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Takizawa F, Hashimoto K, Miyazawa R, Ohta Y, Veríssimo A, Flajnik MF, Parra D, Tokunaga K, Suetake H, Sunyer JO, Dijkstra JM. CD4 and LAG-3 from sharks to humans: related molecules with motifs for opposing functions. Front Immunol 2023; 14:1267743. [PMID: 38187381 PMCID: PMC10768021 DOI: 10.3389/fimmu.2023.1267743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
CD4 and LAG-3 are related molecules that are receptors for MHC class II molecules. Their major functional differences are situated in their cytoplasmic tails, in which CD4 has an activation motif and LAG-3 an inhibitory motif. Here, we identify shark LAG-3 and show that a previously identified shark CD4-like gene has a genomic location, expression pattern, and motifs similar to CD4 in other vertebrates. In nurse shark (Ginglymostoma cirratum) and cloudy catshark (Scyliorhinus torazame), the highest CD4 expression was consistently found in the thymus whereas such was not the case for LAG-3. Throughout jawed vertebrates, the CD4 cytoplasmic tail possesses a Cx(C/H) motif for binding kinase LCK, and the LAG-3 cytoplasmic tail possesses (F/Y)xxL(D/E) including the previously determined FxxL inhibitory motif resembling an immunoreceptor tyrosine-based inhibition motif (ITIM). On the other hand, the acidic end of the mammalian LAG-3 cytoplasmic tail, which is believed to have an inhibitory function as well, was acquired later in evolution. The present study also identified CD4-1, CD4-2, and LAG-3 in the primitive ray-finned fishes bichirs, sturgeons, and gars, and experimentally determined these sequences for sterlet sturgeon (Acipenser ruthenus). Therefore, with CD4-1 and CD4-2 already known in teleosts (modern ray-finned fish), these two CD4 lineages have now been found within all major clades of ray-finned fish. Although different from each other, the cytoplasmic tails of ray-finned fish CD4-1 and chondrichthyan CD4 not only contain the Cx(C/H) motif but also an additional highly conserved motif which we expect to confer a function. Thus, although restricted to some species and gene copies, in evolution both CD4 and LAG-3 molecules appear to have acquired functional motifs besides their canonical Cx(C/H) and ITIM-like motifs, respectively. The presence of CD4 and LAG-3 molecules with seemingly opposing functions from the level of sharks, the oldest living vertebrates with a human-like adaptive immune system, underlines their importance for the jawed vertebrate immune system. It also emphasizes the general need of the immune system to always find a balance, leading to trade-offs, between activating and inhibiting processes.
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Affiliation(s)
- Fumio Takizawa
- Faculty of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui, Japan
| | - Keiichiro Hashimoto
- Emeritus Professor, Center for Medical Science, Fujita Health University, Toyoake, Aichi, Japan
| | - Ryuichiro Miyazawa
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Yuko Ohta
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, United States
| | - Ana Veríssimo
- CIBIO‐InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Martin F. Flajnik
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, United States
| | | | | | - Hiroaki Suetake
- Faculty of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui, Japan
| | - J. Oriol Sunyer
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Van Ryk D, Vimonpatranon S, Hiatt J, Ganesan S, Chen N, McMurry J, Garba S, Min S, Goes LR, Girard A, Yolitz J, Licavoli I, Wei D, Huang D, Soares MA, Martinelli E, Cicala C, Arthos J. The V2 domain of HIV gp120 mimics an interaction between CD4 and integrin ⍺4β7. PLoS Pathog 2023; 19:e1011860. [PMID: 38064524 PMCID: PMC10732398 DOI: 10.1371/journal.ppat.1011860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/20/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023] Open
Abstract
The CD4 receptor, by stabilizing TCR-MHC II interactions, plays a central role in adaptive immunity. It also serves as the HIV docking receptor. The HIV gp120 envelope protein binds directly to CD4. This interaction is a prerequisite for viral entry. gp120 also binds to ⍺4β7, an integrin that is expressed on a subset of memory CD4+ T cells. HIV tropisms for CD4+ T cells and gut tissues are central features of HIV pathogenesis. We report that CD4 binds directly to ⍺4β7 in a dynamic way, consistent with a cis regulatory interaction. The molecular details of this interaction are related to the way in which gp120 interacts with both receptors. Like MAdCAM-1 and VCAM-1, two recognized ligands of ⍺4β7, the binding interface on CD4 includes 2 sites (1° and accessory), distributed across its two N-terminal IgSF domains (D1 and D2). The 1° site includes a sequence in the G β-strand of CD4 D2, KIDIV, that binds directly to ⍺4β7. This pentapeptide sequence occurs infrequently in eukaryotic proteins. However, a closely related and conserved sequence, KLDIV, appears in the V2 domain of gp120. KLDIV mediates gp120-⍺4β7 binding. The accessory ⍺4β7 binding site on CD4 includes Phe43. The Phe43 aromatic ring protrudes outward from one edge of a loop connecting the C'C" strands of CD4 D1. Phe43 is a principal contact for HIV gp120. It interacts with conserved residues in the recessed CD4 binding pocket. Substitution of Phe43 abrogates CD4 binding to both gp120 and ⍺4β7. As such, the interactions of gp120 with both CD4 and ⍺4β7 reflect elements of their interactions with each other. These findings indicate that gp120 specificities for CD4 and ⍺4β7 are interrelated and suggest that selective pressures which produced a CD4 tropic virus that replicates in gut tissues are linked to a dynamic interaction between these two receptors.
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Affiliation(s)
- Donald Van Ryk
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Sinmanus Vimonpatranon
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
- Department of Retrovirology, Armed Forces Research Institute of Medical Sciences–United States Component, Bangkok, Thailand
| | - Joe Hiatt
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Sundar Ganesan
- Biological Imaging Section, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Nathalie Chen
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Jordan McMurry
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Saadiq Garba
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Susie Min
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Livia R. Goes
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
- Oncovirology Program, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Alexandre Girard
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Jason Yolitz
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Isabella Licavoli
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Danlan Wei
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Dawei Huang
- Lymphoid Malignancies Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Marcelo A. Soares
- Oncovirology Program, Instituto Nacional de Câncer, Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Elena Martinelli
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Claudia Cicala
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - James Arthos
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
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3
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Zenere G, Wu C, Midkiff CC, Johnson NM, Grice CP, Wimley WC, Kaur A, Braun SE. Extracellular domain, hinge, and transmembrane determinants affecting surface CD4 expression of a novel anti-HIV chimeric antigen receptor (CAR) construct. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.563930. [PMID: 37961145 PMCID: PMC10634810 DOI: 10.1101/2023.10.25.563930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Chimeric antigen receptor (CAR)-T cells have demonstrated clinical potential, but current receptors still need improvements to be successful against chronic HIV infection. In this study, we address some requirements of CAR motifs for strong surface expression of a novel anti-HIV CAR by evaluating important elements in the extracellular, hinge, and transmembrane (TM) domains. When combining a truncated CD4 extracellular domain and CD8α hinge/TM, the novel CAR did not express extracellularly but was detectable intracellularly. By shortening the CD8α hinge, CD4-CAR surface expression was partially recovered and addition of the LYC motif at the end of the CD8α TM fully recovered both intracellular and extracellular CAR expression. Mutation of LYC to TTA or TTC showed severe abrogation of CAR expression by flow cytometry and confocal microscopy. Additionally, we determined that CD4-CAR surface expression could be maximized by the removal of FQKAS motif at the junction of the extracellular domain and the hinge region. CD4-CAR surface expression also resulted in cytotoxic CAR T cell killing of HIV Env+ target cells. In this study, we identified elements that are crucial for optimal CAR surface expression, highlighting the need for structural analysis studies to establish fundamental guidelines of CAR designs.
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Affiliation(s)
- Giorgio Zenere
- Tulane National Primate Research Center, Covington, LA 70433
- BioMedical Sciences Program, Tulane University School of Medicine, New Orleans, LA 70112
| | - Chengxiang Wu
- Tulane National Primate Research Center, Covington, LA 70433
| | | | - Nathan M. Johnson
- Tulane National Primate Research Center, Covington, LA 70433
- BioMedical Sciences Program, Tulane University School of Medicine, New Orleans, LA 70112
| | - Christopher P. Grice
- Tulane National Primate Research Center, Covington, LA 70433
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112
| | - William C. Wimley
- Department of BioChemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Amitinder Kaur
- Tulane National Primate Research Center, Covington, LA 70433
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112
| | - Stephen E. Braun
- Tulane National Primate Research Center, Covington, LA 70433
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112
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Abstract
The marvel of X-ray crystallography is the beauty and precision of the atomic structures deduced from diffraction patterns. Since these patterns record only amplitudes, phases for the diffracted waves must also be evaluated for systematic structure determination. Thus, we have the phase problem as a central complication, both intellectually for the field and practically so for many analyses. Here, I discuss how we - myself, my laboratory and the diffraction community - have faced the phase problem, considering the evolution of methods for phase evaluation as structural biology developed to the present day. During the explosive growth of macromolecular crystallography, practice in diffraction analysis evolved from a universal reliance on isomorphous replacement to the eventual domination of anomalous diffraction for de novo structure determination. As the Protein Data Bank (PDB) grew and familial relationships among proteins became clear, molecular replacement overtook all other phasing methods; however, experimental phasing remained essential for molecules without obvious precedents, with multi- and single-wavelength anomalous diffraction (MAD and SAD) predominating. While the mathematics-based direct methods had proved to be inadequate for typical macromolecules, they returned to crack substantial selenium substructures in SAD analyses of selenomethionyl proteins. Native SAD, exploiting the intrinsic S and P atoms of biomolecules, has become routine. Selenomethionyl SAD and MAD were the mainstays of structural genomics efforts to populate the PDB with novel proteins. A recent dividend has been paid in the success of PDB-trained artificial intelligence approaches for protein structure prediction. Currently, molecular replacement with AlphaFold models often obviates the need for experimental phase evaluation. For multiple reasons, we are now unfazed by the phase problem. Cryo-EM analysis is an attractive alternative to crystallography for many applications faced by today's structural biologists. It simply finesses the phase problem; however, the principles and procedures of diffraction analysis remain pertinent and are adopted in single-particle cryo-EM studies of biomolecules.
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Affiliation(s)
- Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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5
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Glögl M, Friedrich N, Cerutti G, Lemmin T, Kwon YD, Gorman J, Maliqi L, Mittl PRE, Hesselman MC, Schmidt D, Weber J, Foulkes C, Dingens AS, Bylund T, Olia AS, Verardi R, Reinberg T, Baumann NS, Rusert P, Dreier B, Shapiro L, Kwong PD, Plückthun A, Trkola A. Trapping the HIV-1 V3 loop in a helical conformation enables broad neutralization. Nat Struct Mol Biol 2023; 30:1323-1336. [PMID: 37605043 PMCID: PMC10497408 DOI: 10.1038/s41594-023-01062-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/11/2023] [Indexed: 08/23/2023]
Abstract
The third variable (V3) loop on the human immunodeficiency virus 1 (HIV-1) envelope glycoprotein trimer is indispensable for virus cell entry. Conformational masking of V3 within the trimer allows efficient neutralization via V3 only by rare, broadly neutralizing glycan-dependent antibodies targeting the closed prefusion trimer but not by abundant antibodies that access the V3 crown on open trimers after CD4 attachment. Here, we report on a distinct category of V3-specific inhibitors based on designed ankyrin repeat protein (DARPin) technology that reinstitute the CD4-bound state as a key neutralization target with up to >90% breadth. Broadly neutralizing DARPins (bnDs) bound V3 solely on open envelope and recognized a four-turn amphipathic α-helix in the carboxy-terminal half of V3 (amino acids 314-324), which we termed 'αV3C'. The bnD contact surface on αV3C was as conserved as the CD4 binding site. Molecular dynamics and escape mutation analyses underscored the functional relevance of αV3C, highlighting the potential of αV3C-based inhibitors and, more generally, of postattachment inhibition of HIV-1.
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Affiliation(s)
- Matthias Glögl
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Nikolas Friedrich
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Gabriele Cerutti
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Thomas Lemmin
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Young D Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Liridona Maliqi
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Peer R E Mittl
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Maria C Hesselman
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Daniel Schmidt
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Jacqueline Weber
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Caio Foulkes
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Adam S Dingens
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thomas Reinberg
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Nicolas S Baumann
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Peter Rusert
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Alexandra Trkola
- Institute for Medical Virology, University of Zurich (UZH), Zurich, Switzerland.
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6
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Olia AS, Cheng C, Zhou T, Biju A, Harris DR, Changela A, Duan H, Ivleva VB, Kong WP, Ou L, Rawi R, Tsybovsky Y, Van Wazer DJ, Corrigan AR, Gonelli CA, Lee M, McKee K, Narpala S, O’Dell S, Parchment DK, Stancofski ESD, Stephens T, Tan I, Teng IT, Wang S, Wei Q, Yang Y, Yang Z, Zhang B, Novak J, Renfrow MB, Doria-Rose NA, Koup RA, McDermott AB, Gall JG, Lei QP, Mascola JR, Kwong PD. Soluble prefusion-closed HIV-envelope trimers with glycan-covered bases. iScience 2023; 26:107403. [PMID: 37554450 PMCID: PMC10404741 DOI: 10.1016/j.isci.2023.107403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/23/2023] [Accepted: 07/12/2023] [Indexed: 08/10/2023] Open
Abstract
Soluble HIV-1-envelope (Env) trimers elicit immune responses that target their solvent-exposed protein bases, the result of removing these trimers from their native membrane-bound context. To assess whether glycosylation could limit these base responses, we introduced sequons encoding potential N-linked glycosylation sites (PNGSs) into base-proximal regions. Expression and antigenic analyses indicated trimers bearing six-introduced PNGSs to have reduced base recognition. Cryo-EM analysis revealed trimers with introduced PNGSs to be prone to disassembly and introduced PNGS to be disordered. Protein-base and glycan-base trimers induced reciprocally symmetric ELISA responses, in which only a small fraction of the antibody response to glycan-base trimers recognized protein-base trimers and vice versa. EM polyclonal epitope mapping revealed glycan-base trimers -even those that were stable biochemically- to elicit antibodies that recognized disassembled trimers. Introduced glycans can thus mask the protein base but their introduction may yield neo-epitopes that dominate the immune response.
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Affiliation(s)
- Adam S. Olia
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cheng Cheng
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrea Biju
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darcy R. Harris
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anita Changela
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hongying Duan
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vera B. Ivleva
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wing-Pui Kong
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Ou
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - David J. Van Wazer
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Angela R. Corrigan
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Myungjin Lee
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Krisha McKee
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandeep Narpala
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijy O’Dell
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Tyler Stephens
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Ivy Tan
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - I-Ting Teng
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qing Wei
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yongping Yang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhengrong Yang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Jan Novak
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Matthew B. Renfrow
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Richard A. Koup
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adrian B. McDermott
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason G. Gall
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Q. Paula Lei
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - John R. Mascola
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA
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7
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Zhou T, Chen L, Gorman J, Wang S, Kwon YD, Lin BC, Louder MK, Rawi R, Stancofski ESD, Yang Y, Zhang B, Quigley AF, McCoy LE, Rutten L, Verrips T, Weiss RA, Doria-Rose NA, Shapiro L, Kwong PD. Structural basis for llama nanobody recognition and neutralization of HIV-1 at the CD4-binding site. Structure 2022; 30:862-875.e4. [PMID: 35413243 PMCID: PMC9177634 DOI: 10.1016/j.str.2022.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/15/2021] [Accepted: 03/17/2022] [Indexed: 11/30/2022]
Abstract
Nanobodies can achieve remarkable neutralization of genetically diverse pathogens, including HIV-1. To gain insight into their recognition, we determined crystal structures of four llama nanobodies (J3, A12, C8, and D7), all of which targeted the CD4-binding site, in complex with the HIV-1 envelope (Env) gp120 core, and determined a cryoelectron microscopy (cryo-EM) structure of J3 with the Env trimer. Crystal and cryo-EM structures of J3 complexes revealed this nanobody to mimic binding to the prefusion-closed trimer for the primary site of CD4 recognition as well as a secondary quaternary site. In contrast, crystal structures of A12, C8, and D7 with gp120 revealed epitopes that included portions of the gp120 inner domain, inaccessible on the prefusion-closed trimer. Overall, these structures explain the broad and potent neutralization of J3 and limited neutralization of A12, C8, and D7, which utilized binding modes incompatible with the neutralization-targeted prefusion-closed conformation of Env.
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Affiliation(s)
- Tongqing Zhou
- 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
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Young D Kwon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bob C Lin
- 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
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erik-Stephane D Stancofski
- 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
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna Forsman Quigley
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Lucy Rutten
- University of Utrecht, Utrecht, the Netherlands
| | | | - Robin A Weiss
- Division of Infection and Immunity, University College London, London NW3 2PP, UK
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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8
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Kuramochi M, Dong Y, Yang Y, Arai T, Okada R, Shinkai Y, Doi M, Aoyama K, Sekiguchi H, Mio K, Tsuda S, Sasaki YC. Dynamic motions of ice-binding proteins in living Caenorhabditis elegans using diffracted X-ray blinking and tracking. Biochem Biophys Rep 2022; 29:101224. [PMID: 35146137 PMCID: PMC8819013 DOI: 10.1016/j.bbrep.2022.101224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 11/15/2022] Open
Affiliation(s)
- Masahiro Kuramochi
- Graduate School of Science and Engineering, Ibaraki University, Hitachi, 316-8511, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, 277-8565, Japan
- Corresponding author. Graduate School of Science and Engineering, Ibaraki University, Hitachi, 316-8511, Japan.
| | - Yige Dong
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Yue Yang
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Tatsuya Arai
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Rio Okada
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
| | - Yoichi Shinkai
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Japan
| | - Motomichi Doi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Japan
| | - Kouki Aoyama
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Hiroshi Sekiguchi
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Kazuhiro Mio
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, 277-8565, Japan
| | - Sakae Tsuda
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, 277-8565, Japan
| | - Yuji C. Sasaki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, 277-8565, Japan
- Center for Synchrotron Radiation Research, Japan Synchrotron Radiation Research Institute, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
- Corresponding author. Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8561, Japan.
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9
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Chiliveri SC, Louis JM, Bax A. Concentration‐Dependent Structural Transition of the HIV‐1 gp41 MPER Peptide into α‐Helical Trimers. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202008804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics National Institute of Diabetes and Digestive and Kidney Diseases Bethesda MD 20892 USA
| | - John M. Louis
- Laboratory of Chemical Physics National Institute of Diabetes and Digestive and Kidney Diseases Bethesda MD 20892 USA
| | - Ad Bax
- Laboratory of Chemical Physics National Institute of Diabetes and Digestive and Kidney Diseases Bethesda MD 20892 USA
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10
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Three functional mutation sites affect the immune response of pigs through altering the expression pattern and IgV domain of the CD4 protein. BMC Mol Cell Biol 2020; 21:91. [PMID: 33297958 PMCID: PMC7724863 DOI: 10.1186/s12860-020-00333-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 11/24/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The CD4 protein is an important surface marker of T lymphocytes, which can mediate the antigen presentation process by interacting with MHC II and TCR molecules in human and mouse. RESULTS In this study, two haplotypes (A and B) of the CD4 gene were found within Chinese indigenous and Western commercial pig breeds. These two haplotypes were defined by 22 fully linked SNPs in the CDS region of the CD4 gene. The expression level and localization of the CD4 protein were significantly different between haplotypes A and B. Transcriptome analysis revealed that the immune response-related genes and signaling pathways were down-regulated in genotype AA. Finally, three linked functional SNPs were identified, which affected the expression level and membrane localization of the CD4 protein in pigs. These three SNPs led to the replacements of two amino acids in the IgV1 domain of the CD4 protein, and related to the function of the CD4 protein in the immune response. CONCLUSION These three linked SNPs were the key functional mutation sites in the CD4 gene, which played important roles in the immune response, and could be utilized as new molecular markers in breeding for disease resistance in pigs.
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11
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Chiliveri SC, Louis JM, Bax A. Concentration-Dependent Structural Transition of the HIV-1 gp41 MPER Peptide into α-Helical Trimers. Angew Chem Int Ed Engl 2020; 60:166-170. [PMID: 32916024 DOI: 10.1002/anie.202008804] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/20/2020] [Indexed: 11/12/2022]
Abstract
The membrane proximal external region (MPER) of HIV-1 gp41 contains epitopes for at least four broadly neutralizing antibodies. Depending on solution conditions and construct design, different structures have been reported for this segment. We show that in aqueous solution the MPER fragment (gp160660-674 ) exists in a monomer-trimer equilibrium with an association constant in the micromolar range. Thermodynamic analysis reveals that the association is exothermic, more favorable in D2 O than H2 O, and increases with ionic strength, indicating hydrophobically driven intermolecular interactions. Circular dichroism, 13 Cα chemical shifts, NOE, and hydrogen exchange rates reveal that MPER undergoes a structural transition from predominately unfolded monomer at low concentrations to an α-helical trimer at high concentrations. This result has implications for antibody recognition of MPER prior to and during the process where gp41 switches from a pre-hairpin intermediate to its post-fusion 6-helical bundle state.
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Affiliation(s)
- Sai Chaitanya Chiliveri
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892, USA
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12
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Warren CJ, Meyerson NR, Dirasantha O, Feldman ER, Wilkerson GK, Sawyer SL. Selective use of primate CD4 receptors by HIV-1. PLoS Biol 2019; 17:e3000304. [PMID: 31181085 PMCID: PMC6586362 DOI: 10.1371/journal.pbio.3000304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 06/20/2019] [Accepted: 05/15/2019] [Indexed: 12/15/2022] Open
Abstract
Individuals chronically infected with HIV-1 harbor complex viral populations within their bloodstreams. Recently, it has come to light that when these people infect others, the new infection is typically established by only one or a small number of virions from within this complex viral swarm. An important goal is to characterize the biological properties of HIV-1 virions that seed and exist early in new human infections because these are potentially the only viruses against which a prophylactic HIV-1 vaccine would need to elicit protection. This includes understanding how the Envelope (Env) protein of these virions interacts with the T-cell receptor CD4, which supports attachment and entry of HIV-1 into target cells. We examined early HIV-1 isolates for their ability to infect cells via the CD4 receptor of 15 different primate species. Primates were the original source of HIV-1 and now serve as valuable animal models for studying HIV-1. We find that most primary isolates of HIV-1 from the blood, including early isolates, are highly selective and enter cells through some primate CD4 receptor orthologs but not others. This phenotype is remarkably consistent, regardless of route of transmission, viral subtype, or time of isolation post infection. We show that the weak CD4 binding affinity of blood-derived HIV-1 isolates is what makes them sensitive to the small sequence differences in CD4 from one primate species to the next. To substantiate this, we engineered an early HIV-1 Env to have high, medium, or low binding affinity to CD4, and we show that it loses the ability to enter cells via the CD4 receptor of many primate species as the binding affinity gets weaker. Based on the phenotype of selective use of primate CD4, we find that weak CD4 binding appears to be a nearly universal property of HIV-1 circulating in the bloodstream. Therefore, weak binding to CD4 must be a selected and important property in the biology of HIV-1 in the body. We identify six primate species that encode CD4 receptors that fully support the entry of early HIV-1 isolates despite their low binding affinity for CD4. These findings will help inform long-standing efforts to model HIV-1 transmission and early disease in primates. The current animal model for HIV, the macaque, encodes a CD4 receptor that is non-permissive for HIV entry. This paper reveals that six primate species encode CD4 receptors compatible with HIV infection, potentially making them powerful tools for the study of HIV biology. Furthermore, weak CD4 binding is a nearly constant, and apparently selected, property of HIV circulating in the human bloodstream.
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Affiliation(s)
- Cody J. Warren
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Nicholas R. Meyerson
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Obaiah Dirasantha
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Emily R. Feldman
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
| | - Gregory K. Wilkerson
- Department of Comparative Medicine, Michale E. Keeling Center for Comparative Medicine and Research, The University of Texas MD Anderson Cancer Center, Bastrop, Texas, United States of America
| | - Sara L. Sawyer
- BioFrontiers Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
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13
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A glycan shield on chimpanzee CD4 protects against infection by primate lentiviruses (HIV/SIV). Proc Natl Acad Sci U S A 2019; 116:11460-11469. [PMID: 31113887 DOI: 10.1073/pnas.1813909116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Pandemic HIV-1 (group M) emerged following the cross-species transmission of a simian immunodeficiency virus from chimpanzees (SIVcpz) to humans. Primate lentiviruses (HIV/SIV) require the T cell receptor CD4 to enter into target cells. By surveying the sequence and function of CD4 in 50 chimpanzee individuals, we find that all chimpanzee CD4 alleles encode a fixed, chimpanzee-specific substitution (34T) that creates a glycosylation site on the virus binding surface of the CD4 receptor. Additionally, a single nucleotide polymorphism (SNP) has arisen in chimpanzee CD4 (68T) that creates a second glycosylation site on the same virus-binding interface. This substitution is not yet fixed, but instead alleles containing this SNP are still circulating within chimpanzee populations. Thus, all allelic versions of chimpanzee CD4 are singly glycosylated at the virus binding surface, and some allelic versions are doubly glycosylated. Doubly glycosylated forms of chimpanzee CD4 reduce HIV-1 and SIVcpz infection by as much as two orders of magnitude. Full restoration of virus infection in cells bearing chimpanzee CD4 requires reversion of both threonines at sites 34 and 68, destroying both of the glycosylation sites, suggesting that the effects of the glycans are additive. Differentially glycosylated CD4 receptors were biochemically purified and used in neutralization assays and microscale thermophoresis to show that the glycans on chimpanzee CD4 reduce binding affinity with the lentiviral surface glycoprotein, Env. These glycans create a shield that protects CD4 from being engaged by viruses, demonstrating a powerful form of host resistance against deadly primate lentiviruses.
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14
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eCD4-Ig Variants That More Potently Neutralize HIV-1. J Virol 2018; 92:JVI.02011-17. [PMID: 29593050 DOI: 10.1128/jvi.02011-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 02/28/2018] [Indexed: 12/23/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) entry inhibitor eCD4-Ig is a fusion of CD4-Ig and a coreceptor-mimetic peptide. eCD4-Ig is markedly more potent than CD4-Ig, with neutralization efficiencies approaching those of HIV-1 broadly neutralizing antibodies (bNAbs). However, unlike bNAbs, eCD4-Ig neutralized all HIV-1, HIV-2, and simian immunodeficiency virus (SIV) isolates that it has been tested against, suggesting that it may be useful in clinical settings, where antibody escape is a concern. Here, we characterize three new eCD4-Ig variants, each with a different architecture and each utilizing D1.22, a stabilized form of CD4 domain 1. These variants were 10- to 20-fold more potent than our original eCD4-Ig variant, with a construct bearing four D1.22 domains (eD1.22-HL-Ig) exhibiting the greatest potency. However, this variant mediated less efficient antibody-dependent cell-mediated cytotoxicity (ADCC) activity than eCD4-Ig itself or several other eCD4-Ig variants, including the smallest variant (eD1.22-Ig). A variant with the same architecture as the original eCD4-Ig (eD1.22-D2-Ig) showed modestly higher thermal stability and best prevented the promotion of infection of CCR5-positive, CD4-negative cells. All three variants, and eCD4-Ig itself, mediated more efficient shedding of the HIV-1 envelope glycoprotein gp120 than did CD4-Ig. Finally, we show that only three D1.22 mutations contributed to the potency of eD1.22-D2-Ig and that introduction of these changes into eCD4-Ig resulted in a variant 9-fold more potent than eCD4-Ig and 2-fold more potent than eD1.22-D2-Ig. These studies will assist in developing eCD4-Ig variants with properties optimized for prophylaxis, therapy, and cure applications.IMPORTANCE HIV-1 bNAbs have properties different from those of antiretroviral compounds. Specifically, antibodies can enlist immune effector cells to eliminate infected cells, whereas antiretroviral compounds simply interfere with various steps in the viral life cycle. Unfortunately, HIV-1 is adept at evading antibody recognition, limiting the utility of antibodies as a treatment for HIV-1 infection or as part of an effort to eradicate latently infected cells. eCD4-Ig is an antibody-like entry inhibitor that closely mimics HIV-1's obligate receptors. eCD4-Ig appears to be qualitatively different from antibodies, since it neutralizes all HIV-1, HIV-2, and SIV isolates. Here, we characterize three new structurally distinct eCD4-Ig variants and show that each excels in a key property useful to prevent, treat, or cure an HIV-1 infection. For example, one variant neutralized HIV-1 most efficiently, while others best enlisted natural killer cells to eliminate infected cells. These observations will help generate eCD4-Ig variants optimized for different clinical applications.
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15
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Abstract
The egg coat, an extracellular matrix made up of glycoprotein filaments, plays a key role in animal fertilization by acting as a gatekeeper for sperm. Egg coat components polymerize using a common zona pellucida (ZP) "domain" module that consists of two related immunoglobulin-like domains, called ZP-N and ZP-C. The ZP module has also been recognized in a large number of other secreted proteins with different biological functions, whose mutations are linked to severe human diseases. During the last decade, tremendous progress has been made toward understanding the atomic architecture of the ZP module and the structural basis of its polymerization. Moreover, sperm-binding regions at the N-terminus of mollusk and mammalian egg coat subunits were found to consist of domain repeats that also adopt a ZP-N fold. This discovery revealed an unexpected link between invertebrate and vertebrate fertilization and led to the first structure of an egg coat-sperm protein recognition complex. In this review we summarize these exciting findings, discuss their functional implications, and outline future challenges that must be addressed in order to develop a comprehensive view of this family of biomedically important extracellular molecules.
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Affiliation(s)
- Marcel Bokhove
- Department of Biosciences and Nutrition & Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Luca Jovine
- Department of Biosciences and Nutrition & Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden.
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16
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Zhou CY, Wang RN, Wen Q, He WT, Zhang SM, Du XL, Yang JH, Ma L. Alanine Mutagenesis in the Complementarity Determining Region 3 of the MTB and HIV-1 Peptide-Bispecific T Cell Receptor Beta Chain Affects Ligand Recognition. Front Immunol 2017; 8:983. [PMID: 28861087 PMCID: PMC5561015 DOI: 10.3389/fimmu.2017.00983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/31/2017] [Indexed: 11/22/2022] Open
Abstract
Mycobacterium tuberculosis/human immunodeficiency virus (MTB/HIV) coinfection presents a special challenge to the prevention and treatment of tuberculosis and HIV/AIDS. Adoptive transfer of high-affinity T cell receptor (TCR) gene-modified T cells against MTB and HIV antigens is a promising approach to treating MTB/HIV coinfected patients whose cellular immunity is obviously disordered. We have previously successfully identified that a bispecific TCR screened out from peripheral blood mononuclear cells of a HLA-A*0201+ healthy individual using the complementarity determining region 3 (CDR3) spectratype analysis recognizes both MTB Ag85B199–207 and HIV-1 Env120–128 peptide. However, it has not been known how residues on CDR3 loops, which have been shown to play a leading role in antigen binding and specificity contribute to the bispecific TCR contact with the peptide–major histocompatibility complex (MHC) complexes. In this study, we provided an extensive investigation of residues in the predicted CDR3 of the bispecific TCR beta (β) chain using alanine scanning mutagenesis. Our data showed that three of the five substituted residues (G115A, T116A, A117G) in CDR3β of the bispecific TCR caused a significantly diminished T cell response to antigen, whereas the remaining two substituted residues (D114A, S118A) resulted in completely eliminated response, thus identifying the two residues that were particularly critical for the recognition of peptide–MHC in the bispecific TCR. These findings will provide an imperative foundation for generating an improved high-affinity bispecific TCR for use in T cell adoptive immunotherapy for MTB/HIV coinfected individuals.
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Affiliation(s)
- Chao-Ying Zhou
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Rui-Ning Wang
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Qian Wen
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Wen-Ting He
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Shi-Meng Zhang
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Xia-Lin Du
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Jia-Hui Yang
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Li Ma
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
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17
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Bui VC, Nguyen TH. Insights into the interaction of CD4 with anti-CD4 antibodies. Immunobiology 2016; 222:148-154. [PMID: 27773661 DOI: 10.1016/j.imbio.2016.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/15/2016] [Indexed: 01/13/2023]
Abstract
Knowledge about the mechanism by which some antibodies can block HIV-1 entry is critical to our understanding of their function and may offer new avenues for controlling the adhesion of HIV-1 to the host cells. While much progress has been made, this mechanism remains unclear. Here, atomic force microscopy, isothermal titration calorimetry (ITC), and circular dichroism spectroscopy were used to measure some biophysical characteristics of the interaction of four-domains (D1-D4) membrane protein CD4 with anti-D3 antibody OKT4 and with HIV-1 entry blocking anti-D1 antibody Leu3a. The results showed that at 37°C they bind with similar binding strength, thermodynamics, and kinetics but with different assembly states. Further analyzing the interactions at different temperatures by ITC showed that binding of CD4 with Leu3a is characteristic for specific hydrophobic binding as well as for protein folding while with OKT4 comes from an extensive additional hydration upon binding and charge-related interactions within the binding site. Comparing these characteristics with those of HIV-1 gp120-CD4 interaction revealed that Leu3a binds to CD4 faster than HIV-1 followed by changing local structure of D1 to which HIV-1 binds leading to a prevention of viral entry.
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Affiliation(s)
- Van-Chien Bui
- Center for Innovation Competence, Humoral Immune Reactions in Cardiovascular Diseases, University Medicine Greifswald, 17489 Greifswald, Germany; Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Thi-Huong Nguyen
- Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, 17475 Greifswald, Germany.
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18
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Cereda PM, Palù G, Rassu M, Toni M, Malwood W, Dettin M, di Bello C. Anti-HIV-1 Activity of CD4 Synthetic Oligopeptides Representative of the Putative gp120 Binding Site. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029100200305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Two CD4 oligopeptides, corresponding to residues (37–53) and (37–55) of the V1 domain of CD4, which recent structural studies propose as the most likely binding site of HIV-1 gp120, have been chemically synthesized by solid-phase techniques, modified by the addition of two side-chain protected cysteines at both termini and purified by HPLC. Their ability to inhibit the infectivity of human immunodeficiency virus type 1 (HIV-1) (HTLV-IIIB, RF and GB8 strains) in different cell lines was monitored by the production of progeny virus, p24 and reverse transcriptase activity in the culture supernatants and by electron microscopy. The results indicated that the peptides inhibited HIV-1 infectivity in a dose-dependent fashion without any detectable cytotoxicity.
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Affiliation(s)
- P. M. Cereda
- Institute of Microbiology, University of Pavia, Via Brambilla, Italy
| | - G. Palù
- Institute of Microbiology, University of Padova, Via Gabelli, Italy
| | - M. Rassu
- Institute of Microbiology, University of Padova, Via Gabelli, Italy
| | - M. Toni
- Institute of Microbiology, University of Padova, Via Gabelli, Italy
| | - W. Malwood
- National Institute for Medical Research, Mill Hill, London, UK
| | - M. Dettin
- Institute of Industrial Chemistry, University of Padova, Via Marzolo, Italy
| | - C. di Bello
- Institute of Industrial Chemistry, University of Padova, Via Marzolo, Italy
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19
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Owen GR, Channell JA, Forsyth VT, Haertlein M, Mitchell EP, Capovilla A, Papathanasopoulos M, Cerutti NM. Human CD4 Metastability Is a Function of the Allosteric Disulfide Bond in Domain 2. Biochemistry 2016; 55:2227-37. [DOI: 10.1021/acs.biochem.6b00154] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gavin R. Owen
- HIV
Pathogenesis Research Unit, Department of Molecular Medicine and Haematology,
Faculty of Health Sciences, University of the Witwatersrand, 7
York Road, Parktown, 2193, Johannesburg, South Africa
| | - Jennifer A. Channell
- Faculty
of Natural Sciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
- Life
Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, 38042, Grenoble, France
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - V. Trevor Forsyth
- Faculty
of Natural Sciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
- Life
Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Michael Haertlein
- Life
Sciences Group, Institut Laue-Langevin, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Edward P. Mitchell
- Faculty
of Natural Sciences, Keele University, Keele, Staffordshire ST5 5BG, United Kingdom
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Alexio Capovilla
- HIV
Pathogenesis Research Unit, Department of Molecular Medicine and Haematology,
Faculty of Health Sciences, University of the Witwatersrand, 7
York Road, Parktown, 2193, Johannesburg, South Africa
| | - Maria Papathanasopoulos
- HIV
Pathogenesis Research Unit, Department of Molecular Medicine and Haematology,
Faculty of Health Sciences, University of the Witwatersrand, 7
York Road, Parktown, 2193, Johannesburg, South Africa
| | - Nichole M. Cerutti
- HIV
Pathogenesis Research Unit, Department of Molecular Medicine and Haematology,
Faculty of Health Sciences, University of the Witwatersrand, 7
York Road, Parktown, 2193, Johannesburg, South Africa
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20
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Bui VC, Nguyen TH. The role of CD4 on mechanical properties of live cell membrane. J Biomed Mater Res A 2015; 104:239-44. [DOI: 10.1002/jbm.a.35559] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/13/2015] [Accepted: 09/03/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Van-Chien Bui
- Center for Innovation Competence - Humoral Immune Reactions in Cardiovascular Diseases (ZIK HIKE); University of Greifswald; 17489 Greifswald Germany
| | - Thi-Huong Nguyen
- Center for Innovation Competence - Humoral Immune Reactions in Cardiovascular Diseases (ZIK HIKE); University of Greifswald; 17489 Greifswald Germany
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21
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Hou W, Fang C, Liu J, Yu H, Qi J, Zhang Z, Yuan R, Xiong D, Gao S, Adam Yuan Y, Li S, Gu Y, Xia N. Molecular insights into the inhibition of HIV-1 infection using a CD4 domain-1-specific monoclonal antibody. Antiviral Res 2015; 122:101-11. [PMID: 26259811 DOI: 10.1016/j.antiviral.2015.08.004] [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: 10/17/2014] [Revised: 08/01/2015] [Accepted: 08/07/2015] [Indexed: 12/19/2022]
Abstract
An HIV-1 infection in a host cell occurs through an ordered process that involves HIV-1 attachment to the host's cellular CD4 receptor, co-receptor binding to CCR5 or CXCR4, and the subsequent fusion with the cellular membrane. The natural viral entry pathway into a host cell provides an opportunity to develop agents for the treatment of HIV-1 infections. Several engineered monoclonal antibodies specifically targeting CD4 have shown antiviral activities in clinical trials. Here, we report on an anti-CD4 mAb (15A7) that displays a unique binding specificity for domain 1 of CD4, whose epitope partially overlaps with the gp120 binding region. Moreover, 15A7 displays a much stronger binding affinity to CD4(+) cell lines after HIV infection. 15A7 is able to block and neutralize a broad range of primary HIV-1 isolates and T cell-line passage strains. Notably, the bivalent F(ab')2 form of 15A7 is more effective than the Fab form in blocking HIV-1 infection, which is further supported by molecular docking analyses. Together, these results suggest that this novel antibody may exert its antiviral activity by blocking gp120 targeting to the CD4 receptor or competing with gp120 for CD4 receptor binding and might present post-attachment neutralization activity. This antibody could provide a new candidate to efficiently block HIV-1 infection or provide new starting materials for HIV treatment, especially when HIV-1-resistant strains against the current CD4 mAb treatments have already been identified.
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Affiliation(s)
- Wangheng Hou
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Chu Fang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Jiayan Liu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Hai Yu
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361005, China
| | - Jialong Qi
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361005, China
| | - Zhiqing Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Ruixue Yuan
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Dan Xiong
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Shuangquan Gao
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361005, China
| | - Y Adam Yuan
- National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361005, China; National University of Singapore (Suzhou) Research Institute, Suzhou 215123, China
| | - Shaowei Li
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China; National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361005, China
| | - Ying Gu
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China; National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361005, China.
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361005, China; National Institute of Diagnostics and Vaccine Development in Infectious Disease, School of Public Health, Xiamen University, Xiamen 361005, China
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22
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Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Cell 2015; 161:1280-92. [PMID: 26004070 DOI: 10.1016/j.cell.2015.05.007] [Citation(s) in RCA: 246] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 03/19/2015] [Accepted: 03/25/2015] [Indexed: 01/16/2023]
Abstract
The site on the HIV-1 gp120 glycoprotein that binds the CD4 receptor is recognized by broadly reactive antibodies, several of which neutralize over 90% of HIV-1 strains. To understand how antibodies achieve such neutralization, we isolated CD4-binding-site (CD4bs) antibodies and analyzed 16 co-crystal structures -8 determined here- of CD4bs antibodies from 14 donors. The 16 antibodies segregated by recognition mode and developmental ontogeny into two types: CDR H3-dominated and VH-gene-restricted. Both could achieve greater than 80% neutralization breadth, and both could develop in the same donor. Although paratope chemistries differed, all 16 gp120-CD4bs antibody complexes showed geometric similarity, with antibody-neutralization breadth correlating with antibody-angle of approach relative to the most effective antibody of each type. The repertoire for effective recognition of the CD4 supersite thus comprises antibodies with distinct paratopes arrayed about two optimal geometric orientations, one achieved by CDR H3 ontogenies and the other achieved by VH-gene-restricted ontogenies.
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23
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Reinherz EL, Wang JH. Codification of bidentate pMHC interaction with TCR and its co-receptor. Trends Immunol 2015; 36:300-6. [PMID: 25818864 PMCID: PMC4420642 DOI: 10.1016/j.it.2015.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 02/03/2023]
Abstract
A 1983 Immunology Today rostrum hypothesized that each T cell has two recognition units: a T cell receptor (TCR) complex, which binds antigen associated with a polymorphic region of a MHC molecule (pMHC), and a CD4 or CD8 molecule that binds to a conserved region of that same MHC gene product (class II or I, respectively). Structural biology has since precisely revealed those bidentate pMHC interactions. TCRαβ ligates the membrane-distal antigen-binding MHC platform, whereas CD8 clamps a membrane-proximal MHCI α3 domain loop and CD4 docks to a hydrophobic crevice between MHCII α2 and β2 domains. Here, we review how MHC class-restricted binding impacts signaling and lineage commitment, discussing TCR force-driven conformational transitions that may optimally expose the co-receptor docking site on MHC.
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Affiliation(s)
- Ellis L Reinherz
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Jia-huai Wang
- Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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24
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Kong L, Wilson IA, Kwong PD. Crystal structure of a fully glycosylated HIV-1 gp120 core reveals a stabilizing role for the glycan at Asn262. Proteins 2015; 83:590-6. [PMID: 25546301 DOI: 10.1002/prot.24747] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 12/10/2014] [Indexed: 01/27/2023]
Abstract
The crystal structure of a fully glycosylated HIV-1 gp120 core in complex with CD4 receptor and Fab 17b at 4.5-Å resolution reveals 9 of the 15 N-linked glycans of core gp120 to be partially ordered. The glycan at position Asn262 had the most extensive and well-ordered electron density, and a GlcNAc(2)Man(7) was modeled. The GlcNAc stem of this glycan is largely buried in a cleft in gp120, suggesting a role in gp120 folding and stability. Its arms interact with the stems of neighboring glycans from the oligomannose patch, which is a major target for broadly neutralizing antibodies.
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Affiliation(s)
- Leopold Kong
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland, 20892; Department of Integrative Structural and Computational Biology, the Scripps Research Institute, La Jolla, California; International AIDS Vaccine Initiative Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery, the Scripps Research Institute, La Jolla, California; Scripps Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, the Scripps Research Institute, La Jolla, California
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25
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Abstract
When I entered graduate school in 1963, the golden age of molecular biology had just begun, and myoglobin was the only protein with a known high-resolution structure. The romance of working out the structure of a virus by X-ray crystallography nonetheless captured both my imagination and the ensuing 15 years of my scientific life, during which "protein crystallography" began to morph into "structural biology." The course of the research recounted here follows the broader, 50-year trajectory of structural biology, as I could rarely resist opportunities to capitalize on new technologies when they opened some interesting part of biology to three-dimensional rigor. That fascination shows no sign of subsiding.
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Affiliation(s)
- Stephen C Harrison
- Harvard Medical School, Boston Children's Hospital, and Howard Hughes Medical Institute, Boston, Massachusetts 02115;
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26
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Perez-Jimenez R, Alonso-Caballero A, Berkovich R, Franco D, Chen MW, Richard P, Badilla CL, Fernandez JM. Probing the effect of force on HIV-1 receptor CD4. ACS NANO 2014; 8:10313-10320. [PMID: 25299596 PMCID: PMC4212800 DOI: 10.1021/nn503557w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 10/09/2014] [Indexed: 05/29/2023]
Abstract
Cell-surface proteins are central for the interaction of cells with their surroundings and are also associated with numerous diseases. These molecules are exposed to mechanical forces, but the exact relation between force and the functions and pathologies associated with cell-surface proteins is unclear. An important cell-surface protein is CD4, the primary receptor of HIV-1. Here we show that mechanical force activates conformational and chemical changes on CD4 that may be important during viral attachment. We have used single-molecule force spectroscopy and analysis on HIV-1 infectivity to demonstrate that the mechanical extension of CD4 occurs in a time-dependent manner and correlates with HIV-1 infectivity. We show that Ibalizumab, a monoclonal antibody that blocks HIV-1, prevents the mechanical extension of CD4 domains 1 and 2. Furthermore, we demonstrate that thiol/disulfide exchange in CD4 requires force for exposure of cryptic disulfide bonds. This mechanical perspective provides unprecedented information that can change our understanding on how viruses interact with their hosts.
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Affiliation(s)
- Raul Perez-Jimenez
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48013, Spain
- CIC nanoGUNE, San Sebastian, E-20018, Spain
| | | | - Ronen Berkovich
- Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - David Franco
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York 10065, United States
| | - Ming-Wei Chen
- Aaron Diamond AIDS Research Center, The Rockefeller University, New York, New York 10065, United States
| | - Patricia Richard
- Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Carmen L. Badilla
- Department of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Julio M. Fernandez
- Department of Biological Sciences, Columbia University, New York, New York 10027, United States
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27
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Zhou B, Baldus IB, Li W, Edwards SA, Gräter F. Identification of allosteric disulfides from prestress analysis. Biophys J 2014; 107:672-681. [PMID: 25099806 PMCID: PMC4129481 DOI: 10.1016/j.bpj.2014.06.025] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/11/2014] [Accepted: 06/16/2014] [Indexed: 11/23/2022] Open
Abstract
Disulfide bonds serve to form physical cross-links between residues in protein structures, thereby stabilizing the protein fold. Apart from this purely structural role, they can also be chemically active, participating in redox reactions, and they may even potentially act as allosteric switches controlling protein functions. Specific types of disulfide bonds have been identified in static protein structures from their distinctive pattern of dihedral bond angles, and the allosteric function of such bonds is purported to be related to the torsional strain they store. Using all-atom molecular-dynamics simulations for ∼700 disulfide bonded proteins, we analyzed the intramolecular mechanical forces in 20 classes of disulfide bonds. We found that two particular classes, the -RHStaple and the -/+RHHook disulfides, are indeed more stressed than other disulfide bonds, but the stress is carried primarily by stretching of the S-S bond and bending of the neighboring bond angles, rather than by dihedral torsion. This stress corresponds to a tension force of magnitude ∼200 pN, which is balanced by repulsive van der Waals interactions between the cysteine Cα atoms. We confirm stretching of the S-S bond to be a general feature of the -RHStaples and the -/+RHHooks by analyzing ∼20,000 static protein structures. Given that forced stretching of S-S bonds is known to accelerate their cleavage, we propose that prestress of allosteric disulfide bonds has the potential to alter the reactivity of a disulfide, thereby allowing us to readily switch between functional states.
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Affiliation(s)
- Beifei Zhou
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai, China; Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Ilona B Baldus
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Wenjin Li
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois
| | - Scott A Edwards
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai, China; College of Physics Science and Technology, Shenzhen University, Shenzhen, Guangdong, China
| | - Frauke Gräter
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai, China; Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
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28
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The immunology connection--my first T cell receptor structure projects. Protein Cell 2014; 5:649-52. [PMID: 25087847 PMCID: PMC4145086 DOI: 10.1007/s13238-014-0091-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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29
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Abstract
X-ray diffraction patterns from crystals of biological macromolecules contain sufficient information to define atomic structures, but atomic positions are inextricable without having electron-density images. Diffraction measurements provide amplitudes, but the computation of electron density also requires phases for the diffracted waves. The resonance phenomenon known as anomalous scattering offers a powerful solution to this phase problem. Exploiting scattering resonances from diverse elements, the methods of MAD (multiwavelength anomalous diffraction) and SAD (single-wavelength anomalous diffraction) now predominate for de novo determinations of atomic-level biological structures. This review describes the physical underpinnings of anomalous diffraction methods, the evolution of these methods to their current maturity, the elements, procedures and instrumentation used for effective implementation, and the realm of applications.
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Affiliation(s)
- Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, and Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032 USA. New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027 USA
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30
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Roy S, Huang H, Liu S, Kornberg TB. Cytoneme-mediated contact-dependent transport of the Drosophila decapentaplegic signaling protein. Science 2014; 343:1244624. [PMID: 24385607 DOI: 10.1126/science.1244624] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Decapentaplegic (Dpp), a Drosophila morphogen signaling protein, transfers directly at synapses made at sites of contact between cells that produce Dpp and cytonemes that extend from recipient cells. The Dpp that cytonemes receive moves together with activated receptors toward the recipient cell body in motile puncta. Genetic loss-of-function conditions for diaphanous, shibire, neuroglian, and capricious perturbed cytonemes by reducing their number or only the synapses they make with cells they target, and reduced cytoneme-mediated transport of Dpp and Dpp signaling. These experiments provide direct evidence that cells use cytonemes to exchange signaling proteins, that cytoneme-based exchange is essential for signaling and normal development, and that morphogen distribution and signaling can be contact-dependent, requiring cytoneme synapses.
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Affiliation(s)
- Sougata Roy
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
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31
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Kong L, Giang E, Nieusma T, Kadam RU, Cogburn KE, Hua Y, Dai X, Stanfield RL, Burton DR, Ward AB, Wilson IA, Law M. Hepatitis C virus E2 envelope glycoprotein core structure. Science 2013; 342:1090-4. [PMID: 24288331 DOI: 10.1126/science.1243876] [Citation(s) in RCA: 311] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hepatitis C virus (HCV), a Hepacivirus, is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. HCV envelope glycoproteins E1 and E2 mediate fusion and entry into host cells and are the primary targets of the humoral immune response. The crystal structure of the E2 core bound to broadly neutralizing antibody AR3C at 2.65 angstroms reveals a compact architecture composed of a central immunoglobulin-fold β sandwich flanked by two additional protein layers. The CD81 receptor binding site was identified by electron microscopy and site-directed mutagenesis and overlaps with the AR3C epitope. The x-ray and electron microscopy E2 structures differ markedly from predictions of an extended, three-domain, class II fusion protein fold and therefore provide valuable information for HCV drug and vaccine design.
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Affiliation(s)
- Leopold Kong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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32
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Liu Y, Schön A, Freire E. Optimization of CD4/gp120 inhibitors by thermodynamic-guided alanine-scanning mutagenesis. Chem Biol Drug Des 2013; 81:72-8. [PMID: 23066870 DOI: 10.1111/cbdd.12075] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
As protein/protein interactions usually trigger signalling processes, inhibitors of those interactions must preclude protein binding without eliciting the signalling process themselves. To accomplish those goals, small molecules need to target those protein residues that contribute the most to binding (binding hotspots) without disturbing those residues that initiate signalling processes (allosteric hotspots). The availability of a blueprint identifying binding and allosteric hotspots will significantly aid inhibitor design and optimization. In this study, we show that in some situations the blueprint can be constructed by combining the standard technique of alanine-scanning mutagenesis with isothermal titration calorimetry (ITC). We demonstrate the approach by developing the combined binding and allosteric hotspots blueprint for CD4/gp120, the initial interaction leading to HIV-1 cell infection. A major finding of these studies is that not all binding hotspots are allosteric hotspots opening the possibility for the rational design of inhibitors and antagonist or agonist modulators.
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Affiliation(s)
- Yingyun Liu
- Department of Biology, The Johns Hopkins University, 3400 North Charles, Baltimore, MD 21218, USA
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33
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Kassler K, Sticht H. Molecular mechanism of HIV-1 gp120 mutations that reduce CD4 binding affinity. J Biomol Struct Dyn 2013; 32:52-64. [DOI: 10.1080/07391102.2012.746946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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34
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Li L, Shi X, Lu Q, Zhang S, Wang X, Jiang X, Liu Y, Wang G, Zhu W, Lei R, Wu H. Role of human CD4 D1D2 domain in HIV-1 infection. Immunol Invest 2012; 42:106-21. [PMID: 23252862 DOI: 10.3109/08820139.2012.736115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Broadly neutralizing antibodies and appropriate immunogens are critical for preexposure prophylaxis and therapeutic HIV vaccines. In this study, we aimed to explore effective antibodies against the genetically diverse HIV-1 strains by investigating the roles of human CD4 D1D2 domain and nonvariable immugens. The human CD4 D1D2 domain and the chimeric protein of mouse D1 domain/human D2 domain were expressed in Sf9 insect cells and purified by gel-filtration chromatography. The human CD4 D1D2 domain potently inhibited the infection of 77.8% HIV-1 pseudoviruses, including the clades AE, B' and BC, with less than 20 μg/mL of IC(50). pcDNA3.1-mhD1D2m and pcDNA3.1-mhD2m plasmids were used for the production of mouse anti-human CD4 polyclonal antibodies. The neutralizing activities of the polyclonal antibodies were determined by using pseudotyped HIV-1 viruses. The antibodies induced by plasmids containing human CD4 D1D2 domain were able to potently inhibit all pseudotyped HIV-1 strains. The antibodies from mhD1D2m-immunized mice also showed strong binding capacity to CD4 expressed on the surface of TZM-bl cells. The potent and broad inhibitory activity of antibodies against the human CD4 D1D2 domain may be used to develop effective passive immunization agent to control the spread of HIV infection.
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Affiliation(s)
- Lan Li
- Department of Infectious Diseases, Beijing You'an Hospital, Capital Medical University, Beijing, China
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35
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Meier J, Kassler K, Sticht H, Eichler J. Peptides presenting the binding site of human CD4 for the HIV-1 envelope glycoprotein gp120. Beilstein J Org Chem 2012; 8:1858-66. [PMID: 23209523 PMCID: PMC3511023 DOI: 10.3762/bjoc.8.214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 09/24/2012] [Indexed: 01/31/2023] Open
Abstract
Based on the structure of the HIV-1 glycoprotein gp120 in complex with its cellular receptor CD4, we have designed and synthesized peptides that mimic the binding site of CD4 for gp120. The ability of these peptides to bind to gp120 can be strongly enhanced by increasing their conformational stability through cyclization, as evidenced by binding assays, as well as through molecular-dynamics simulations of peptide–gp120 complexes. The specificity of the peptide–gp120 interaction was demonstrated by using peptide variants, in which key residues for the interaction with gp120 were replaced by alanine or D-amino acids.
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Affiliation(s)
- Julia Meier
- Department of Chemistry and Pharmacy, Universität Erlangen-Nürnberg, Schuhstrasse 19, 91052 Erlangen, Germany
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36
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Abstract
Antibody-based therapeutics have been successfully used for the treatment of various diseases and as research tools. Several well characterized, broadly neutralizing monoclonal antibodies (bnmAbs) targeting HIV-1 envelope glycoproteins or related host cell surface proteins show sterilizing protection of animals, but they are not effective when used for therapy of an established infection in humans. Recently, a number of novel bnmAbs, engineered antibody domains (eAds), and multifunctional fusion proteins have been reported which exhibit exceptionally potent and broad neutralizing activity against a wide range of HIV-1 isolates from diverse genetic subtypes. eAds could be more effective in vivo than conventional full-size antibodies generated by the human immune system. Because of their small size (12∼15 kD), they can better access sterically restricted epitopes and penetrate densely packed tissue where HIV-1 replicates than the larger full-size antibodies. HIV-1 possesses a number of mechanisms to escape neutralization by full-size antibodies but could be less likely to develop resistance to eAds. Here, we review the in vitro and in vivo antiviral efficacies of existing HIV-1 bnmAbs, summarize the development of eAds and multispecific fusion proteins as novel types of HIV-1 inhibitors, and discuss possible strategies to generate more potent antibody-based candidate therapeutics against HIV-1, including some that could be used to eradicate the virus.
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Affiliation(s)
- Rui Gong
- Protein Interactions Group, Frederick National Laboratory for Cancer Research, National Institutes of Health, Frederick, MD 21702-1201, USA.
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37
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Ryu SE, Hendrickson WA. Structure and design of broadly-neutralizing antibodies against HIV. Mol Cells 2012; 34:231-7. [PMID: 22736269 PMCID: PMC3823542 DOI: 10.1007/s10059-012-0104-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 05/29/2012] [Accepted: 06/04/2012] [Indexed: 10/28/2022] Open
Abstract
Since the discovery more than 30 years ago of human immunodeficiency virus (HIV) as the causative agent of the deadly disease, acquired immune deficiency disease (AIDS), there have been no efficient vaccines against the virus. For the infection of the virus, the HIV surface glycoprotein gp120 first recognizes the CD4 receptor on the target helper T-cell, which initiates HIV fusion with the target cell and, if unchecked, leads to destruction of the patient's immune system. Despite the difficulty of developing appropriate immune responses in HIV-infected individuals, patient sera often contain antibodies that have broad neutralization activity, indicating the possibility of immunological treatment and prevention. Recently, through extensive structural studies of neutralizing antibodies of HIV in complex with gp120, the critical mechanisms of broad neutralization against HIV have been elucidated. Based on these discoveries, the structure-aided designs of antibodies and novel scaffolds were performed to create extremely potent neutralizing antibodies against HIV. These new discoveries and advances shed light on the road to development of efficient immunological therapies against AIDS.
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Affiliation(s)
- Seong Eon Ryu
- Department of Bioengineering, College of Engineering, Hanyang University, Seoul 133-070,
Korea
- Institute of Biopharmaceutical Research, Hanyang University, Seoul 133-070,
Korea
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032,
USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032,
USA
- Howard Hughes Medical Institute, Columbia University, New York, NY 10032,
USA
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38
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Structural Basis for Species Selectivity in the HIV-1 gp120-CD4 Interaction: Restoring Affinity to gp120 in Murine CD4 Mimetic Peptides. Adv Bioinformatics 2012; 2011:736593. [PMID: 22312332 PMCID: PMC3270550 DOI: 10.1155/2011/736593] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 11/07/2011] [Accepted: 11/23/2011] [Indexed: 11/18/2022] Open
Abstract
The first step of HIV-1 infection involves interaction between the viral glycoprotein gp120 and the human cellular receptor CD4. Inhibition of the gp120-CD4 interaction represents an attractive strategy to block HIV-1 infection. In an attempt to explore the known lack of affinity of murine CD4 to gp120, we have investigated peptides presenting the putative gp120-binding site of murine CD4 (mCD4). Molecular modeling indicates that mCD4 protein cannot bind gp120 due to steric clashes, while the larger conformational flexibility of mCD4 peptides allows an interaction. This finding is confirmed by experimental binding assays, which also evidenced specificity of the peptide-gp120 interaction. Molecular dynamics simulations indicate that the mCD4-peptide stably interacts with gp120 via an intermolecular β-sheet, while an important salt-bridge formed by a C-terminal lysine is lost. Fixation of the C-terminus by introducing a disulfide bridge between the N- and C-termini of the peptide significantly enhanced the affinity to gp120.
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39
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Cheng K, El-Boubbou K, Landry CC. Binding of HIV-1 gp120 glycoprotein to silica nanoparticles modified with CD4 glycoprotein and CD4 peptide fragments. ACS APPLIED MATERIALS & INTERFACES 2012; 4:235-243. [PMID: 22117536 DOI: 10.1021/am2013008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
An important step in human immunodeficiency virus infection involves the interaction between the viral envelope glycoprotein gp120 and the human host cell surface receptor CD4. Herein, we describe a CD4-functionalized mesoporous silica-based system to selectively capture HIV-gp120 with high binding efficiency. Using a protection-deprotection strategy developed recently by our group, the external surface of the mesoporous particles was selectively functionalized with soluble CD4 ("sCD4") or an 18-peptide fragment mimicking the gp120 binding region. Confocal microscopy confirmed the CD4 locations and showed that the internal pores can be made accessible after external modification in a controlled manner. An evaluation of the ability of an 18-peptide CD4 fragment versus amide-immobilized sCD4 and sCD4 immobilized through its glycosidic group indicated that while all peptides were selective, the latter method was clearly best, with nearly complete removal of whole gp120 from solution. This study shows, for the first time, that sCD4 bound to mesoporous silica particles actively recognizes and retains high binding affinity for HIV-gp120. It is anticipated that, by proper modification of the accessible internal pores, our methodology can be adopted to develop porous platforms for HIV diagnosis, imaging, drug delivery, and vaccine development.
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Affiliation(s)
- Kai Cheng
- Department of Chemistry, University of Vermont, 82 University Place, Burlington, Vermont 05405, USA
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Toda T, Kuwahara K, Kondo N, Matsuda Z, Maeda Y, Maeda K, Sakaguchi N. Dynamic appearance of antigenic epitopes effective for viral neutralization during membrane fusion initiated by interactions between HIV-1 envelope proteins and CD4/CXCR4. Immunobiology 2011; 217:864-72. [PMID: 22226668 DOI: 10.1016/j.imbio.2011.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Revised: 12/15/2011] [Accepted: 12/16/2011] [Indexed: 11/19/2022]
Abstract
HIV-1 entry into cells is mediated by interactions between the envelope (Env) gp120 and gp41 proteins with CD4 and chemokine receptors via an intermediate called the viral fusion complex (vFC). Here, mAbs were used to find the dynamic changes in expression of antigenic epitopes during vFC formation. A CD4-specific mAb (R275) and anti-vFC mAbs, designated F12-1, F13-6 and F18-4 that recognize the epitopes only appeared by the co-culture of env-transfected 293FT and CD4-transfected 293 cells, were developed by immunizing ganp-gene transgenic mice with an vFC-like structure formed by the same co-culture. The epitopes recognized by the mAbs appeared at different time points during vFC formation: F18-4 appeared first, followed by F13-6, and finally F12-1. The anti-vFC mAbs had little effect on vFC formation or virus neutralization; however, interestingly F12-1 and F18-4 increased exposure of the OKT4-epitope on the domain 3 in the extracellular region of CD4. R275, which recognizes the epitope closely associated with the OKT4-determinant on the domain 3, showed the marked inhibition of vFC formation and viral neutralization activity. The Ab binding to the epitopes appeared during viral membrane fusion might reinforce the appearance of the target epitopes for effective neutralization activity.
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MESH Headings
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- CD4 Antigens/immunology
- CD4 Antigens/metabolism
- Cell Line
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/metabolism
- Gene Order
- Gene Targeting
- HIV Antibodies/immunology
- HIV Antibodies/metabolism
- HIV-1/immunology
- Humans
- Immunoglobulin Fc Fragments/immunology
- Immunoglobulin Fc Fragments/metabolism
- Mice
- Mice, Transgenic
- Neutralization Tests
- Protein Binding
- Receptors, CXCR4/immunology
- Receptors, CXCR4/metabolism
- Virus Internalization
- env Gene Products, Human Immunodeficiency Virus/chemistry
- env Gene Products, Human Immunodeficiency Virus/immunology
- env Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Teppei Toda
- Department of Immunology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8556, Japan
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Metcalfe C, Cresswell P, Ciaccia L, Thomas B, Barclay AN. Labile disulfide bonds are common at the leucocyte cell surface. Open Biol 2011; 1:110010. [PMID: 22645650 PMCID: PMC3352085 DOI: 10.1098/rsob.110010] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 10/31/2011] [Indexed: 12/22/2022] Open
Abstract
Redox conditions change in events such as immune and platelet activation, and during viral infection, but the biochemical consequences are not well characterized. There is evidence that some disulfide bonds in membrane proteins are labile while others that are probably structurally important are not exposed at the protein surface. We have developed a proteomic/mass spectrometry method to screen for and identify non-structural, redox-labile disulfide bonds in leucocyte cell-surface proteins. These labile disulfide bonds are common, with several classes of proteins being identified and around 30 membrane proteins regularly identified under different reducing conditions including using enzymes such as thioredoxin. The proteins identified include integrins, receptors, transporters and cell-cell recognition proteins. In many cases, at least one cysteine residue was identified by mass spectrometry as being modified by the reduction process. In some cases, functional changes are predicted (e.g. in integrins and cytokine receptors) but the scale of molecular changes in membrane proteins observed suggests that widespread effects are likely on many different types of proteins including enzymes, adhesion proteins and transporters. The results imply that membrane protein activity is being modulated by a 'redox regulator' mechanism.
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Affiliation(s)
- Clive Metcalfe
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - Peter Cresswell
- Department of Immunobiology, Howard Hughes Medical Institute, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06520-8011, USA
| | - Laura Ciaccia
- Department of Immunobiology, Howard Hughes Medical Institute, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06520-8011, USA
| | - Benjamin Thomas
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | - A. Neil Barclay
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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Engineered single human CD4 domains as potent HIV-1 inhibitors and components of vaccine immunogens. J Virol 2011; 85:9395-405. [PMID: 21715496 DOI: 10.1128/jvi.05119-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Soluble forms of the HIV-1 receptor CD4 (sCD4) have been extensively characterized for more than 2 decades as promising inhibitors and components of vaccine immunogens. However, they were mostly based on the first two CD4 domains (D1D2), and numerous attempts to develop functional, high-affinity, stable soluble one-domain sCD4 (D1) have not been successful because of the strong interactions between the two domains. We have hypothesized that combining the power of structure-based design with sequential panning of large D1 mutant libraries against different HIV-1 envelope glycoproteins (Envs) and screening for soluble mutants could not only help solve the fundamental stability problem of isolated D1, but may also allow improvement of D1 affinity while preserving its cross-reactivity. By using this strategy, we identified two stable monomeric D1 mutants, mD1.1 and mD1.2, which were significantly more soluble and bound Env gp120s more strongly (50-fold) than D1D2, neutralized a panel of HIV-1 primary isolates from different clades more potently than D1D2, induced conformational changes in gp120, and sensitized HIV-1 for neutralization by CD4-induced antibodies. mD1.1 and mD1.2 exhibited much lower binding to human blood cell lines than D1D2; moreover, they preserved a β-strand secondary structure and stability against thermally induced unfolding, trypsin digestion, and degradation by human serum. Because of their superior properties, mD1.1 and mD1.2 could be potentially useful as candidate therapeutics, components of vaccine immunogens, and research reagents for exploration of HIV-1 entry and immune responses. Our approach could be applied to other cases where soluble isolated protein domains are needed.
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Cicala C, Arthos J, Fauci AS. HIV-1 envelope, integrins and co-receptor use in mucosal transmission of HIV. J Transl Med 2011; 9 Suppl 1:S2. [PMID: 21284901 PMCID: PMC3105502 DOI: 10.1186/1479-5876-9-s1-s2] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
It is well established that HIV-1 infection typically involves an interaction between the viral envelope protein gp120/41 and the CD4 molecule followed by a second interaction with a chemokine receptor, usually CCR5 or CXCR4. In the early stages of an HIV-1 infection CCR5 using viruses (R5 viruses) predominate. In some viral subtypes there is a propensity to switch to CXCR4 usage (X4 viruses). The receptor switch occurs in ~ 40% of the infected individuals and is associated with faster disease progression. This holds for subtypes B and D, but occurs less frequently in subtypes A and C. There are several hypotheses to explain the preferential transmission of R5 viruses and the mechanisms that lead to switching of co-receptor usage; however, there is no definitive explanation for either. One important consideration regarding transmission is that signaling by R5 gp120 may facilitate transmission of R5 viruses by inducing a permissive environment for HIV replication. In the case of sexual transmission, infection by HIV requires the virus to breach the mucosal barrier to gain access to the immune cell targets that it infects; however, the immediate events that follow HIV exposure at genital mucosal sites are not well understood. Upon transmission, the HIV quasispecies that is replicating in an infected donor contracts through a “genetic bottleneck”, and often infection results from a single infectious event. Many details surrounding this initial infection remain unresolved. In mucosal tissues, CD4+ T cells express high levels of CCR5, and a subset of these CD4+/CCR5high cells express the integrin α4β7, the gut homing receptor. CD4+/CCR5high/ α4β7high T cells are highly susceptible to infection by HIV-1 and are ideal targets for an efficient productive infection at the point of transmission. In this context we have demonstrated that the HIV-1 envelope protein gp120 binds to α4β7 on CD4+ T cells. On CD4+/CCR5high/ α4β7high T cells, α4β7 is closely associated with CD4 and CCR5. Furthermore, α4β7 is ~3 times the size of CD4 on the cell surface, that makes it a prominent receptor for an efficient virus capture. gp120-α4β7 interactions mediate the activation of the adhesion-associated integrin LFA-1. LFA-1 facilitates the formation of virological synapses and cell-to-cell spread of HIV-1. gp120 binding to α4β7 is mediated by a tripeptide located in the V1/V2 domain of gp120. Of note, the V1/V2 domain of gp120 has been linked to variations in transmission fitness among viral isolates raising the intriguing possibility that gp120-α4β7 interactions may be linked to transmission fitness. Although many details remain unresolved, we hypothesize that gp120-α4β7 interactions play an important role in the very early events following sexual transmission of HIV and may have important implication in the design of vaccine strategies for the prevention of acquisition of HIV infection
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Affiliation(s)
- Claudia Cicala
- Laboratory of Immunoregulation National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Stains CI, Furman JL, Porter JR, Rajagopal S, Li Y, Wyatt RT, Ghosh I. A general approach for receptor and antibody-targeted detection of native proteins utilizing split-luciferase reassembly. ACS Chem Biol 2010; 5:943-52. [PMID: 20681584 DOI: 10.1021/cb100143m] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The direct detection of native proteins in heterogeneous solutions remains a challenging problem. Standard methodologies rely on a separation step to circumvent nonspecific signal generation. We hypothesized that a simple and general method for the detection of native proteins in solution could be achieved through ternary complexation, where the conditional signal generation afforded by split-protein reporters could be married to the specificity afforded by either native receptors or specific antibodies. Toward this goal, we describe a solution phase split-luciferase assay for native protein detection, where we fused fragmented halves of firefly luciferase to separate receptor fragments or single-chain antibodies, allowing for conditional luciferase complementation in the presence of several biologically significant protein targets. To demonstrate the utility of this strategy, we have developed and validated assay platforms for the vascular endothelial growth factor, the gp120 coat protein from HIV-1, and the human epidermal growth factor receptor 2 (HER2), a marker for breast cancer. The specificities of the recognition elements, CD4 and the 17b single-chain antibody, employed in the gp120 sensor allowed us to parse gp120s from different clades. Our rationally designed HER2 sensing platform was capable of discriminating between HER2 expression levels in several tumor cell lines. In addition, luminescence from reassembled luciferase was linear across a panel of cell lines with increasing HER2 expression. We envision that the proof of principle studies presented herein may allow for the potential detection of a broad range of biological analytes utilizing ternary split-protein systems.
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Affiliation(s)
- Cliff I. Stains
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721
| | - Jennifer L. Furman
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721
| | - Jason R. Porter
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721
| | - Srivats Rajagopal
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721
| | - Yuxing Li
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland 20892
| | - Richard T. Wyatt
- Vaccine Research Center, National Institutes of Health, Bethesda, Maryland 20892
| | - Indraneel Ghosh
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721
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Local conformational stability of HIV-1 gp120 in unliganded and CD4-bound states as defined by amide hydrogen/deuterium exchange. J Virol 2010; 84:10311-21. [PMID: 20660185 DOI: 10.1128/jvi.00688-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The binding reaction of the HIV-1 gp120 envelope glycoprotein to the CD4 receptor involves exceptional changes in enthalpy and entropy. Crystal structures of gp120 in unliganded and various ligand-bound states, meanwhile, reveal an inner domain able to fold into diverse conformations, a structurally invariant outer domain, and, in the CD4-bound state, a bridging sheet minidomain. These studies, however, provide only hints as to the flexibility of each state. Here we use amide hydrogen/deuterium exchange coupled to mass spectrometry to provide quantifications of local conformational stability for HIV-1 gp120 in unliganded and CD4-bound states. On average, unliganded core gp120 displayed >10,000-fold slower exchange of backbone-amide hydrogens than a theoretically unstructured protein of the same composition, with binding by CD4 reducing the rate of gp120 amide exchange a further 10-fold. For the structurally constant CD4, alterations in exchange correlated well with alterations in binding surface (P value = 0.0004). For the structurally variable gp120, however, reductions in flexibility extended outside the binding surface, and regions of expected high structural diversity (inner domain/bridging sheet) displayed roughly 20-fold more rapid exchange in the unliganded state than regions of low diversity (outer domain). Thus, despite an extraordinary reduction in entropy, neither unliganded gp120 nor free CD4 was substantially unstructured, suggesting that most of the diverse conformations that make up the gp120 unliganded state are reasonably ordered. The results provide a framework for understanding how local conformational stability influences entropic change, conformational diversity, and structural rearrangements in the gp120-CD4 binding reaction.
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Owens RM, Gu X, Shin M, Springer TA, Jin MM. Engineering of single Ig superfamily domain of intercellular adhesion molecule 1 (ICAM-1) for native fold and function. J Biol Chem 2010; 285:15906-15. [PMID: 20304924 PMCID: PMC2871458 DOI: 10.1074/jbc.m110.104349] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Revised: 03/11/2010] [Indexed: 11/06/2022] Open
Abstract
The immunoglobulin (Ig) superfamily is one of the largest families in the vertebrate genome, found most frequently in cell surface molecules. Intercellular adhesion molecule-1 (ICAM-1) contains five extracellular Ig superfamily domains (D1-D5) of which the first domain, D1, is the binding site for the integrin lymphocyte function-associated antigen-1 (LFA-1) and human rhinovirus. Despite the modular nature of many Ig superfamily domains with respect to domain folding and ligand recognition, D1 does not fold on its own due to the loss of its interaction with the second domain. The goal of this study was to engineer ICAM-1 D1 by introducing mutations that would stabilize the Ig superfamily domain fold while retaining its ability to bind to LFA-1 and rhinovirus. First, with a directed evolution approach, we isolated mutations in D1 that showed binding to conformation-specific antibodies and the ligand binding domain of LFA-1 called the inserted, or I, domain. Then, with a rational design approach we introduced mutations that contributed to the stability of ICAM-1 D1 in solution. The mutations that restored native folding of D1 in isolation were those that would convert hydrogen bond networks in buried regions into hydrophobic contacts. Notably, for most mutations, identical or similar types of substitutions were found in ICAM-1 molecules of different species and other ICAM family members. The systematic approach demonstrated in this study to engineer a single Ig superfamily fold in ICAM-1 can be broadly applicable to the engineering of modular Ig superfamily domains in other cell surface molecules.
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Affiliation(s)
- Róisín M. Owens
- From the Department of Biomedical Engineering, Cornell University, Ithaca, New York 14853 and
| | - Xiaoling Gu
- From the Department of Biomedical Engineering, Cornell University, Ithaca, New York 14853 and
| | - Miran Shin
- From the Department of Biomedical Engineering, Cornell University, Ithaca, New York 14853 and
| | - Timothy A. Springer
- the Immune Disease Institute, Harvard Medical School, Boston, Massachusetts 02115
| | - Moonsoo M. Jin
- From the Department of Biomedical Engineering, Cornell University, Ithaca, New York 14853 and
- the Immune Disease Institute, Harvard Medical School, Boston, Massachusetts 02115
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Epitope mapping of ibalizumab, a humanized anti-CD4 monoclonal antibody with anti-HIV-1 activity in infected patients. J Virol 2010; 84:6935-42. [PMID: 20463063 DOI: 10.1128/jvi.00453-10] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ibalizumab is a humanized monoclonal antibody that binds human CD4, the primary receptor for human immunodeficiency virus type 1 (HIV-1). With its unique specificity for domain 2 of CD4, this antibody potently and broadly blocks HIV-1 infection in vitro by inhibiting a postbinding step required for viral entry but without interfering with major histocompatibility complex class II (MHC-II)-mediated immune function. In clinical trials, ibalizumab has demonstrated anti-HIV-1 activity in patients without causing immunosuppression. Thus, a characterization of the ibalizumab epitope was conducted in an attempt to gain insight into the underlying mechanism of its antiviral activity as well as its safety profile. By studying mouse/human chimeric CD4 molecules and site-directed point mutants of CD4, amino acids L96, P121, P122, and Q163 in domain 2 were found to be important for ibalizumab binding, with E77 and S79 in domain 1 also contributing. All these residues appear to cluster on the interface between domains 1 and 2 of human CD4 on a surface opposite the site where gp120 and the MHC-II molecule bind on domain 1. Separately, the epitope of M-T441, a weakly neutralizing mouse monoclonal antibody that competes with ibalizumab, was localized entirely within domain 2 on residues 123 to 125 and 138 to 140. The results reported herein not only provide an appreciation for why ibalizumab has not had significant adverse immunological consequences in infected patients to date but also raise possible steric hindrance mechanisms by which this antibody blocks HIV-1 entry into a CD4-positive cell.
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Grosdidier S, Totrov M, Fernández-Recio J. Computer applications for prediction of protein-protein interactions and rational drug design. Adv Appl Bioinform Chem 2009; 2:101-23. [PMID: 21918619 PMCID: PMC3169948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
In recent years, protein-protein interactions are becoming the object of increasing attention in many different fields, such as structural biology, molecular biology, systems biology, and drug discovery. From a structural biology perspective, it would be desirable to integrate current efforts into the structural proteomics programs. Given that experimental determination of many protein-protein complex structures is highly challenging, and in the context of current high-performance computational capabilities, different computer tools are being developed to help in this task. Among them, computational docking aims to predict the structure of a protein-protein complex starting from the atomic coordinates of its individual components, and in recent years, a growing number of docking approaches are being reported with increased predictive capabilities. The improvement of speed and accuracy of these docking methods, together with the modeling of the interaction networks that regulate the most critical processes in a living organism, will be essential for computational proteomics. The ultimate goal is the rational design of drugs capable of specifically inhibiting or modifying protein-protein interactions of therapeutic significance. While rational design of protein-protein interaction inhibitors is at its very early stage, the first results are promising.
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Affiliation(s)
- Solène Grosdidier
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Juan Fernández-Recio
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain,Correspondence: Juan Fernandez-Recio, Life Sciences Department, Barcelona Supercomputing Center, C/Jordi Girona 29, 08034 Barcelona, Spain, Tel +34 934137729, Fax +34 934137721, Email
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Meyuhas R, Noy H, Fishman S, Margalit A, Montefiori DC, Gross G. Enhanced HIV-1 neutralization by a CD4-VH3-IgG1 fusion protein. Biochem Biophys Res Commun 2009; 386:402-6. [PMID: 19538939 DOI: 10.1016/j.bbrc.2009.06.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Accepted: 06/12/2009] [Indexed: 10/20/2022]
Abstract
HIV-1 gp120 is an alleged B cell superantigen, binding certain VH3+ human antibodies. We reasoned that a CD4-VH3 fusion protein could possess higher affinity for gp120 and improved HIV-1 inhibitory capacity. To test this we produced several human IgG1 immunoligands harboring VH3. Unlike VH3-IgG1 or VH3-CD4-IgG1, CD4-VH3-IgG1 bound gp120 considerably stronger than CD4-IgG1. CD4-VH3-IgG1 exhibited approximately 1.5-2.5-fold increase in neutralization of two T-cell laboratory-adapted strains when compared to CD4-IgG1. CD4-VH3-IgG1 improved neutralization of 7/10 clade B primary isolates or pseudoviruses, exceeding 20-fold for JR-FL and 13-fold for Ba-L. It enhanced neutralization of 4/8 clade C viruses, and had negligible effect on 1/4 clade A pseudoviruses. We attribute this improvement to possible pairing of VH3 with CD4 D1 and stabilization of an Ig Fv-like structure, rather than to superantigen interactions. These novel findings support the current notion that CD4 fusion proteins can act as better HIV-1 entry inhibitors with potential clinical implications.
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Affiliation(s)
- Ronit Meyuhas
- Laboratory of Immunology, MIGAL, Kiryat Shmona 11016, Israel
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