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Miller NL, Raman R, Clark T, Sasisekharan R. Complexity of Viral Epitope Surfaces as Evasive Targets for Vaccines and Therapeutic Antibodies. Front Immunol 2022; 13:904609. [PMID: 35784339 PMCID: PMC9247215 DOI: 10.3389/fimmu.2022.904609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/16/2022] [Indexed: 11/29/2022] Open
Abstract
The dynamic interplay between virus and host plays out across many interacting surfaces as virus and host evolve continually in response to one another. In particular, epitope-paratope interactions (EPIs) between viral antigen and host antibodies drive much of this evolutionary race. In this review, we describe a series of recent studies examining aspects of epitope complexity that go beyond two interacting protein surfaces as EPIs are typically understood. To structure our discussion, we present a framework for understanding epitope complexity as a spectrum along a series of axes, focusing primarily on 1) epitope biochemical complexity (e.g., epitopes involving N-glycans) and 2) antigen conformational/dynamic complexity (e.g., epitopes with differential properties depending on antigen state or fold-axis). We highlight additional epitope complexity factors including epitope tertiary/quaternary structure, which contribute to epistatic relationships between epitope residues within- or adjacent-to a given epitope, as well as epitope overlap resulting from polyclonal antibody responses, which is relevant when assessing antigenic pressure against a given epitope. Finally, we discuss how these different forms of epitope complexity can limit EPI analyses and therapeutic antibody development, as well as recent efforts to overcome these limitations.
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Affiliation(s)
- Nathaniel L. Miller
- Harvard Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Rahul Raman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Thomas Clark
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ram Sasisekharan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
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New p35 (H3L) Epitope Involved in Vaccinia Virus Neutralization and Its Deimmunization. Viruses 2022; 14:v14061224. [PMID: 35746695 PMCID: PMC9227246 DOI: 10.3390/v14061224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 01/07/2023] Open
Abstract
Vaccinia virus (VACV) is a promising oncolytic agent because it exhibits many characteristic features of an oncolytic virus. However, its effectiveness is limited by the strong antiviral immune response induced by this virus. One possible approach to overcome this limitation is to develop deimmunized recombinant VACV. It is known that VACV p35 is a major protein for B- and T-cell immune response. Despite the relevance of p35, its epitope structure remains insufficiently studied. To determine neutralizing epitopes, a panel of recombinant p35 variants was designed, expressed, and used for mice immunization. Plaque-reduction neutralization tests demonstrated that VACV was only neutralized by sera from mice that were immunized with variants containing both N- and C- terminal regions of p35. This result was confirmed by the depletion of anti-p35 mice sera with recombinant p35 variants. At least nine amino acid residues affecting the immunogenic profile of p35 were identified. Substitutions of seven residues led to disruption of B-cell epitopes, whereas substitutions of two residues resulted in the recognition of the mutant p35 solely by non-neutralizing antibodies.
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3
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Safari M, Jayaraman B, Yang S, Smith C, Fernandes JD, Frankel AD. Functional and structural segregation of overlapping helices in HIV-1. eLife 2022; 11:e72482. [PMID: 35511220 PMCID: PMC9119678 DOI: 10.7554/elife.72482] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Overlapping coding regions balance selective forces between multiple genes. One possible division of nucleotide sequence is that the predominant selective force on a particular nucleotide can be attributed to just one gene. While this arrangement has been observed in regions in which one gene is structured and the other is disordered, we sought to explore how overlapping genes balance constraints when both protein products are structured over the same sequence. We use a combination of sequence analysis, functional assays, and selection experiments to examine an overlapped region in HIV-1 that encodes helical regions in both Env and Rev. We find that functional segregation occurs even in this overlap, with each protein spacing its functional residues in a manner that allows a mutable non-binding face of one helix to encode important functional residues on a charged face in the other helix. Additionally, our experiments reveal novel and critical functional residues in Env and have implications for the therapeutic targeting of HIV-1.
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Affiliation(s)
- Maliheh Safari
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Bhargavi Jayaraman
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Shumin Yang
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- School of Medicine, Tsinghua UniversityBeijingChina
| | - Cynthia Smith
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Jason D Fernandes
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
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4
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Miller NL, Clark T, Raman R, Sasisekharan R. Insights on the mutational landscape of the SARS-CoV-2 Omicron variant receptor-binding domain. Cell Rep Med 2022; 3:100527. [PMID: 35233548 PMCID: PMC8784435 DOI: 10.1016/j.xcrm.2022.100527] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/23/2021] [Accepted: 01/19/2022] [Indexed: 11/27/2022]
Abstract
The Omicron variant features enhanced transmissibility and antibody escape. Here, we describe the Omicron receptor-binding domain (RBD) mutational landscape using amino acid interaction (AAI) networks, which are well suited for interrogating constellations of mutations that function in an epistatic manner. Using AAI, we map Omicron mutations directly and indirectly driving increased escape breadth and depth in class 1-4 antibody epitopes. Further, we present epitope networks for authorized therapeutic antibodies and assess perturbations to each antibody's epitope. Since our initial modeling following the identification of Omicron, these predictions have been realized by experimental findings of Omicron neutralization escape from therapeutic antibodies ADG20, AZD8895, and AZD1061. Importantly, the AAI predicted escape resulting from indirect epitope perturbations was not captured by previous sequence or point mutation analyses. Finally, for several Omicron RBD mutations, we find evidence for a plausible role in enhanced transmissibility via disruption of RBD-down conformational stability at the RBDdown-RBDdown interface.
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Affiliation(s)
- Nathaniel L. Miller
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Thomas Clark
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rahul Raman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ram Sasisekharan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Singapore-MIT Alliance in Research and Technology (SMART), Singapore 138602, Singapore
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5
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Li Z, Khanna M, Grimley SL, Ellenberg P, Gonelli CA, Lee WS, Amarasena TH, Kelleher AD, Purcell DFJ, Kent SJ, Ranasinghe C. Mucosal IL-4R antagonist HIV vaccination with SOSIP-gp140 booster can induce high-quality cytotoxic CD4 +/CD8 + T cells and humoral responses in macaques. Sci Rep 2020; 10:22077. [PMID: 33328567 PMCID: PMC7744512 DOI: 10.1038/s41598-020-79172-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/02/2020] [Indexed: 11/09/2022] Open
Abstract
Inducing humoral, cellular and mucosal immunity is likely to improve the effectiveness of HIV-1 vaccine strategies. Here, we tested a vaccine regimen in pigtail macaques using an intranasal (i.n.) recombinant Fowl Pox Virus (FPV)-gag pol env-IL-4R antagonist prime, intramuscular (i.m.) recombinant Modified Vaccinia Ankara Virus (MVA)-gag pol-IL-4R antagonist boost followed by an i.m SOSIP-gp140 boost. The viral vector-expressed IL-4R antagonist transiently inhibited IL-4/IL-13 signalling at the vaccination site. The SOSIP booster not only induced gp140-specific IgG, ADCC (antibody-dependent cellular cytotoxicity) and some neutralisation activity, but also bolstered the HIV-specific cellular and humoral responses. Specifically, superior sustained systemic and mucosal HIV Gag-specific poly-functional/cytotoxic CD4+ and CD8+ T cells were detected with the IL-4R antagonist adjuvanted strategy compared to the unadjuvanted control. In the systemic compartment elevated Granzyme K expression was linked to CD4+ T cells, whilst Granzyme B/TIA-1 to CD8+ T cells. In contrast, the cytotoxic marker expression by mucosal CD4+ and CD8+ T cells differed according to the mucosal compartment. This vector-based mucosal IL-4R antagonist/SOSIP booster strategy, which promotes cytotoxic mucosal CD4+ T cells at the first line of defence, and cytotoxic CD4+ and CD8+ T cells plus functional antibodies in the blood, may prove valuable in combating mucosal infection with HIV-1 and warrants further investigation.
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Affiliation(s)
- Z Li
- Molecular Mucosal Vaccine Immunology Group, Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - M Khanna
- Molecular Mucosal Vaccine Immunology Group, Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.,Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA
| | - S L Grimley
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - P Ellenberg
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - C A Gonelli
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Wen Shi Lee
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - T H Amarasena
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - A D Kelleher
- Immunovirology and Pathogenesis Program, Kirby Institute, University of New South Wales, Sydney, NSW, 2052, Australia
| | - D F J Purcell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - S J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - C Ranasinghe
- Molecular Mucosal Vaccine Immunology Group, Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.
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Song K, Viskovska M. Design and Engineering of Deimmunized Vaccinia Viral Vectors. Biomedicines 2020; 8:E491. [PMID: 33187060 PMCID: PMC7697509 DOI: 10.3390/biomedicines8110491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 12/31/2022] Open
Abstract
Vaccinia viral (VV) vectors are increasingly used in oncolytic virus therapy and vaccine development for cancer and infectious diseases. However, their effectiveness is hindered by the strong anti-viral immune response induced by the viral vector. In this review, we discuss the strategies to deimmunize vaccinia viral vector. One approach is to mask the virus from the neutralization antibody responses by mapping and eliminating of B-cell epitopes on the viral membrane proteins. The recombinant VVs contain one or more viral glycoproteins with mutations in the neutralizing antibody epitopes, resulting in viral escape from neutralization. In addition, a regulator of complement activation (e.g., CD55) can be expressed on the surface of the virus particle, leading to increased resistance to complement-mediated neutralization.
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Affiliation(s)
| | - Mariya Viskovska
- Icell Kealex Therapeutics, 2450 Holcombe Blvd Suite J, JALBS@TMC, Houston, TX 77021, USA;
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Salimi H, Johnson J, Flores MG, Zhang MS, O'Malley Y, Houtman JC, Schlievert PM, Haim H. The lipid membrane of HIV-1 stabilizes the viral envelope glycoproteins and modulates their sensitivity to antibody neutralization. J Biol Chem 2019; 295:348-362. [PMID: 31757809 DOI: 10.1074/jbc.ra119.009481] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 11/19/2019] [Indexed: 11/06/2022] Open
Abstract
The envelope glycoproteins (Envs) of HIV-1 are embedded in the cholesterol-rich lipid membrane of the virus. Chemical depletion of cholesterol from HIV-1 particles inactivates their infectivity. We observed that diverse HIV-1 strains exhibit a range of sensitivities to such treatment. Differences in sensitivity to cholesterol depletion could not be explained by variation in Env components known to interact with cholesterol, including the cholesterol-recognition motif and cytoplasmic tail of gp41. Using antibody-binding assays, measurements of virus infectivity, and analyses of lipid membrane order, we found that depletion of cholesterol from HIV-1 particles decreases the conformational stability of Env. It enhances exposure of partially cryptic epitopes on the trimer and increases sensitivity to structure-perturbing treatments such as antibodies and cold denaturation. Substitutions in the cholesterol-interacting motif of gp41 induced similar effects as depletion of cholesterol. Surface-acting agents, which are incorporated into the virus lipid membrane, caused similar effects as disruption of the Env-cholesterol interaction. Furthermore, substitutions in gp120 that increased structural stability of Env (i.e. induced a "closed" conformation of the trimer) increased virus resistance to cholesterol depletion and to the surface-acting agents. Collectively, these results indicate a critical contribution of the viral membrane to the stability of the Env trimer and to neutralization resistance against antibodies. Our findings suggest that the potency of poorly neutralizing antibodies, which are commonly elicited in vaccinated individuals, may be markedly enhanced by altering the lipid composition of the viral membrane.
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Affiliation(s)
- Hamid Salimi
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Jacklyn Johnson
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Manuel G Flores
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Michael S Zhang
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Yunxia O'Malley
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Jon C Houtman
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Patrick M Schlievert
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Hillel Haim
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242.
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HIV-1 Envelope Glycoprotein Amino Acids Signatures Associated with Clade B Transmitted/Founder and Recent Viruses. Viruses 2019; 11:v11111012. [PMID: 31683782 PMCID: PMC6893788 DOI: 10.3390/v11111012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/10/2019] [Accepted: 10/29/2019] [Indexed: 12/01/2022] Open
Abstract
Background: HIV-1 transmitted/founder viruses (TF) are selected during the acute phase of infection from a multitude of virions present during transmission. They possess the capacity to establish infection and viral dissemination in a new host. Deciphering the discrete genetic determinant of infectivity in their envelope may provide clues for vaccine design. Methods: One hundred twenty-six clade B HIV-1 consensus envelope sequences from untreated acute and early infected individuals were compared to 105 sequences obtained from chronically infected individuals using next generation sequencing and molecular analyses. Results: We identified an envelope amino acid signature associated with TF viruses. They are more likely to have an isoleucine (I) in position 841 instead of an arginine (R). This mutation of R to I (R841I) in the gp41 cytoplasmic tail (gp41CT), specifically in lentivirus lytic peptides segment 1 (LLP-1), is significantly enriched compared to chronic viruses (OR = 0.2, 95% CI (0.09, 0.44), p = 0.00001). Conversely, a mutation of lysine (K) to isoleucine (I) located in position six (K6I) of the envelope signal peptide was selected by chronic viruses and compared to TF (OR = 3.26, 95% CI (1.76–6.02), p = 0.0001). Conclusions: The highly conserved gp41 CT_ LLP-1 domain plays a major role in virus replication in mediating intracellular traffic and Env incorporation into virions in interacting with encoded matrix protein. The presence of an isoleucine in gp41 in the TF viruses’ envelope may sustain its role in the successful establishment of infection during the acute stage.
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He W, Mazzuca P, Yuan W, Varney K, Bugatti A, Cagnotto A, Giagulli C, Rusnati M, Marsico S, Diomede L, Salmona M, Caruso A, Lu W, Caccuri F. Identification of amino acid residues critical for the B cell growth-promoting activity of HIV-1 matrix protein p17 variants. Biochim Biophys Acta Gen Subj 2018; 1863:13-24. [PMID: 30248376 DOI: 10.1016/j.bbagen.2018.09.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND HIV-1 matrix protein p17 variants (vp17s) detected in HIV-1-infected patients with non-Hodgkin's lymphoma (HIV-NHL) display, differently from the wild-type protein (refp17), B cell growth-promoting activity. Biophysical analysis revealed that vp17s are destabilized as compared to refp17, motivating us to explore structure-function relationships. METHODS We used: biophysical techniques (circular dichroism (CD), nuclear magnetic resonance (NMR) and thermal/GuHCL denaturation) to study protein conformation and stability; Surface plasmon resonance (SPR) to study interactions; Western blot to investigate signaling pathways; and Colony Formation and Soft Agar assays to study B cell proliferation and clonogenicity. RESULTS By forcing the formation of a disulfide bridge between Cys residues at positions 57 and 87 we obtained a destabilized p17 capable of promoting B cell proliferation. This finding prompted us to dissect refp17 to identify the functional epitope. A synthetic peptide (F1) spanning from amino acid (aa) 2 to 21 was found to activate Akt and promote B cell proliferation and clonogenicity. Three positively charged aa (Arg15, Lys18 and Arg20) proved critical for sustaining the proliferative activity of both F1 and HIV-NHL-derived vp17s. Lack of any interaction of F1 with the known refp17 receptors suggests an alternate one involved in cell proliferation. CONCLUSIONS The molecular reasons for the proliferative activity of vp17s, compared to refp17, relies on the exposure of a functional epitope capable of activating Akt. GENERAL SIGNIFICANCE Our findings pave the way for identifying the receptor(s) responsible for B cell proliferation and offer new opportunities to identify novel treatment strategies in combating HIV-related NHL.
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Affiliation(s)
- Wangxiao He
- Center for Translational Medicine, Xi'an Jiaotong University School of Life Science and Technology, Xi'an, China.
| | - Pietro Mazzuca
- Department of Molecular and Translational Medicine, University of Brescia Medical School, Brescia, Italy.
| | - Weirong Yuan
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA.
| | - Kristen Varney
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA.
| | - Antonella Bugatti
- Department of Molecular and Translational Medicine, University of Brescia Medical School, Brescia, Italy.
| | - Alfredo Cagnotto
- IRCCS Istituto Ricerche Farmacologiche "Mario Negri", Milan, Italy.
| | - Cinzia Giagulli
- Department of Molecular and Translational Medicine, University of Brescia Medical School, Brescia, Italy.
| | - Marco Rusnati
- Department of Molecular and Translational Medicine, University of Brescia Medical School, Brescia, Italy.
| | - Stefania Marsico
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata di Rende, Italy.
| | - Luisa Diomede
- IRCCS Istituto Ricerche Farmacologiche "Mario Negri", Milan, Italy.
| | - Mario Salmona
- IRCCS Istituto Ricerche Farmacologiche "Mario Negri", Milan, Italy.
| | - Arnaldo Caruso
- Department of Molecular and Translational Medicine, University of Brescia Medical School, Brescia, Italy.
| | - Wuyuan Lu
- Center for Translational Medicine, Xi'an Jiaotong University School of Life Science and Technology, Xi'an, China; Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA.
| | - Francesca Caccuri
- Department of Molecular and Translational Medicine, University of Brescia Medical School, Brescia, Italy.
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Kumar R, Ozorowski G, Kumar V, Holden LG, Shrivastava T, Patil S, Deshpande S, Ward AB, Bhattacharya J. Characterization of a stable HIV-1 B/C recombinant, soluble, and trimeric envelope glycoprotein (Env) highly resistant to CD4-induced conformational changes. J Biol Chem 2017; 292:15849-15858. [PMID: 28743743 PMCID: PMC5612115 DOI: 10.1074/jbc.m117.803056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/22/2017] [Indexed: 11/06/2022] Open
Abstract
The HIV-1 envelope (Env) is a glycoprotein consisting of a trimer of heterodimers containing gp120 and gp41 subunits that mediates virus entry and is a major target of broadly neutralizing antibodies (bnAbs) developed during infection in some individuals. The engagement of the HIV-1 gp120 glycoprotein to the host CD4 protein triggers conformational changes in gp120 that allow its binding to co-receptors and is necessary for virus entry to establish infection. Native-like HIV-1 Env immunogens representing distinct clades have been proposed to improve immunogenicity. In the present study, we examined the basis of resistance of an HIV-1 B/C recombinant Env (LT5.J4b12C) to non-neutralizing antibodies targeting CD4-induced Env epitopes in the presence of soluble CD4 (sCD4). Using native polyacrylamide gel shift assay and negative-stain EM, we found that the prefusion conformational state of LT5.J4b12C trimeric Env was largely unaffected in the presence of excess sCD4 with most Env trimers appearing to be in a ligand-free state. This resistance to CD4-induced conformational changes was associated with a lower affinity for CD4. Moreover, the LT5.J4b12C trimeric Env preferentially bound to the neutralizing antibodies compared with non-neutralizing antibodies. Taken together, we report on an HIV-1 B/C recombinant, native-like trimeric Env protein that is highly resistant to CD4-induced conformational changes but displays epitopes recognized by a diverse array of bnAbs. Such features make this B/C recombinant trimeric Env a useful addition to the pool of other recently identified native-like HIV-1 Env trimers suitable for use as antigenic bait for bnAb isolation, structural studies, and use as potential immunogens.
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Affiliation(s)
- Rajesh Kumar
- From the HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, International AIDS Vaccine Initiative Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California 92037, and
| | - Vivek Kumar
- From the HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Lauren G Holden
- Department of Integrative Structural and Computational Biology, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, International AIDS Vaccine Initiative Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California 92037, and
| | - Tripti Shrivastava
- From the HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Shilpa Patil
- From the HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Suprit Deshpande
- From the HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, Haryana 121001, India
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, International AIDS Vaccine Initiative Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery, The Scripps Research Institute, La Jolla, California 92037, and
| | - Jayanta Bhattacharya
- From the HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, Haryana 121001, India, .,International AIDS Vaccine Initiative, New York, New York 10004
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11
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Reduced Potency and Incomplete Neutralization of Broadly Neutralizing Antibodies against Cell-to-Cell Transmission of HIV-1 with Transmitted Founder Envs. J Virol 2017; 91:JVI.02425-16. [PMID: 28148796 DOI: 10.1128/jvi.02425-16] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 01/18/2017] [Indexed: 12/28/2022] Open
Abstract
Broadly neutralizing antibodies (bNAbs) have been isolated from HIV-1 patients and can potently block infection of a wide spectrum of HIV-1 subtypes. These antibodies define common epitopes shared by many viral isolates. While bNAbs potently antagonize infection with cell-free virus, inhibition of HIV-1 transmission from infected to uninfected CD4+ T cells through virological synapses (VS) has been found to require greater amounts of antibody. In this study, we examined two well-studied molecular clones and two transmitted/founder (T/F) clones for their sensitivities to a panel of bNAbs in cell-free and cell-to-cell infection assays. We observed resistance of cell-to-cell transmission to antibody neutralization that was reflected not only by reductions of antibody potency but also by decreases in maximum neutralization capacity relative to the levels seen with cell-free infections. BNAbs targeting different epitopes exhibited incomplete neutralization against cell-associated virus with T/F Envs, which was not observed with the cell-free form of the same virus. We further identified the membrane-proximal internal tyrosine-based sorting motif as a determinant that can affect the incomplete neutralization of these T/F clones in cell-to-cell infection. These findings indicate that the signal that affects surface expression and/or internalization of Env from the plasma membrane can modulate the presentation of neutralizing epitopes on infected cells. These results highlight that a fraction of virus can escape from high concentrations of antibody through cell-to-cell infection while remaining sensitive to neutralization in cell-free infection. The ability to fully inhibit cell-to-cell transmission may represent an important consideration in the development of antibodies for treatment or prophylaxis.IMPORTANCE In recent years, isolation of new-generation HIV-1 bNAbs has invigorated HIV vaccine research. These bNAbs display remarkable potency and breadth of coverage against cell-free virus; however, they exhibit a diminished ability to block HIV-1 cell-to-cell transmission. The mechanism(s) by which HIV-1 resists neutralization when transmitting through VS remains uncertain. We examined a panel of bNAbs for their ability to neutralize HIV-1 T/F viruses in cell-to-cell infection assays. We found that some antibodies exhibit not only reduced potency but also decreased maximum neutralization capacity or in vitro efficacy against cell-to-cell infection of HIV-1 with T/F Envs compared to cell-free infection of the same virus. We further identified the membrane-proximal internal tyrosine-based sorting motif YXXL as a determinant that can affect the incomplete neutralization phenotype of these T/F clones. When the maximum neutralization capacity falls short of 100%, this can have a major impact on the ability of antibodies to halt viral replication.
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HIV-1 Cell-Free and Cell-to-Cell Infections Are Differentially Regulated by Distinct Determinants in the Env gp41 Cytoplasmic Tail. J Virol 2015; 89:9324-37. [PMID: 26136566 DOI: 10.1128/jvi.00655-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/23/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The HIV-1 envelope (Env) glycoprotein mediates viral entry during both cell-free and cell-to-cell infection of CD4(+) T cells. The highly conserved long cytoplasmic tail (CT) of Env is required in a cell type-dependent manner for optimal infectivity of cell-free virus. To probe the role of the CT in cell-to-cell infection, we tested a panel of mutations in the CT region that maintain or attenuate cell-free infection to investigate whether the functions of the CT are conserved during cell-free and cell-to-cell infection. The mutations tested included truncations of structural motifs in the gp41 CT and two point mutations in lentiviral lytic peptide 3 (LLP-3) previously described as disrupting the infectivity of cell-free virus. We found that small truncations of 28 to 43 amino acids (aa) or two LLP-3 point mutations, YW_SL and LL_RQ, severely impaired single-round cell-free infectivity 10-fold or more relative to wild-type full-length CT. These mutants showed a modest 2-fold reduction in cell-to-cell infection assays. Conversely, large truncations of 93 to 124 aa severely impaired cell-to-cell infectivity 20-fold or more while resulting in a 50% increase in infectivity of cell-free viral particles when produced in 293T cells. Intermediate truncations of 46 to 90 aa showed profound impairment of both modes of infection. Our results show that the abilities of Env to support cell-free and cell-to-cell infection are genetically distinct. These differences are cell type dependent for large-CT-truncation mutants. Additionally, point mutants in LLP-3 can maintain multiround propagation from cell-to-cell in primary CD4(+) T cells. IMPORTANCE The functions of HIV Env gp41 CT remain poorly understood despite being widely studied in the context of cell-free infection. We have identified domains of the gp41 CT responsible for striking selective deficiencies in either cell-free or cell-to-cell infectivity. These differences may reflect a different intrinsic regulatory influence of the CT on cell-associated versus particle-associated Env or differential interaction with host or viral proteins. Our findings provide novel insight into the key regulatory potential of the gp41 CT in cell-free and cell-to-cell HIV-1 infection, particularly for short-truncation mutants of ≤43 amino acids or mutants with point mutations in the LLP-3 helical domain of the CT, which are able to propagate via cell-to-cell infection in the absence of infectious cell-free virus production. These mutants may also serve as tools to further define the contributions of cell-free and cell-to-cell infection in vitro and in vivo.
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Potempa M, Lee SK, Wolfenden R, Swanstrom R. The triple threat of HIV-1 protease inhibitors. Curr Top Microbiol Immunol 2015; 389:203-41. [PMID: 25778681 DOI: 10.1007/82_2015_438] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Newly released human immunodeficiency virus type 1 (HIV-1) particles obligatorily undergo a maturation process to become infectious. The HIV-1 protease (PR) initiates this step, catalyzing the cleavage of the Gag and Gag-Pro-Pol structural polyproteins. Proper organization of the mature virus core requires that cleavage of these polyprotein substrates proceeds in a highly regulated, specific series of events. The vital role the HIV-1 PR plays in the viral life cycle has made it an extremely attractive target for inhibition and has accordingly fostered the development of a number of highly potent substrate-analog inhibitors. Though the PR inhibitors (PIs) inhibit only the HIV-1 PR, their effects manifest at multiple different stages in the life cycle due to the critical importance of the PR in preparing the virus for these subsequent events. Effectively, PIs masquerade as entry inhibitors, reverse transcription inhibitors, and potentially even inhibitors of post-reverse transcription steps. In this chapter, we review the triple threat of PIs: the intermolecular cooperativity in the form of a cooperative dose-response for inhibition in which the apparent potency increases with increasing inhibition; the pleiotropic effects of HIV-1 PR inhibition on entry, reverse transcription, and post-reverse transcription steps; and their potency as transition state analogs that have the potential for further improvement that could lead to an inability of the virus to evolve resistance in the context of single drug therapy.
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Affiliation(s)
- Marc Potempa
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA
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14
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Tedbury PR, Freed EO. The cytoplasmic tail of retroviral envelope glycoproteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 129:253-84. [PMID: 25595807 DOI: 10.1016/bs.pmbts.2014.10.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Retroviruses comprise a large, diverse group that infects a broad range of host organisms. Pathogenicity varies widely; the human immunodeficiency virus is the causative agent of acquired immunodeficiency syndrome, one of the world's leading infectious causes of death, while many nonhuman retroviruses cause cancer in the host. Retroviruses have been studied intensively, and great strides have been made in understanding aspects of retroviral biology. While the principal functions of the viral structural proteins are well understood, there remain many incompletely characterized domains. One of these is the cytoplasmic tail (CT) of the envelope glycoprotein. Several functions of the CT are highly conserved, whereas other properties are unique to a specific retrovirus. For example, the lentiviruses encode envelope glycoproteins with particularly large cytoplasmic domains. The functions of the long lentiviral envelope CT are still being deciphered. The reported functions of retroviral envelope CTs are discussed in this chapter.
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Affiliation(s)
- Philip R Tedbury
- Virus-Cell Interaction Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA.
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Boscia AL, Akabori K, Benamram Z, Michel JA, Jablin MS, Steckbeck JD, Montelaro RC, Nagle JF, Tristram-Nagle S. Membrane structure correlates to function of LLP2 on the cytoplasmic tail of HIV-1 gp41 protein. Biophys J 2014; 105:657-66. [PMID: 23931314 DOI: 10.1016/j.bpj.2013.06.042] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 06/18/2013] [Accepted: 06/24/2013] [Indexed: 11/30/2022] Open
Abstract
Mutation studies previously showed that the lentivirus lytic peptide (LLP2) sequence of the cytoplasmic C-terminal tail of the HIV-1 gp41 envelope protein inhibited viral-initiated T-cell death and T-cell syncytium formation, at which time in the HIV life cycle the gp41 protein is embedded in the T-cell membrane. In striking contrast, the mutants did not affect virion infectivity, during which time the gp41 protein is embedded in the HIV envelope membrane. To examine the role of LLP2/membrane interactions, we applied synchrotron x-radiation to determine structure of hydrated membranes. We focused on WT LLP2 peptide (+3 charge) and MX2 mutant (-1 charge) with membrane mimics for the T-cell and the HIV-1 membranes. To investigate the influence of electrostatics, cholesterol content, and peptide palmitoylation, we also studied three other LLP2 variants and HIV-1 mimics without negatively charged lipids or cholesterol as well as extracted HIV-1 lipids. All LLP2 peptides bound strongly to T-cell membrane mimics, as indicated by changes in membrane structure and bending. In contrast, none of the weakly bound LLP2 variants changed the HIV-1 membrane mimic structure or properties. This correlates well with, and provides a biophysical basis for, previously published results that reported lack of a mutant effect in HIV virion infectivity in contrast to an inhibitory effect in T-cell syncytium formation. It shows that interaction of LLP2 with the T-cell membrane modulates biological function.
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Affiliation(s)
- Alexander L Boscia
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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16
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Kuhlmann AS, Steckbeck JD, Sturgeon TJ, Craigo JK, Montelaro RC. Unique functional properties of conserved arginine residues in the lentivirus lytic peptide domains of the C-terminal tail of HIV-1 gp41. J Biol Chem 2014; 289:7630-40. [PMID: 24497632 PMCID: PMC3953275 DOI: 10.1074/jbc.m113.529339] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/20/2014] [Indexed: 11/06/2022] Open
Abstract
A previous study from our laboratory reported a preferential conservation of arginine relative to lysine in the C-terminal tail (CTT) of HIV-1 envelope (Env). Despite substantial overall sequence variation in the CTT, specific arginines are highly conserved in the lentivirus lytic peptide (LLP) motifs and are scarcely substituted by lysines, in contrast to gp120 and the ectodomain of gp41. However, to date, no explanation has been provided to explain the selective incorporation and conservation of arginines over lysines in these motifs. Herein, we address the functions in virus replication of the most conserved arginines by performing conservative mutations of arginine to lysine in the LLP1 and LLP2 motifs. The presence of lysine in place of arginine in the LLP1 motif resulted in significant impairment of Env expression and consequently virus replication kinetics, Env fusogenicity, and incorporation. By contrast, lysine exchanges in LLP2 only affected the level of Env incorporation and fusogenicity. Our findings demonstrate that the conservative lysine substitutions significantly affect Env functional properties indicating a unique functional role for the highly conserved arginines in the LLP motifs. These results provide for the first time a functional explanation to the preferred incorporation of arginine, relative to lysine, in the CTT of HIV-1 Env. We propose that these arginines may provide unique functions for Env interaction with viral or cellular cofactors that then influence overall Env functional properties.
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Affiliation(s)
- Anne-Sophie Kuhlmann
- From the Center for Vaccine Research and
- the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Jonathan D. Steckbeck
- From the Center for Vaccine Research and
- the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | | | - Jodi K. Craigo
- From the Center for Vaccine Research and
- the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Ronald C. Montelaro
- From the Center for Vaccine Research and
- the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
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17
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Affranchino JL, González SA. Understanding the process of envelope glycoprotein incorporation into virions in simian and feline immunodeficiency viruses. Viruses 2014; 6:264-83. [PMID: 24441862 PMCID: PMC3917442 DOI: 10.3390/v6010264] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/01/2014] [Accepted: 01/06/2014] [Indexed: 12/18/2022] Open
Abstract
The lentiviral envelope glycoproteins (Env) mediate virus entry by interacting with specific receptors present at the cell surface, thereby determining viral tropism and pathogenesis. Therefore, Env incorporation into the virions formed by assembly of the viral Gag polyprotein at the plasma membrane of the infected cells is a key step in the replication cycle of lentiviruses. Besides being useful models of human immunodeficiency virus (HIV) infections in humans and valuable tools for developing AIDS therapies and vaccines, simian and feline immunodeficiency viruses (SIV and FIV, respectively) are relevant animal retroviruses; the study of which provides important information on how lentiviral replication strategies have evolved. In this review, we discuss the molecular mechanisms underlying the incorporation of the SIV and FIV Env glycoproteins into viral particles.
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Affiliation(s)
- José L Affranchino
- Laboratorio de Virología, CONICET-Universidad de Belgrano (UB), Buenos Aires C1426BMJ, Argentina.
| | - Silvia A González
- Laboratorio de Virología, CONICET-Universidad de Belgrano (UB), Buenos Aires C1426BMJ, Argentina.
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18
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Steckbeck JD, Kuhlmann AS, Montelaro RC. Structural and functional comparisons of retroviral envelope protein C-terminal domains: still much to learn. Viruses 2014; 6:284-300. [PMID: 24441863 PMCID: PMC3917443 DOI: 10.3390/v6010284] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/06/2014] [Indexed: 01/24/2023] Open
Abstract
Retroviruses are a family of viruses that cause a broad range of pathologies in animals and humans, from the apparently harmless, long-term genomic insertion of endogenous retroviruses, to tumors induced by the oncogenic retroviruses and acquired immunodeficiency syndrome (AIDS) resulting from human immunodeficiency virus infection. Disease can be the result of diverse mechanisms, including tumorigenesis induced by viral oncogenes or immune destruction, leading to the gradual loss of CD4 T-cells. Of the virally encoded proteins common to all retroviruses, the envelope (Env) displays perhaps the most diverse functionality. Env is primarily responsible for binding the cellular receptor and for effecting the fusion process, with these functions mediated by protein domains localized to the exterior of the virus. The remaining C-terminal domain may have the most variable functionality of all retroviral proteins. The C-terminal domains from three prototypical retroviruses are discussed, focusing on the different structures and functions, which include fusion activation, tumorigenesis and viral assembly and lifecycle influences. Despite these genetic and functional differences, however, the C-terminal domains of these viruses share a common feature in the modulation of Env ectodomain conformation. Despite their differences, perhaps each system still has information to share with the others.
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Affiliation(s)
- Jonathan D Steckbeck
- Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
| | - Anne-Sophie Kuhlmann
- Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
| | - Ronald C Montelaro
- Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
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Computational prediction of broadly neutralizing HIV-1 antibody epitopes from neutralization activity data. PLoS One 2013; 8:e80562. [PMID: 24312481 PMCID: PMC3846483 DOI: 10.1371/journal.pone.0080562] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 10/03/2013] [Indexed: 11/19/2022] Open
Abstract
Broadly neutralizing monoclonal antibodies effective against the majority of circulating isolates of HIV-1 have been isolated from a small number of infected individuals. Definition of the conformational epitopes on the HIV spike to which these antibodies bind is of great value in defining targets for vaccine and drug design. Drawing on techniques from compressed sensing and information theory, we developed a computational methodology to predict key residues constituting the conformational epitopes on the viral spike from cross-clade neutralization activity data. Our approach does not require the availability of structural information for either the antibody or antigen. Predictions of the conformational epitopes of ten broadly neutralizing HIV-1 antibodies are shown to be in good agreement with new and existing experimental data. Our findings suggest that our approach offers a means to accelerate epitope identification for diverse pathogenic antigens.
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20
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Chenine AL, Wieczorek L, Sanders-Buell E, Wesberry M, Towle T, Pillis DM, Molnar S, McLinden R, Edmonds T, Hirsch I, O’Connell R, McCutchan FE, Montefiori DC, Ochsenbauer C, Kappes JC, Kim JH, Polonis VR, Tovanabutra S. Impact of HIV-1 backbone on neutralization sensitivity: neutralization profiles of heterologous envelope glycoproteins expressed in native subtype C and CRF01_AE backbone. PLoS One 2013; 8:e76104. [PMID: 24312165 PMCID: PMC3843658 DOI: 10.1371/journal.pone.0076104] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 08/20/2013] [Indexed: 01/24/2023] Open
Abstract
Standardized assays to assess vaccine and antiviral drug efficacy are critical for the development of protective HIV-1 vaccines and drugs. These immune assays will be advanced by the development of standardized viral stocks, such as HIV-1 infectious molecular clones (IMC), that i) express a reporter gene, ii) are representative of globally diverse subtypes and iii) are engineered to easily exchange envelope (env) genes for expression of sequences of interest. Thus far, a subtype B IMC backbone expressing Renilla luciferase (LucR), and into which the ectodomain of heterologous env coding sequences can be expressed has been successfully developed but as execution of HIV-1 vaccine efficacy trials shifts increasingly to non-subtype B epidemics (Southern African and Southeast Asia), non-subtype B HIV-1 reagents are needed to support vaccine development. Here we describe two IMCs derived from subtypes C and CRF01_AE HIV-1 primary isolates expressing LucR (IMC.LucR) that were engineered to express heterologous gp160 Envs. 18 constructs expressing various subtypes C and CRF01_AE Envs, mostly acute, in subtype-matched and -unmatched HIV backbones were tested for functionality and neutralization sensitivity. Our results suggest a possible effect of non-env HIV-1 genes on the interaction of Env and neutralizing antibodies and highlight the need to generate a library of IMCs representative of the HIV-1 subtype spectrum to be used as standardized neutralization assay reagents for assessing HIV-1 vaccine efficacy.
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Affiliation(s)
- Agnès-Laurence Chenine
- The Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Military HIV Research Program, Silver Spring, Maryland, United States of America
- * E-mail:
| | - Lindsay Wieczorek
- The Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Eric Sanders-Buell
- The Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Maggie Wesberry
- The Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Teresa Towle
- The Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Devin M. Pillis
- The Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Sebastian Molnar
- The Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Robert McLinden
- The Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Military HIV Research Program, Silver Spring, Maryland, United States of America
| | - Tara Edmonds
- University of Alabama, Birmingham, Birmingham, Alabama, United States of America
| | - Ivan Hirsch
- Inserm UMR891, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Robert O’Connell
- Military HIV Research Program, Silver Spring, Maryland, United States of America
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | | | | | | | - John C. Kappes
- University of Alabama, Birmingham, Birmingham, Alabama, United States of America
| | - Jerome H. Kim
- Military HIV Research Program, Silver Spring, Maryland, United States of America
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Victoria R. Polonis
- Military HIV Research Program, Silver Spring, Maryland, United States of America
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Sodsai Tovanabutra
- The Henry M. Jackson Foundation, Bethesda, Maryland, United States of America
- Military HIV Research Program, Silver Spring, Maryland, United States of America
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21
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Bakouche N, Vandenbroucke AT, Goubau P, Ruelle J. Study of the HIV-2 Env cytoplasmic tail variability and its impact on Tat, Rev and Nef. PLoS One 2013; 8:e79129. [PMID: 24223892 PMCID: PMC3815105 DOI: 10.1371/journal.pone.0079129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/18/2013] [Indexed: 11/24/2022] Open
Abstract
Background The HIV-2 env’s 3’ end encodes the cytoplasmic tail (CT) of the Env protein. This genomic region also encodes the rev, Tat and Nef protein in overlapping reading frames. We studied the variability in the CT coding region in 46 clinical specimens and in 2 reference strains by sequencing and by culturing. The aims were to analyse the variability of Env CT and the evolution of proteins expressed from overlapping coding sequences. Results A 70% reduction of the length of the CT region affected the HIV-2 ROD and EHO strains invitro due to a premature stop codon in the env gene. In clinical samples this wasn’t observed, but the CT length varied due to insertions and deletions. We noted 3 conserved and 3 variable regions in the CT. The conserved regions were those containing residues involved in Env endocytosis, the potential HIV-2 CT region implicated in the NF-kB activation and the potential end of the lentiviral lytic peptide one. The variable regions were the potential HIV-2 Kennedy region, the potential lentiviral lytic peptide two and the beginning of the potential lentiviral lytic peptide one. A very hydrophobic region was coded downstream of the premature stop codon observed invitro, suggesting a membrane spanning region. Interestingly, the nucleotides that are responsible for the variability of the CT don’t impact rev and Nef. However, in the Kennedy-like coding region variability resulted only from nucleotide changes that impacted Env and Tat together. Conclusion The HIV-2 Env, Tat and Rev C-terminal part are subject to major length variations in both clinical samples and cultured strains. The HIV-2 Env CT contains variable and conserved regions. These regions don’t affect the rev and Nef amino acids composition which evolves independently. In contrast, Tat co-evolves with the Env CT.
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Affiliation(s)
- Nordine Bakouche
- Institut de recherche expérimentale et clinique, Université catholique de Louvain, Brussels, Belgium
| | | | - Patrick Goubau
- Institut de recherche expérimentale et clinique, Université catholique de Louvain, Brussels, Belgium
| | - Jean Ruelle
- Institut de recherche expérimentale et clinique, Université catholique de Louvain, Brussels, Belgium
- * E-mail:
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A next-generation cleaved, soluble HIV-1 Env trimer, BG505 SOSIP.664 gp140, expresses multiple epitopes for broadly neutralizing but not non-neutralizing antibodies. PLoS Pathog 2013; 9:e1003618. [PMID: 24068931 PMCID: PMC3777863 DOI: 10.1371/journal.ppat.1003618] [Citation(s) in RCA: 740] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 07/30/2013] [Indexed: 01/17/2023] Open
Abstract
A desirable but as yet unachieved property of a human immunodeficiency virus type 1 (HIV-1) vaccine candidate is the ability to induce broadly neutralizing antibodies (bNAbs). One approach to the problem is to create trimeric mimics of the native envelope glycoprotein (Env) spike that expose as many bNAb epitopes as possible, while occluding those for non-neutralizing antibodies (non-NAbs). Here, we describe the design and properties of soluble, cleaved SOSIP.664 gp140 trimers based on the subtype A transmitted/founder strain, BG505. These trimers are highly stable, more so even than the corresponding gp120 monomer, as judged by differential scanning calorimetry. They are also homogenous and closely resemble native virus spikes when visualized by negative stain electron microscopy (EM). We used several techniques, including ELISA and surface plasmon resonance (SPR), to determine the relationship between the ability of monoclonal antibodies (MAbs) to bind the soluble trimers and neutralize the corresponding virus. In general, the concordance was excellent, in that virtually all bNAbs against multiple neutralizing epitopes on HIV-1 Env were highly reactive with the BG505 SOSIP.664 gp140 trimers, including quaternary epitopes (CH01, PG9, PG16 and PGT145). Conversely, non-NAbs to the CD4-binding site, CD4-induced epitopes or gp41ECTO did not react with the trimers, even when their epitopes were present on simpler forms of Env (e.g. gp120 monomers or dissociated gp41 subunits). Three non-neutralizing MAbs to V3 epitopes did, however, react strongly with the trimers but only by ELISA, and not at all by SPR and to only a limited extent by EM. These new soluble trimers are useful for structural studies and are being assessed for their performance as immunogens.
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Steckbeck JD, Sun C, Sturgeon TJ, Montelaro RC. Detailed topology mapping reveals substantial exposure of the "cytoplasmic" C-terminal tail (CTT) sequences in HIV-1 Env proteins at the cell surface. PLoS One 2013; 8:e65220. [PMID: 23724133 PMCID: PMC3664582 DOI: 10.1371/journal.pone.0065220] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 04/24/2013] [Indexed: 01/20/2023] Open
Abstract
Substantial controversy surrounds the membrane topology of the HIV-1 gp41 C-terminal tail (CTT). While few studies have been designed to directly address the topology of the CTT, results from envelope (Env) protein trafficking studies suggest that the CTT sequence is cytoplasmically localized, as interactions with intracellular binding partners are required for proper Env targeting. However, previous studies from our lab demonstrate the exposure of a short CTT sequence, the Kennedy epitope, at the plasma membrane of intact Env-expressing cells, the exposure of which is not observed on viral particles. To address the topology of the entire CTT sequence, we serially replaced CTT sequences with a VSV-G epitope tag sequence and examined reactivity of cell- and virion-surface Env to an anti-VSV-G monoclonal antibody. Our results demonstrate that the majority of the CTT sequence is accessible to antibody binding on the surface of Env expressing cells, and that the CTT-exposed Env constitutes 20–50% of the cell-surface Env. Cell surface CTT exposure was also apparent in virus-infected cells. Passive transfer of Env through cell culture media to Env negative (non-transfected) cells was not responsible for the apparent cell surface CTT exposure. In contrast to the cell surface results, CTT-exposed Env was not detected on infectious pseudoviral particles containing VSV-G-substituted Env. Finally, a monoclonal antibody directed to the Kennedy epitope neutralized virus in a temperature-dependent manner in a post-attachment neutralization assay. Collectively, these results suggest that the membrane topology of the HIV gp41 CTT is more complex than the widely accepted intracytoplasmic model.
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Affiliation(s)
- Jonathan D. Steckbeck
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Chengqun Sun
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Timothy J. Sturgeon
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ronald C. Montelaro
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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Clustering and mobility of HIV-1 Env at viral assembly sites predict its propensity to induce cell-cell fusion. J Virol 2013; 87:7516-25. [PMID: 23637402 DOI: 10.1128/jvi.00790-13] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
HIV-1 Env mediates virus attachment to and fusion with target cell membranes, and yet, while Env is still situated at the plasma membrane of the producer cell and before its incorporation into newly formed particles, Env already interacts with the viral receptor CD4 on target cells, thus enabling the formation of transient cell contacts that facilitate the transmission of viral particles. During this first encounter with the receptor, Env must not induce membrane fusion, as this would prevent the producer cell and the target cell from separating upon virus transmission, but how Env's fusion activity is controlled remains unclear. To gain a better understanding of the Env regulation that precedes viral transmission, we examined the nanoscale organization of Env at the surface of producer cells. Utilizing superresolution microscopy (stochastic optical reconstruction microscopy [STORM]) and fluorescence recovery after photobleaching (FRAP), we quantitatively assessed the clustering and dynamics of Env upon its arrival at the plasma membrane. We found that Gag assembly induced the aggregation of small Env clusters into larger domains and that these domains were completely immobile. Truncation of the cytoplasmic tail (CT) of Env abrogated Gag's ability to induce Env clustering and restored Env mobility at assembly sites, both of which correlated with increased Env-induced fusion of infected and uninfected cells. Hence, while Env trapping by Gag secures Env incorporation into viral particles, Env clustering and its sequestration at assembly sites likely also leads to the repression of its fusion function, and thus, by preventing the formation of syncytia, Gag helps to secure efficient transfer of viral particles to target cells.
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Steckbeck JD, Kuhlmann AS, Montelaro RC. C-terminal tail of human immunodeficiency virus gp41: functionally rich and structurally enigmatic. J Gen Virol 2012; 94:1-19. [PMID: 23079381 PMCID: PMC3542723 DOI: 10.1099/vir.0.046508-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome (AIDS) pandemic is amongst the most important current worldwide public health threats. While much research has been focused on AIDS vaccines that target the surface viral envelope (Env) protein, including gp120 and the gp41 ectodomain, the C-terminal tail (CTT) of gp41 has received relatively little attention. Despite early studies highlighting the immunogenicity of a particular CTT sequence, the CTT has been classically portrayed as a type I membrane protein limited to functioning in Env trafficking and virion incorporation. Recent studies demonstrate, however, that the Env CTT has other important functions. The CTT has been shown to additionally modulate Env ectodomain structure on the cell and virion surface, affect Env reactivity and viral sensitivity to conformation-dependent neutralizing antibodies, and alter cell–cell and virus–cell fusogenicity of Env. This review provides an overview of the Env structure and function with a particular emphasis on the CTT and recent studies that highlight its functionally rich nature.
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Affiliation(s)
- Jonathan D. Steckbeck
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Anne-Sophie Kuhlmann
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Ronald C. Montelaro
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15261, USA
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA, 15261, USA
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26
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Bhowmick A, Salunke DM. Limited conformational flexibility in the paratope may be responsible for degenerate specificity of HIV epitope recognition. Int Immunol 2012; 25:77-90. [DOI: 10.1093/intimm/dxs093] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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27
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Checkley MA, Luttge BG, Freed EO. HIV-1 envelope glycoprotein biosynthesis, trafficking, and incorporation. J Mol Biol 2011; 410:582-608. [PMID: 21762802 PMCID: PMC3139147 DOI: 10.1016/j.jmb.2011.04.042] [Citation(s) in RCA: 328] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Revised: 04/14/2011] [Accepted: 04/15/2011] [Indexed: 12/13/2022]
Abstract
The HIV-1 envelope (Env) glycoproteins play an essential role in the virus replication cycle by mediating the fusion between viral and cellular membranes during the entry process. The Env glycoproteins are synthesized as a polyprotein precursor (gp160) that is cleaved by cellular proteases to the mature surface glycoprotein gp120 and the transmembrane glycoprotein gp41. During virus assembly, the gp120/gp41 complex is incorporated as heterotrimeric spikes into the lipid bilayer of nascent virions. These gp120/gp41 complexes then initiate the infection process by binding receptor and coreceptor on the surface of target cells. Much is currently known about the HIV-1 Env glycoprotein trafficking pathway and the structure of gp120 and the extracellular domain of gp41. However, the mechanism by which the Env glycoprotein complex is incorporated into virus particles remains incompletely understood. Genetic data support a major role for the cytoplasmic tail of gp41 and the matrix domain of Gag in Env glycoprotein incorporation. Still to be defined are the identities of host cell factors that may promote Env incorporation and the role of specific membrane microdomains in this process. Here, we review our current understanding of HIV-1 Env glycoprotein trafficking and incorporation into virions.
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Affiliation(s)
- Mary Ann Checkley
- Virus-Cell Interaction Section, HIV Drug Resistance Program National Cancer Institute Frederick, MD 21702
| | - Benjamin G. Luttge
- Virus-Cell Interaction Section, HIV Drug Resistance Program National Cancer Institute Frederick, MD 21702
| | - Eric O. Freed
- Virus-Cell Interaction Section, HIV Drug Resistance Program National Cancer Institute Frederick, MD 21702
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Electrochemical analysis of HIV-1 reverse transcriptase serum level: Exploiting protein binding to a functionalized nanostructured surface. Talanta 2011; 85:770-8. [DOI: 10.1016/j.talanta.2011.04.070] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 04/26/2011] [Accepted: 04/27/2011] [Indexed: 11/21/2022]
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29
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Steckbeck JD, Craigo JK, Barnes CO, Montelaro RC. Highly conserved structural properties of the C-terminal tail of HIV-1 gp41 protein despite substantial sequence variation among diverse clades: implications for functions in viral replication. J Biol Chem 2011; 286:27156-66. [PMID: 21659530 DOI: 10.1074/jbc.m111.258855] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Although the HIV-1 Env gp120 and gp41 ectodomain have been extensively characterized in terms of structure and function, similar characterizations of the C-terminal tail (CTT) of HIV gp41 remain relatively limited and contradictory. The current study was designed to examine in detail CTT sequence conservation relative to gp120 and the gp41 ectodomain and to examine the conservation of predicted physicochemical and structural properties across a number of divergent HIV clades and groups. Results demonstrate that CTT sequences display intermediate levels of sequence evolution and diversity in comparison to the more diverse gp120 and the more conserved gp41 ectodomain. Despite the relatively high level of CTT sequence variation, the physicochemical properties of the lentivirus lytic peptide domains (LLPs) within the CTT are evidently highly conserved across clades/groups. Additionally, predictions using PEP-FOLD indicate a high level of structural similarity in the LLP regions that was confirmed by circular dichroism measurements of secondary structure of LLP peptides from clades B, C, and group O. Results demonstrate that LLP peptides adopt helical structure in the presence of SDS or trifluoroethanol but are predominantly unstructured in aqueous buffer. Thus, these data for the first time demonstrate strong conservations of characteristic CTT physicochemical and structural properties despite substantial sequence diversity, apparently indicating a delicate balance between evolutionary pressures and the conservation of CTT structure and associated functional roles in virus replication.
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Affiliation(s)
- Jonathan D Steckbeck
- Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261, USA
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30
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A bioorganometallic approach for rapid electrochemical analysis of human immunodeficiency virus type-1 reverse transcriptase in serum. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.03.063] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Labib M, Shipman PO, Martić S, Kraatz HB. Towards an early diagnosis of HIV infection: an electrochemical approach for detection ofHIV-1 reverse transcriptase enzyme. Analyst 2011; 136:708-15. [DOI: 10.1039/c0an00741b] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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32
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Steckbeck JD, Sun C, Sturgeon TJ, Montelaro RC. Topology of the C-terminal tail of HIV-1 gp41: differential exposure of the Kennedy epitope on cell and viral membranes. PLoS One 2010; 5:e15261. [PMID: 21151874 PMCID: PMC2998427 DOI: 10.1371/journal.pone.0015261] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 11/03/2010] [Indexed: 01/05/2023] Open
Abstract
The C-terminal tail (CTT) of the HIV-1 gp41 envelope (Env) protein is increasingly recognized as an important determinant of Env structure and functional properties, including fusogenicity and antigenicity. While the CTT has been commonly referred to as the “intracytoplasmic domain” based on the assumption of an exclusive localization inside the membrane lipid bilayer, early antigenicity studies and recent biochemical analyses have produced a credible case for surface exposure of specific CTT sequences, including the classical “Kennedy epitope” (KE) of gp41, leading to an alternative model of gp41 topology with multiple membrane-spanning domains. The current study was designed to test these conflicting models of CTT topology by characterizing the exposure of native CTT sequences and substituted VSV-G epitope tags in cell- and virion-associated Env to reference monoclonal antibodies (MAbs). Surface staining and FACS analysis of intact, Env-expressing cells demonstrated that the KE is accessible to binding by MAbs directed to both an inserted VSV-G epitope tag and the native KE sequence. Importantly, the VSV-G tag was only reactive when inserted into the KE; no reactivity was observed in cells expressing Env with the VSV-G tag inserted into the LLP2 domain. In contrast to cell-surface expressed Env, no binding of KE-directed MAbs was observed to Env on the surface of intact virions using either immune precipitation or surface plasmon resonance spectroscopy. These data indicate apparently distinct CTT topologies for virion- and cell-associated Env species and add to the case for a reconsideration of CTT topology that is more complex than currently envisioned.
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Affiliation(s)
- Jonathan D. Steckbeck
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chengqun Sun
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Timothy J. Sturgeon
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ronald C. Montelaro
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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33
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Kirchherr JL, Hamilton J, Lu X, Gnanakaran S, Muldoon M, Daniels M, Kasongo W, Chalwe V, Mulenga C, Mwananyanda L, Musonda RM, Yuan X, Montefiori DC, Korber BT, Haynes BF, Gao F. Identification of amino acid substitutions associated with neutralization phenotype in the human immunodeficiency virus type-1 subtype C gp120. Virology 2010; 409:163-74. [PMID: 21036380 DOI: 10.1016/j.virol.2010.09.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 08/22/2010] [Accepted: 09/27/2010] [Indexed: 10/18/2022]
Abstract
Neutralizing antibodies (Nabs) are thought to play an important role in prevention and control of HIV-1 infection and should be targeted by an AIDS vaccine. It is critical to understand how HIV-1 induces Nabs by analyzing viral sequences in both tested viruses and sera. Neutralization susceptibility to antibodies in autologous and heterologous plasma was determined for multiple Envs (3-6) from each of 15 subtype-C-infected individuals. Heterologous neutralization was divided into two distinct groups: plasma with strong, cross-reactive neutralization (n=9) and plasma with weak neutralization (n=6). Plasma with cross-reactive heterologous Nabs also more potently neutralized contemporaneous autologous viruses. Analysis of Env sequences in plasma from both groups revealed a three-amino-acid substitution pattern in the V4 region that was associated with greater neutralization potency and breadth. Identification of such potential neutralization signatures may have important implications for the development of HIV-1 vaccines capable of inducing Nabs to subtype C HIV-1.
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Affiliation(s)
- Jennifer L Kirchherr
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
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Abstract
PURPOSE OF REVIEW HIV-1 neutralizing antibodies are directed to the Envelope glycoprotein trimer on the surface of the virion and block entry into target cells in vitro. During infection, closely related but distinct variants arise in infected individuals, and the interplay of Envelope and neutralizing antibodies is a dynamic process. Vaccines that generate neutralizing antibodies and drugs that inhibit entry must address the issue of variation of subtypes worldwide. The purpose of this review is to summarize major advances in the neutralizing antibody field published during 2005 and early 2006. RECENT FINDINGS The main themes that are covered in this review include new findings in the development of neutralizing antibodies during natural and experimental infection, characterization of monoclonal antibodies with neutralizing activity, Envelope structural data, the development of novel Envelope constructs, and novel approaches designed to generate neutralizing antibodies by vaccination. SUMMARY Advances leading to a better understanding of the structure of the Envelope and the character of neutralizing antibodies that develop during the course of infection have provided important clues to guide the design of better immunogens and drugs to block attachment. These findings have implications for prophylactic and therapeutic vaccine approaches, drugs, and antibody-based therapies to reduce HIV transmission.
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35
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Matrix and envelope coevolution revealed in a patient monitored since primary infection with human immunodeficiency virus type 1. J Virol 2009; 83:9875-89. [PMID: 19625403 DOI: 10.1128/jvi.01213-09] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Lentiviruses, including human immunodeficiency virus type 1 (HIV-1), typically encode envelope glycoproteins (Env) with long cytoplasmic tails (CTs). The strong conservation of CT length in primary isolates of HIV-1 suggests that this factor plays a key role in viral replication and persistence in infected patients. However, we report here the emergence and dominance of a primary HIV-1 variant carrying a natural 20-amino-acid truncation of the CT in vivo. We demonstrated that this truncation was deleterious for viral replication in cell culture. We then identified a compensatory amino acid substitution in the matrix protein that reversed the negative effects of CT truncation. The loss or rescue of infectivity depended on the level of Env incorporation into virus particles. Interestingly, we found that a virus mutant with defective Env incorporation was able to spread by cell-to-cell transfer. The effects on viral infectivity of compensation between the CT and the matrix protein have been suggested by in vitro studies based on T-cell laboratory-adapted virus mutants, but we provide here the first demonstration of the natural occurrence of similar mechanisms in an infected patient. Our findings provide insight into the potential of HIV-1 to evolve in vivo and its ability to overcome major structural alterations.
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36
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Kulkarni SS, Lapedes A, Tang H, Gnanakaran S, Daniels MG, Zhang M, Bhattacharya T, Li M, Polonis VR, McCutchan FE, Morris L, Ellenberger D, Butera ST, Bollinger RC, Korber BT, Paranjape RS, Montefiori DC. Highly complex neutralization determinants on a monophyletic lineage of newly transmitted subtype C HIV-1 Env clones from India. Virology 2009; 385:505-20. [PMID: 19167740 PMCID: PMC2677301 DOI: 10.1016/j.virol.2008.12.032] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 12/01/2008] [Accepted: 12/16/2008] [Indexed: 10/21/2022]
Abstract
Little is known about the neutralization properties of HIV-1 in India to optimally design and test vaccines. For this reason, a functional Env clone was obtained from each of ten newly acquired, heterosexually transmitted HIV-1 infections in Pune, Maharashtra. These clones formed a phylogenetically distinct genetic lineage within subtype C. As Env-pseudotyped viruses the clones were mostly resistant to IgG1b12, 2G12 and 2F5 but all were sensitive to 4E10. When compared to a large multi-subtype panel of Env-pseudotyped viruses (subtypes B, C and CRF02_AG) in neutralization assays with a multi-subtype panel of HIV-1-positive plasma samples, the Indian Envs were remarkably complex. With the exception of the Indian Envs, results of a hierarchical clustering analysis showed a strong subtype association with the patterns of neutralization susceptibility. From these patterns we were able to identify 19 neutralization cluster-associated amino acid signatures in gp120 and 14 signatures in the ectodomain and cytoplasmic tail of gp41. We conclude that newly transmitted Indian Envs are antigenically complex in spite of close genetic similarity. Delineation of neutralization-associated amino acid signatures provides a deeper understanding of the antigenic structure of HIV-1 Env.
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Affiliation(s)
| | - Alan Lapedes
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Haili Tang
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710
| | - S. Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Marcus G. Daniels
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Ming Zhang
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Ming Li
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710
| | - Victoria R. Polonis
- Walter Reed Army Institute of Research and the Henry M. Jackson Foundation, Rockville, Maryland 20850
| | - Francine E. McCutchan
- Walter Reed Army Institute of Research and the Henry M. Jackson Foundation, Rockville, Maryland 20850
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | | | | | - Robert C. Bollinger
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Bette T. Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico
| | | | - David C. Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710
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Xiao L, Zhang J, Yin Y, Chen C, Li K, Chang A, Sirois P. Molecular diagnosis of HIV and relevant novel technologies in mutation analysis. Biotechnol Adv 2008; 26:389-97. [DOI: 10.1016/j.biotechadv.2008.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 04/01/2008] [Accepted: 04/27/2008] [Indexed: 12/12/2022]
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White JM, Delos SE, Brecher M, Schornberg K. Structures and mechanisms of viral membrane fusion proteins: multiple variations on a common theme. Crit Rev Biochem Mol Biol 2008; 43:189-219. [PMID: 18568847 DOI: 10.1080/10409230802058320] [Citation(s) in RCA: 665] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recent work has identified three distinct classes of viral membrane fusion proteins based on structural criteria. In addition, there are at least four distinct mechanisms by which viral fusion proteins can be triggered to undergo fusion-inducing conformational changes. Viral fusion proteins also contain different types of fusion peptides and vary in their reliance on accessory proteins. These differing features combine to yield a rich diversity of fusion proteins. Yet despite this staggering diversity, all characterized viral fusion proteins convert from a fusion-competent state (dimers or trimers, depending on the class) to a membrane-embedded homotrimeric prehairpin, and then to a trimer-of-hairpins that brings the fusion peptide, attached to the target membrane, and the transmembrane domain, attached to the viral membrane, into close proximity thereby facilitating the union of viral and target membranes. During these conformational conversions, the fusion proteins induce membranes to progress through stages of close apposition, hemifusion, and then the formation of small, and finally large, fusion pores. Clearly, highly divergent proteins have converged on the same overall strategy to mediate fusion, an essential step in the life cycle of every enveloped virus.
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Affiliation(s)
- Judith M White
- Department of Cell Biology, University of Virginia, Charlottesville, Virginia 22908-0732, USA.
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39
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Gray ES, Moore PL, Bibollet-Ruche F, Li H, Decker JM, Meyers T, Shaw GM, Morris L. 4E10-resistant variants in a human immunodeficiency virus type 1 subtype C-infected individual with an anti-membrane-proximal external region-neutralizing antibody response. J Virol 2008; 82:2367-75. [PMID: 18094155 PMCID: PMC2258954 DOI: 10.1128/jvi.02161-07] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2007] [Accepted: 12/12/2007] [Indexed: 01/24/2023] Open
Abstract
The broadly neutralizing monoclonal antibody (MAb) 4E10 recognizes a linear epitope in the C terminus of the membrane-proximal external region (MPER) of gp41. This epitope is particularly attractive for vaccine design because it is highly conserved among human immunodeficiency virus type 1 (HIV-1) strains and neutralization escape in vivo has not been observed. Multiple env genes were cloned from an HIV-1 subtype C virus isolated from a 7-year-old perinatally infected child who had anti-MPER neutralizing antibodies. One clone (TM20.13) was resistant to 4E10 neutralization as a result of an F673L substitution in the MPER. Frequency analysis showed that F673L was present in 33% of the viral variants and in all cases was linked to the presence of an intact 2F5 epitope. Two other envelope clones were sensitive to 4E10 neutralization, but TM20.5 was 10-fold less sensitive than TM20.6. Substitutions at positions 674 and 677 within the MPER rendered TM20.5 more sensitive to 4E10 but had no effect on TM20.6. Using chimeric and mutant constructs of these two variants, we further demonstrated that the lentivirus lytic peptide-2 domain in the cytoplasmic tail affected the accessibility of the 4E10 epitope, as well as virus infectivity. Collectively, these genetic changes in the face of a neutralizing antibody response to the MPER strongly suggested immune escape from antibody responses targeting this region.
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Affiliation(s)
- Elin S Gray
- National Institute for Communicable Diseases, Johannesburg, Private Bag X4, Sandringham 2131, Johannesburg, South Africa
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Valas S, Rolland M, Perrin C, Perrin G, Mamoun RZ. Characterization of a new 5' splice site within the caprine arthritis encephalitis virus genome: evidence for a novel auxiliary protein. Retrovirology 2008; 5:22. [PMID: 18312636 PMCID: PMC2291067 DOI: 10.1186/1742-4690-5-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 02/29/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lentiviral genomes encode multiple structural and regulatory proteins. Expression of the full complement of viral proteins is accomplished in part by alternative splicing of the genomic RNA. Caprine arthritis encephalitis virus (CAEV) and maedi-visna virus (MVV) are two highly related small-ruminant lentiviruses (SRLVs) that infect goats and sheep. Their genome seems to be less complex than those of primate lentiviruses since SRLVs encode only three auxiliary proteins, namely, Tat, Rev, and Vif, in addition to the products of gag, pol, and env genes common to all retroviruses. Here, we investigated the central part of the SRLV genome to identify new splice elements and their relevance in viral mRNA and protein expression. RESULTS We demonstrated the existence of a new 5' splice (SD) site located within the central part of CAEV genome, 17 nucleotides downstream from the SD site used for the rev mRNA synthesis, and perfectly conserved among SRLV strains. This new SD site was found to be functional in both transfected and infected cells, leading to the production of a transcript containing an open reading frame generated by the splice junction with the 3' splice site used for the rev mRNA synthesis. This open reading frame encodes two major protein isoforms of 18- and 17-kDa, named Rtm, in which the N-terminal domain shared by the Env precursor and Rev proteins is fused to the entire cytoplasmic tail of the transmembrane glycoprotein. Immunoprecipitations using monospecific antibodies provided evidence for the expression of the Rtm isoforms in infected cells. The Rtm protein interacts specifically with the cytoplasmic domain of the transmembrane glycoprotein in vitro, and its expression impairs the fusion activity of the Env protein. CONCLUSION The characterization of a novel CAEV protein, named Rtm, which is produced by an additional multiply-spliced mRNA, indicated that the splicing pattern of CAEV genome is more complex than previously reported, generating greater protein diversity. The high conservation of the SD site used for the rtm mRNA synthesis among CAEV and MVV strains strongly suggests that the Rtm protein plays a role in SRLV propagation in vivo, likely by competing with Env protein functions.
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Affiliation(s)
- Stephen Valas
- AFSSA-Niort, Laboratoire d'Etudes et de Recherches Caprines, 79012 Niort, France.
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41
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Elena SF, Sanjuán R. Virus Evolution: Insights from an Experimental Approach. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2007. [DOI: 10.1146/annurev.ecolsys.38.091206.095637] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 València, Spain;
| | - Rafael Sanjuán
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, 46022 València, Spain;
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Zhu Y, Lu L, Chao L, Chen YH. Important changes in biochemical properties and function of mutated LLP12 domain of HIV-1 gp41. Chem Biol Drug Des 2007; 70:311-8. [PMID: 17850282 PMCID: PMC7188357 DOI: 10.1111/j.1747-0285.2007.00564.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The human immunodeficiency virus type 1 gp41 possesses an unusually long and conserved cytoplasmic region. Mutations in the LLP12 domain in this region have been shown to significantly affect viral competence. It is likely that the impaired infectivity of this mutated virus involves certain biochemical aspects of the peptide LLP12. To test our assumptions, some important biochemical properties and functions of LLP12 domain were studied. The recombinant peptide LLP12 (LLP12 domain on gp41, including LLP1 and LLP2 domains) was prepared via bacterial expression system. Biochemical analysis directly demonstrated its multimeric potential and membrane-binding ability. Several arginine residues in this domain were observed to be extremely highly conserved. Interestingly, the LLP12 mutants constructed by substitution of these arginine residues with alanine (separate mutations in LLP1 or LLP2 or both) showed apparent decreases in their multimeric potential and membrane-binding ability. Comparing our results with independent data on human immunodeficiency virus from other researchers, it appears that both the multimeric state and the membrane affinity of the LLP12 domain of human immunodeficiency virus type 1 gp41 could be involved in viral competence and in the mechanism of human immunodeficiency virus type 1 Env-mediated cell fusion.
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Affiliation(s)
- Yun Zhu
- Laboratory of Immunology, Department of Biology, Tsinghua University and Protein Science Laboratory of the Ministry of Education, Beijing 100084, China
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43
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Chen P, Hübner W, Spinelli MA, Chen BK. Predominant mode of human immunodeficiency virus transfer between T cells is mediated by sustained Env-dependent neutralization-resistant virological synapses. J Virol 2007; 81:12582-95. [PMID: 17728240 PMCID: PMC2169007 DOI: 10.1128/jvi.00381-07] [Citation(s) in RCA: 334] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Cell-free human immunodeficiency virus type 1 (HIV-1) can initiate infections, but contact between infected and uninfected T cells can enhance viral spread through intercellular structures called virological synapses (VS). The relative contribution of VS to cell-free viral transfer has not been carefully measured. Using an ultrasensitive, fluorescent virus transfer assay, we estimate that when VS between HIV-expressing Jurkat T cells and primary CD4(+) T cells are formed, cell-associated transfer of virus is 18,000-fold more efficient than uptake of cell-free virus. Furthermore, in contrast to cell-free virus uptake, the VS deposits virus rapidly into focal, trypsin-resistant compartments in target T cells. This massive virus internalization requires Env-CD4 receptor interactions but is resistant to inhibition by patient-derived neutralizing antisera that inhibit homologous cell-free virus. Deleting the Env cytoplasmic tail does not abrogate VS-mediated transfer, but it renders the VS sensitive to neutralizing antibodies, suggesting that the tail limits exposure of VS-neutralizing epitopes on the surface of infected cells. Dynamic live imaging of the VS reveals that HIV-expressing cells are polarized and make sustained, Env-dependent contacts with target cells through uropod-like structures. The polarized T-cell morphology, Env-CD4 coordinated adhesion, and viral transfer from HIV-infected to uninfected cells suggest that VS allows HIV-1 to evade antibody neutralization and to disseminate efficiently. Future studies will discern to what extent this massive viral transfer contributes to productive infection or viral dissemination through the migration of virus-carrying T cells.
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Affiliation(s)
- Ping Chen
- Department of Medicine, Division of Infectious Diseases, Immunology Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
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44
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Kirchherr JL, Lu X, Kasongo W, Chalwe V, Mwananyanda L, Musonda RM, Xia SM, Scearce RM, Liao HX, Montefiori DC, Haynes BF, Gao F. High throughput functional analysis of HIV-1 env genes without cloning. J Virol Methods 2007; 143:104-11. [PMID: 17416428 PMCID: PMC1948023 DOI: 10.1016/j.jviromet.2007.02.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 02/23/2007] [Accepted: 02/27/2007] [Indexed: 11/16/2022]
Abstract
Functional human immunodeficiency virus type 1 (HIV-1) env genes have been widely used for vaccine design, neutralization assays, and pathogenesis studies. However, obtaining bona fide functional env clones is a time consuming and labor intensive process. A new high throughput method has been developed to characterize HIV-1 env genes. Multiple rev/env gene cassettes were obtained from each of seven HIV-1 strains using single genome amplification (SGA) PCR. The cytomegalovirus (CMV) promoter was amplified separately by PCR. A promoter PCR (pPCR) method was developed to link both PCR products using an overlapping PCR method. Pseudovirions were generated by cotransfection of pPCR products and pSG3 Delta env backbone into 293T cells. After infecting TZM-bl cells, 75 out of 87 (86%) of the rev/env gene cassettes were functional. Pseudoviruses generated with pPCR products or corresponding plasmid DNA showed similar sensitivity to six HIV-1 positive sera and three monoclonal antibodies, suggesting neutralization properties are not altered in pPCR pseudovirions. Furthermore, sufficient amounts of pseudovirions can be obtained for a large number of neutralization assays. The new pPCR method eliminates cloning, transformation, and plasmid DNA preparation steps in the generation of HIV-1 pseudovirions. This allows for quick analysis of multiple env genes from HIV-1 infected individuals.
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Affiliation(s)
- Jennifer L Kirchherr
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
| | - Webster Kasongo
- The Tropical Disease Research Centre, PO Box 71769 Ndola, Zambia
| | - Victor Chalwe
- The Tropical Disease Research Centre, PO Box 71769 Ndola, Zambia
| | | | | | - Shi-Mao Xia
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
| | - Richard M Scearce
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
| | - David C Montefiori
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
| | - Barton F Haynes
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
| | - Feng Gao
- Duke Human Vaccine Institute and Center for HIV-AIDS Vaccine Immunology, Duke University Medical Center, Durham, NC 27710 USA
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45
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Newman JT, Sturgeon TJ, Gupta P, Montelaro RC. Differential functional phenotypes of two primary HIV-1 strains resulting from homologous point mutations in the LLP domains of the envelope gp41 intracytoplasmic domain. Virology 2007; 367:102-16. [PMID: 17582453 PMCID: PMC2034414 DOI: 10.1016/j.virol.2007.05.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 04/09/2007] [Accepted: 05/21/2007] [Indexed: 01/10/2023]
Abstract
We previously reported that selected mutations of highly conserved arginine residues within the LLP regions of HIV-1(ME46) gp41 had diverse effects on Env function. In the current study, we sought to test if the observed LLP mutant phenotypes would be similar in HIV-1(89.6). The results of the current studies revealed that the LLP-1 mutations conferred reduced Env incorporation, infectivity, and replication phenotypes in both viruses, while homologous LLP-2 mutations had differential phenotypical effects between the two strains. In particular, several of the 89.6 LLP-2 mutant viruses were replication defective in CEMX174 cells despite having increased levels of Env incorporation, and with both strains, there were differential effects on infectivity. This comparison of homologous point mutations in two different strains of HIV supports the role of LLPs as determinants of Env function, but reveals for the first time the influence of virus strain on LLP mutant phenotypes.
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Affiliation(s)
- Jason T Newman
- Department of Molecular Genetics and Biochemistry, School of Medicine, University of Pittsburgh, PA 15261, USA
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46
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Korotkova N, Chattopadhyay S, Tabata TA, Beskhlebnaya V, Vigdorovich V, Kaiser BK, Strong RK, Dykhuizen DE, Sokurenko EV, Moseley SL. Selection for functional diversity drives accumulation of point mutations in Dr adhesins of Escherichia coli. Mol Microbiol 2007; 64:180-94. [PMID: 17376081 DOI: 10.1111/j.1365-2958.2007.05648.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Immune escape is considered to be the driving force behind structural variability of major antigens on the surface of bacterial pathogens, such as fimbriae. In the Dr family of Escherichia coli adhesins, structural and adhesive functions are carried out by the same subunit. Dr adhesins have been shown to bind decay-accelerating factor (DAF), collagen IV, and carcinoembryonic antigen-related cell adhesion molecules (CEACAMs). We show that genes encoding Dr adhesins from 100 E. coli strains form eight structural groups with a high level of amino acid sequence diversity between them. However, genes comprising each group differ from each other by only a small number of point mutations. Out of 66 polymorphisms identified within the groups, only three were synonymous mutations, indicating strong positive selection for amino acid replacements. Functional analysis of intragroup variants comprising the Dr haemagglutinin (DraE) group revealed that the point mutations result in distinctly different binding phenotypes, with a tendency of increased affinity to DAF, decreased sensitivity of DAF binding to inhibition by chloramphenicol, and loss of binding capability to collagen, CEACAM3 and CEACAM6. Thus, variability by point mutation of major antigenic proteins on the bacterial surface can be a signature of selection for functional modification.
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Affiliation(s)
- Natalia Korotkova
- Department of Microbiology, University of Washington, Seattle, WA 98195-7242, USA
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47
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Sheppard NC, Davies SL, Jeffs SA, Vieira SM, Sattentau QJ. Production and characterization of high-affinity human monoclonal antibodies to human immunodeficiency virus type 1 envelope glycoproteins in a mouse model expressing human immunoglobulins. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2006; 14:157-67. [PMID: 17167037 PMCID: PMC1797789 DOI: 10.1128/cvi.00274-06] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human (Hu) monoclonal antibodies (MAbs) against the human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins (Env) are useful tools in the structural and functional analysis of Env, are under development both as potential prophylaxis and as therapy for established HIV-1 infection, and have crucial roles in guiding the design of preventative vaccines. Despite representing more than 50% of infections globally, no MAbs have been generated in any species against C clade HIV-1 Env. To generate HuMAbs to a novel Chinese C clade Env vaccine candidate (primary isolate strain HIV-1(97CN54)), we used BAB5 mice that express a human immunoglobulin (Ig) M antibody repertoire in place of endogenous murine immunoglobulins. When immunized with HIV-1(97CN54) Env, these mice developed antigen-specific IgM antibodies. Hybridoma fusions using splenocytes from these mice enabled the isolation of two Env-specific IgM HuMAbs: N3C5 and N03B11. N3C5 bound to HIV-1 Env from clades A and C, whereas N03B11 bound two geographically distant clade C isolates but not Env from other clades. These HuMAbs bind conformational epitopes within the immunodominant region of the gp41 ectodomain. N3C5 weakly neutralized the autologous isolate in the absence of complement and weakly enhanced infection in the presence of complement. N03B11 has no effect on infectivity in either the presence or the absence of complement. These novel HuMAbs are useful reagents for the study of HIV-1 Env relevant to the global pandemic, and mice producing human immunoglobulin present a tool for the production of such antibodies.
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Affiliation(s)
- Neil C Sheppard
- The Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom.
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48
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Poon AFY, Lewis FI, Pond SLK, Frost SDW. Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope. PLoS Comput Biol 2006; 3:e11. [PMID: 17238283 PMCID: PMC1779302 DOI: 10.1371/journal.pcbi.0030011] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Accepted: 12/07/2006] [Indexed: 11/18/2022] Open
Abstract
The addition of asparagine (N)-linked polysaccharide chains (i.e., glycans) to the gp120 and gp41 glycoproteins of human immunodeficiency virus type 1 (HIV-1) envelope is not only required for correct protein folding, but also may provide protection against neutralizing antibodies as a "glycan shield." As a result, strong host-specific selection is frequently associated with codon positions where nonsynonymous substitutions can create or disrupt potential N-linked glycosylation sites (PNGSs). Moreover, empirical data suggest that the individual contribution of PNGSs to the neutralization sensitivity or infectivity of HIV-1 may be critically dependent on the presence or absence of other PNGSs in the envelope sequence. Here we evaluate how glycan-glycan interactions have shaped the evolution of HIV-1 envelope sequences by analyzing the distribution of PNGSs in a large-sequence alignment. Using a "covarion"-type phylogenetic model, we find that the rates at which individual PNGSs are gained or lost vary significantly over time, suggesting that the selective advantage of having a PNGS may depend on the presence or absence of other PNGSs in the sequence. Consequently, we identify specific interactions between PNGSs in the alignment using a new paired-character phylogenetic model of evolution, and a Bayesian graphical model. Despite the fundamental differences between these two methods, several interactions are jointly identified by both. Mapping these interactions onto a structural model of HIV-1 gp120 reveals that negative (exclusive) interactions occur significantly more often between colocalized glycans, while positive (inclusive) interactions are restricted to more distant glycans. Our results imply that the adaptive repertoire of alternative configurations in the HIV-1 glycan shield is limited by functional interactions between the N-linked glycans. This represents a potential vulnerability of rapidly evolving HIV-1 populations that may provide useful glycan-based targets for neutralizing antibodies.
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Affiliation(s)
- Art F Y Poon
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America.
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49
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Waheed AA, Ablan SD, Mankowski MK, Cummins JE, Ptak RG, Schaffner CP, Freed EO. Inhibition of HIV-1 replication by amphotericin B methyl ester: selection for resistant variants. J Biol Chem 2006; 281:28699-711. [PMID: 16882663 DOI: 10.1074/jbc.m603609200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Membrane cholesterol plays an important role in human immunodeficiency virus type 1 (HIV-1) particle production and infectivity. Here, we have investigated the target and mechanism of action of a cholesterol-binding compound, the polyene antifungal antibiotic amphotericin B methyl ester (AME). We found that AME potently inhibited the replication of a highly divergent panel of HIV-1 isolates in various T-cell lines and primary cells irrespective of clade or target cell tropism. The defects in HIV-1 replication caused by AME were due to profoundly impaired viral infectivity as well as a defect in viral particle production. To elucidate further the mechanism of action of AME, we selected for and characterized AME-resistant HIV-1 variants. Mutations responsible for AME resistance mapped to a highly conserved and functionally important endocytosis motif in the cytoplasmic tail of the transmembrane glycoprotein gp41. Interestingly, truncation of the gp41 cytoplasmic tail in the context of either HIV-1 or rhesus macaque simian immunodeficiency virus also conferred resistance to AME. The infectivity of HIV-1 virions bearing murine leukemia virus or vesicular stomatitis virus glycoproteins was unaffected by AME. Our data define the target and mechanism of action of AME and provide support for the concept that cholesterol-binding compounds should be pursued as antiretroviral drugs to disrupt HIV-1 replication.
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Affiliation(s)
- Abdul A Waheed
- Virus-Cell Interaction Section, HIV Drug Resistance Program, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702-1201, USA
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50
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Davis MR, Jiang J, Zhou J, Freed EO, Aiken C. A mutation in the human immunodeficiency virus type 1 Gag protein destabilizes the interaction of the envelope protein subunits gp120 and gp41. J Virol 2006; 80:2405-17. [PMID: 16474147 PMCID: PMC1395406 DOI: 10.1128/jvi.80.5.2405-2417.2006] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Gag protein of human immunodeficiency virus type 1 (HIV-1) associates with the envelope protein complex during virus assembly. The available evidence indicates that this interaction involves recognition of the gp41 cytoplasmic tail (CT) by the matrix protein (MA) region of Pr55(Gag). Here we show that substitution of Asp for Leu at position 49 (L49D) in MA results in a specific reduction in particle-associated gp120 without affecting the levels of gp41. Mutant virions were markedly reduced in single-cycle infectivity despite a relatively modest defect in fusion with target cells. Studies with HIV-1 particles containing decreased levels of envelope proteins suggested that the L49D mutation also inhibits a postentry step in infection. Truncation of the gp41 tail, or pseudotyping by vesicular stomatitis virus glycoprotein, restored both the fusion and infectivity of L49D mutant virions to wild-type levels. Truncation of gp41 also resulted in equivalent levels of gp120 on particles with and without the MA mutation and enhanced the replication of the L49D mutant virus in T cells. The impaired fusion and infectivity of L49D mutant particles were also complemented by a single point mutation in the gp41 CT that disrupted the tyrosine-containing endocytic motif. Our results suggest that an altered interaction between the MA domain of Gag and the gp41 cytoplasmic tail leads to dissociation of gp120 from gp41 during HIV-1 particle assembly, thus resulting in impaired fusion and infectivity.
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Affiliation(s)
- Melody R Davis
- Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232-2363, USA
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