Antigenic and 3D structural characterization of soluble X4 and hybrid X4-R5 HIV-1 Env trimers

Retrovirology

Ralf Dürr⁵  Ursula Dietrich²  Patrick Bartholomäus⁶  Robert Tampé⁷  Volker Gatterdam⁷  Jürgen Markl¹  Tim-Michael Decker⁸  Svenja Weiß²  Patricia Himmels³  Philipp Arnold⁴ 

[1]Institute of Zoology, Johannes Gutenberg University, Mainz, Germany

[2]Molecular Virology, Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany

[3]Current address: Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany

[4]Current address: Anatomical Institute, Christian-Albrecht’s University, Kiel, Germany

[5]Current address: Department of Pathology, New York University, School of Medicine, New York City, USA

[6]Current address: Institute for Experimental Infection Research, Twincore, Center for Experimental and Clinical Infection Research, Hannover, Germany

[7]Institute of Biochemistry, Goethe University, Frankfurt, Germany

[8]Current address: Department of Molecular Epigenetics, Helmholtz Center Munich, Center for Integrated Protein Science Munich (CIPSM), Munich, Germany

关键词: Open structure;    CD4 binding site;    Single particle analysis;    3D EM;    V3 loop;    Tropism;    CCR5;    CXCR4;    Soluble gp140 Env;    HIV-1;   

Others  :  801697
DOI  :  10.1186/1742-4690-11-42

 received in 2013-10-09, accepted in 2014-05-16,  发布年份 2014

【 摘 要 】

Background

HIV-1 is decorated with trimeric glycoprotein spikes that enable infection by engaging CD4 and a chemokine coreceptor, either CCR5 or CXCR4. The variable loop 3 (V3) of the HIV-1 envelope protein (Env) is the main determinant for coreceptor usage. The predominant CCR5 using (R5) HIV-1 Env has been intensively studied in function and structure, whereas the trimeric architecture of the less frequent, but more cytopathic CXCR4 using (X4) HIV-1 Env is largely unknown, as are the consequences of sequence changes in and near V3 on antigenicity and trimeric Env structure.

Results

Soluble trimeric gp140 Env constructs were used as immunogenic mimics of the native spikes to analyze their antigenic properties in the context of their overall 3D structure. We generated soluble, uncleaved, gp140 trimers from a prototypic T-cell line-adapted (TCLA) X4 HIV-1 strain (NL4-3) and a hybrid (NL4-3/ADA), in which the V3 spanning region was substituted with that from the primary R5 isolate ADA. Compared to an ADA (R5) gp140, the NL4-3 (X4) construct revealed an overall higher antibody accessibility, which was most pronounced for the CD4 binding site (CD4bs), but also observed for mAbs against CD4 induced (CD4i) epitopes and gp41 mAbs. V3 mAbs showed significant binding differences to the three constructs, which were refined by SPR analysis. Of interest, the NL4-3/ADA construct with the hybrid NL4-3/ADA CD4bs showed impaired CD4 and CD4bs mAb reactivity despite the presence of the essential elements of the CD4bs epitope. We obtained 3D reconstructions of the NL4-3 and the NL4-3/ADA gp140 trimers via electron microscopy and single particle analysis, which indicates that both constructs inherit a propeller-like architecture. The first 3D reconstruction of an Env construct from an X4 TCLA HIV-1 strain reveals an open conformation, in contrast to recently published more closed structures from R5 Env. Exchanging the X4 V3 spanning region for that of R5 ADA did not alter the open Env architecture as deduced from its very similar 3D reconstruction.

Conclusions

3D EM analysis showed an apparent open trimer configuration of X4 NL4-3 gp140 that is not modified by exchanging the V3 spanning region for R5 ADA.

【 授权许可】

   
2014 Arnold et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]Blumenthal R, Durell S, Viard M: HIV entry and envelope glycoprotein-mediated fusion. J Biol Chem 2012, 287:40841-40849.
• [2]Caffrey M: HIV envelope: challenges and opportunities for development of entry inhibitors. Trends Microbiol 2011, 19:191-197.
• [3]Harrison SC: Viral membrane fusion. Nat Struct Mol Biol 2008, 15:690-698.
• [4]Mosier DE: How HIV changes its tropism: evolution and adaptation? Curr Opin HIV AIDS 2009, 4:125-130.
• [5]Regoes RR, Bonhoeffer S: The HIV coreceptor switch: a population dynamical perspective. Trends Microbiol 2005, 13:269-277.
• [6]Cocchi F, DeVico AL, Garzino-Demo A, Cara A, Gallo RC, Lusso P: The V3 domain of the HIV-1 gp120 envelope glycoprotein is critical for chemokine-mediated blockade of infection. Nat Med 1996, 2:1244-1247.
• [7]Hartley O, Klasse PJ, Sattentau QJ, Moore JP: V3: HIV’s switch-hitter. AIDS Res Hum Retrovir 2005, 21:171-189.
• [8]Poveda E, Alcami J, Paredes R, Cordoba J, Gutierrez F, Llibre JM, Delgado R, Pulido F, Iribarren JA, Garcia Deltoro M, Hernandez Quero J, Moreno S, Garcia F: Genotypic determination of HIV tropism - clinical and methodological recommendations to guide the therapeutic use of CCR5 antagonists. AIDS Rev 2010, 12:135-148.
• [9]Rosen O, Sharon M, Quadt-Akabayov SR, Anglister J: Molecular switch for alternative conformations of the HIV-1 V3 region: implications for phenotype conversion. Proc Natl Acad Sci U S A 2006, 103:13950-13955.
• [10]Sharon M, Kessler N, Levy R, Zolla-Pazner S, Gorlach M, Anglister J: Alternative conformations of HIV-1 V3 loops mimic beta hairpins in chemokines, suggesting a mechanism for coreceptor selectivity. Structure 2003, 11:225-236.
• [11]Andrabi R, Williams C, Wang XH, Li L, Choudhary AK, Wig N, Biswas A, Luthra K, Nadas A, Seaman MS, Nyambi P, Zolla-Pazner S, Gorny MK: Cross-neutralizing activity of human anti-V3 monoclonal antibodies derived from non-B clade HIV-1 infected individuals. Virology 2013, 439:81-88.
• [12]Gorny MK, Revesz K, Williams C, Volsky B, Louder MK, Anyangwe CA, Krachmarov C, Kayman SC, Pinter A, Nadas A, Nyambi PN, Mascola JR, Zolla-Pazner S: The v3 loop is accessible on the surface of most human immunodeficiency virus type 1 primary isolates and serves as a neutralization epitope. J Virol 2004, 78:2394-2404.
• [13]Gorny MK, Williams C, Volsky B, Revesz K, Cohen S, Polonis VR, Honnen WJ, Kayman SC, Krachmarov C, Pinter A, Zolla-Pazner S: Human monoclonal antibodies specific for conformation-sensitive epitopes of V3 neutralize human immunodeficiency virus type 1 primary isolates from various clades. J Virol 2002, 76:9035-9045.
• [14]Zolla-Pazner S: Improving on nature: focusing the immune response on the V3 loop. Hum Antibodies 2005, 14:69-72.
• [15]Derby NR, Gray S, Wayner E, Campogan D, Vlahogiannis G, Kraft Z, Barnett SW, Srivastava IK, Stamatatos L: Isolation and characterization of monoclonal antibodies elicited by trimeric HIV-1 Env gp140 protein immunogens. Virology 2007, 366:433-445.
• [16]Nkolola JP, Peng H, Settembre EC, Freeman M, Grandpre LE, Devoy C, Lynch DM, La Porte A, Simmons NL, Bradley R, Montefiori DC, Seaman MS, Chen B, Barouch DH: Breadth of neutralizing antibodies elicited by stable, homogeneous clade A and clade C HIV-1 gp140 envelope trimers in guinea pigs. J Virol 2010, 84:3270-3279.
• [17]Zhang CW, Chishti Y, Hussey RE, Reinherz EL: Expression, purification, and characterization of recombinant HIV gp140. The gp41 ectodomain of HIV or simian immunodeficiency virus is sufficient to maintain the retroviral envelope glycoprotein as a trimer. J Biol Chem 2001, 276:39577-39585.
• [18]Binley JM, Sanders RW, Clas B, Schuelke N, Master A, Guo Y, Kajumo F, Anselma DJ, Maddon PJ, Olson WC, Moore JP: 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, 74:627-643.
• [19]Sanders RW, Vesanen M, Schuelke N, Master A, Schiffner L, Kalyanaraman R, Paluch M, Berkhout B, Maddon PJ, Olson WC, Lu M, Moore JP: Stabilization of the soluble, cleaved, trimeric form of the envelope glycoprotein complex of human immunodeficiency virus type 1. J Virol 2002, 76:8875-8889.
• [20]Mao Y, Wang L, Gu C, Herschhorn A, Desormeaux A, Finzi A, Xiang SH, Sodroski JG: Molecular architecture of the uncleaved HIV-1 envelope glycoprotein trimer. Proc Natl Acad Sci U S A 2013, 110:12438-12443.
• [21]Mao Y, Wang L, Gu C, Herschhorn A, Xiang SH, Haim H, Yang X, Sodroski J: Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer. Nat Struct Mol Biol 2012, 19:893-899.
• [22]Moscoso CG, Sun Y, Poon S, Xing L, Kan E, Martin L, Green D, Lin F, Vahlne AG, Barnett S, Srivastava I, Cheng RH: Quaternary structures of HIV Env immunogen exhibit conformational vicissitudes and interface diminution elicited by ligand binding. Proc Natl Acad Sci U S A 2011, 108:6091-6096.
• [23]Depetris RS, Julien JP, Khayat R, Lee JH, Pejchal R, Katpally U, Cocco N, Kachare M, Massi E, David KB, Cupo A, Marozsan AJ, Olson WC, Ward AB, Wilson IA, Sanders RW, Moore JP: Partial enzymatic deglycosylation preserves the structure of cleaved recombinant HIV-1 envelope glycoprotein trimers. J Biol Chem 2012, 287:24239-24254.
• [24]Harris A, Borgnia MJ, Shi D, Bartesaghi A, He H, Pejchal R, Kang YK, Depetris R, Marozsan AJ, Sanders RW, Klasse PJ, Milne JL, Wilson IA, Olson WC, Moore JP, Subramaniam S: 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 U S A 2011, 108:11440-11445.
• [25]Hu G, Liu J, Taylor KA, Roux KH: Structural comparison of HIV-1 envelope spikes with and without the V1/V2 loop. J Virol 2011, 85:2741-2750.
• [26]Julien JP, Cupo A, Sok D, Stanfield RL, Lyumkis D, Deller MC, Klasse PJ, Burton DR, Sanders RW, Moore JP, Ward AB, Wilson IA: Crystal structure of a soluble cleaved HIV-1 envelope trimer. Science 2013, 342:1477-1483.
• [27]Julien JP, Lee JH, Cupo A, Murin CD, Derking R, Hoffenberg S, Caulfield MJ, King CR, Marozsan AJ, Klasse PJ, Sanders RW, Moore JP, Wilson IA, Ward AB: Asymmetric recognition of the HIV-1 trimer by broadly neutralizing antibody PG9. Proc Natl Acad Sci U S A 2013, 110:4351-4356.
• [28]Julien JP, Sok D, Khayat R, Lee JH, Doores KJ, Walker LM, Ramos A, Diwanji DC, Pejchal R, Cupo A, Katpally U, Depetris RS, Stanfield RL, McBride R, Marozsan AJ, Paulson JC, Sanders RW, Moore JP, Burton DR, Poignard P, Ward AB, Wilson IA: Broadly neutralizing antibody PGT121 allosterically modulates CD4 binding via recognition of the HIV-1 gp120 V3 base and multiple surrounding glycans. PLoS Pathog 2013, 9:e1003342.
• [29]Khayat R, Lee JH, Julien JP, Cupo A, Klasse PJ, Sanders RW, Moore JP, Wilson IA, Ward AB: Structural Characterization of Cleaved, Soluble HIV-1 Envelope Glycoprotein Trimers. J Virol 2013, 87:9865-9872.
• [30]Lyumkis D, Julien JP, De Val N, Cupo A, Potter CS, Klasse PJ, Burton DR, Sanders RW, Moore JP, Carragher B, Wilson IA, Ward AB: Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. Science 2013, 342:1484-1490.
• [31]Sanders RW, Derking R, Cupo A, Julien JP, Yasmeen A, De Val N, Kim HJ, Blattner C, de la Pena AT, Korzun J, Golabek M, De Los Reyes K, Ketas TJ, Van Gils MJ, King CR, Wilson IA, Ward AB, Klasse PJ, Moore JP: 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.
• [32]Tran EE, Borgnia MJ, Kuybeda O, Schauder DM, Bartesaghi A, Frank GA, Sapiro G, Milne JL, Subramaniam S: Structural mechanism of trimeric HIV-1 envelope glycoprotein activation. PLoS Pathog 2012, 8:e1002797.
• [33]Tan Q, Zhu Y, Li J, Chen Z, Han GW, Kufareva I, Li T, Ma L, Fenalti G, Zhang W, Xie X, Yang H, Jiang H, Cherezov V, Liu H, Stevens RC, Zhao Q, Wu B: Structure of the CCR5 chemokine receptor-HIV entry inhibitor maraviroc complex. Science 2013, 341:1387-1390.
• [34]Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC, Hamel DJ, Kuhn P, Handel TM, Cherezov V, Stevens RC: Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 2010, 330:1066-1071.
• [35]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, 20:1352-1357.
• [36]Lusso P, Earl PL, Sironi F, Santoro F, Ripamonti C, Scarlatti G, Longhi R, Berger EA, Burastero SE: Cryptic nature of a conserved, CD4-inducible V3 loop neutralization epitope in the native envelope glycoprotein oligomer of CCR5-restricted, but not CXCR4-using, primary human immunodeficiency virus type 1 strains. J Virol 2005, 79:6957-6968.
• [37]Gorny MK, Conley AJ, Karwowska S, Buchbinder A, Xu JY, Emini EA, Koenig S, Zolla-Pazner S: Neutralization of diverse human immunodeficiency virus type 1 variants by an anti-V3 human monoclonal antibody. J Virol 1992, 66:7538-7542.
• [38]Myers R, Meiller T, Falkler JW, Patel J, Joseph J: A Human Monoclonal Antibody to a Cryptic gp41 Epitope on HIV-1 Infected Cells. Abstr Gen Meet Am Soc Microbiol 1993, 93:444.
• [39]Gershoni JM, Denisova G, Raviv D, Smorodinsky NI, Buyaner D: HIV binding to its receptor creates specific epitopes for the CD4/gp120 complex. FASEB J 1993, 7:1185-1187.
• [40]Wu X, Yang ZY, Li Y, Hogerkorp CM, Schief WR, Seaman MS, Zhou T, Schmidt SD, Wu L, Xu L, Longo NS, McKee K, O’Dell S, Louder MK, Wycuff DL, Feng Y, Nason M, Doria-Rose N, Connors M, Kwong PD, Roederer M, Wyatt RT, Nabel GJ, Mascola JR: Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1. Science 2010, 329:856-861.
• [41]Burton DR, Barbas CF 3rd, Persson MA, Koenig S, Chanock RM, Lerner RA: A large array of human monoclonal antibodies to type 1 human immunodeficiency virus from combinatorial libraries of asymptomatic seropositive individuals. Proc Natl Acad Sci U S A 1991, 88:10134-10137.
• [42]Posner MR, Hideshima T, Cannon T, Mukherjee M, Mayer KH, Byrn RA: An IgG human monoclonal antibody that reacts with HIV-1/GP120, inhibits virus binding to cells, and neutralizes infection. J Immunol 1991, 146:4325-4332.
• [43]EMDB 2657: EMData Bank. http://www.emdatabank.org/ webcite
• [44]EMDB 2659: EMData Bank. http://www.emdatabank.org/ webcite
• [45]Zhou T, Xu L, Dey B, Hessell AJ, Van Ryk D, Xiang SH, Yang X, Zhang MY, Zwick MB, Arthos J, Burton DR, Dimitrov DS, Sodroski J, Wyatt R, Nabel GJ, Kwong PD: Structural definition of a conserved neutralization epitope on HIV-1 gp120. Nature 2007, 445:732-737.
• [46]Adachi A, Gendelman HE, Koenig S, Folks T, Willey R, Rabson A, Martin MA: Production of acquired immunodeficiency syndrome-associated retrovirus in human and nonhuman cells transfected with an infectious molecular clone. J Virol 1986, 59:284-291.
• [47]LaBranche CC, Hoffman TL, Romano J, Haggarty BS, Edwards TG, Matthews TJ, Doms RW, Hoxie JA: Determinants of CD4 independence for a human immunodeficiency virus type 1 variant map outside regions required for coreceptor specificity. J Virol 1999, 73:10310-10319.
• [48]Sato H, Kato K, Takebe Y: Functional complementation of the envelope hypervariable V3 loop of human immunodeficiency virus type 1 subtype B by the subtype E V3 loop. Virology 1999, 257:491-501.
• [49]Steidl S, Stitz J, Schmitt I, Konig R, Flory E, Schweizer M, Cichutek K: Coreceptor Switch of [MLV(SIVagm)] pseudotype vectors by V3-loop exchange. Virology 2002, 300:205-216.
• [50]Cardozo T, Kimura T, Philpott S, Weiser B, Burger H, Zolla-Pazner S: Structural basis for coreceptor selectivity by the HIV type 1 V3 loop. AIDS Res Hum Retrovir 2007, 23:415-426.
• [51]White TA, Bartesaghi A, Borgnia MJ, Meyerson JR, de la Cruz MJ, Bess JW, Nandwani R, Hoxie JA, Lifson JD, Milne JL, Subramaniam S: Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure. PLoS Pathog 2010, 6:e1001249.
• [52]White TA, Bartesaghi A, Borgnia MJ, de la Cruz MJ, Nandwani R, Hoxie JA, Bess JW, Lifson JD, Milne JL, Subramaniam S: Three-dimensional structures of soluble CD4-bound states of trimeric simian immunodeficiency virus envelope glycoproteins determined by using cryo-electron tomography. J Virol 2011, 85:12114-12123.
• [53]Liu J, Bartesaghi A, Borgnia MJ, Sapiro G, Subramaniam S: Molecular architecture of native HIV-1 gp120 trimers. Nature 2008, 455:109-113.
• [54]Meyerson JR, Tran EE, Kuybeda O, Chen W, Dimitrov DS, Gorlani A, Verrips T, Lifson JD, Subramaniam S: Molecular structures of trimeric HIV-1 Env in complex with small antibody derivatives. Proc Natl Acad Sci U S A 2013, 110:513-518.
• [55]Moore JP, Ho DD: HIV-1 neutralization: the consequences of viral adaptation to growth on transformed T cells. AIDS 1995, 9:S117-S136.
• [56]York J, Follis KE, Trahey M, Nyambi PN, Zolla-Pazner S, Nunberg JH: Antibody binding and neutralization of primary and T-cell line-adapted isolates of human immunodeficiency virus type 1. J Virol 2001, 75:2741-2752.
• [57]Zhuang K, Finzi A, Tasca S, Shakirzyanova M, Knight H, Westmoreland S, Sodroski J, Cheng-Mayer C: Adoption of an “Open” Envelope Conformation Facilitating CD4 Binding and Structural Remodeling Precedes Coreceptor Switch in R5 SHIV-Infected Macaques. PLoS ONE 2011, 6:e21350.
• [58]Zhuang K, Finzi A, Toma J, Frantzell A, Huang W, Sodroski J, Cheng-Mayer C: Identification of interdependent variables that influence coreceptor switch in R5 SHIV(SF162P3N)-infected macaques. Retrovirology 2012, 9:106. BioMed Central Full Text
• [59]Chen L, Kwon YD, Zhou T, Wu X, O’Dell S, Cavacini L, Hessell AJ, Pancera M, Tang M, Xu L, Yang ZY, Zhang MY, Arthos J, Burton DR, Dimitrov DS, Nabel GJ, Posner MR, Sodroski J, Wyatt R, Mascola JR, Kwong PD: Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120. Science 2009, 326:1123-1127.
• [60]Li Y, O’Dell S, Walker LM, Wu X, Guenaga J, Feng Y, Schmidt SD, McKee K, Louder MK, Ledgerwood JE, Graham BS, Haynes BF, Burton DR, Wyatt RT, Mascola JR: Mechanism of neutralization by the broadly neutralizing HIV-1 monoclonal antibody VRC01. J Virol 2011, 85:8954-8967.
• [61]Dimonte S, Mercurio F, Svicher V, D’Arrigo R, Perno CF, Ceccherini-Silberstein F: Selected amino acid mutations in HIV-1 B subtype gp41 are associated with specific gp120v signatures in the regulation of co-receptor usage. Retrovirology 2011, 8:33. BioMed Central Full Text
• [62]Pastore C, Nedellec R, Ramos A, Pontow S, Ratner L, Mosier DE: Human immunodeficiency virus type 1 coreceptor switching: V1/V2 gain-of-fitness mutations compensate for V3 loss-of-fitness mutations. J Virol 2006, 80:750-758.
• [63]Ludtke SJ, Baldwin PR, Chiu W: EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol 1999, 128:82-97.
• [64]Markl J, Moeller A, Martin AG, Rheinbay J, Gebauer W, Depoix F: 10-A cryoEM structure and molecular model of the Myriapod (Scutigera) 6x6mer hemocyanin: understanding a giant oxygen transport protein. J Mol Biol 2009, 392:362-380.
• [65]Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE: UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem 2004, 25:1605-1612.