2Nef dimers are present in intact cells, but surprisingly self-association was dependent on R105, but not D123. SIV(MAC239)Nef can be cross-linked at its only cysteine, C55, and SF2Nef is also cross-linked, but at C206 instead of C55, suggesting that Nefs exhibit multiple dimeric structures. ClusPro dimerization analysis of HIV-1Nef homodimers and HIV-1Nef/SIVNef heterodimers identified a new potential dimerization interface, including a dibasic motif at R105-R106 and a six amino acid hydrophobic surface. CONCLUSIONS We have demonstrated significant levels of intracellular Nef oligomers by immunoprecipitation from cellular extracts. However, our results are contrary to the identification of salt bridges between R105 and D123 as necessary for self-association. Importantly, binding between HIV-1Nef and SIVNef demonstrates evolutionary conservation and therefore significant function(s) for oligomerization. Based on modeling studies of Nef self-association, we propose a new dimerization interface. Finally, our findings support a stochastic model of Nef function with a dispersed intracellular distribution of Nef oligomers.
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Affiliation(s)
- Youn Tae Kwak
- Baylor Institute for Immunology Research, 3434 Live Oak, Dallas, TX 75204, USA
| | - Alexa Raney
- Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Y9.206, Dallas, Texas 75390, USA
| | - Lillian S Kuo
- Department of Internal Medicine, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Y9.206, Dallas, Texas 75390, USA
| | - Sarah J Denial
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina 27599-7042, USA
| | - Brenda RS Temple
- Department of Biochemistry and Biophysics, R. L. Juliano Structural Bioinformatics Core, University of North Carolina, Chapel Hill, North Carolina 27599-7042, USA
| | - J Victor Garcia
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina 27599-7042, USA
| | - John L Foster
- Division of Infectious Diseases, Center for AIDS Research, University of North Carolina, Chapel Hill, North Carolina 27599-7042, USA
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25
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Pushker R, Jacqué JM, Shields DC. Meta-analysis to test the association of HIV-1 nef amino acid differences and deletions with disease progression. J Virol 2010; 84:3644-53. [PMID: 20071583 PMCID: PMC2838144 DOI: 10.1128/jvi.01959-09] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 12/30/2009] [Indexed: 11/20/2022] Open
Abstract
Previous relatively small studies have associated particular amino acid replacements and deletions in the HIV-1 nef gene with differences in the rate of HIV disease progression. We tested more rigorously whether particular nef amino acid differences and deletions are associated with HIV disease progression. Amino acid replacements and deletions in patients' consensus sequences were investigated for 153 progressor (P), 615 long-term nonprogressor (LTNP), and 2,311 unknown progressor sequences from 582 subtype B HIV-infected patients. LTNPs had more defective nefs (interrupted by frameshifts or stop codons), but on a per-patient basis there was no excess of LTNP patients with one or more defective nef sequences compared to the Ps (P = 0.47). The high frequency of amino acid replacement at residues S(8), V(10), I(11), A(15), V(85), V(133), N(157), S(163), V(168), D(174), R(178), E(182), and R(188) in LTNPs was also seen in permuted datasets, implying that these are simply rapidly evolving residues. Permutation testing revealed that residues showing the greatest excess over expectation (A(15), V(85), N(157), S(163), V(168), D(174), R(178), and R(188)) were not significant (P = 0.77). Exploratory analysis suggested a hypothetical excess of frameshifting in the regions (9)SVIG and (118)QGYF among LTNPs. The regions V(10) and (152)KVEEA of nef were commonly deleted in LTNPs. However, permutation testing indicated that none of the regions displayed significantly excessive deletion in LTNPs. In conclusion, meta-analysis of HIV-1 nef sequences provides no clear evidence of whether defective nef sequences or particular regions of the protein play a significant role in disease progression.
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Affiliation(s)
- Ravindra Pushker
- UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Science, Centre for Research in Infectious Diseases, University College Dublin, Belfield, Dublin 4, Ireland
| | - Jean-Marc Jacqué
- UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Science, Centre for Research in Infectious Diseases, University College Dublin, Belfield, Dublin 4, Ireland
| | - Denis C. Shields
- UCD Complex and Adaptive Systems Laboratory, UCD Conway Institute of Biomolecular and Biomedical Research, School of Medicine and Medical Science, Centre for Research in Infectious Diseases, University College Dublin, Belfield, Dublin 4, Ireland
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26
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Gómez-Icazbalceta G, Larralde C. [Linking Nef with the immunological and virological determinants of AIDS]. Rev Invest Clin 2009; 61:243-251. [PMID: 19736813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Nef is an accessory protein from HIV-1 involved in viral replication, depletion of CD4 + T cells and progression to AIDS. The participation of Nef in altering several of the cellular and subcellular components has been studied in detail. The finding that infected patients over 15 years with HIV-1 variants that expressed a defective nef gene had not progressed to AIDS, suggested that Nef played a decisive role in the outcome of AIDS, through the regulation of different virological and immunological components. In addition, the mere expression of Nef is able to induce AIDS in transgenic mice and alter the kinetics of replication of the virus in infected monkeys. This review examines the relationship between the expression of Nef and the ultimate consequences of HIV-1 infection, taking into account the most relevant clinical parameters: viral load, counting of CD4 + T cells and progression to AIDS. Under this approach, it is emphasized the role of Nef as immunomodulator and also as independent mediator of damage to the immune system.
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27
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de Virgilio M, De Marchis F, Bellucci M, Mainieri D, Rossi M, Benvenuto E, Arcioni S, Vitale A. The human immunodeficiency virus antigen Nef forms protein bodies in leaves of transgenic tobacco when fused to zeolin. J Exp Bot 2008; 59:2815-29. [PMID: 18540021 PMCID: PMC2486477 DOI: 10.1093/jxb/ern143] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2008] [Revised: 03/31/2008] [Accepted: 04/28/2008] [Indexed: 05/03/2023]
Abstract
Protein bodies (PB) are stable polymers naturally formed by certain seed storage proteins within the endoplasmic reticulum (ER). The human immunodeficiency virus negative factor (Nef) protein, a potential antigen for the development of an anti-viral vaccine, is highly unstable when introduced into the plant secretory pathway, probably because of folding defects in the ER environment. The aim of this study was to promote the formation of Nef-containing PB in tobacco (Nicotiana tabacum) leaves by fusing the Nef sequence to the N-terminal domains of the maize storage protein gamma-zein or to the chimeric protein zeolin (which efficiently forms PB and is composed of the vacuolar storage protein phaseolin fused to the N-terminal domains of gamma-zein). Protein blots and pulse-chase indicate that fusions between Nef and the same gamma-zein domains present in zeolin are degraded by ER quality control. Consistently, a mutated zeolin, in which wild-type phaseolin was substituted with a defective version known to be degraded by ER quality control, is unstable in plant cells. Fusion of Nef to the entire zeolin sequence instead allows the formation of PB detectable by electron microscopy and subcellular fractionation, leading to zeolin-Nef accumulation higher than 1% of total soluble protein, consistently reproduced in independent transgenic plants. It is concluded that zeolin, but not its gamma-zein portion, has a positive dominant effect over ER quality control degradation. These results provide insights into the requirements for PB formation and avoidance of quality-control degradation, and indicate a strategy for enhancing foreign protein accumulation in plants.
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MESH Headings
- Amino Acid Sequence
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/metabolism
- Gene Expression
- Humans
- Inclusion Bodies/chemistry
- Inclusion Bodies/genetics
- Inclusion Bodies/metabolism
- Molecular Sequence Data
- Plant Leaves/chemistry
- Plant Leaves/genetics
- Plant Leaves/metabolism
- Plants, Genetically Modified/chemistry
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Protein Engineering
- Protein Structure, Tertiary
- Protein Transport
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Nicotiana/chemistry
- Nicotiana/genetics
- Nicotiana/metabolism
- Zea mays/genetics
- Zein/chemistry
- Zein/genetics
- Zein/metabolism
- nef Gene Products, Human Immunodeficiency Virus/chemistry
- nef Gene Products, Human Immunodeficiency Virus/genetics
- nef Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Maddalena de Virgilio
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, via Bassini 15, 20133 Milano, Italy, EU
| | - Francesca De Marchis
- Istituto di Genetica Vegetale, Consiglio Nazionale delle Ricerche, Articolazione Territoriale di Perugia, via della Madonna Alta 130, 06128 Perugia, Italy, EU
| | - Michele Bellucci
- Istituto di Genetica Vegetale, Consiglio Nazionale delle Ricerche, Articolazione Territoriale di Perugia, via della Madonna Alta 130, 06128 Perugia, Italy, EU
| | - Davide Mainieri
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, via Bassini 15, 20133 Milano, Italy, EU
| | - Marika Rossi
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, via Bassini 15, 20133 Milano, Italy, EU
| | - Eugenio Benvenuto
- ENEA-BIOTEC Sezione Genetica e Genomica Vegetale, C.R. Casaccia, 00060 Roma, Italy, EU
| | - Sergio Arcioni
- Istituto di Genetica Vegetale, Consiglio Nazionale delle Ricerche, Articolazione Territoriale di Perugia, via della Madonna Alta 130, 06128 Perugia, Italy, EU
| | - Alessandro Vitale
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, via Bassini 15, 20133 Milano, Italy, EU
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28
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Betzi S, Restouin A, Opi S, Arold ST, Parrot I, Guerlesquin F, Morelli X, Collette Y. Protein protein interaction inhibition (2P2I) combining high throughput and virtual screening: Application to the HIV-1 Nef protein. Proc Natl Acad Sci U S A 2007; 104:19256-61. [PMID: 18042718 PMCID: PMC2148277 DOI: 10.1073/pnas.0707130104] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Indexed: 11/18/2022] Open
Abstract
Protein-protein recognition is the cornerstone of multiple cellular and pathological functions. Therefore, protein-protein interaction inhibition (2P2I) is endowed with great therapeutic potential despite the initial belief that 2P2I was refractory to small-molecule intervention. Improved knowledge of complex molecular binding surfaces has recently stimulated renewed interest for 2P2I, especially after identification of "hot spots" and first inhibitory compounds. However, the combination of target complexity and lack of starting compound has thwarted experimental results and created intellectual barriers. Here we combined virtual and experimental screening when no previously known inhibitors can be used as starting point in a structure-based research program that targets an SH3 binding surface of the HIV type I Nef protein. High-throughput docking and application of a pharmacophoric filter on one hand and search for analogy on the other hand identified drug-like compounds that were further confirmed to bind Nef in the micromolar range (isothermal titration calorimetry), to target the Nef SH3 binding surface (NMR experiments), and to efficiently compete for Nef-SH3 interactions (cell-based assay, GST pull-down). Initial identification of these compounds by virtual screening was validated by screening of the very same library of compounds in the cell-based assay, demonstrating that a significant enrichment factor was attained by the in silico screening. To our knowledge, our results identify the first set of drug-like compounds that functionally target the HIV-1 Nef SH3 binding surface and provide the basis for a powerful discovery process that should help to speed up 2P2I strategies and open avenues for new class of antiviral molecules.
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Affiliation(s)
- Stéphane Betzi
- *Bioénergétique et Ingénierie des Protéines Laboratory, Centre National de la Recherche Scientifique/Institut de Biologie Structurale et Microbiologie, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Audrey Restouin
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 599, Centre de Recherche en Cancérologie de Marseille, F-13009 Marseille, France
- Institut Paoli-Calmettes, F-13009 Marseille, France
- Université de la Méditerranée, F-13007 Marseille, France
| | - Sandrine Opi
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 599, Centre de Recherche en Cancérologie de Marseille, F-13009 Marseille, France
- Institut Paoli-Calmettes, F-13009 Marseille, France
- Université de la Méditerranée, F-13007 Marseille, France
| | - Stefan T. Arold
- Institut National de la Santé et de la Recherche Médicale, Unité 554, and Université de Montpellier, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Centre de Biochimie Structurale, 29, Rue de Navacelles, 34090 Montpellier Cedex, France; and
| | - Isabelle Parrot
- Institut des Biomolécules Max Mousseron, Unité Mixte de Recherche 5247, Centre National de la Recherche Scientifique–Universités Montpellier I et II, Faculté de Pharmacie, 34093 Montpellier, France
| | - Françoise Guerlesquin
- *Bioénergétique et Ingénierie des Protéines Laboratory, Centre National de la Recherche Scientifique/Institut de Biologie Structurale et Microbiologie, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Xavier Morelli
- *Bioénergétique et Ingénierie des Protéines Laboratory, Centre National de la Recherche Scientifique/Institut de Biologie Structurale et Microbiologie, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Yves Collette
- Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche 599, Centre de Recherche en Cancérologie de Marseille, F-13009 Marseille, France
- Institut Paoli-Calmettes, F-13009 Marseille, France
- Université de la Méditerranée, F-13007 Marseille, France
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29
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Wolf D, Giese SI, Witte V, Krautkrämer E, Trapp S, Sass G, Haller C, Blume K, Fackler OT, Baur AS. Novel (n)PKC kinases phosphorylate Nef for increased HIV transcription, replication and perinuclear targeting. Virology 2007; 370:45-54. [PMID: 17904606 DOI: 10.1016/j.virol.2007.08.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Revised: 05/28/2007] [Accepted: 08/08/2007] [Indexed: 10/22/2022]
Abstract
The N-terminus of the human immunodeficiency virus (HIV) pathogenicity factor Nef associates with a protein complex (NAKC for Nef-associated kinase complex) that contains at least two kinases: the tyrosine kinase Lck and a serine kinase activity which was found to phosphorylate Lck and the Nef N-terminus. Here we show that this serine kinase activity is mediated by members of the novel Protein Kinase C (nPKC) subfamily, PKCdelta and theta. Association with the Nef N-terminus was sufficient to activate PKC leading to phosphorylation of Nef in vitro on a conserved serine residue at position 6. Mutation of serine 6 or coexpression of a transdominant negative PKC mutant significantly reduced Nef-stimulated HIV transcription and replication in resting PBMC. When analyzing the molecular mechanisms, we found that mutating serine 6 moderately affected myristoylation of Nef and its association with Pak2 activity, whereas CD4 downmodulation was not inhibited. More interestingly, this mutation abolished the typical perinuclear localization of Nef in T cells. We conclude that the activation of nPKCs by Nef is required to increase viral replication/infectivity and direct the subcellular localization of Nef.
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Affiliation(s)
- Dietlinde Wolf
- University of Miami, Miller School of Medicine, Department of Microbiology and Immunology, BCRI 739, Miami, FL 33136, USA
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30
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Raney A, Shaw AY, Foster JL, Garcia JV. Structural constraints on human immunodeficiency virus type 1 Nef function. Virology 2007; 368:7-16. [PMID: 17632197 PMCID: PMC3026346 DOI: 10.1016/j.virol.2007.02.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2007] [Revised: 01/23/2007] [Accepted: 02/20/2007] [Indexed: 10/23/2022]
Abstract
HIV-1 Nef is a multifunctional protein that exerts its activities through interactions with multiple cellular partners. Nef uses different domains and mechanisms to exert its functions including cell surface down-modulation of CD4 and MHC-I receptors and activation of the serine/threonine kinase PAK-2. We inserted tags at the C-terminus and proximal to the N-terminus of Nef and the effects on Nef's structure/function relationships were examined. We discovered significant defects in MHC-I down-modulation with the insertion of HA/FLAG tags at either region. We also found impaired PAK-2 activation with a C-terminal fusion with GFP. Interestingly, Nef-GFP and Nef-GH(7) induced MHC-I down-modulation, suggesting that the negative charge of the HA/FLAG tag could contribute to the observed defect. Together, these observations highlight elements of Nef's functional complexity and demonstrate previously unsuspected structural requirements for PAK-2 activation and MHC-1 down-modulation in Nef's flexible N- and C-terminal regions.
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Affiliation(s)
- Alexa Raney
- University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard Y9.206, Dallas, TX, 75390, U.S.A
| | - Alice Y. Shaw
- University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard Y9.206, Dallas, TX, 75390, U.S.A
| | - John L. Foster
- University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard Y9.206, Dallas, TX, 75390, U.S.A
| | - J. Victor Garcia
- University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard Y9.206, Dallas, TX, 75390, U.S.A
- Corresponding author. , Phone: (214) 648-9970, Fax: (214) 648-0231
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Zhai S, Kang WZ, Yu X, Wang SY, Walker BD, Altfeld M, Sun YT. [Specific immune responses to human immunodeficiency virus type 1 Gag, Tat, Rev and Nef proteins]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 2005; 21:175-9. [PMID: 15766402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
AIM To investigate the features of HIV-1-Gag-, Tat-, Rev- and Nef- specific cytotoxic T-lymphocyte (CTL) responses in infected individuals in China. METHODS The HIV-1-specific CTL responses were analyzed with an IFN-gamma ELISPOT assay by using 220 overlapping peptides spanning the entire HIV-1 Clade B (HIV-1B) and C (HIV-1C) Gag, Tat, Rev and Nef proteins consensus sequences. RESULTS For either HIV-1B or HIV-1C, Gag and Nef were preferentially targeted by HIV-1 specific CTLs, Rev and Tat proteins were also recognized to different extent. In comparison of the immune responses between HIV-1B and HIV-1C, the magnitude and frequency were roughly identical but there were some differences in the immunodominant regions. For HIV-1B, the highest response magnitude was detected in 288-313 amino acids of Gag p24, and for HIV-1C, in 155-181 amino acids of Gag p24. The most frequently recognized region was located in 106-143 amino acids of Nef either in HIV-1B or in HIV-1C (48.1%). CONCLUSION HIV-1-specific CTLs mainly directed against HIV-1 Gag and Nef in Chinese, and there is some difference between HIV-1B and HIV-1C. There exists the cross-recognition between the Clade B and Clade C. These data suggest that the study on HIV-1-specific CTL responses in Chinese will provide strategies for the vaccine design in China.
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Affiliation(s)
- Song Zhai
- Center of Diagnosis and Treatment for Infectious Diseases of Chinese PLA, Tangdu Hospital, Fourth Military Medical University, Xi'an 710038, China
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