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Bradley T, Trama A, Tumba N, Gray E, Lu X, Madani N, Jahanbakhsh F, Eaton A, Xia SM, Parks R, Lloyd KE, Sutherland LL, Scearce RM, Bowman CM, Barnett S, Abdool-Karim SS, Boyd SD, Melillo B, Smith AB, Sodroski J, Kepler TB, Alam SM, Gao F, Bonsignori M, Liao HX, Moody MA, Montefiori D, Santra S, Morris L, Haynes BF. Amino Acid Changes in the HIV-1 gp41 Membrane Proximal Region Control Virus Neutralization Sensitivity. EBioMedicine 2016; 12:196-207. [PMID: 27612593 PMCID: PMC5078591 DOI: 10.1016/j.ebiom.2016.08.045] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/26/2016] [Accepted: 08/30/2016] [Indexed: 01/21/2023] Open
Abstract
Most HIV-1 vaccines elicit neutralizing antibodies that are active against highly sensitive (tier-1) viruses or rare cases of vaccine-matched neutralization-resistant (tier-2) viruses, but no vaccine has induced antibodies that can broadly neutralize heterologous tier-2 viruses. In this study, we isolated antibodies from an HIV-1-infected individual that targeted the gp41 membrane-proximal external region (MPER) that may have selected single-residue changes in viral variants in the MPER that resulted in neutralization sensitivity to antibodies targeting distal epitopes on the HIV-1 Env. Similarly, a single change in the MPER in a second virus from another infected-individual also conferred enhanced neutralization sensitivity. These gp41 single-residue changes thus transformed tier-2 viruses into tier-1 viruses that were sensitive to vaccine-elicited tier-1 neutralizing antibodies. These data demonstrate that Env amino acid changes within the MPER bnAb epitope of naturally-selected escape viruses can increase neutralization sensitivity to multiple types of neutralizing antibodies, and underscore the critical importance of the MPER for maintaining the integrity of the tier-2 HIV-1 trimer. Amino acid changes in the HIV gp41 MPER can regulate neutralization sensitivity of distal epitopes. MPER antibodies isolated early are resistant to MPER changes that enhance neutralization sensitivity. HIV gp41 MPER is critical for determining overall HIV envelope conformations.
The HIV-1 envelope protein (Env) is the primary target for neutralizing antibodies. Most HIV-1 vaccines elicit neutralizing antibodies that are active against highly neutralization-sensitive (tier-1) or rare vaccine-matched more neutralization-resistant (tier-2) viruses, but no vaccine has induced antibodies that can broadly neutralize heterologous tier-2 viruses. In this study, we identified changes that occurred in two HIV-1-infected individuals in the membrane proximal region of the HIV-1 Env that resulted in neutralization sensitivity to antibodies targeting distal epitopes on the HIV Env. These single-residue changes thus transformed tier-2 viruses into tier-1 viruses, highlighting the importance of MPER residues in maintaining neutralization-resistant virus.
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Affiliation(s)
- Todd Bradley
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA.
| | - Ashley Trama
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Nancy Tumba
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Elin Gray
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Navid Madani
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Krissey E Lloyd
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Laura L Sutherland
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Richard M Scearce
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Cindy M Bowman
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Susan Barnett
- Novartis Vaccines and Diagnostics, Inc., Cambridge, MA, USA
| | - Salim S Abdool-Karim
- Center for AIDS Program of Research in South Africa, University of KwaZulu-Natal, Durban 4013, South Africa; Columbia University, New York, NY 10032, USA
| | | | - Bruno Melillo
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amos B Smith
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph Sodroski
- Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - S Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - David Montefiori
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Lynn Morris
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa; Center for AIDS Program of Research in South Africa, University of KwaZulu-Natal, Durban 4013, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2131, South Africa
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA.
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352
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Minimally Mutated HIV-1 Broadly Neutralizing Antibodies to Guide Reductionist Vaccine Design. PLoS Pathog 2016; 12:e1005815. [PMID: 27560183 PMCID: PMC4999182 DOI: 10.1371/journal.ppat.1005815] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 07/19/2016] [Indexed: 11/19/2022] Open
Abstract
An optimal HIV vaccine should induce broadly neutralizing antibodies (bnAbs) that neutralize diverse viral strains and subtypes. However, potent bnAbs develop in only a small fraction of HIV-infected individuals, all contain rare features such as extensive mutation, insertions, deletions, and/or long complementarity-determining regions, and some are polyreactive, casting doubt on whether bnAbs to HIV can be reliably induced by vaccination. We engineered two potent VRC01-class bnAbs that minimized rare features. According to a quantitative features frequency analysis, the set of features for one of these minimally mutated bnAbs compared favorably with all 68 HIV bnAbs analyzed and was similar to antibodies elicited by common vaccines. This same minimally mutated bnAb lacked polyreactivity in four different assays. We then divided the minimal mutations into spatial clusters and dissected the epitope components interacting with those clusters, by mutational and crystallographic analyses coupled with neutralization assays. Finally, by synthesizing available data, we developed a working-concept boosting strategy to select the mutation clusters in a logical order following a germline-targeting prime. We have thus developed potent HIV bnAbs that may be more tractable vaccine goals compared to existing bnAbs, and we have proposed a strategy to elicit them. This reductionist approach to vaccine design, guided by antibody and antigen structure, could be applied to design candidate vaccines for other HIV bnAbs or protective Abs against other pathogens. Many HIV vaccine design efforts aim to elicit so-called broadly neutralizing antibodies that bind and neutralize diverse strains and subtypes of the virus. However, these efforts are guided by very unusual antibodies isolated from HIV-infected individuals. These antibodies have rare features that limit their use as direct vaccine templates, because it is unlikely that any vaccine could consistently elicit similar antibodies. We engineered HIV broadly neutralizing antibodies that minimized these rare features and may therefore serve as better leads for HIV vaccine design. Antibodies generally gain affinity for their target epitope by accumulating mutations in a natural process of maturation. Figuring out how to use vaccines to elicit particular kinds of antibodies, with particular kinds of helpful mutations, is a major unsolved challenge for vaccine design. We were able to determine which mutations in our new antibodies are most important and which epitope structures are needed to induce those mutations. This analysis allowed us to deduce a logical strategy, which remains to be tested, for how to guide the maturation of these types of antibodies by vaccination. We propose that this reductionist approach to vaccine design, guided by molecular structure and engineering-oriented to allow for optimization, has promise for designing vaccines against HIV and many other pathogens.
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353
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Louis JM, Baber JL, Ghirlando R, Aniana A, Bax A, Roche J. Insights into the Conformation of the Membrane Proximal Regions Critical to the Trimerization of the HIV-1 gp41 Ectodomain Bound to Dodecyl Phosphocholine Micelles. PLoS One 2016; 11:e0160597. [PMID: 27513582 PMCID: PMC4981318 DOI: 10.1371/journal.pone.0160597] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 07/21/2016] [Indexed: 01/06/2023] Open
Abstract
The transitioning of the ectodomain of gp41 from a pre-hairpin to a six-helix bundle conformation is a crucial aspect of virus-cell fusion. To gain insight into the intermediary steps of the fusion process we have studied the pH and dodecyl phosphocholine (DPC) micelle dependent trimer association of gp41 by systematic deletion analysis of an optimized construct termed 17-172 (residues 528 to 683 of Env) that spans the fusion peptide proximal region (FPPR) to the membrane proximal external region (MPER) of gp41, by sedimentation velocity and double electron-electron resonance (DEER) EPR spectroscopy. Trimerization at pH 7 requires the presence of both the FPPR and MPER regions. However, at pH 4, the protein completely dissociates to monomers. DEER measurements reveal a partial fraying of the C-terminal MPER residues in the 17-172 trimer while the other regions, including the FPPR, remain compact. In accordance, truncating nine C-terminal MPER residues (675-683) in the 17-172 construct does not shift the trimer-monomer equilibrium significantly. Thus, in the context of the gp41 ectodomain spanning residues 17-172, trimerization is clearly dependent on FPPR and MPER regions even when the terminal residues of MPER unravel. The antibody Z13e1, which spans both the 2F5 and 4E10 epitopes in MPER, binds to 17-172 with a Kd of 1 ± 0.12 μM. Accordingly, individual antibodies 2F5 and 4E10 also recognize the 17-172 trimer/DPC complex. We propose that binding of the C-terminal residues of MPER to the surface of the DPC micelles models a correct positioning of the trimeric transmembrane domain anchored in the viral membrane.
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Affiliation(s)
- John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (JL)); (JR)
| | - James L. Baber
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
- * E-mail: (JL)); (JR)
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354
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Benureau Y, Colin P, Staropoli I, Gonzalez N, Garcia-Perez J, Alcami J, Arenzana-Seisdedos F, Lagane B. Guidelines for cloning, expression, purification and functional characterization of primary HIV-1 envelope glycoproteins. J Virol Methods 2016; 236:184-195. [PMID: 27451265 DOI: 10.1016/j.jviromet.2016.07.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/13/2016] [Accepted: 07/19/2016] [Indexed: 12/14/2022]
Abstract
The trimeric HIV-1 envelope (Env) glycoproteins gp120 and gp41 mediate virus entry into target cells by engaging CD4 and the coreceptors CCR5 or CXCR4 at the cell surface and driving membrane fusion. Receptor/gp120 interactions regulate the virus life cycle, HIV infection transmission and pathogenesis. Env is also the target of neutralizing antibodies. Efforts have thus been made to produce soluble HIV-1 glycoproteins to develop vaccines and study the role and mechanisms of HIV/receptor interactions. However, production and purification of Env glycoproteins and their functional assessment has to cope with multiple obstacles. These include difficulties in amplifying and cloning env sequences and setting up receptor binding assays that are suitable for studies on large collections of glycoproteins, flexible enough to adapt to Env and receptor structural heterogeneities, and allow recapitulating the receptor binding properties of virion-associated Env trimers. Here we identify these difficulties and present protocols to produce primary gp120 and determination of their binding properties to receptors. The receptor binding assays confirmed that the produced glycoproteins are competent for binding CD4 and undergo proper CD4-induced conformational changes required for interaction with CCR5. These assays may help elucidate the role of gp120/receptor interactions in the pathophysiology of HIV infection and develop HIV-1 entry inhibitors.
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Affiliation(s)
- Yann Benureau
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
| | - Philippe Colin
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
| | - Isabelle Staropoli
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
| | - Nuria Gonzalez
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
| | - Javier Garcia-Perez
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
| | - Jose Alcami
- AIDS Immunopathogenesis Unit, Instituto de Salud Carlos III, 28220, Majadahonda, Madrid, Spain.
| | - Fernando Arenzana-Seisdedos
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
| | - Bernard Lagane
- INSERM U1108, Institut Pasteur, 75015 Paris, France; Viral Pathogenesis Unit, Department of Virology, Institut Pasteur, 75015 Paris, France.
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355
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Woodham AW, Skeate JG, Sanna AM, Taylor JR, Da Silva DM, Cannon PM, Kast WM. Human Immunodeficiency Virus Immune Cell Receptors, Coreceptors, and Cofactors: Implications for Prevention and Treatment. AIDS Patient Care STDS 2016; 30:291-306. [PMID: 27410493 DOI: 10.1089/apc.2016.0100] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In the last three decades, extensive research on human immunodeficiency virus (HIV) has highlighted its capability to exploit a variety of strategies to enter and infect immune cells. Although CD4(+) T cells are well known as the major HIV target, with infection occurring through the canonical combination of the cluster of differentiation 4 (CD4) receptor and either the C-C chemokine receptor type 5 (CCR5) or C-X-C chemokine receptor type 4 (CXCR4) coreceptors, HIV has also been found to enter other important immune cell types such as macrophages, dendritic cells, Langerhans cells, B cells, and granulocytes. Interestingly, the expression of distinct cellular cofactors partially regulates the rate in which HIV infects each distinct cell type. Furthermore, HIV can benefit from the acquisition of new proteins incorporated into its envelope during budding events. While several publications have investigated details of how HIV manipulates particular cell types or subtypes, an up-to-date comprehensive review on HIV tropism for different immune cells is lacking. Therefore, this review is meant to focus on the different receptors, coreceptors, and cofactors that HIV exploits to enter particular immune cells. Additionally, prophylactic approaches that have targeted particular molecules associated with HIV entry and infection of different immune cells will be discussed. Unveiling the underlying cellular receptors and cofactors that lead to HIV preference for specific immune cell populations is crucial in identifying novel preventative/therapeutic targets for comprehensive strategies to eliminate viral infection.
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Affiliation(s)
- Andrew W. Woodham
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, California
| | - Joseph G. Skeate
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, California
| | - Adriana M. Sanna
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
| | - Julia R. Taylor
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, California
| | - Diane M. Da Silva
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
- Department of Obstetrics & Gynecology, University of Southern California, Los Angeles, California
| | - Paula M. Cannon
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, California
| | - W. Martin Kast
- Department of Molecular Microbiology and Immunology, University of Southern California, Los Angeles, California
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California
- Department of Obstetrics & Gynecology, University of Southern California, Los Angeles, California
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356
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HIV Genome-Wide Protein Associations: a Review of 30 Years of Research. Microbiol Mol Biol Rev 2016; 80:679-731. [PMID: 27357278 DOI: 10.1128/mmbr.00065-15] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The HIV genome encodes a small number of viral proteins (i.e., 16), invariably establishing cooperative associations among HIV proteins and between HIV and host proteins, to invade host cells and hijack their internal machineries. As a known example, the HIV envelope glycoprotein GP120 is closely associated with GP41 for viral entry. From a genome-wide perspective, a hypothesis can be worked out to determine whether 16 HIV proteins could develop 120 possible pairwise associations either by physical interactions or by functional associations mediated via HIV or host molecules. Here, we present the first systematic review of experimental evidence on HIV genome-wide protein associations using a large body of publications accumulated over the past 3 decades. Of 120 possible pairwise associations between 16 HIV proteins, at least 34 physical interactions and 17 functional associations have been identified. To achieve efficient viral replication and infection, HIV protein associations play essential roles (e.g., cleavage, inhibition, and activation) during the HIV life cycle. In either a dispensable or an indispensable manner, each HIV protein collaborates with another viral protein to accomplish specific activities that precisely take place at the proper stages of the HIV life cycle. In addition, HIV genome-wide protein associations have an impact on anti-HIV inhibitors due to the extensive cross talk between drug-inhibited proteins and other HIV proteins. Overall, this study presents for the first time a comprehensive overview of HIV genome-wide protein associations, highlighting meticulous collaborations between all viral proteins during the HIV life cycle.
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357
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Li H, Wang S, Kong R, Ding W, Lee FH, Parker Z, Kim E, Learn GH, Hahn P, Policicchio B, Brocca-Cofano E, Deleage C, Hao X, Chuang GY, Gorman J, Gardner M, Lewis MG, Hatziioannou T, Santra S, Apetrei C, Pandrea I, Alam SM, Liao HX, Shen X, Tomaras GD, Farzan M, Chertova E, Keele BF, Estes JD, Lifson JD, Doms RW, Montefiori DC, Haynes BF, Sodroski JG, Kwong PD, Hahn BH, Shaw GM. Envelope residue 375 substitutions in simian-human immunodeficiency viruses enhance CD4 binding and replication in rhesus macaques. Proc Natl Acad Sci U S A 2016; 113:E3413-22. [PMID: 27247400 PMCID: PMC4914158 DOI: 10.1073/pnas.1606636113] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Most simian-human immunodeficiency viruses (SHIVs) bearing envelope (Env) glycoproteins from primary HIV-1 strains fail to infect rhesus macaques (RMs). We hypothesized that inefficient Env binding to rhesus CD4 (rhCD4) limits virus entry and replication and could be enhanced by substituting naturally occurring simian immunodeficiency virus Env residues at position 375, which resides at a critical location in the CD4-binding pocket and is under strong positive evolutionary pressure across the broad spectrum of primate lentiviruses. SHIVs containing primary or transmitted/founder HIV-1 subtype A, B, C, or D Envs with genotypic variants at residue 375 were constructed and analyzed in vitro and in vivo. Bulky hydrophobic or basic amino acids substituted for serine-375 enhanced Env affinity for rhCD4, virus entry into cells bearing rhCD4, and virus replication in primary rhCD4 T cells without appreciably affecting antigenicity or antibody-mediated neutralization sensitivity. Twenty-four RMs inoculated with subtype A, B, C, or D SHIVs all became productively infected with different Env375 variants-S, M, Y, H, W, or F-that were differentially selected in different Env backbones. Notably, SHIVs replicated persistently at titers comparable to HIV-1 in humans and elicited autologous neutralizing antibody responses typical of HIV-1. Seven animals succumbed to AIDS. These findings identify Env-rhCD4 binding as a critical determinant for productive SHIV infection in RMs and validate a novel and generalizable strategy for constructing SHIVs with Env glycoproteins of interest, including those that in humans elicit broadly neutralizing antibodies or bind particular Ig germ-line B-cell receptors.
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Affiliation(s)
- Hui Li
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Shuyi Wang
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Rui Kong
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Wenge Ding
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Fang-Hua Lee
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Zahra Parker
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Eunlim Kim
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Gerald H Learn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Paul Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Ben Policicchio
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261
| | | | - Claire Deleage
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702
| | - Xingpei Hao
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Matthew Gardner
- Department of Infectious Disease, Scripps Research Institute, Jupiter, FL 33458
| | | | | | - Sampa Santra
- Center of Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02215
| | - Cristian Apetrei
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261
| | - Ivona Pandrea
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15261
| | - S Munir Alam
- Department of Medicine, Duke University, Durham, NC 27710
| | - Hua-Xin Liao
- Department of Medicine, Duke University, Durham, NC 27710
| | - Xiaoying Shen
- Department of Medicine, Duke University, Durham, NC 27710
| | | | - Michael Farzan
- Department of Infectious Disease, Scripps Research Institute, Jupiter, FL 33458
| | - Elena Chertova
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702
| | - Brandon F Keele
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702
| | - Jacob D Estes
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702
| | - Jeffrey D Lifson
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702
| | - Robert W Doms
- Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | | | | | - Joseph G Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215
| | - Peter D Kwong
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory, Frederick, MD 21702
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104;
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358
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Wu X, Kong XP. Antigenic landscape of the HIV-1 envelope and new immunological concepts defined by HIV-1 broadly neutralizing antibodies. Curr Opin Immunol 2016; 42:56-64. [PMID: 27289425 DOI: 10.1016/j.coi.2016.05.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/20/2016] [Indexed: 10/21/2022]
Abstract
The isolation of HIV-1 broadly neutralizing antibodies (bnAbs) has demonstrated the ability of the human immune system to mount effective antibody responses against the virus. To harness this immune potential to elicit similar antibody responses by vaccination, it is important to understand the immunological processes that produce them. Here we review recent advances in crystal structural determinations of HIV-1 bnAb epitopes that directly portray the antigenic landscape of the HIV-1 envelope glycoprotein. We also summarize new immunological concepts implicated in bnAb sequences and their lineage studies.
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Affiliation(s)
- Xueling Wu
- Aaron Diamond AIDS Research Center, New York, NY 10016, USA.
| | - Xiang-Peng Kong
- New York University, School of Medicine, New York, NY 10016, USA.
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359
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Choi UB, Zhao M, Zhang Y, Lai Y, Brunger AT. Complexin induces a conformational change at the membrane-proximal C-terminal end of the SNARE complex. eLife 2016; 5. [PMID: 27253060 PMCID: PMC4927292 DOI: 10.7554/elife.16886] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/01/2016] [Indexed: 01/14/2023] Open
Abstract
Complexin regulates spontaneous and activates Ca2+-triggered neurotransmitter release, yet the molecular mechanisms are still unclear. Here we performed single molecule fluorescence resonance energy transfer experiments and uncovered two conformations of complexin-1 bound to the ternary SNARE complex. In the cis conformation, complexin-1 induces a conformational change at the membrane-proximal C-terminal end of the ternary SNARE complex that specifically depends on the N-terminal, accessory, and central domains of complexin-1. The complexin-1 induced conformation of the ternary SNARE complex may be related to a conformation that is juxtaposing the synaptic vesicle and plasma membranes. In the trans conformation, complexin-1 can simultaneously interact with a ternary SNARE complex via the central domain and a binary SNARE complex consisting of syntaxin-1A and SNAP-25A via the accessory domain. The cis conformation may be involved in activation of synchronous neurotransmitter release, whereas both conformations may be involved in regulating spontaneous release. DOI:http://dx.doi.org/10.7554/eLife.16886.001 Nerve cells communicate via electrical signals that travel at high speeds. However, these signals cannot pass across the gaps – called synapses – that separate one nerve cell from the next. Instead, signals pass between nerve cells via molecules called neurotransmitters that are released from the membrane of the first cell and recognized by receptors in the membrane of the next. Prior to being released, neurotransmitters are packaged inside bubble-like structures called vesicles. The synaptic vesicles must fuse with the cell membrane in order to release their contents into the synaptic cleft. Proteins called SNAREs work together with other proteins to allow this membrane fusion to occur rapidly after the electrical signal arrives. Complexin is a synaptic protein that binds tightly to a complex of SNARE proteins to regulate membrane fusion. This protein activates the quick release of neurotransmitters, which is triggered by an increase in calcium ions as the electrical signal reachess the synapse. Complexin also regulates a different type of neurotransmitter release, which is known as “spontaneous release”. The complexin protein is made up of different regions, each of which is required for one or more of the protein’s activities. However, it is not clear how these regions, or domains, interact with SNAREs and other proteins to enable complexin to perform these roles. Choi et al. have now investigated whether the different activities of mammalian complexin are related to the structure that it adopts when it interacts with the SNARE complex. Complexes of SNARE proteins were assembled with one of the SNARE proteins tethered to a surface for imaging. Next, a light-based imaging technique called single molecule Förster resonance energy transfer (or FRET) was used to monitor how complexin interacts with the SNARE complex. This technique allows individual proteins that have been labeled with fluorescent markers to be followed under a microscope and can show how they interact in real-time. Using this approach, Choi et al. showed that complexin could adopt two different shapes or conformations when it binds to the SNARE complex. In one, complexin interacted closely with the SNARE complex so that it made part of the complex change shape. In the other, complexin was able to bridge two SNARE complexes. Complexin can therefore interact with SNARE complexes in different ways by using different regions of the protein. These findings provide insight into how complexin may regulate membrane fusion via the SNARE complex. In the future, single molecule FRET could be used to study other proteins found at synapses and understand the other steps that regulate the release of neurotransmitters. DOI:http://dx.doi.org/10.7554/eLife.16886.002
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Affiliation(s)
- Ucheor B Choi
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Structural Biology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Minglei Zhao
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Structural Biology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Yunxiang Zhang
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Structural Biology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Ying Lai
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Structural Biology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Structural Biology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
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360
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Florian PE, Rouillé Y, Ruta S, Nichita N, Roseanu A. Recent advances in human viruses imaging studies. J Basic Microbiol 2016; 56:591-607. [PMID: 27059598 DOI: 10.1002/jobm.201500575] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/27/2016] [Indexed: 12/13/2022]
Abstract
Microscopy techniques are often exploited by virologists to investigate molecular details of critical steps in viruses' life cycles such as host cell recognition and entry, genome replication, intracellular trafficking, and release of mature virions. Fluorescence microscopy is the most attractive tool employed to detect intracellular localizations of various stages of the viral infection and monitor the pathogen-host interactions associated with them. Super-resolution microscopy techniques have overcome the technical limitations of conventional microscopy and offered new exciting insights into the formation and trafficking of human viruses. In addition, the development of state-of-the art electron microscopy techniques has become particularly important in studying virus morphogenesis by revealing ground-braking ultrastructural details of this process. This review provides recent advances in human viruses imaging in both, in vitro cell culture systems and in vivo, in the animal models recently developed. The newly available imaging technologies bring a major contribution to our understanding of virus pathogenesis and will become an important tool in early diagnosis of viral infection and the development of novel therapeutics to combat the disease.
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Affiliation(s)
- Paula Ecaterina Florian
- Department of , Ligand-Receptor Interactions, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Yves Rouillé
- Center for Infection and Immunity of Lille (CIIL), Inserm U1019, CNRS UMR8204, Institut Pasteur de Lille, Université Lille Nord de France, Lille, France
| | - Simona Ruta
- Department of Emergent Diseases, Stefan S. Nicolau Institute of Virology, Bucharest, 030304, Romania
| | - Norica Nichita
- Department of Viral Glycoproteins, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
| | - Anca Roseanu
- Department of , Ligand-Receptor Interactions, Institute of Biochemistry of the Romanian Academy, Bucharest, Romania
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361
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Kong R, Xu K, Zhou T, Acharya P, Lemmin T, Liu K, Ozorowski G, Soto C, Taft JD, Bailer RT, Cale EM, Chen L, Choi CW, Chuang GY, Doria-Rose NA, Druz A, Georgiev IS, Gorman J, Huang J, Joyce MG, Louder MK, Ma X, McKee K, O'Dell S, Pancera M, Yang Y, Blanchard SC, Mothes W, Burton DR, Koff WC, Connors M, Ward AB, Kwong PD, Mascola JR. Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody. Science 2016; 352:828-33. [PMID: 27174988 DOI: 10.1126/science.aae0474] [Citation(s) in RCA: 279] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 03/30/2016] [Indexed: 12/13/2022]
Abstract
The HIV-1 fusion peptide, comprising 15 to 20 hydrophobic residues at the N terminus of the Env-gp41 subunit, is a critical component of the virus-cell entry machinery. Here, we report the identification of a neutralizing antibody, N123-VRC34.01, which targets the fusion peptide and blocks viral entry by inhibiting conformational changes in gp120 and gp41 subunits of Env required for entry. Crystal structures of N123-VRC34.01 liganded to the fusion peptide, and to the full Env trimer, revealed an epitope consisting of the N-terminal eight residues of the gp41 fusion peptide and glycan N88 of gp120, and molecular dynamics showed that the N-terminal portion of the fusion peptide can be solvent-exposed. These results reveal the fusion peptide to be a neutralizing antibody epitope and thus a target for vaccine design.
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Affiliation(s)
- Rui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kai Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Priyamvada Acharya
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas Lemmin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Cinque Soto
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin D Taft
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evan M Cale
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lei Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chang W Choi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aliaksandr Druz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivelin S Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinghe Huang
- HIV-Specific Immunity Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaochu Ma
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marie Pancera
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scott C Blanchard
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY 10021, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science, International AIDS Vaccine Initiative Neutralizing Antibody Center, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, MA 02142, USA
| | - Wayne C Koff
- International AIDS Vaccine Initiative, New York, NY 10038, USA
| | - Mark Connors
- HIV-Specific Immunity Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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362
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Moody MA, Gao F, Gurley TC, Amos JD, Kumar A, Hora B, Marshall DJ, Whitesides JF, Xia SM, Parks R, Lloyd KE, Hwang KK, Lu X, Bonsignori M, Finzi A, Vandergrift NA, Alam SM, Ferrari G, Shen X, Tomaras GD, Kamanga G, Cohen MS, Sam NE, Kapiga S, Gray ES, Tumba NL, Morris L, Zolla-Pazner S, Gorny MK, Mascola JR, Hahn BH, Shaw GM, Sodroski JG, Liao HX, Montefiori DC, Hraber PT, Korber BT, Haynes BF. Strain-Specific V3 and CD4 Binding Site Autologous HIV-1 Neutralizing Antibodies Select Neutralization-Resistant Viruses. Cell Host Microbe 2016; 18:354-62. [PMID: 26355218 DOI: 10.1016/j.chom.2015.08.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 04/14/2015] [Accepted: 08/14/2015] [Indexed: 11/19/2022]
Abstract
The third variable (V3) loop and the CD4 binding site (CD4bs) of the HIV-1 envelope are frequently targeted by neutralizing antibodies (nAbs) in infected individuals. In chronic infection, HIV-1 escape mutants repopulate the plasma, and V3 and CD4bs nAbs emerge that can neutralize heterologous tier 1 easy-to-neutralize but not tier 2 difficult-to-neutralize HIV-1 isolates. However, neutralization sensitivity of autologous plasma viruses to this type of nAb response has not been studied. We describe the development and evolution in vivo of antibodies distinguished by their target specificity for V3 and CD4bs epitopes on autologous tier 2 viruses but not on heterologous tier 2 viruses. A surprisingly high fraction of autologous circulating viruses was sensitive to these antibodies. These findings demonstrate a role for V3 and CD4bs antibodies in constraining the native envelope trimer in vivo to a neutralization-resistant phenotype, explaining why HIV-1 transmission generally occurs by tier 2 neutralization-resistant viruses.
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Affiliation(s)
- M Anthony Moody
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA; Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
| | - Thaddeus C Gurley
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Joshua D Amos
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Amit Kumar
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Bhavna Hora
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Dawn J Marshall
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - John F Whitesides
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Krissey E Lloyd
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Kwan-Ki Hwang
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM and Department of Microbiology, Infectology and Immunology, Université de Montréal, Montreal, QC H2X 0A9, Canada and Department of Microbiology and Immunology, McGill University, Montreal, QC H2X 1P1, Canada
| | - Nathan A Vandergrift
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA; Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Guido Ferrari
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiaoying Shen
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Gift Kamanga
- University of North Carolina Project, Kamuzu Central Hospital, Lilongwe, Malawi
| | - Myron S Cohen
- Departments of Medicine, Epidemiology, Microbiology, and Immunology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Noel E Sam
- Kilimanjaro Christian Medical Center, Moshi 25102, Tanzania
| | - Saidi Kapiga
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Elin S Gray
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Nancy L Tumba
- National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Lynn Morris
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; National Institute for Communicable Diseases, Johannesburg 2131, South Africa
| | - Susan Zolla-Pazner
- Department of Pathology, New York University School of Medicine, New York, NY 10010, USA; Veterans Affairs New York Harbor Healthcare System, New York, NY 10010, USA
| | - Miroslaw K Gorny
- Department of Pathology, New York University School of Medicine, New York, NY 10010, USA
| | - John R Mascola
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Beatrice H Hahn
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - George M Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph G Sodroski
- Department of Cancer Immunology & AIDS, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Hua-Xin Liao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - David C Montefiori
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Peter T Hraber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Bette T Korber
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA; Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA; Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.
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363
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Sakin V, Paci G, Lemke EA, Müller B. Labeling of virus components for advanced, quantitative imaging analyses. FEBS Lett 2016; 590:1896-914. [PMID: 26987299 DOI: 10.1002/1873-3468.12131] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 12/31/2022]
Abstract
In recent years, investigation of virus-cell interactions has moved from ensemble measurements to imaging analyses at the single-particle level. Advanced fluorescence microscopy techniques provide single-molecule sensitivity and subdiffraction spatial resolution, allowing observation of subviral details and individual replication events to obtain detailed quantitative information. To exploit the full potential of these techniques, virologists need to employ novel labeling strategies, taking into account specific constraints imposed by viruses, as well as unique requirements of microscopic methods. Here, we compare strengths and limitations of various labeling methods, exemplify virological questions that were successfully addressed, and discuss challenges and future potential of novel approaches in virus imaging.
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Affiliation(s)
- Volkan Sakin
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
| | - Giulia Paci
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Edward A Lemke
- Structural and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Germany
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364
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Swanstrom AE, Haggarty B, Jordan APO, Romano J, Leslie GJ, Aye PP, Marx PA, Lackner AA, Del Prete GQ, Robinson JE, Betts MR, Montefiori DC, LaBranche CC, Hoxie JA. Derivation and Characterization of a CD4-Independent, Non-CD4-Tropic Simian Immunodeficiency Virus. J Virol 2016; 90:4966-4980. [PMID: 26937037 PMCID: PMC4859711 DOI: 10.1128/jvi.02851-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/24/2016] [Indexed: 12/16/2022] Open
Abstract
UNLABELLED CD4 tropism is conserved among all primate lentiviruses and likely contributes to viral pathogenesis by targeting cells that are critical for adaptive antiviral immune responses. Although CD4-independent variants of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) have been described that can utilize the coreceptor CCR5 or CXCR4 in the absence of CD4, these viruses typically retain their CD4 binding sites and still can interact with CD4. We describe the derivation of a novel CD4-independent variant of pathogenic SIVmac239, termed iMac239, that was used to derive an infectious R5-tropic SIV lacking a CD4 binding site. Of the seven mutations that differentiate iMac239 from wild-type SIVmac239, a single change (D178G) in the V1/V2 region was sufficient to confer CD4 independence in cell-cell fusion assays, although other mutations were required for replication competence. Like other CD4-independent viruses, iMac239 was highly neutralization sensitive, although mutations were identified that could confer CD4-independent infection without increasing its neutralization sensitivity. Strikingly, iMac239 retained the ability to replicate in cell lines and primary cells even when its CD4 binding site had been ablated by deletion of a highly conserved aspartic acid at position 385, which, for HIV-1, plays a critical role in CD4 binding. iMac239, with and without the D385 deletion, exhibited an expanded host range in primary rhesus peripheral blood mononuclear cells that included CCR5(+) CD8(+) T cells. As the first non-CD4-tropic SIV, iMac239-ΔD385 will afford the opportunity to directly assess the in vivo role of CD4 targeting on pathogenesis and host immune responses. IMPORTANCE CD4 tropism is an invariant feature of primate lentiviruses and likely plays a key role in pathogenesis by focusing viral infection onto cells that mediate adaptive immune responses and in protecting virions attached to cells from neutralizing antibodies. Although CD4-independent viruses are well described for HIV and SIV, these viruses characteristically retain their CD4 binding site and can engage CD4 if available. We derived a novel CD4-independent, CCR5-tropic variant of the pathogenic molecular clone SIVmac239, termed iMac239. The genetic determinants of iMac239's CD4 independence provide new insights into mechanisms that underlie this phenotype. This virus remained replication competent even after its CD4 binding site had been ablated by mutagenesis. As the first truly non-CD4-tropic SIV, lacking the capacity to interact with CD4, iMac239 will provide the unique opportunity to evaluate SIV pathogenesis and host immune responses in the absence of the immunomodulatory effects of CD4(+) T cell targeting and infection.
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Affiliation(s)
- Adrienne E Swanstrom
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Beth Haggarty
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Andrea P O Jordan
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Josephine Romano
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - George J Leslie
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pyone P Aye
- Tulane National Primate Research Center, Covington, and Department of Tropical Medicine, Tulane University, New Orleans, Louisiana, USA
| | - Preston A Marx
- Tulane National Primate Research Center, Covington, and Department of Tropical Medicine, Tulane University, New Orleans, Louisiana, USA
| | - Andrew A Lackner
- Tulane National Primate Research Center, Covington, and Department of Tropical Medicine, Tulane University, New Orleans, Louisiana, USA
| | - Gregory Q Del Prete
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - James E Robinson
- Department of Pediatrics, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Michael R Betts
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - Celia C LaBranche
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA
| | - James A Hoxie
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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365
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Takeda S, Takizawa M, Miyauchi K, Urano E, Fujino M, Murakami T, Murakami T, Komano J. Conformational properties of the third variable loop of HIV-1AD8 envelope glycoprotein in the liganded conditions. Biochem Biophys Res Commun 2016; 475:113-8. [PMID: 27178216 DOI: 10.1016/j.bbrc.2016.05.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 05/10/2016] [Indexed: 10/21/2022]
Abstract
The conformational dynamics of the HIV-1 envelope glycoprotein gp120 and gp41 (Env) remains poorly understood. Here we examined how the V3 loop conformation is regulated in the liganded state using a panel of recombinant HIV-1NL4-3 clones bearing HIV-1AD8 Env by two experimental approaches, one adopting a monoclonal neutralizing antibody KD-247 (suvizumab) that recognizes the tip of the V3 loop, and the other assessing the function of the V3 loop. A significant positive correlation of the Env-KD-247 binding was detected between the liganded and unliganded conditions. Namely, the mutation D163G located in the V2 loop, which enhances viral susceptibility to KD-247 by 59.4-fold, had little effect on the sCD4-induced increment of the virus-KD-247 binding. By contrast, a virus with the S370N mutation in the C3 region increased the virus-KD-247 binding by 91.4-fold, although it did not influence the KD-247-mediated neutralization. Co-receptor usage and the susceptibility to CCR5 inhibitor Maraviroc were unaffected by D163G and S370N mutations. Collectively, these data suggest that the conformation of the liganded V3-loop of HIV-1AD8 Env is still under regulation of other Env domains aside from the V3 loop, including V2 and C3. Our results give an insight into the structural properties of HIV-1 Env and viral resistance to entry inhibitors by non-V3 loop mutations.
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Affiliation(s)
- Satoshi Takeda
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama Shinjuku, Tokyo, 162-0053, Japan
| | - Mari Takizawa
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama Shinjuku, Tokyo, 162-0053, Japan
| | - Kosuke Miyauchi
- Laboratory for Cytokine Regulation, Research Center for Integrative Medical Science (IMS), RIKEN Yokohama Institute, Suehiro-cho 1-7-22, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Emiko Urano
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama Shinjuku, Tokyo, 162-0053, Japan
| | - Masayuki Fujino
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama Shinjuku, Tokyo, 162-0053, Japan
| | - Toshio Murakami
- The Chemo-Sero-Therapeutic Research Institute, 1314-1 Kawabe Kyokushi, Kikuchi, Kumamoto, 869-1298, Japan
| | - Tsutomu Murakami
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama Shinjuku, Tokyo, 162-0053, Japan
| | - Jun Komano
- AIDS Research Center, National Institute of Infectious Diseases, 1-23-1 Toyama Shinjuku, Tokyo, 162-0053, Japan; Department of Clinical Laboratory, Nagoya Medical Center, 1-1 4-Chome, Sannomaru, Naka-ku, Nagoya, 460-0001, Japan.
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366
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Berinyuy E, Soliman MES. Identification of Novel Potential gp120 of HIV-1 Antagonist Using Per-Residue Energy Contribution-Based Pharmacophore modelling. Interdiscip Sci 2016; 9:406-418. [PMID: 27165479 DOI: 10.1007/s12539-016-0174-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 04/11/2016] [Accepted: 04/15/2016] [Indexed: 01/01/2023]
Abstract
Inhibition of HIV-1 target cell entry, by targeting gp120, has been identified as a promising approach for the identification and development of prophylactic and salvage HIV infection inhibitors. A small molecule compound 18A is an important chemotype in the development of novel and diverse viral cell entry inhibitors, as it inhibits a wide variety of HIV strains by disrupting allosteric structuring on gp120. This study combines residue energy contribution (REC) pharmacophore mapping of 18A and in silico molecular docking in a virtual screening campaign to identify novel and diverse antagonists of gp120. The binding free energy of a validated docked complex of gp120-18A and the quantitative contribution of interacting residues were obtained with a more accurate molecular mechanics/generalised born surface area (MM/GBSA) method followed by mapping the energetically favourable residue contributions onto atom centres in 18A to obtain a pharmacophore model. The generated pharmacophore hypothesis was used to search the ZINC database for 3D structures that match the pharmacophore. Further, molecular docking, molecular dynamics simulations and binding free energy analysis were performed on retrieved hits in order to rank hits based on their affinity and interactions in the CD4 binding cavity of a gp120. Interestingly, the top scoring compound designated with ZINC database ID as ZINC64700951 (docking score = -8.8 kcal/mol, ∆G = -43.77 kcal/mol) showed higher affinity compared to compound 18A docking score = -7.3 kcal/mol, ∆G = -31.97 kcal/mol) and interaction of ZN64700951 with validated allosteric hot spot residues, Asp368 and Met426, and binding hot spot residues, Asn425, Glu370, Gly473, Trp427 and Met475 in gp120, suggest that ZN64700951 is a promising antagonist of gp120. Thus, ZN64700951 could serve as an additional prototype for further optimisation as an HIV target cell viral entry inhibitor.
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Affiliation(s)
- Emiliene Berinyuy
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4000, South Africa
| | - Mahmoud E S Soliman
- Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban, 4000, South Africa.
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367
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de Taeye SW, Ozorowski G, Torrents de la Peña A, Guttman M, Julien JP, van den Kerkhof TLGM, Burger JA, Pritchard LK, Pugach P, Yasmeen A, Crampton J, Hu J, Bontjer I, Torres JL, Arendt H, DeStefano J, Koff WC, Schuitemaker H, Eggink D, Berkhout B, Dean H, LaBranche C, Crotty S, Crispin M, Montefiori DC, Klasse PJ, Lee KK, Moore JP, Wilson IA, Ward AB, Sanders RW. Immunogenicity of Stabilized HIV-1 Envelope Trimers with Reduced Exposure of Non-neutralizing Epitopes. Cell 2016; 163:1702-15. [PMID: 26687358 DOI: 10.1016/j.cell.2015.11.056] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/29/2015] [Accepted: 11/23/2015] [Indexed: 12/22/2022]
Abstract
The envelope glycoprotein trimer mediates HIV-1 entry into cells. The trimer is flexible, fluctuating between closed and more open conformations and sometimes sampling the fully open, CD4-bound form. We hypothesized that conformational flexibility and transient exposure of non-neutralizing, immunodominant epitopes could hinder the induction of broadly neutralizing antibodies (bNAbs). We therefore modified soluble Env trimers to stabilize their closed, ground states. The trimer variants were indeed stabilized in the closed conformation, with a reduced ability to undergo receptor-induced conformational changes and a decreased exposure of non-neutralizing V3-directed antibody epitopes. In rabbits, the stabilized trimers induced similar autologous Tier-1B or Tier-2 NAb titers to those elicited by the corresponding wild-type trimers but lower levels of V3-directed Tier-1A NAbs. Stabilized, closed trimers might therefore be useful components of vaccines aimed at inducing bNAbs.
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Affiliation(s)
- Steven W de Taeye
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alba Torrents de la Peña
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Jean-Philippe Julien
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tom L G M van den Kerkhof
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands; Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Laura K Pritchard
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Pavel Pugach
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Anila Yasmeen
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Jordan Crampton
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, Center for HIV-1/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA 92037, USA
| | - Joyce Hu
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, Center for HIV-1/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA 92037, USA
| | - Ilja Bontjer
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Heather Arendt
- International AIDS Vaccine Initiative, New York, NY 10004, USA
| | | | - Wayne C Koff
- International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Hanneke Schuitemaker
- Department of Experimental Immunology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Dirk Eggink
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Ben Berkhout
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands
| | - Hansi Dean
- International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Shane Crotty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, Center for HIV-1/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA 92037, USA
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - P J Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA.
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368
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Liang Y, Guttman M, Davenport TM, Hu SL, Lee KK. Probing the Impact of Local Structural Dynamics of Conformational Epitopes on Antibody Recognition. Biochemistry 2016; 55:2197-213. [PMID: 27003615 PMCID: PMC5479570 DOI: 10.1021/acs.biochem.5b01354] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Antibody-antigen interactions are governed by recognition of specific residues and structural complementarity between the antigen epitope and antibody paratope. While X-ray crystallography has provided detailed insights into static conformations of antibody-antigen complexes, factors such as conformational flexibility and dynamics, which are not readily apparent in the structures, can also have an impact on the binding event. Here we investigate the contribution of dynamics in the HIV-1 gp120 glycoprotein to antibody recognition of conserved conformational epitopes, including the CD4- and coreceptor-binding sites, and an inner domain site that is targeted by ADCC-active antibodies. Hydrogen/deuterium-exchange mass spectrometry (HDX-MS) was used to measure local structural dynamics across a panel of variable loop truncation mutants of HIV-1 gp120, including full-length gp120, ΔV3, ΔV1/V2, and extended core, which includes ΔV1/V2 and V3 loop truncations. CD4-bound full-length gp120 was also examined as a reference state. HDX-MS revealed a clear trend toward an increased level of order of the conserved subunit core resulting from loop truncation. Combined with biolayer interferometry and enzyme-linked immunosorbent assay measurements of antibody-antigen binding, we demonstrate that an increased level of ordering of the subunit core was associated with better recognition by an array of antibodies targeting complex conformational epitopes. These results provide detailed insight into the influence of structural dynamics on antibody-antigen interactions and suggest the importance of characterizing the structural stability of vaccine candidates to improve antibody recognition of complex epitopes.
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Affiliation(s)
- Yu Liang
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Thaddeus M. Davenport
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Shiu-Lok Hu
- Department of Pharmaceutics, University of Washington, Seattle, Washington 98195, United States
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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369
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Range of CD4-Bound Conformations of HIV-1 gp120, as Defined Using Conditional CD4-Induced Antibodies. J Virol 2016; 90:4481-4493. [PMID: 26889042 DOI: 10.1128/jvi.03206-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/14/2016] [Indexed: 01/23/2023] Open
Abstract
UNLABELLED The HIV envelope binds cellular CD4 and undergoes a range of conformational changes that lead to membrane fusion and delivery of the viral nucleocapsid into the cellular cytoplasm. This binding to CD4 reveals cryptic and highly conserved epitopes, the molecular nature of which is still not fully understood. The atomic structures of CD4 complexed with gp120 core molecules (a form of gp120 in which the V1, V2, and V3 loops and N and C termini have been truncated) have indicated that a hallmark feature of the CD4-bound conformation is the bridging sheet minidomain. Variations in the orientation of the bridging sheet hairpins have been revealed when CD4-liganded gp120 was compared to CD4-unliganded trimeric envelope structures. Hence, there appears to be a number of conformational transitions possible in HIV-1 monomeric gp120 that are affected by CD4 binding. The spectrum of CD4-bound conformations has been interrogated in this study by using a well-characterized panel of conditional, CD4-induced (CD4i) monoclonal antibodies (MAbs) that bind HIV-1 gp120 and its mutations under various conditions. Two distinct CD4i epitopes of the outer domain were studied: the first comprises the bridging sheet, while the second contains elements of the V2 loop. Furthermore, we show that the unliganded extended monomeric core of gp120 (coree) assumes an intermediate CD4i conformation in solution that further undergoes detectable rearrangements upon association with CD4. These discoveries impact both accepted paradigms concerning gp120 structure and the field of HIV immunogen design. IMPORTANCE Elucidation of the conformational transitions that the HIV-1 envelope protein undergoes during the course of entry into CD4(+)cells is fundamental to our understanding of HIV biology. The binding of CD4 triggers a range of gp120 structural rearrangements that could present targets for future drug design and development of preventive vaccines. Here we have systematically interrogated and scrutinized these conformational transitions using a panel of antibody probes that share a specific preference for the CD4i conformations. These have been employed to study a collection of gp120 mutations and truncations. Through these analyses, we propose 4 distinct sequential steps in CD4i transitions of gp120 conformations, each defined by antibody specificities and structural requirements of the HIV envelope monomer. As a result, we not only provide new insights into this dynamic process but also define probes to further investigate HIV infection.
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370
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White JM, Whittaker GR. Fusion of Enveloped Viruses in Endosomes. Traffic 2016; 17:593-614. [PMID: 26935856 PMCID: PMC4866878 DOI: 10.1111/tra.12389] [Citation(s) in RCA: 282] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 02/25/2016] [Accepted: 02/25/2016] [Indexed: 12/12/2022]
Abstract
Ari Helenius launched the field of enveloped virus fusion in endosomes with a seminal paper in the Journal of Cell Biology in 1980. In the intervening years, a great deal has been learned about the structures and mechanisms of viral membrane fusion proteins as well as about the endosomes in which different enveloped viruses fuse and the endosomal cues that trigger fusion. We now recognize three classes of viral membrane fusion proteins based on structural criteria and four mechanisms of fusion triggering. After reviewing general features of viral membrane fusion proteins and viral fusion in endosomes, we delve into three characterized mechanisms for viral fusion triggering in endosomes: by low pH, by receptor binding plus low pH and by receptor binding plus the action of a protease. We end with a discussion of viruses that may employ novel endosomal fusion‐triggering mechanisms. A key take‐home message is that enveloped viruses that enter cells by fusing in endosomes traverse the endocytic pathway until they reach an endosome that has all of the environmental conditions (pH, proteases, ions, intracellular receptors and lipid composition) to (if needed) prime and (in all cases) trigger the fusion protein and to support membrane fusion.
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Affiliation(s)
- Judith M White
- Department of Cell Biology, University of Virginia, Charlottesville, VA, USA
| | - Gary R Whittaker
- Department of Microbiology & Immunology, Cornell University, Ithaca, NY, USA
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371
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Oum YH, Desai TM, Marin M, Melikyan GB. Click labeling of unnatural sugars metabolically incorporated into viral envelope glycoproteins enables visualization of single particle fusion. J Virol Methods 2016; 233:62-71. [PMID: 27033181 DOI: 10.1016/j.jviromet.2016.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 02/11/2016] [Indexed: 10/22/2022]
Abstract
Enveloped viruses infect target cells by fusing their membrane with cellular membrane through a process that is mediated by specialized viral glycoproteins. The inefficient and highly asynchronous nature of viral fusion complicates studies of virus entry on a population level. Single virus imaging in living cells has become an important tool for delineating the entry pathways and for mechanistic studies of viral fusion. We have previously demonstrated that incorporation of fluorescent labels into the viral membrane and trapping fluorescent proteins in the virus interior enables the visualization of single virus fusion in living cells. Here, we implement a new approach to non-invasively label the viral membrane glycoproteins through metabolic incorporation of unnatural sugars followed by click-reaction with organic fluorescent dyes. This approach allows for efficient labeling of diverse viral fusion glycoproteins on the surface of HIV pseudoviruses. Incorporation of a content marker into surface-labeled viral particles enables sensitive detection of single virus fusion with live cells.
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Affiliation(s)
- Yoon Hyeun Oum
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, USA
| | - Tanay M Desai
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, USA
| | - Mariana Marin
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, USA
| | - Gregory B Melikyan
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, USA; Children's Healthcare of Atlanta, Atlanta, GA, USA.
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372
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Lee JH, Ozorowski G, Ward AB. Cryo-EM structure of a native, fully glycosylated, cleaved HIV-1 envelope trimer. Science 2016; 351:1043-8. [PMID: 26941313 DOI: 10.1126/science.aad2450] [Citation(s) in RCA: 356] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The envelope glycoprotein trimer (Env) on the surface of HIV-1 recognizes CD4(+) T cells and mediates viral entry. During this process, Env undergoes substantial conformational rearrangements, making it difficult to study in its native state. Soluble stabilized trimers have provided valuable insights into the Env structure, but they lack the hydrophobic membrane proximal external region (MPER, an important target of broadly neutralizing antibodies), the transmembrane domain, and the cytoplasmic tail. Here we present (i) a cryogenic electron microscopy (cryo-EM) structure of a clade B virus Env, which lacks only the cytoplasmic tail and is stabilized by the broadly neutralizing antibody PGT151, at a resolution of 4.2 angstroms and (ii) a reconstruction of this form of Env in complex with PGT151 and MPER-targeting antibody 10E8 at a resolution of 8.8 angstroms. These structures provide new insights into the wild-type Env structure.
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Affiliation(s)
- Jeong Hyun Lee
- 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, CA 92037, USA
| | - 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, CA 92037, USA
| | - 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, CA 92037, USA
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373
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de Taeye SW, Moore JP, Sanders RW. HIV-1 Envelope Trimer Design and Immunization Strategies To Induce Broadly Neutralizing Antibodies. Trends Immunol 2016; 37:221-232. [PMID: 26869204 DOI: 10.1016/j.it.2016.01.007] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/12/2016] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
Abstract
The identification of multiple broadly neutralizing antibodies (bNAbs) against the HIV-1 envelope glycoprotein (Env) trimer has facilitated its structural characterization and guided Env immunogen design. Several recent studies constitute progress in utilizing this knowledge for the development of an HIV-1 vaccine that induces bNAbs. Native-like Env trimers can induce autologous NAb responses against resistant (Tier-2) viruses in several animal models. Here we review recent studies aimed at addressing the challenge of driving the strong but narrowly focused NAb responses to Env trimers towards ones with much greater breadth. Among strategies that merit pursuing are using multiple trimers as sequential or simultaneous immunogens, targeting the germline precursors of bNAbs, delivering sequential lineages of trimers derived from infected individuals who developed bNAbs, and presenting trimers as particulate antigens.
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Affiliation(s)
- Steven W de Taeye
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA.
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374
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Yokoyama M, Nomaguchi M, Doi N, Kanda T, Adachi A, Sato H. In silico Analysis of HIV-1 Env-gp120 Reveals Structural Bases for Viral Adaptation in Growth-Restrictive Cells. Front Microbiol 2016; 7:110. [PMID: 26903989 PMCID: PMC4746247 DOI: 10.3389/fmicb.2016.00110] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/21/2016] [Indexed: 12/17/2022] Open
Abstract
Variable V1/V2 and V3 loops on human immunodeficiency virus type 1 (HIV-1) envelope-gp120 core play key roles in modulating viral competence to recognize two infection receptors, CD4 and chemokine-receptors. However, molecular bases for the modulation largely remain unclear. To address these issues, we constructed structural models for a full-length gp120 in CD4-free and -bound states. The models showed topologies of gp120 surface loop that agree with those in reported structural data. Molecular dynamics simulation showed that in the unliganded state, V1/V2 loop settled into a thermodynamically stable arrangement near V3 loop for conformational masking of V3 tip, a potent neutralization epitope. In the CD4-bound state, however, V1/V2 loop was rearranged near the bound CD4 to support CD4 binding. In parallel, cell-based adaptation in the absence of anti-viral antibody pressures led to the identification of amino acid substitutions that individually enhance viral entry and growth efficiencies in association with reduced sensitivity to CCR5 antagonist TAK-779. Notably, all these substitutions were positioned on the receptors binding surfaces in V1/V2 or V3 loop. In silico structural studies predicted some physical changes of gp120 by substitutions with alterations in viral replication phenotypes. These data suggest that V1/V2 loop is critical for creating a gp120 structure that masks co-receptor binding site compatible with maintenance of viral infectivity, and for tuning a functional balance of gp120 between immune escape ability and infectivity to optimize HIV-1 replication fitness.
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Affiliation(s)
- Masaru Yokoyama
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases Tokyo, Japan
| | - Masako Nomaguchi
- Department of Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School Tokushima, Japan
| | - Naoya Doi
- Department of Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School Tokushima, Japan
| | - Tadahito Kanda
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious DiseasesTokyo, Japan; Department of Research Promotion, Division of Infectious Disease Research, Japan Agency for Medical Research and DevelopmentTokyo, Japan
| | - Akio Adachi
- Department of Microbiology, Institute of Biomedical Sciences, Tokushima University Graduate School Tokushima, Japan
| | - Hironori Sato
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases Tokyo, Japan
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375
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DeSantis MC, Cheng W. Label-free detection and manipulation of single biological nanoparticles. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 8:717-29. [PMID: 26846164 DOI: 10.1002/wnan.1392] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 12/23/2015] [Accepted: 01/05/2016] [Indexed: 11/11/2022]
Abstract
In the past several years, there have been significant advances in the field of nanoparticle detection for various biological applications. Of considerable interest are synthetic nanoparticles being designed as potential drug delivery systems as well as naturally occurring or biological nanoparticles, including viruses and extracellular vesicles. Many infectious diseases and several human cancers are attributed to individual virions. Because these particles likely display different degrees of heterogeneity under normal physiological conditions, characterization of these natural nanoparticles with single-particle sensitivity is necessary for elucidating information on their basic structure and function as well as revealing novel targets for therapeutic intervention. Additionally, biodefense and point-of-care clinical testing demand ultrasensitive detection of viral pathogens particularly with high specificity. Consequently, the ability to perform label-free virus sensing has motivated the development of multiple electrical-, mechanical-, and optical-based detection techniques, some of which may even have the potential for nanoparticle sorting and multi-parametric analysis. For each technique, the challenges associated with label-free detection and measurement sensitivity are discussed as are their potential contributions for future real-world applications. WIREs Nanomed Nanobiotechnol 2016, 8:717-729. doi: 10.1002/wnan.1392 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Michael C DeSantis
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Wei Cheng
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA.,Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
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376
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Zolla-Pazner S, Cohen SS, Boyd D, Kong XP, Seaman M, Nussenzweig M, Klein F, Overbaugh J, Totrov M. Structure/Function Studies Involving the V3 Region of the HIV-1 Envelope Delineate Multiple Factors That Affect Neutralization Sensitivity. J Virol 2016; 90:636-49. [PMID: 26491157 PMCID: PMC4702699 DOI: 10.1128/jvi.01645-15] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 10/04/2015] [Indexed: 01/13/2023] Open
Abstract
UNLABELLED Antibodies (Abs) specific for the V3 loop of the HIV-1 gp120 envelope neutralize most tier 1 and many tier 2 viruses and are present in essentially all HIV-infected individuals as well as immunized humans and animals. Vaccine-induced V3 Abs are associated with reduced HIV infection rates in humans and affect the nature of transmitted viruses in infected vaccinees, despite the fact that V3 is often occluded in the envelope trimer. Here, we link structural and experimental data showing how conformational alterations of the envelope trimer render viruses exceptionally sensitive to V3 Abs. The experiments interrogated the neutralization sensitivity of pseudoviruses with single amino acid mutations in various regions of gp120 that were predicted to alter packing of the V3 loop in the Env trimer. The results indicate that the V3 loop is metastable in the envelope trimer on the virion surface, flickering between states in which V3 is either occluded or available for binding to chemokine receptors (leading to infection) and to V3 Abs (leading to virus neutralization). The spring-loaded V3 in the envelope trimer is easily released by disruption of the stability of the V3 pocket in the unliganded trimer or disruption of favorable V3/pocket interactions. Formation of the V3 pocket requires appropriate positioning of the V1V2 domain, which is, in turn, dependent on the conformation of the bridging sheet and on the stability of the V1V2 B-C strand-connecting loop. IMPORTANCE The levels of antibodies to the third variable region (V3) of the HIV envelope protein correlate with reduced HIV infection rates. Previous studies showed that V3 is often occluded, as it sits in a pocket of the envelope trimer on the surface of virions; however, the trimer is flexible, allowing occluded portions of the envelope (like V3) to flicker into an exposed position that binds antibodies. Here we provide a systematic interrogation of mechanisms by which single amino acid changes in various regions of gp120 (i) render viruses sensitive to neutralization by V3 antibodies, (ii) result in altered packing of the V3 loop, and (iii) activate an open conformation that exposes V3 to the effects of V3 Abs. Taken together, these and previous studies explain how V3 antibodies can protect against HIV-1 infection and why they should be one of the targets of vaccine-induced antibodies.
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Affiliation(s)
- Susan Zolla-Pazner
- Veterans Affairs New York Harbor Healthcare System, New York, New York, USA Departments of Pathology and Biochemistry, New York University School of Medicine, New York, New York, USA
| | - Sandra Sharpe Cohen
- Departments of Pathology and Biochemistry, New York University School of Medicine, New York, New York, USA
| | - David Boyd
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Xiang-Peng Kong
- Departments of Pathology and Biochemistry, New York University School of Medicine, New York, New York, USA
| | - Michael Seaman
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | | | | | - Julie Overbaugh
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Max Totrov
- Molsoft, L.L.C., San Diego, California, USA
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377
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Dynamic Viral Glycoprotein Machines: Approaches for Probing Transient States That Drive Membrane Fusion. Viruses 2016; 8:v8010015. [PMID: 26761026 PMCID: PMC4728575 DOI: 10.3390/v8010015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 12/11/2015] [Accepted: 12/31/2015] [Indexed: 01/10/2023] Open
Abstract
The fusion glycoproteins that decorate the surface of enveloped viruses undergo dramatic conformational changes in the course of engaging with target cells through receptor interactions and during cell entry. These refolding events ultimately drive the fusion of viral and cellular membranes leading to delivery of the genetic cargo. While well-established methods for structure determination such as X-ray crystallography have provided detailed structures of fusion proteins in the pre- and post-fusion fusion states, to understand mechanistically how these fusion glycoproteins perform their structural calisthenics and drive membrane fusion requires new analytical approaches that enable dynamic intermediate states to be probed. Methods including structural mass spectrometry, small-angle X-ray scattering, and electron microscopy have begun to provide new insight into pathways of conformational change and fusion protein function. In combination, the approaches provide a significantly richer portrait of viral fusion glycoprotein structural variation and fusion activation as well as inhibition by neutralizing agents. Here recent studies that highlight the utility of these complementary approaches will be reviewed with a focus on the well-characterized influenza virus hemagglutinin fusion glycoprotein system.
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378
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Sliepen K, Sanders RW. HIV-1 envelope glycoprotein immunogens to induce broadly neutralizing antibodies. Expert Rev Vaccines 2016; 15:349-65. [PMID: 26654478 DOI: 10.1586/14760584.2016.1129905] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The long pursuit for a vaccine against human immunodeficiency virus 1 (HIV-1) has recently been boosted by a number of exciting developments. An HIV-1 subunit vaccine ideally should elicit potent broadly neutralizing antibodies (bNAbs), but raising bNAbs by vaccination has proved extremely difficult because of the characteristics of the HIV-1 envelope glycoprotein complex (Env). However, the isolation of bNAbs from HIV-1-infected patients demonstrates that the human humoral immune system is capable of making such antibodies. Therefore, a focus of HIV-1 vaccinology is the elicitation of bNAbs by engineered immunogens and by using vaccination strategies aimed at mimicking the bNAb maturation pathways in HIV-infected patients. Important clues can also be taken from the successful subunit vaccines against hepatitis B virus and human papillomavirus. Here, we review the different types of HIV-1 immunogens and vaccination strategies that are being explored in the search for an HIV-1 vaccine that induces bNAbs.
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Affiliation(s)
- Kwinten Sliepen
- a Department of Medical Microbiology, Academic Medical Center , University of Amsterdam , Amsterdam , The Netherlands
| | - Rogier W Sanders
- a Department of Medical Microbiology, Academic Medical Center , University of Amsterdam , Amsterdam , The Netherlands.,b Department of Microbiology and Immunology , Weill Medical College of Cornell University , New York , NY , USA
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379
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Klasse PJ. How to assess the binding strength of antibodies elicited by vaccination against HIV and other viruses. Expert Rev Vaccines 2016; 15:295-311. [PMID: 26641943 DOI: 10.1586/14760584.2016.1128831] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Vaccines that protect against viral infections generally induce neutralizing antibodies. When vaccines are evaluated, the need arises to assess the affinity maturation of the antibody responses. Binding titers of polyclonal sera depend not only on the affinities of the constituent antibodies but also on their individual concentrations, which are difficult to ascertain. Therefore an assay based on chaotrope disruption of antibody-antigen complexes was designed for measuring binding strength. This assay works well with many viral antigens but gives differential results depending on the conformational dependence of epitopes on complex antigens such as the envelope glycoprotein of HIV-1. Kinetic binding assays might offer alternatives, since they can measure average off-rate constants for polyclonal antibodies in a serum. Here, potentials and fallacies of these techniques are discussed.
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Affiliation(s)
- P J Klasse
- a Department of Microbiology and Immunology, Weill Cornell Medical College , Cornell University , New York , NY , USA
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380
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Gorman J, Soto C, Yang MM, Davenport TM, Guttman M, Bailer RT, Chambers M, Chuang GY, DeKosky BJ, Doria-Rose NA, Druz A, Ernandes MJ, Georgiev IS, Jarosinski MC, Joyce MG, Lemmin TM, Leung S, Louder MK, McDaniel JR, Narpala S, Pancera M, Stuckey J, Wu X, Yang Y, Zhang B, Zhou T, NISC Comparative Sequencing Program, Mullikin JC, Baxa U, Georgiou G, McDermott AB, Bonsignori M, Haynes BF, Moore PL, Morris L, Lee KK, Shapiro L, Mascola JR, Kwong PD. Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design. Nat Struct Mol Biol 2016; 23:81-90. [PMID: 26689967 PMCID: PMC4833398 DOI: 10.1038/nsmb.3144] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 11/17/2015] [Indexed: 12/20/2022]
Abstract
Broadly neutralizing antibodies (bNAbs) against HIV-1 Env V1V2 arise in multiple donors. However, atomic-level interactions had previously been determined only with antibodies from a single donor, thus making commonalities in recognition uncertain. Here we report the cocrystal structure of V1V2 with antibody CH03 from a second donor and model Env interactions of antibody CAP256-VRC26 from a third donor. These V1V2-directed bNAbs used strand-strand interactions between a protruding antibody loop and a V1V2 strand but differed in their N-glycan recognition. Ontogeny analysis indicated that protruding loops develop early, and glycan interactions mature over time. Altogether, the multidonor information suggested that V1V2-directed bNAbs form an 'extended class', for which we engineered ontogeny-specific antigens: Env trimers with chimeric V1V2s that interacted with inferred ancestor and intermediate antibodies. The ontogeny-based design of vaccine antigens described here may provide a general means for eliciting antibodies of a desired class.
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Affiliation(s)
- Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Cinque Soto
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Max M. Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | | | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington
| | - Robert T. Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Michael Chambers
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Brandon J. DeKosky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas
| | - Nicole A. Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Aliaksandr Druz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Michael J. Ernandes
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Ivelin S. Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Marissa C. Jarosinski
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - M. Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Thomas M. Lemmin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Sherman Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Mark K. Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jonathan R. McDaniel
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas
| | - Sandeep Narpala
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Marie Pancera
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jonathan Stuckey
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Xueling Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | | | - James C. Mullikin
- NIH Intramural Sequenicng Center (NISC), National Human Geonome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Ulrich Baxa
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas
| | - Adrian B. McDermott
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Mattia Bonsignori
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Barton F. Haynes
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Penny L. Moore
- Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, South Africa
| | - Lynn Morris
- Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, South Africa
| | - Kelly K. Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
- Department of Biochemistry & Molecular Biophysics and Department of Systems Biology, Columbia University, New York
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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381
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Immunogenicity of a Prefusion HIV-1 Envelope Trimer in Complex with a Quaternary-Structure-Specific Antibody. J Virol 2015; 90:2740-55. [PMID: 26719262 DOI: 10.1128/jvi.02380-15] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/10/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The HIV-1 envelope trimer (Env) is the target of broadly neutralizing antibodies and is being explored as a vaccine candidate to elicit protective antibodies. One of the most promising antigenic and structural mimics of HIV-1 Env is the SOSIP.664-stabilized soluble trimer from the clade A strain BG505, which is preferentially recognized by broadly neutralizing antibodies. Trimer immunization elicits high-titer neutralization of the autologous tier 2 BG505 strain; however, breadth is limited, and substantial interest has focused on understanding and improving trimer immunogenicity. We sought to improve the antigenic specificity of BG505 SOSIP.664 by reducing recognition of the variable loop 3 (V3) region, which elicits only weakly neutralizing antibodies. To stabilize the trimer in its prefusion closed conformation, we complexed trimeric BG505 SOSIP.664 with the antigen-binding fragment (Fab) of PGT145, a broadly neutralizing quaternary-structure-specific antibody. Compared to the ligand-free trimer, the PGT145 Fab-BG505 SOSIP.664 complex displayed increased melting temperature stability and reduced V3 recognition. In guinea pigs, immunization with the PGT145 Fab-BG505 SOSIP.664 complex elicited ∼100-fold lower V3-directed binding and neutralization titers than those obtained with ligand-free BG505 SOSIP.664. Both complexed and ligand-free BG505 SOSIP.664 elicited comparable neutralization of the autologous BG505 virus, and in both cases, BG505 neutralization mapped to the outer domain of gp120 for some guinea pigs. Our results indicate that it is possible to reduce immune recognition of the V3 region of the trimer while maintaining the antigenic profile needed to induce autologous neutralizing antibodies. These data suggest that appropriate modifications of trimer immunogens could further focus the immune response on key neutralization epitopes. IMPORTANCE HIV-1 Env trimers have been proposed as preferred HIV-1 vaccine immunogens. One version, BG505 SOSIP.664, a soluble stabilized trimer, was recently shown to elicit high-titer autologous neutralizing antibodies (NAbs) in rabbits. Here we compared two immunogens: the ligand-free BG505 SOSIP.664 trimer and the same trimer bound to the antigen-binding fragment (Fab) of the PGT145 antibody, a broadly neutralizing antibody which recognizes the trimer at its membrane-distal apex. We hypothesized that the Fab-bound complex would stabilize BG505 SOSIP.664 in its prefusion closed conformation and limit reactivity to weakly neutralizing antibodies targeting the variable loop 3 (V3) region. In guinea pigs, the Fab-complexed trimer induced 100-fold lower responses to the V3 region, while both ligand-free and Fab-complexed trimers elicited similar levels of autologous NAbs. Our findings demonstrate the potential to reduce "off-target" immunogenicity while maintaining the capacity to generate autologous NAbs.
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382
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Scharf L, Wang H, Gao H, Chen S, McDowall AW, Bjorkman PJ. Broadly Neutralizing Antibody 8ANC195 Recognizes Closed and Open States of HIV-1 Env. Cell 2015; 162:1379-90. [PMID: 26359989 DOI: 10.1016/j.cell.2015.08.035] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 06/19/2015] [Accepted: 07/28/2015] [Indexed: 10/23/2022]
Abstract
The HIV-1 envelope (Env) spike contains limited epitopes for broadly neutralizing antibodies (bNAbs); thus, most neutralizing antibodies are strain specific. The 8ANC195 epitope, defined by crystal and electron microscopy (EM) structures of bNAb 8ANC195 complexed with monomeric gp120 and trimeric Env, respectively, spans the gp120 and gp41 Env subunits. To investigate 8ANC195's gp41 epitope at higher resolution, we solved a 3.58 Å crystal structure of 8ANC195 complexed with fully glycosylated Env trimer, revealing 8ANC195 insertion into a glycan shield gap to contact gp120 and gp41 glycans and protein residues. To determine whether 8ANC195 recognizes the CD4-bound open Env conformation that leads to co-receptor binding and fusion, one of several known conformations of virion-associated Env, we solved EM structures of an Env/CD4/CD4-induced antibody/8ANC195 complex. 8ANC195 binding partially closed the CD4-bound trimer, confirming structural plasticity of Env by revealing a previously unseen conformation. 8ANC195's ability to bind different Env conformations suggests advantages for potential therapeutic applications.
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Affiliation(s)
- Louise Scharf
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Haoqing Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Songye Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alasdair W McDowall
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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383
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van Oijen AM, Dixon NE. Probing molecular choreography through single-molecule biochemistry. Nat Struct Mol Biol 2015; 22:948-52. [DOI: 10.1038/nsmb.3119] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/06/2015] [Indexed: 01/09/2023]
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384
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Pan J, Zhang S, Chou A, Borchers CH. Higher-order structural interrogation of antibodies using middle-down hydrogen/deuterium exchange mass spectrometry. Chem Sci 2015; 7:1480-1486. [PMID: 29910905 PMCID: PMC5975933 DOI: 10.1039/c5sc03420e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/24/2015] [Indexed: 01/05/2023] Open
Abstract
Specific restricted proteolysis combined with subzero temperature HPLC and online ETD facilitates structural characterization of antibodies at high resolution.
Although X-ray crystallography is the “gold standard” method for protein higher-order structure analysis, the challenges of antibody crystallization and the time-consuming data analysis involved make this technique unsuitable for routine structural studies of antibodies. In addition, crystallography cannot be used for the structural characterization of an antibody in solution, under conditions where antibody drugs are active. Intact antibodies are also too large and too complex for NMR. Top-down mass spectrometry coupled to hydrogen/deuterium exchange (HDX) is a powerful tool for high-resolution protein structural characterization, but its success declines rapidly as protein size increases. Here we report for the first time a new hybrid “middle-down” HDX approach that overcomes this limitation through enabling the nonspecific enzyme pepsin to perform specific restricted digestion at low pH prior to HPLC separation at subzero temperatures and online electron transfer dissociation (ETD). Three large specific peptic fragments (12 to 25 kDa) were observed from the heavy chain and light chain of a therapeutic antibody Herceptin, together with a few smaller fragments from the middle portion of the heavy chain. The average amino-acid resolutions obtained by ETD were around two residues, with single-residue resolution in many regions. This middle-down approach is also applicable to other antibodies. It provided HDX information on the entire light chain, and 95.3% of the heavy chain, representing 96.8% of the entire antibody (150 kDa). The structural effects of glycosylation on Herceptin were determined at close-to-single residue level by this method.
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Affiliation(s)
- Jingxi Pan
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , #3101-4464 Markham St. , Victoria , BC V8Z 7X8 , Canada .
| | - Suping Zhang
- MRM Proteomics Inc. , 4464 Markham Street, Suite #2108 , Victoria , British Columbia V8Z 7X8 , Canada
| | - Albert Chou
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , #3101-4464 Markham St. , Victoria , BC V8Z 7X8 , Canada .
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , #3101-4464 Markham St. , Victoria , BC V8Z 7X8 , Canada . .,Department of Biochemistry & Microbiology , University of Victoria , Petch Building Room 207, 3800 Finnerty Rd. , Victoria , BC V8P 5C2 , Canada
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385
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Peptide triazole inactivators of HIV-1: how do they work and what is their potential? Future Med Chem 2015; 7:2305-10. [PMID: 26599515 DOI: 10.4155/fmc.15.152] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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386
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Sommerstein R, Flatz L, Remy MM, Malinge P, Magistrelli G, Fischer N, Sahin M, Bergthaler A, Igonet S, ter Meulen J, Rigo D, Meda P, Rabah N, Coutard B, Bowden TA, Lambert PH, Siegrist CA, Pinschewer DD. Arenavirus Glycan Shield Promotes Neutralizing Antibody Evasion and Protracted Infection. PLoS Pathog 2015; 11:e1005276. [PMID: 26587982 PMCID: PMC4654586 DOI: 10.1371/journal.ppat.1005276] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/22/2015] [Indexed: 01/05/2023] Open
Abstract
Arenaviruses such as Lassa virus (LASV) can cause severe hemorrhagic fever in humans. As a major impediment to vaccine development, delayed and weak neutralizing antibody (nAb) responses represent a unifying characteristic of both natural infection and all vaccine candidates tested to date. To investigate the mechanisms underlying arenavirus nAb evasion we engineered several arenavirus envelope-chimeric viruses and glycan-deficient variants thereof. We performed neutralization tests with sera from experimentally infected mice and from LASV-convalescent human patients. NAb response kinetics in mice correlated inversely with the N-linked glycan density in the arenavirus envelope protein’s globular head. Additionally and most intriguingly, infection with fully glycosylated viruses elicited antibodies, which neutralized predominantly their glycan-deficient variants, both in mice and humans. Binding studies with monoclonal antibodies indicated that envelope glycans reduced nAb on-rate, occupancy and thereby counteracted virus neutralization. In infected mice, the envelope glycan shield promoted protracted viral infection by preventing its timely elimination by the ensuing antibody response. Thus, arenavirus envelope glycosylation impairs the protective efficacy rather than the induction of nAbs, and thereby prevents efficient antibody-mediated virus control. This immune evasion mechanism imposes limitations on antibody-based vaccination and convalescent serum therapy. Neutralizing antibodies (nAbs) represent a key principle of antiviral immunity. Protective vaccines aim at inducing nAbs to prevent viral infection, and infusion of nAbs in convalescent patient serum can offer a potent antiviral therapy. Certain viruses, however, have found ways to evade nAb control. Amongst them are high-risk pathogens of the arenavirus family such as Lassa virus (LASV), which is a frequent cause of hemorrhagic fever in West Africa. Here we unveil the molecular strategy by which arenaviruses escape antibody neutralization and avoid efficient immune control. We show that their surface is decorated with sugar moieties, serving to shield the virus against the neutralizing effect of the host’s antibodies. This immune evasion strategy differs from those described for other viruses, in which sugars impair primarily the induction of antibodies or allow for viral mutational escape. The arenavirus sugar coat renders the host nAb response inefficient and as a consequence thereof, the host fails to promptly control the infection. Our results offer a compelling explanation for the long history of failures in trying to make a nAb-based vaccine against LASV or in using convalescent serum for therapy. These mechanistic insights will support vaccine development efforts against arenaviruses such as LASV.
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Affiliation(s)
- Rami Sommerstein
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- World Health Organization Collaborating Centre for Vaccine Immunology, University of Geneva, Geneva, Switzerland
| | - Lukas Flatz
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Melissa M. Remy
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- Division of Experimental Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | | | | | - Mehmet Sahin
- Division of Experimental Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Andreas Bergthaler
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Sebastien Igonet
- Institut Pasteur, Département de Virologie, Unité de Virologie Structurale and CNRS UMR 3569 Virologie, Paris, France
| | - Jan ter Meulen
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Dorothée Rigo
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Paolo Meda
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Nadia Rabah
- AFMB, UMR7257 CNRS/Aix Marseille Université, Marseille, France
| | - Bruno Coutard
- AFMB, UMR7257 CNRS/Aix Marseille Université, Marseille, France
| | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Paul-Henri Lambert
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- World Health Organization Collaborating Centre for Vaccine Immunology, University of Geneva, Geneva, Switzerland
| | - Claire-Anne Siegrist
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- World Health Organization Collaborating Centre for Vaccine Immunology, University of Geneva, Geneva, Switzerland
| | - Daniel D. Pinschewer
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- World Health Organization Collaborating Centre for Vaccine Immunology, University of Geneva, Geneva, Switzerland
- Division of Experimental Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
- * E-mail:
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387
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Coevolution Analysis of HIV-1 Envelope Glycoprotein Complex. PLoS One 2015; 10:e0143245. [PMID: 26579711 PMCID: PMC4651434 DOI: 10.1371/journal.pone.0143245] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/02/2015] [Indexed: 11/19/2022] Open
Abstract
The HIV-1 Env spike is the main protein complex that facilitates HIV-1 entry into CD4+ host cells. HIV-1 entry is a multistep process that is not yet completely understood. This process involves several protein-protein interactions between HIV-1 Env and a variety of host cell receptors along with many conformational changes within the spike. HIV-1 Env developed due to high mutation rates and plasticity escape strategies from immense immune pressure and entry inhibitors. We applied a coevolution and residue-residue contact detecting method to identify coevolution patterns within HIV-1 Env protein sequences representing all group M subtypes. We identified 424 coevolving residue pairs within HIV-1 Env. The majority of predicted pairs are residue-residue contacts and are proximal in 3D structure. Furthermore, many of the detected pairs have functional implications due to contributions in either CD4 or coreceptor binding, or variable loop, gp120-gp41, and interdomain interactions. This study provides a new dimension of information in HIV research. The identified residue couplings may not only be important in assisting gp120 and gp41 coordinate structure prediction, but also in designing new and effective entry inhibitors that incorporate mutation patterns of HIV-1 Env.
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388
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Inhibitors of HIV-1 attachment: The discovery and structure-activity relationships of tetrahydroisoquinolines as replacements for the piperazine benzamide in the 3-glyoxylyl 6-azaindole pharmacophore. Bioorg Med Chem Lett 2015; 26:160-7. [PMID: 26584882 DOI: 10.1016/j.bmcl.2015.11.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/02/2015] [Accepted: 11/04/2015] [Indexed: 11/22/2022]
Abstract
6,6-Fused ring systems including tetrahydroisoquinolines and tetrahydropyrido[3,4-d]pyrimidines have been explored as possible replacements for the piperazine benzamide portion of the HIV-1 attachment inhibitor BMS-663068. In initial studies, the tetrahydroisoquinoline compounds demonstrate sub-nanomolar activity in a HIV-1 pseudotype viral infection assay used as the initial screen for inhibitory activity. Analysis of SARs and approaches to optimization for an improved drug-like profile are examined herein.
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389
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Genotypic Differences in Dengue Virus Neutralization Are Explained by a Single Amino Acid Mutation That Modulates Virus Breathing. mBio 2015; 6:e01559-15. [PMID: 26530385 PMCID: PMC4631804 DOI: 10.1128/mbio.01559-15] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Flaviviruses sample an ensemble of virion conformations resulting from the conformational flexibility of their structural proteins. To investigate how sequence variation among strains impacts virus breathing, we performed studies with the monoclonal antibody (MAb) E111, which binds an inaccessible domain III envelope (E) protein epitope of dengue virus serotype 1 (DENV1). Prior studies indicated that an observed ~200-fold difference in neutralization between the DENV1 strains Western Pacific-74 (West Pac-74) and 16007 could not be explained by differences in the affinity of MAb E111 for each strain. Through neutralization studies with wild-type and variant viruses carrying genes encoding reciprocal mutations at all 13 amino acid differences between the E proteins of West Pac-74 and 16007, we found that E111 neutralization susceptibility mapped solely to the presence of a lysine or arginine at E domain II residue 204, located distally from the E111 epitope. This same residue correlated with neutralization differences observed for MAbs specific for epitopes distinct from E111, suggesting that this amino acid dictates changes in the conformational ensembles sampled by the virus. Furthermore, an observed twofold difference in the stability of infectious West Pac-74 versus 16007 in solution also mapped to E residue 204. Our results demonstrate that neutralization susceptibility can be altered in an epitope-independent manner by natural strain variation that influences the structures sampled by DENV. That different conformational ensembles of flaviviruses may affect the landscape available for antibody binding, as well as virus stability, has important implications for functional studies of antibody potency, a critical aspect of vaccine development. The global burden of dengue virus (DENV) is growing, with recent estimates of ~390 million human infections each year. Antibodies play a crucial role in protection from DENV infection, and vaccines that elicit a robust antibody response are being actively pursued. We report here the identification of a single amino acid residue in the envelope protein of DENV serotype 1 that results in global changes to virus structure and stability when it is changed. Our results indicate that naturally occurring variation at this particular site among virus strains impacts the ensemble of structures sampled by the virus, a process referred to as virus breathing. The finding that such limited and conservative sequence changes can modulate the landscape available for antibody binding has important implications for both vaccine development and the study of DENV-reactive antibodies.
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390
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Chemical Cross-Linking Stabilizes Native-Like HIV-1 Envelope Glycoprotein Trimer Antigens. J Virol 2015; 90:813-28. [PMID: 26512083 PMCID: PMC4702668 DOI: 10.1128/jvi.01942-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/21/2015] [Indexed: 01/26/2023] Open
Abstract
Major neutralizing antibody immune evasion strategies of the HIV-1 envelope glycoprotein (Env) trimer include conformational and structural instability. Stabilized soluble trimers such as BG505 SOSIP.664 mimic the structure of virion-associated Env but nevertheless sample different conformational states. Here we demonstrate that treating BG505 SOSIP.664 trimers with glutaraldehyde or a heterobifunctional cross-linker introduces additional stability with relatively modest effects on antigenicity. Thus, most broadly neutralizing antibody (bNAb) epitopes were preserved after cross-linking, whereas the binding of most weakly or nonneutralizing antibodies (non-NAb) was reduced. Cross-linking stabilized all Env conformers present within a mixed population, and individual conformers could be isolated by bNAb affinity chromatography. Both positive selection of cross-linked conformers using the quaternary epitope-specific bNAbs PGT145, PGT151, and 3BC315 and negative selection with non-NAbs against the V3 region enriched for trimer populations with improved antigenicity for bNAbs. Similar results were obtained using the clade B B41 SOSIP.664 trimer. The cross-linking method may, therefore, be useful for countering the natural conformational heterogeneity of some HIV-1 Env proteins and, by extrapolation, also vaccine immunogens from other pathogens. IMPORTANCE The development of a vaccine to induce protective antibodies against HIV-1 is of primary public health importance. Recent advances in immunogen design have provided soluble recombinant envelope glycoprotein trimers with near-native morphology and antigenicity. However, these trimers are conformationally flexible, potentially reducing B-cell recognition of neutralizing antibody epitopes. Here we show that chemical cross-linking increases trimer stability, reducing binding of nonneutralizing antibodies while largely maintaining neutralizing antibody binding. Cross-linking followed by positive or negative antibody affinity selection of individual stable conformational variants further improved the antigenic and morphological characteristics of the trimers. This approach may be generally applicable to HIV-1 Env and also to other conformationally flexible pathogen antigens.
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391
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Rationally Targeted Mutations at the V1V2 Domain of the HIV-1 Envelope to Augment Virus Neutralization by Anti-V1V2 Monoclonal Antibodies. PLoS One 2015; 10:e0141233. [PMID: 26491873 PMCID: PMC4619609 DOI: 10.1371/journal.pone.0141233] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/06/2015] [Indexed: 01/25/2023] Open
Abstract
HIV-1 envelope glycoproteins (Env) are the only viral antigens present on the virus surface and serve as the key targets for virus-neutralizing antibodies. However, HIV-1 deploys multiple strategies to shield the vulnerable sites on its Env from neutralizing antibodies. The V1V2 domain located at the apex of the HIV-1 Env spike is known to encompass highly variable loops, but V1V2 also contains immunogenic conserved elements recognized by cross-reactive antibodies. This study evaluates human monoclonal antibodies (mAbs) against V2 epitopes which overlap with the conserved integrin α4β7-binding LDV/I motif, designated as the V2i (integrin) epitopes. We postulate that the V2i Abs have weak or no neutralizing activities because the V2i epitopes are often occluded from antibody recognition. To gain insights into the mechanisms of the V2i occlusion, we evaluated three elements at the distal end of the V1V2 domain shown in the structure of V2i epitope complexed with mAb 830A to be important for antibody recognition of the V2i epitope. Amino-acid substitutions at position 179 that restore the LDV/I motif had minimal effects on virus sensitivity to neutralization by most V2i mAbs. However, a charge change at position 153 in the V1 region significantly increased sensitivity of subtype C virus ZM109 to most V2i mAbs. Separately, a disulfide bond introduced to stabilize the hypervariable region of V2 loop also enhanced virus neutralization by some V2i mAbs, but the effects varied depending on the virus. These data demonstrate that multiple elements within the V1V2 domain act independently and in a virus-dependent fashion to govern the antibody recognition and accessibility of V2i epitopes, suggesting the need for multi-pronged strategies to counter the escape and the shielding mechanisms obstructing the V2i Abs from neutralizing HIV-1.
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392
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Yu Y, Fu L, Shi Y, Guan S, Yang L, Gong X, Yin H, He X, Liu D, Kuai Z, Shan Y, Wang S, Kong W. Elicitation of HIV-1 neutralizing antibodies by presentation of 4E10 and 10E8 epitopes on Norovirus P particles. Immunol Lett 2015; 168:271-8. [PMID: 26455781 DOI: 10.1016/j.imlet.2015.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/15/2015] [Accepted: 10/05/2015] [Indexed: 01/12/2023]
Abstract
Eliciting efficient broadly neutralizing antibodies (BnAbs) is a major goal in vaccine development against human immunodeficiency virus type 1 (HIV-1). Conserved epitopes in the membrane-proximal external region (MPER) of HIV-1 are a significant target. In this study, Norovirus P particles (NoV PPs) were used as carriers to display conformational 4E10 and 10E8 epitopes in different patterns with an appropriate linker. Immune responses to the recombinant NoV PPs were characterized in guinea pigs and Balb/c mice and could induce high levels of MPER-binding antibodies. Modest neutralizing activities could be detected in sera of guinea pigs but not of Balb/c mice. The 4E10 or 10E8 epitopes dispersed on three loops on the outermost surface of NoV PPs (4E10-loop123 PP or 10E8-loop123 PP) elicited higher neutralizing activities than the equivalent number of epitopes presented on loop 2 only (4E10-3loop2 PP or 10E8-3loop2 PP). The epitopes on different loops of the PP were well-exposed and likely formed an appropriate conformation to induce neutralizing antibodies. Although sera of immunized guinea pigs could neutralize several HIV envelope-pseudoviruses, a vaccine candidate for efficiently inducing HIV-1 BnAbs remains to be developed.
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Affiliation(s)
- Yongjiao Yu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Lu Fu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Yuhua Shi
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Shanshan Guan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Lan Yang
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Xin Gong
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - He Yin
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Xiaoqiu He
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Dongni Liu
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Ziyu Kuai
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China
| | - Yaming Shan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China; Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun, Jilin, China.
| | - Song Wang
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin, China.
| | - Wei Kong
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, Jilin, China; Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun, Jilin, China
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393
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Berinyuy E, Soliman MES. A broad spectrum anti-HIV inhibitor significantly disturbs V1/V2 domain rearrangements of HIV-1 gp120 and inhibits virus entry. J Recept Signal Transduct Res 2015; 36:119-29. [PMID: 26446906 DOI: 10.3109/10799893.2015.1056307] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Inhibition of human immunodeficiency virus (HIV) entry into target human cells is considered as a critical strategy for preventing HIV infection. Conformational shifts of the HIV-1 envelope glycoprotein (gp120) facilitates the attachment of the virus to target cells, therefore gp120 remains an attractive target for antiretroviral therapy development. Compound 18A has been recently identified as a broad-spectrum anti-HIV inhibitor. It was proposed that 18A disrupts rearrangements of V1/V2 region in gp120; however, the precise mechanism by which 18A interferes with the inherent motion of V1/V2 domain remains obscure. In this report, we elaborate on the binding mode of compound 18A to the closed conformation of a soluble cleaved gp120 and further examine the dynamic motion of V1/V2 region in both gp120 and the gp120-18A complex via all-atom molecular dynamics simulations. In this work, comparative molecular dynamic analyses revealed that 18A makes contact with Leu179, Ile194, Ile424, Met426 W427, E370 and Met475 in the main hydrophobic cavity of the unliganded gp120 and disrupts the restructuring of V1/V2 domain observed in apo gp120. The unwinding of α1 and slight inversion of β2 in gp120 leads to the shift of VI/V2 domain away from the V3 N-terminal regions and toward the outer domain. Stronger contacts between Trp425 and Trp112 rings may contribute to the reduced flexibility of α1 observed upon 18A binding thereby inhibiting the shifts of the V1/V2 region. Binding of 18A to gp120: (1) decreases the overall flexibility of the protein and (2) inhibits the formation a gp120 conformation that closely ressembles a CD4-bound-like conformation. Information gained from this report not only elaborates on important dynamic features of gp120, but will also assist with the future designs of potent gp120 inhibitors as anti-HIV.
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Affiliation(s)
- Emiliene Berinyuy
- a Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal , Westville , Durban , South Africa
| | - Mahmoud E S Soliman
- a Molecular Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal , Westville , Durban , South Africa
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394
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Pham S, Tabarin T, Garvey M, Pade C, Rossy J, Monaghan P, Hyatt A, Böcking T, Leis A, Gaus K, Mak J. Cryo-electron microscopy and single molecule fluorescent microscopy detect CD4 receptor induced HIV size expansion prior to cell entry. Virology 2015; 486:121-33. [PMID: 26432024 DOI: 10.1016/j.virol.2015.09.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 10/23/2022]
Abstract
Viruses are often thought to have static structure, and they only remodel after the viruses have entered target cells. Here, we detected a size expansion of virus particles prior to viral entry using cryo-electron microscopy (cryo-EM) and single molecule fluorescence imaging. HIV expanded both under cell-free conditions with soluble receptor CD4 (sCD4) targeting the CD4 binding site on the HIV-1 envelope protein (Env) and when HIV binds to receptor on cellular membrane. We have shown that the HIV Env is needed to facilitate receptor induced virus size expansions, showing that the 'lynchpin' for size expansion is highly specific. We demonstrate that the size expansion required maturation of HIV and an internal capsid core with wild type stability, suggesting that different HIV compartments are linked and are involved in remodelling. Our work reveals a previously unknown event in HIV entry, and we propose that this pre-entry priming process enables HIV particles to facilitate the subsequent steps in infection.
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Affiliation(s)
- Son Pham
- Deakin University, Victoria 3216, Australia; CSIRO Australian Animal Health Laboratory, Victoria 3220, Australia
| | - Thibault Tabarin
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, New South Wales 3220, Australia
| | - Megan Garvey
- Deakin University, Victoria 3216, Australia; CSIRO Australian Animal Health Laboratory, Victoria 3220, Australia
| | - Corinna Pade
- Deakin University, Victoria 3216, Australia; CSIRO Australian Animal Health Laboratory, Victoria 3220, Australia
| | - Jérémie Rossy
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, New South Wales 3220, Australia
| | - Paul Monaghan
- CSIRO Australian Animal Health Laboratory, Victoria 3220, Australia
| | - Alex Hyatt
- CSIRO Australian Animal Health Laboratory, Victoria 3220, Australia
| | - Till Böcking
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, New South Wales 3220, Australia
| | - Andrew Leis
- CSIRO Australian Animal Health Laboratory, Victoria 3220, Australia
| | - Katharina Gaus
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, New South Wales 3220, Australia.
| | - Johnson Mak
- Deakin University, Victoria 3216, Australia; CSIRO Australian Animal Health Laboratory, Victoria 3220, Australia.
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395
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Lee JH, Leaman DP, Kim AS, Torrents de la Peña A, Sliepen K, Yasmeen A, Derking R, Ramos A, de Taeye SW, Ozorowski G, Klein F, Burton DR, Nussenzweig MC, Poignard P, Moore JP, Klasse PJ, Sanders RW, Zwick MB, Wilson IA, Ward AB. Antibodies to a conformational epitope on gp41 neutralize HIV-1 by destabilizing the Env spike. Nat Commun 2015; 6:8167. [PMID: 26404402 PMCID: PMC4586043 DOI: 10.1038/ncomms9167] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 07/27/2015] [Indexed: 01/16/2023] Open
Abstract
The recent identification of three broadly neutralizing antibodies (bnAbs) against gp120–gp41 interface epitopes has expanded the targetable surface on the HIV-1 envelope glycoprotein (Env) trimer. By using biochemical, biophysical and computational methods, we map the previously unknown trimer epitopes of two related antibodies, 3BC315 and 3BC176. A cryo-EM reconstruction of a soluble Env trimer bound to 3BC315 Fab at 9.3 Å resolution reveals that the antibody binds between two gp41 protomers, and neutralizes the virus by accelerating trimer decay. In contrast, bnAb 35O22 binding to a partially overlapping quaternary epitope at the gp120–gp41 interface does not induce decay. A conserved gp41-proximal glycan at N88 was also shown to play a role in the binding kinetics of 3BC176 and 3BC315. Finally, our data suggest that the dynamic structure of the Env trimer influences exposure of bnAb epitopes. The envelope glycoprotein (Env) trimer is the only antigenic target for broadly neutralizing antibodies on the surface of the HIV-1 virus. Here the authors show that two related monoclonal antibodies bind between gp41 protomers and neutralize HIV-1 by accelerating Env trimer decay.
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Affiliation(s)
- Jeong Hyun Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla California 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Daniel P Leaman
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Arthur S Kim
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Alba Torrents de la Peña
- Department of Medicinal Microbiology, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands
| | - Kwinten Sliepen
- Department of Medicinal Microbiology, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands
| | - Anila Yasmeen
- Weill Medical College of Cornell University, New York, New York 10065, USA
| | - Ronald Derking
- Department of Medicinal Microbiology, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands
| | - Alejandra Ramos
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla California 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Steven W de Taeye
- Department of Medicinal Microbiology, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla California 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Florian Klein
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA
| | - Dennis R Burton
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla California 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA.,Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts 02114, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York 10065, USA.,Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
| | - Pascal Poignard
- International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla California 92037, USA.,Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - John P Moore
- Weill Medical College of Cornell University, New York, New York 10065, USA
| | - Per Johan Klasse
- Weill Medical College of Cornell University, New York, New York 10065, USA
| | - Rogier W Sanders
- Department of Medicinal Microbiology, Academic Medical Center, 1105 AZ Amsterdam, The Netherlands.,Weill Medical College of Cornell University, New York, New York 10065, USA
| | - Michael B Zwick
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla California 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA.,Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA.,International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla California 92037, USA.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, California 92037, USA
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396
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Conformational Masking and Receptor-Dependent Unmasking of Highly Conserved Env Epitopes Recognized by Non-Neutralizing Antibodies That Mediate Potent ADCC against HIV-1. Viruses 2015; 7:5115-32. [PMID: 26393642 PMCID: PMC4584300 DOI: 10.3390/v7092856] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/12/2015] [Accepted: 08/18/2015] [Indexed: 01/11/2023] Open
Abstract
The mechanism of antibody-mediated protection is a major focus of HIV-1 vaccine development and a significant issue in the control of viremia. Virus neutralization, Fc-mediated effector function, or both, are major mechanisms of antibody-mediated protection against HIV-1, although other mechanisms, such as virus aggregation, are known. The interplay between virus neutralization and Fc-mediated effector function in protection against HIV-1 is complex and only partially understood. Passive immunization studies using potent broadly neutralizing antibodies (bnAbs) show that both neutralization and Fc-mediated effector function provides the widest dynamic range of protection; however, a vaccine to elicit these responses remains elusive. By contrast, active immunization studies in both humans and non-human primates using HIV-1 vaccine candidates suggest that weakly neutralizing or non-neutralizing antibodies can protect by Fc-mediated effector function, albeit with a much lower dynamic range seen for passive immunization with bnAbs. HIV-1 has evolved mechanisms to evade each type of antibody-mediated protection that must be countered by a successful AIDS vaccine. Overcoming the hurdles required to elicit bnAbs has become a major focus of HIV-1 vaccine development. Here, we discuss a less studied problem, the structural basis of protection (and its evasion) by antibodies that protect only by potent Fc-mediated effector function.
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397
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Rashad AA, Kalyana Sundaram RV, Aneja R, Duffy C, Chaiken I. Macrocyclic Envelope Glycoprotein Antagonists that Irreversibly Inactivate HIV-1 before Host Cell Encounter. J Med Chem 2015; 58:7603-8. [PMID: 26331669 DOI: 10.1021/acs.jmedchem.5b00935] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We derived macrocyclic HIV-1 antagonists as a new class of peptidomimetic drug leads. Cyclic peptide triazoles (cPTs) retained the gp120 inhibitory and virus-inactivating signature of parent PTs, arguing that cyclization locked an active conformation. The six-residue cPT 9 (AAR029b) exhibited submicromolar antiviral potencies in inhibiting cell infection and triggering gp120 shedding that causes irreversible virion inactivation. Importantly, cPTs were stable to trypsin and chymotrypsin compared to substantial susceptibility of corresponding linear PTs.
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Affiliation(s)
- Adel A Rashad
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine , 245 North 15th Street, Philadelphia, Pennsylvania 19102 United States
| | - Ramalingam Venkat Kalyana Sundaram
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine , 245 North 15th Street, Philadelphia, Pennsylvania 19102 United States.,School of Biomedical Engineering, Science and Health Systems, Drexel University , Philadelphia, Pennsylvania 19104 United States
| | - Rachna Aneja
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine , 245 North 15th Street, Philadelphia, Pennsylvania 19102 United States
| | - Caitlin Duffy
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine , 245 North 15th Street, Philadelphia, Pennsylvania 19102 United States
| | - Irwin Chaiken
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine , 245 North 15th Street, Philadelphia, Pennsylvania 19102 United States
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398
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Design and structure of two HIV-1 clade C SOSIP.664 trimers that increase the arsenal of native-like Env immunogens. Proc Natl Acad Sci U S A 2015; 112:11947-52. [PMID: 26372963 DOI: 10.1073/pnas.1507793112] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A key challenge in the quest toward an HIV-1 vaccine is design of immunogens that can generate a broadly neutralizing antibody (bnAb) response against the enormous sequence diversity of the HIV-1 envelope glycoprotein (Env). We previously demonstrated that a recombinant, soluble, fully cleaved SOSIP.664 trimer based on the clade A BG505 sequence is a faithful antigenic and structural mimic of the native trimer in its prefusion conformation. Here, we sought clade C native-like trimers with comparable properties. We identified DU422 and ZM197M SOSIP.664 trimers as being appropriately thermostable (Tm of 63.4 °C and 62.7 °C, respectively) and predominantly native-like, as determined by negative-stain electron microscopy (EM). Size exclusion chromatography, ELISA, and surface plasmon resonance further showed that these trimers properly display epitopes for all of the major bnAb classes, including quaternary-dependent, trimer-apex (e.g., PGT145) and gp120/gp41 interface (e.g., PGT151) epitopes. A cryo-EM reconstruction of the ZM197M SOSIP.664 trimer complexed with VRC01 Fab against the CD4 binding site at subnanometer resolution revealed a striking overall similarity to its BG505 counterpart with expected local conformational differences in the gp120 V1, V2, and V4 loops. These stable clade C trimers contribute additional diversity to the pool of native-like Env immunogens as key components of strategies to induce bnAbs to HIV-1.
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Influences on the Design and Purification of Soluble, Recombinant Native-Like HIV-1 Envelope Glycoprotein Trimers. J Virol 2015; 89:12189-210. [PMID: 26311893 DOI: 10.1128/jvi.01768-15] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 08/20/2015] [Indexed: 12/27/2022] Open
Abstract
UNLABELLED We have investigated factors that influence the production of native-like soluble, recombinant trimers based on the env genes of two isolates of human immunodeficiency virus type 1 (HIV-1), specifically 92UG037.8 (clade A) and CZA97.012 (clade C). When the recombinant trimers based on the env genes of isolates 92UG037.8 and CZA97.012 were made according to the SOSIP.664 design and purified by affinity chromatography using broadly neutralizing antibodies (bNAbs) against quaternary epitopes (PGT145 and PGT151, respectively), the resulting trimers are highly stable and they are fully native-like when visualized by negative-stain electron microscopy. They also have a native-like (i.e., abundant) oligomannose glycan composition and display multiple bNAb epitopes while occluding those for nonneutralizing antibodies. In contrast, uncleaved, histidine-tagged Foldon (Fd) domain-containing gp140 proteins (gp140UNC-Fd-His), based on the same env genes, very rarely form native-like trimers, a finding that is consistent with their antigenic and biophysical properties and glycan composition. The addition of a 20-residue flexible linker (FL20) between the gp120 and gp41 ectodomain (gp41ECTO) subunits to make the uncleaved 92UG037.8 gp140-FL20 construct is not sufficient to create a native-like trimer, but a small percentage of native-like trimers were produced when an I559P substitution in gp41ECTO was also present. The further addition of a disulfide bond (SOS) to link the gp120 and gp41 subunits in the uncleaved gp140-FL20-SOSIP protein increases native-like trimer formation to ∼20 to 30%. Analysis of the disulfide bond content shows that misfolded gp120 subunits are abundant in uncleaved CZA97.012 gp140UNC-Fd-His proteins but very rare in native-like trimer populations. The design and stabilization method and the purification strategy are, therefore, all important influences on the quality of trimeric Env proteins and hence their suitability as vaccine components. IMPORTANCE Soluble, recombinant multimeric proteins based on the HIV-1 env gene are current candidate immunogens for vaccine trials in humans. These proteins are generally designed to mimic the native trimeric envelope glycoprotein (Env) that is the target of virus-neutralizing antibodies on the surfaces of virions. The underlying hypothesis is that an Env-mimetic protein may be able to induce antibodies that can neutralize the virus broadly and potently enough for a vaccine to be protective. Multiple different designs for Env-mimetic trimers have been put forth. Here, we used the CZA97.012 and 92UG037.8 env genes to compare some of these designs and determine which ones best mimic virus-associated Env trimers. We conclude that the most widely used versions of CZA97.012 and 92UG037.8 oligomeric Env proteins do not resemble the trimeric Env glycoprotein on HIV-1 viruses, which has implications for the design and interpretation of ongoing or proposed clinical trials of these proteins.
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Sanders RW, van Gils MJ, Derking R, Sok D, Ketas TJ, Burger JA, Ozorowski G, Cupo A, Simonich C, Goo L, Arendt H, Kim HJ, Lee JH, Pugach P, Williams M, Debnath G, Moldt B, van Breemen MJ, Isik G, Medina-Ramírez M, Back JW, Koff WC, Julien JP, Rakasz EG, Seaman MS, Guttman M, Lee KK, Klasse PJ, LaBranche C, Schief WR, Wilson IA, Overbaugh J, Burton DR, Ward AB, Montefiori DC, Dean H, Moore JP. HIV-1 VACCINES. HIV-1 neutralizing antibodies induced by native-like envelope trimers. Science 2015; 349:aac4223. [PMID: 26089353 PMCID: PMC4498988 DOI: 10.1126/science.aac4223] [Citation(s) in RCA: 430] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/05/2015] [Indexed: 12/22/2022]
Abstract
A challenge for HIV-1 immunogen design is the difficulty of inducing neutralizing antibodies (NAbs) against neutralization-resistant (tier 2) viruses that dominate human transmissions. We show that a soluble recombinant HIV-1 envelope glycoprotein trimer that adopts a native conformation, BG505 SOSIP.664, induced NAbs potently against the sequence-matched tier 2 virus in rabbits and similar but weaker responses in macaques. The trimer also consistently induced cross-reactive NAbs against more sensitive (tier 1) viruses. Tier 2 NAbs recognized conformational epitopes that differed between animals and in some cases overlapped with those recognized by broadly neutralizing antibodies (bNAbs), whereas tier 1 responses targeted linear V3 epitopes. A second trimer, B41 SOSIP.664, also induced a strong autologous tier 2 NAb response in rabbits. Thus, native-like trimers represent a promising starting point for the development of HIV-1 vaccines aimed at inducing bNAbs.
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Affiliation(s)
- Rogier W Sanders
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA. Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, Netherlands.
| | - Marit J van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
| | - Ronald Derking
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
| | - Devin Sok
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thomas J Ketas
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Judith A Burger
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
| | - Gabriel Ozorowski
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Albert Cupo
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Cassandra Simonich
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Leslie Goo
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Heather Arendt
- International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Helen J Kim
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeong Hyun Lee
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Pavel Pugach
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Melissa Williams
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Gargi Debnath
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Brian Moldt
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mariëlle J van Breemen
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
| | - Gözde Isik
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
| | - Max Medina-Ramírez
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
| | | | - Wayne C Koff
- International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - Jean-Philippe Julien
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eva G Rakasz
- Wisconsin National Primate Research Center, University of Wisconsin, Madison, WI 53715, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA. Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, MA 02114, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Per Johan Klasse
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - William R Schief
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, New York, NY 10004, USA. Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, MA 02114, USA
| | - Ian A Wilson
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA. Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Dennis R Burton
- Department of Immunology and Microbial Science, Scripps Research Institute, La Jolla, CA 92037, USA. International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Boston, MA 02114, USA
| | - Andrew B Ward
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, and Collaboration for AIDS Vaccine Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, Scripps Research Institute, La Jolla, CA 92037, USA. Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Hansi Dean
- International AIDS Vaccine Initiative, New York, NY 10004, USA
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA.
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