Probing Structural Variation and Dynamics in the HIV-1 Env Fusion Glycoprotein

Author(s): James B. Munro*, Kelly K. Lee*.

Journal Name: Current HIV Research

Volume 16 , Issue 1 , 2018

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Graphical Abstract:


Background: Recent advances in structural characterization of the HIV envelope glycoprotein (Env) have provided a high-resolution glimpse of the architecture of this target for neutralizing antibodies and the machinery responsible for mediating receptor binding and membrane fusion. These structures primarily capture the detailed organization of the receptor-naive, prefusion conformation of Env, but under native solution conditions Env is highly dynamic, sampling multiple conformational states as well as exhibiting local protein flexibility.

Methods: Special emphasis is placed on the use of biophysical methods, including single-molecule fluorescence microscopy and hydrogen/deuterium-exchange mass spectrometry.

Results: Using novel biophysical approaches, striking isolate-specific differences in Env’s dynamic profile have been revealed that appear to underlie phenotypic differences of the viral isolates such as neutralization sensitivity and CD4 receptor reactivity.

Conclusion: Structural studies are complemented by novel biophysical investigations that enable visualization of the dynamics of HIV-1 Env under native conditions. These approaches will also enable us to gain new insights into the mechanisms of action of antibodies and drugs.

Keywords: HIV, Env, glycoprotein, structure, dynamics, neutralizing antibody, FRET, mass spectrometry.

Blumenthal R, Durell S, Viard M. HIV entry and envelope glycoprotein-mediated fusion. J Biol Chem 2012; 287: 40841-9.
Munro JB, Gorman J, Ma X, et al. Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions. Science 2014; 346: 759-63.
Guttman M, Kahn M, Garcia NK, Hu SL, Lee KK. Solution structure, conformational dynamics, and cd4-induced activation in full-length, glycosylated, monomeric HIV gp120. J Virol 2012; 86: 8750-64.
Kong L, Huang CC, Coales SJ, et al. 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.
Liang Y, Guttman M, Davenport TM, Hu SL, Lee KK. Probing the Impact of local structural dynamics of Conformational Epitopes on Antibody Recognition. Biochemistry 2016; 55: 2197-213.
Davenport TM, Guttman M, Guo W, et al. Isolate-specific differences in the conformational dynamics and antigenicity of HIV-1 gp120. J Virol 2013; 87: 10855-73.
Kwong PD, Doyle ML, Casper DJ, et al. HIV-1 evades antibody-mediated neutralization through conformational masking of receptor-binding sites. Nature 2002; 420: 678-82.
Sougrat R, Bartesaghi A, Lifson JD, et al. Electron tomography of the contact between T cells and SIV/HIV-1: implications for viral entry. PLoS pathogens 2007; 3: e63.
Chojnacki J, Staudt T, Glass B, et al. Maturation-dependent HIV-1 surface protein redistribution revealed by fluorescence nanoscopy. Science 2012; 338: 524-8.
Sanders RW, Derking R, Cupo A, et al. A next-generation cleaved, soluble HIV-1 Env Trimer, BG505 SOSIP.664 gp140, expresses multiple epitopes for broadly neutralizing but not non-neutralizing antibodies. PLoS pathog 2013; 9: e1003618.
Binley JM, Sanders RW, Clas B, et al. A recombinant human immunodeficiency virus type 1 envelope glycoprotein complex stabilized by an intermolecular disulfide bond between the gp120 and gp41 subunits is an antigenic mimic of the trimeric virion-associated structure. J Virol 2000; 74: 627-43.
Sanders RW, Vesanen M, Schuelke N, et al. Stabilization of the soluble, cleaved, trimeric form of the envelope glycoprotein complex of human immunodeficiency virus type 1. J Virol 2002; 76: 8875-89.
Lyumkis D, Julien JP, de Val N, et al. Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. Science 2013; 342: 1484-90.
Julien JP, Cupo A, Sok D, et al. Crystal structure of a soluble cleaved HIV-1 envelope trimer. Science 2013; 342: 1477-83.
Pancera M, Zhou T, Druz A, et al. Structure and immune recognition of trimeric pre-fusion HIV-1 Env. Nature 2014; 514: 455-61.
Lee JH, Ozorowski G, Ward AB. Cryo-EM structure of a native, fully glycosylated, cleaved HIV-1 envelope trimer. Science 2016; 351: 1043-8.
Bartesaghi A, Merk A, Borgnia MJ, Milne JL, Subramaniam S. Prefusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy. Nat Struct Mol Biol 2013; 20: 1352-7.
Pancera M, Majeed S, Ban YE, et al. Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility. Proc Natl Acad Sci USA 2010; 107: 1166-71.
Huang CC, Tang M, Zhang MY, et al. Structure of a V3-containing HIV-1 gp120 core. Science 2005; 310: 1025-8.
Kwong PD, Wyatt R, Majeed S, et al. Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Structure 2000; 8: 1329-39.
Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J, Hendrickson WA. Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 1998; 393: 648-59.
Chan DC, Fass D, Berger JM, Kim PS. Core structure of gp41 from the HIV envelope glycoprotein. Cell 1997; 89: 263-73.
Lu M, Blacklow SC, Kim PS. A trimeric structural domain of the HIV-1 transmembrane glycoprotein. Nat Struct Biol 1995; 2: 1075-82.
Tran EE, Borgnia MJ, Kuybeda O, et al. Structural mechanism of trimeric HIV-1 envelope glycoprotein activation. PLoS pathog 2012; 8: e1002797.
Harris A, Borgnia MJ, Shi D, et al. Trimeric HIV-1 glycoprotein gp140 immunogens and native HIV-1 envelope glycoproteins display the same closed and open quaternary molecular architectures. Proc Natl Acad Sci USA 2011; 108: 11440-5.
White TA, Bartesaghi A, Borgnia MJ, et al. Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure. PLoS pathog 2010; 6: e1001249.
Liu J, Bartesaghi A, Borgnia MJ, Sapiro G, Subramaniam S. Molecular architecture of native HIV-1 gp120 trimers. Nature 2008; 455: 109-13.
Lee JH, de Val N, Lyumkis D, Ward AB. Model Building and Refinement of a Natively Glycosylated HIV-1 Env Protein by High-Resolution Cryoelectron Microscopy. Structure 2015; 23: 1943-51.
Stewart-Jones GB, Soto C, Lemmin T, et al. Trimeric HIV-1-Env structures define glycan shields from clades A, B, and G. Cell 2016; 165: 813-26.
Scharf L, Wang H, Gao H, Chen S, McDowall AW, Bjorkman PJ. Broadly neutralizing antibody 8ANC195 recognizes closed and open states of HIV-1 Env. Cell 2015; 162: 1379-90.
Guttman M, Garcia NK, Cupo A, et al. CD4-induced activation in a soluble HIV-1 Env trimer. Structure 2014; 22: 974-84.
Behrens AJ, Vasiljevic S, Pritchard LK, et al. Composition and antigenic effects of individual glycan sites of a trimeric HIV-1 envelope glycoprotein. Cell reports 2016; 14: 2695-706.
Harvey DJ, Scarff CA, Edgeworth M, et al. Travelling wave ion mobility and negative ion fragmentation for the structural determination of N-linked glycans. Electrophoresis 2013; 34: 2368-78.
Guttman M, Cupo A, Julien JP, et al. Antibody potency relates to the ability to recognize the closed, pre-fusion form of HIV Env. Nature Commun 2015; 6: 6144.
Do Kwon Y, Pancera M, Acharya P, et al. Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env. Nat Struct Mol Biol 2015; 22: 522-31.
Zhu P, Liu J, Bess J Jr, Chertova E, Lifson JD, Grise H, et al. Distribution and three-dimensional structure of AIDS virus envelope spikes. Nature 2006; 441: 847-52.
Zhu P, Chertova E, Bess J Jr, et al. Electron tomography analysis of envelope glycoprotein trimers on HIV and simian immunodeficiency virus virions. Proc Natl Acad Sci USA 2003; 100: 15812-7.
Brandenberg OF, Magnus C, Rusert P, Regoes RR, Trkola A. Different infectivity of HIV-1 strains is linked to number of envelope trimers required for entry. PLoS pathog 2015; 11: e1004595.
Blom H, Widengren J. Stimulated emission depletion microscopy. Chem Rev 2017.
Joyner AS, Willis JR, Crowe JE Jr, Aiken C. Maturation-induced cloaking of neutralization epitopes on HIV-1 particles. PLoS pathog 2011; 7: e1002234.
Poignard P, Moulard M, Golez E, et al. Heterogeneity of envelope molecules expressed on primary human immunodeficiency virus type 1 particles as probed by the binding of neutralizing and nonneutralizing antibodies. J Virol 2003; 77: 353-65.
Yang X, Kurteva S, Ren X, Lee S, Sodroski J. Stoichiometry of envelope glycoprotein trimers in the entry of human immunodeficiency virus type 1. J Virol 2005; 79: 12132-47.
Ellens H, Bentz J, Mason D, Zhang F, White JM. Fusion of influenza hemagglutinin-expressing fibroblasts with glycophorin-bearing liposomes: role of hemagglutinin surface density. Biochemistry 1990; 29: 9697-707.
Danieli T, Pelletier SL, Henis YI, White JM. Membrane fusion mediated by the influenza virus hemagglutinin requires the concerted action of at least three hemagglutinin trimers. J Cell Biol 1996; 133: 559-69.
Lee KK. Architecture of a nascent viral fusion pore. The EMBO journal 2010; 29: 1299-311.
Gui L, Ebner JL, Mileant A, Williams JA, Lee KK. Visualization and sequencing of membrane remodeling leading to influenza virus fusion. J Virol 2016; 90: 6948-62.
Leikina E, Mittal A, Cho MS, Melikov K, Kozlov MM, Chernomordik LV. Influenza hemagglutinins outside of the contact zone are necessary for fusion pore expansion. J Biol Chem 2004; 279: 26526-32.
Crooks ET, Tong T, Osawa K, Binley JM. Enzyme digests eliminate nonfunctional Env from HIV-1 particle surfaces, leaving native Env trimers intact and viral infectivity unaffected. J Virol 2011; 85: 5825-39.
Moore PL, Crooks ET, Porter L, et al. Nature of nonfunctional envelope proteins on the surface of human immunodeficiency virus type 1. J Virol 2006; 80: 2515-28.
Dimura M, Peulen TO, Hanke CA, Prakash A, Gohlke H, Seidel CA. Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Curr Opin Struct Biol 2016; 40: 163-85.
Zhou Z, Cironi P, Lin AJ, et al. Genetically encoded short peptide tags for orthogonal protein labeling by Sfp and AcpS phosphopantetheinyl transferases. ACS Chem Biol 2007; 2: 337-46.
Lin CW, Ting AY. Transglutaminase-catalyzed site-specific conjugation of small-molecule probes to proteins in vitro and on the surface of living cells. J Am Chem Soc 2006; 128: 4542-3.
Nikic I, Estrada Girona G, Kang JH, et al. Debugging eukaryotic genetic code expansion for site-specific click-paint super-resolution microscopy. Angew Chem Int Ed Engl 2016; 55: 16172-6.
Maleknia SD, Brenowitz M, Chance MR. Millisecond radiolytic modification of peptides by synchrotron X-rays identified by mass spectrometry. Anal Chem 1999; 71: 3965-73.
Kong R, Xu K, Zhou T, et al. Fusion peptide of HIV-1 as a site of vulnerability to neutralizing antibody. Science 2016; 352: 828-33.
Mao Y, Wang L, Gu C, Herschhorn A, Desormeaux A, Finzi A, et al. Molecular architecture of the uncleaved HIV-1 envelope glycoprotein trimer. Proc Natl Acad Sci USA 2013; 110: 12438-43.
Mao Y, Wang L, Gu C, et al. Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer. Nat Struct Mol Biol 2012; 19: 893-9.
Marcsisin SR, Engen JR. Hydrogen exchange mass spectrometry: what is it and what can it tell us? Anal Bioanal Chem 2010; 397: 967-72.
Guttman M, Lee KK. Isotope Labeling of Biomolecules: Structural Analysis of Viruses by HDX-MS. Methods Enzymol 2016; 566: 405-26.
Kwon YD, Finzi A, Wu X, et al. Unliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops. Proc Natl Acad Sci USA 2012; 109: 5663-8.
Ringe RP, Yasmeen A, Ozorowski G, et al. Influences on the design and purification of soluble, recombinant native-like HIV-1 envelope glycoprotein trimers. J Virol 2015; 89: 12189-210.
Verkerke HP, Williams JA, Guttman M, Simonich CA, Liang Y, Filipavicius M, et al. Epitope-Independent Purification of Native-Like Envelope Trimers from Diverse HIV-1 Isolates. J Virol 2016; 90: 9471-82.
Guttman M, Lee KK. A functional gp41-gp120 interaction is observed in monomeric but not oligomeric, uncleaved HIV-1 Env gp140. J Virol 2013; 87: 11462-75.
de Taeye SW, Ozorowski G, Torrents de la Pena A, et al. Immunogenicity of stabilized HIV-1 envelope trimers with reduced exposure of non-neutralizing epitopes. Cell 2015; 163: 1702-15.
Garcia NK, Guttman M, Ebner JL, Lee KK. Dynamic changes during acid-induced activation of influenza hemagglutinin. Structure 2015; 23: 665-76.
Lim XX, Chandramohan A, Lim XY, et al. Conformational changes in intact dengue virus reveal serotype-specific expansion. Nat Commun 2017; 8: 14339.
Davenport TM, Gorman J, Joyce MG, et al. Somatic hypermutation-induced changes in the structure and dynamics of HIV-1 broadly neutralizing antibodies. Structure 2016; 24: 1346-57.
Li X, Grant OC, Ito K, et al. Structural analysis of the glycosylated intact HIV-1 gp120-b12 antibody complex using hydroxyl radical protein footprinting. Biochemistry 2017; 56(7): 957-70.

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Year: 2018
Page: [5 - 12]
Pages: 8
DOI: 10.2174/1570162X16666171222110025

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