A native-like SOSIP.664 trimer based on an HIV-1 subtype B env gene

Journal of Virology

Volumn 89, Issue 6, 2015, Pages 3380-3395

  Pugach, Pavel ^a   Ozorowski, Gabriel ^b   Cupo, Albert ^a   Ringe, Rajesh ^a   Yasmeen, Anila ^a   de Val, Natalia ^b   Derking, Ronald ^c   Kim, Helen J ^a   Korzun, Jacob ^a   Golabek, Michael ^a   de los Reyes, Kevin ^a   Ketas, Thomas J ^a   Julien, Jean Philippe ^b,e   Burton, Dennis R ^b,d   Wilson, Ian A ^b   Sanders, Rogier W ^a,c   Klasse, P J ^a   Ward, Andrew B ^b   Moore, John P ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF AMSTERDAM   (Netherlands)

^d MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^e HOSPITAL FOR SICK CHILDREN RESEARCH INSTITUTE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ENVELOPE PROTEIN; EPITOPE; HUMAN IMMUNODEFICIENCY VIRUS VACCINE; VIRUS ENVELOPE PROTEIN;

ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; ELECTRON MICROSCOPY; ENVELOPE GENE; GENE EXPRESSION; GENETIC ANALYSIS; HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 SUBTYPE B; IMMUNOGENICITY; IN VITRO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN QUATERNARY STRUCTURE; STRUCTURE ANALYSIS; THERMOSTABILITY; VIRUS STRAIN; CHEMISTRY; CLASSIFICATION; GENETICS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNOLOGY; ISOLATION AND PURIFICATION; PROTEIN MULTIMERIZATION; VIROLOGY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

AIDS VACCINES; ENV GENE PRODUCTS, HUMAN IMMUNODEFICIENCY VIRUS; EPITOPES; HIV INFECTIONS; HIV-1; HUMANS; PROTEIN MULTIMERIZATION;

EID: 84923172318     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.03473-14     Document Type: Article

References (75)

1. Burton DR, Desrosiers RC, Doms RW, Koff WC, Kwong PD, Moore JP, Nabel GJ, Sodroski J, Wilson IA, Wyatt RT. 2004. HIV vaccine design and the neutralizing antibody problem. Nat Immunol 5:233-236. http://dx.doi.org/10.1038/ni0304-233.
2. Burton DR, Hessell AJ, Keele BF, Klasse PJ, Ketas TA, Moldt B, Dunlop DC, Poignard P, Doyle LA, Cavacini L, Veazey RS, Moore JP. 2011. Limited or no protection by weakly or nonneutralizing antibodies against vaginal SHIV challenge of macaques compared with a strongly neutralizing antibody. Proc Natl Acad Sci U S A 108:11181-11186. http://dx.doi .org/10.1073/pnas.1103012108.
3. Burton DR, Poignard P, Stanfield RL, Wilson IA. 2012. Broadly neutralizing antibodies present new prospects to counter highly antigenically diverse viruses. Science 337:183-186. http://dx.doi.org/10.1126/science .1225416.
4. Binley JM, Sanders RW, Clas B, Schuelke N, Master A, Guo Y, Kajumo F, Anselma DJ, Maddon PJ, Olson WC, Moore JP. 2000. 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 74:627-643. http://dx.doi.org/10.1128/JVI.74.2.627-643 .2000.
5. Binley JM, Sanders RW, Master A, Cayanan CS, Wiley CL, Schiffner L, Travis B, Kuhmann S, Burton DR, Hu SL, Olson WC, Moore JP. 2002. Enhancing the proteolytic maturation of human immunodeficiency virus type 1 envelope glycoproteins. J Virol 76:2606-2616. http://dx.doi.org/10 .1128/JVI.76.6.2606-2616.2002.
6. Sanders RW, Vesanen M, Schuelke N, Master A, Schiffner L, Kalyanaraman R, Paluch M, Berkhout B, Maddon PJ, Olson WC, Lu M, Moore JP. 2002. Stabilization of the soluble, cleaved, trimeric form of the envelope glycoprotein complex of human immunodeficiency virus type 1. J Virol 76: 8875-8889. http://dx.doi.org/10.1128/JVI.76.17.8875-8889.2002.
7. Earl PL, Broder CC, Doms RW, Moss B. 1997. Epitope map of human immunodeficiency virus type 1 gp41 derived from 47 monoclonal antibodies produced by immunization with oligomeric envelope protein. J Virol 71:2674-2684.
8. Yang X, Farzan M, Wyatt R, Sodroski J. 2000. Characterization of stable, soluble trimers containing complete ectodomains of human immunodeficiency virus type 1 envelope glycoproteins. J Virol 74:5716-5725. http://dx.doi.org/10.1128/JVI.74.12.5716-5725.2000.
9. Yang X, Florin L, Farzan M, Kolchinsky P, Kwong PD, Sodroski J, Wyatt R. 2000. Modifications that stabilize human immunodeficiency virus envelope glycoprotein trimers in solution. J Virol 74:4746-4754. http://dx.doi.org/10.1128/JVI.74.10.4746-4754.2000.
10. Earl PL, Sugiura W, Montefiori DC, Broder CC, Lee SA, Wild C, Lifson J, Moss B. 2001. Immunogenicity and protective efficacy of oligomeric human immunodeficiency virus type 1 gp140. J Virol 75:645-653. http://dx.doi.org/10.1128/JVI.75.2.645-653.2001.
11. Yang X, Wyatt R, Sodroski J. 2001. Improved elicitation of neutralizing antibodies against primary human immunodeficiency viruses by soluble stabilized envelope glycoprotein trimers. J Virol 75:1165-1171. http://dx .doi.org/10.1128/JVI.75.3.1165-1171.2001.
12. Srivastava IK, Stamatatos L, Legg H, Kan E, Fong A, Coates SR, Leung L, Wininger M, Donnelly JJ, Ulmer JB, Barnett SW. 2002. Purification and characterization of oligomeric envelope glycoprotein from a primary R5 subtype B human immunodeficiency virus. J Virol 76:2835-2847. http://dx.doi.org/10.1128/JVI.76.6.2835-2847.2002.
13. Yang X, Lee J, Mahony EM, Kwong PD, Wyatt R, Sodroski J. 2002. Highly stable trimers formed by human immunodeficiency virus type 1 envelope glycoproteins fused with the trimeric motif of T4 bacteriophage fibritin. J Virol 76:4634-4642. http://dx.doi.org/10.1128/JVI.76.9.4634-4642.2002.
14. Srivastava IK, Stamatatos L, Kan E, Vajdy M, Lian Y, Hilt S, Martin L, Vita C, Zhu P, Roux KH, Vojtech L, D CM, Donnelly J, Ulmer JB, Barnett SW. 2003. Purification, characterization, and immunogenicity of a soluble trimeric envelope protein containing a partial deletion of the V2 loop derived from SF162, an R5-tropic human immunodeficiency virus type 1 isolate. J Virol 77:11244-11259. http://dx.doi.org/10.1128/JVI.77 .20.11244-11259.2003.
15. Srivastava IK, VanDorsten K, Vojtech L, Barnett SW, Stamatatos L. 2003. Changes in the immunogenic properties of soluble gp140 human immunodeficiency virus envelope constructs upon partial deletion of the second hypervariable region. J Virol 77:2310-2320. http://dx.doi.org/10 .1128/JVI.77.4.2310-2320.2003.
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. 2010. Breadth of neutralizing antibodies elicited by stable, homogeneous clade A and clade C HIV-1 gp140 envelope trimers in guinea pigs. J Virol 84:3270-3279. http://dx.doi.org/10.1128/JVI.02252-09.
17. Kovacs JM, Nkolola JP, Peng H, Cheung A, Perry J, Miller CA, Seaman MS, Barouch DH, Chen B. 2012. HIV-1 envelope trimer elicits more potent neutralizing antibody responses than monomeric gp120. Proc Natl Acad Sci USA109:12111-12116. http://dx.doi.org/10.1073/pnas.1204533109.
18. Nkolola JP, Bricault CA, Cheung A, Shields J, Perry J, Kovacs JM, Giorgi E, van Winsen M, Apetri A, Brinkman-van der Linden EC, Chen B, Korber B, Seaman MS, Barouch DH. 2014. Characterization and immunogenicity of a novel mosaic M HIV-1 gp140 trimer. J Virol 88: 9538-9552. http://dx.doi.org/10.1128/JVI.01739-14.
19. Nkolola JP, Cheung A, Perry JR, Carter D, Reed S, Schuitemaker H, Pau MG, Seaman MS, Chen B, Barouch DH. 2014. Comparison of multiple adjuvants on the stability and immunogenicity of a clade C HIV-1 gp140 trimer. Vaccine 32:2109-2116. http://dx.doi.org/10.1016/j .vaccine.2014.02.001.
20. Guttman M, Lee KK. 2013.Afunctional interaction between gp41 and gp120 is observed for monomeric but not oligomeric, uncleaved HIV-1 Env gp140. J Virol 87:11462-11475. http://dx.doi.org/10.1128/JVI.01681-13.
21. Ringe RP, Sanders RW, Yasmeen A, Kim HJ, Lee JH, Cupo A, Korzun J, Derking R, van Montfort T, Julien JP, Wilson IA, Klasse PJ, Ward AB, Moore JP. 2013. Cleavage strongly influences whether soluble HIV-1 envelope glycoprotein trimers adopt a native-like conformation. Proc Natl Acad Sci U S A 110:18256-18261. http://dx.doi.org/10.1073/pnas .1314351110.
22. Moscoso CG, Xing L, Hui J, Hu J, Kalkhoran MB, Yenigun OM, Sun Y, Paavolainen L, Martin L, Vahlne A, Zambonelli C, Barnett SW, Srivastava IK, Cheng RH. 2014. Trimeric HIV Env provides epitope occlusion mediated by hypervariable loops. Sci Rep 4:7025. http://dx.doi.org/10 .1038/srep07025.
23. Sanders RW, Moore JP. 2014. HIV: a stamp on the envelope. Nature 514:437-438. http://dx.doi.org/10.1038/nature13926.
24. Tran K, Poulsen C, Guenaga J, de Val N, Wilson R, Sundling C, Li Y, Stanfield RL, Wilson IA, Ward AB, Karlsson Hedestam GB, Wyatt RT. 2014. Vaccine-elicited primate antibodies use a distinct approach to the HIV-1 primary receptor binding site informing vaccine redesign. Proc Natl Acad Sci U S A 111:E738-E747. http://dx.doi.org/10.1073/pnas .1319512111.
25. Yasmeen A, Ringe R, Derking R, Cupo A, Julien JP, Burton DR, Ward AB, Wilson IA, Sanders RW, Moore JP, Klasse PJ. 2014. Differential binding of neutralizing and non-neutralizing antibodies to native-like soluble HIV-1 Env trimers, uncleaved Env proteins, and monomeric subunits. Retrovirology 11:41. http://dx.doi.org/10.1186/1742-4690-11-41.
26. Kovacs JM, Noeldeke E, Ha HJ, Peng H, Rits-Volloch S, Harrison SC, Chen B. 2014. Stable, uncleaved HIV-1 envelope glycoprotein gp140 forms a tightly folded trimer with a native-like structure. Proc Natl Acad Sci U S A 111:18542-18547. http://dx.doi.org/10.1073/pnas.1422269112.
27. Li Y, O'Dell S, Wilson R, Wu X, Schmidt SD, Hogerkorp CM, Louder MK, Longo NS, Poulsen C, Guenaga J, Chakrabarti BK, Doria-Rose N, Roederer M, Connors M, Mascola JR, Wyatt RT. 2012. HIV-1 neutralizing antibodies display dual recognition of the primary and coreceptor binding sites and preferential binding to fully cleaved envelope glycoproteins. J Virol 86:11231-11241. http://dx.doi.org/10.1128/JVI.01543-12.
28. Blattner C, Lee JH, Sliepen K, Derking R, Falkowska E, de la Pena AT, Cupo A, Julien JP, van Gils M, Lee PS, Peng W, Paulson JC, Poignard P, Burton DR, Moore JP, Sanders RW, Wilson IA, Ward AB. 2014. Structural delineation of a quaternary, cleavage-dependent epitope at the gp41-gp120 interface on intact HIV-1 Env trimers. Immunity 40:669-680. http://dx.doi.org/10.1016/j.immuni.2014.04.008.
29. Falkowska E, Le KM, Ramos A, Doores KJ, Lee JH, Blattner C, Ramirez A, Derking R, van Gils MJ, Liang CH, McBride R, von Bredow B, Shivatare SS, Wu CY, Chan-Hui PY, Liu Y, Feizi T, Zwick MB, Koff WC, Seaman MS, Swiderek K, Moore JP, Evans D, Paulson JC, Wong CH, Ward AB, Wilson IA, Sanders RW, Poignard P, Burton DR. 2014. Broadly neutralizing HIV antibodies define a glycan-dependent epitope on the prefusion conformation of gp41 on cleaved envelope trimers. Immunity 40:657-668. http://dx.doi.org/10.1016/j.immuni.2014.04.009.
30. Huang J, Kang BH, Pancera M, Lee JH, Tong T, Feng Y, Georgiev IS, Chuang GY, Druz A, Doria-Rose NA, Laub L, Sliepen K, van Gils MJ, de la Pena AT, Derking R, Klasse PJ, Migueles SA, Bailer RT, Alam M, Pugach P, Haynes BF, Wyatt RT, Sanders RW, Binley JM, Ward AB, Mascola JR, Kwong PD, Connors M. 2014. Broad and potent HIV-1 neutralization by a human antibody that binds the gp41-gp120 interface. Nature 515:138-142. http://dx.doi.org/10.1038/nature13601.
31. Go EP, Zhang Y, Menon S, Desaire H. 2011. Analysis of the disulfide bond arrangement of the HIV-1 envelope protein CON-S gp140 ΔCFI shows variability in the V1 and V2 regions. J Proteome Res 10:578-591. http://dx.doi.org/10.1021/pr100764a.
32. Go EP, Hua D, Desaire H. 2014. Glycosylation and disulfide bond analysis of transiently and stably expressed clade C HIV-1 gp140 trimers in 293T cells identifies disulfide heterogeneity present in both proteins and differences in O-linked glycosylation. J Proteome Res 13:4012-4027. http://dx.doi.org/10.1021/pr5003643.
33. Pancera M, Wyatt R. 2005. Selective recognition of oligomeric HIV-1 primary isolate envelope glycoproteins by potently neutralizing ligands requires efficient precursor cleavage. Virology 332:145-156. http://dx.doi .org/10.1016/j.virol.2004.10.042.
34. Khayat R, Lee JH, Julien JP, Cupo A, Klasse PJ, Sanders RW, Moore JP, Wilson IA, Ward AB. 2013. Structural characterization of cleaved, soluble HIV-1 envelope glycoprotein trimers. J Virol 87:9865-9872. http://dx .doi.org/10.1128/JVI.01222-13.
35. Klasse PJ, Depetris RS, Pejchal R, Julien JP, Khayat R, Lee JH, Marozsan AJ, Cupo A, Cocco N, Korzun J, Yasmeen A, Ward AB, Wilson IA, Sanders RW, Moore JP. 2013. Influences on trimerization and aggregation of soluble, cleaved HIV-1 SOSIP envelope glycoprotein. J Virol 87: 9873-9885. http://dx.doi.org/10.1128/JVI.01226-13.
36. Wu X, Parast AB, Richardson BA, Nduati R, John-Stewart G, Mbori-Ngacha D, Rainwater SM, Overbaugh J. 2006. Neutralization escape variants of human immunodeficiency virus type 1 are transmitted from mother to infant. J Virol 80:835-844. http://dx.doi.org/10.1128/JVI.80.2 .835-844.2006.
37. Hoffenberg S, Powell R, Carpov A, Wagner D, Wilson A, Kosakovsky Pond S, Lindsay R, Arendt H, Destefano J, Phogat S, Poignard P, Fling SP, Simek M, Labranche C, Montefiori D, Wrin T, Phung P, Burton D, Koff W, King CR, Parks CL, Caulfield MJ. 2013. Identification of an HIV-1 clade A envelope that exhibits broad antigenicity and neutralization sensitivity and elicits antibodies targeting three distinct epitopes. J Virol 87:5372-5383. http://dx.doi.org/10.1128/JVI.02827-12.
38. 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. 2013. 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 9:e1003618. http://dx .doi.org/10.1371/journal.ppat.1003618.
39. Julien JP, Cupo A, Sok D, Stanfield RL, Lyumkis D, Deller MC, Klasse PJ, Burton DR, Sanders RW, Moore JP, Ward AB, Wilson IA. 2013. Crystal structure of a soluble cleaved HIV-1 envelope trimer. Science 342: 1477-1483. http://dx.doi.org/10.1126/science.1245625.
40. 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. 2013. Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. Science 342:1484-1490. http://dx.doi.org/10.1126/science.1245627.
41. Pancera M, Zhou T, Druz A, Georgiev IS, Soto C, Gorman J, Huang J, Acharya P, Chuang GY, Ofek G, Stewart-Jones GB, Stuckey J, Bailer RT, Joyce MG, Louder MK, Tumba N, Yang Y, Zhang B, Cohen MS, Haynes BF, Mascola JR, Morris L, Munro JB, Blanchard SC, Mothes W, Connors M, Kwong PD. 2014. Structure and immune recognition of trimeric pre-fusion HIV-1 Env. Nature 514:455-461. http://dx.doi.org/10 .1038/nature13808.
42. Berman PW, Gregory TJ, Riddle L, Nakamura GR, Champe MA, Porter JP, Wurm FM, Hershberg RD, Cobb EK, Eichberg JW. 1990. Protection of chimpanzees from infection by HIV-1 after vaccination with recombinant glycoprotein gp120 but not gp160. Nature 345:622-625. http://dx .doi.org/10.1038/345622a0.
43. Clements GJ, Price-Jones MJ, Stephens PE, Sutton C, Schulz TF, Clapham PR, McKeating JA, McClure MO, Thomson S, Marsh M, Kay J, Weiss RA, Moore JP. 1991. The V3 loops of the HIV-1 and HIV-2 surface glycoproteins contain proteolytic cleavage sites: a possible function in viral fusion? AIDS Res Hum Retroviruses 7:3-16.
44. Du SX, Xu L, Viswanathan S, Whalen RG. 2008. Inhibition of V3-specific cleavage of recombinant HIV-1 gp120 produced in Chinese hamster ovary cells. Protein Expr Purif 59:223-231. http://dx.doi.org/10.1016/j.pep.2008.02.002.
45. Aggarwal KY, Yu D, Mullberg J, Thakur D, Maranga L, Porter F. 2014. Controlling host-cell based proteolytic activity in CHO cultures: role of different culture parameters, abstr D015. Abstr Cell Cul Eng XIV Conf.
46. Wilen CB, Parrish NF, Pfaff JM, Decker JM, Henning EA, Haim H, Petersen JE, Wojcechowskyj JA, Sodroski J, Haynes BF, Montefiori DC, Tilton JC, Shaw GM, Hahn BH, Doms RW. 2011. Phenotypic and immunologic comparison of clade B transmitted/founder and chronic HIV-1 envelope glycoproteins. J Virol 85:8514-8527. http://dx.doi.org/10.1128/JVI.00736-11.
47. Sellhorn G, Caldwell Z, Mineart C, Stamatatos L. 2009. Improving the expression of recombinant soluble HIV Envelope glycoproteins using pseudo-stable transient transfection. Vaccine 28:430-436. http://dx.doi .org/10.1016/j.vaccine.2009.10.028.
48. Kirschner M, Monrose V, Paluch M, Techodamrongsin N, Rethwilm A, Moore JP. 2006. The production of cleaved, trimeric human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein vaccine antigens and infectious pseudoviruses using linear polyethylenimine as a transfection reagent. Protein Expr Purif 48:61-68. http://dx.doi.org/10.1016/j.pep.2006.02.017.
49. Chung NP, Matthews K, Kim HJ, Ketas TJ, Golabek M, de Los Reyes K, Korzun J, Yasmeen A, Sanders RW, Klasse PJ, Wilson IA, Ward AB, Marozsan AJ, Moore JP, Cupo A. 2014. Stable 293 T and CHO cell lines expressing cleaved, stable HIV-1 envelope glycoprotein trimers for structural and vaccine studies. Retrovirology 11:33. http://dx.doi.org/10.1186/1742-4690-11-33.
50. 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. 2013. Asymmetric recognition of the HIV-1 trimer by broadly neutralizing antibody PG9. Proc Natl Acad SciUSA110:4351-4356. http://dx.doi.org/10.1073/pnas.1217537110.
51. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A. 2005. Protein identification and analysis tools on the ExPASy server. Proteomics protocols handbook, p 571-607. Humana Press, New York, NY.
52. Schülke N, Vesanen MS, Sanders RW, Zhu P, Lu M, Anselma DJ, Villa AR, Parren PW, Binley JM, Roux KH, Maddon PJ, Moore JP, Olson WC. 2002. Oligomeric and conformational properties of a proteolytically mature, disulfide-stabilized human immunodeficiency virus type 1 gp140 envelope glycoprotein. J Virol 76:7760-7776. http://dx.doi.org/10.1128/JVI.76.15.7760-7776.2002.
53. 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. 2013. Broadly neutralizing antibody PGT121 allosterically modulates CD4 binding via recognition of the HIV-1 gp120 V3 base and multiple surrounding glycans. PLoS Pathog 9:e1003342. http://dx.doi.org/10.1371/journal.ppat.1003342.
54. Lander GC, Stagg SM, Voss NR, Cheng A, Fellmann D, Pulokas J, Yoshioka C, Irving C, Mulder A, Lau PW, Lyumkis D, Potter CS, Carragher B. 2009. Appion: an integrated, database-driven pipeline to facilitateEMimage processing. J Struct Biol 166:95-102. http://dx.doi.org/10.1016/j.jsb.2009.01.002.
55. Voss NR, Yoshioka CK, Radermacher M, Potter CS, Carragher B. 2009. DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy. J Struct Biol 166:205-213. http://dx .doi.org/10.1016/j.jsb.2009.01.004.
56. Ogura T, Iwasaki K, Sato C. 2003. Topology representing network enables highly accurate classification of protein images taken by cryo electron-microscope without masking. J Struct Biol 143:185-200. http://dx .doi.org/10.1016/j.jsb.2003.08.005.
57. Sorzano CO, Bilbao-Castro JR, Shkolnisky Y, Alcorlo M, Melero R, Caffarena-Fernandez G, Li M, Xu G, Marabini R, Carazo JM. 2010. A clustering approach to multireference alignment of single-particle projections in electron microscopy. J Struct Biol 171:197-206. http://dx.doi.org/10.1016/j.jsb.2010.03.011.
58. Tang G, Peng L, Baldwin PR, Mann DS, Jiang W, Rees I, Ludtke SJ. 2007. EMAN2: an extensible image processing suite for electron microscopy. J Struct Biol 157:38-46. http://dx.doi.org/10.1016/j.jsb.2006.05.009.
59. Ludtke SJ, Baldwin PR, Chiu W. 1999. EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol 128:82-97. http://dx.doi.org/10.1006/jsbi.1999.4174.
60. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. 2004. UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 25:1605-1612. http://dx.doi.org/10.1002/jcc.20084.
61. Scharf L, Scheid JF, Lee JH, West AP, Jr, Chen C, Gao H, Gnanapragasam PN, Mares R, Seaman MS, Ward AB, Nussenzweig MC, Bjorkman PJ. 2014. Antibody 8ANC195 reveals a site of broad vulnerability on the HIV-1 envelope spike. Cell Rep 7:785-795. http://dx.doi.org/10.1016/j.celrep.2014.04.001.
62. Klasse PJ, Sattentau QJ. 2002. Occupancy and mechanism in antibodymediated neutralization of animal viruses. J Gen Virol 83:2091-2108.
63. Klein F, Mouquet H, Dosenovic P, Scheid JF, Scharf L, Nussenzweig MC. 2013. Antibodies in HIV-1 vaccine development and therapy. Science 341:1199-1204. http://dx.doi.org/10.1126/science.1241144.
64. Guttman M, Cupo A, Julien JP, Sanders RW, Wilson IA, Moore JP, Lee KK. The potency of broadly neutralizing antibodies directly relates to their ability to recognize the closed, pre-fusion form of HIV Env. Nat Commun, in press.
65. Munro JB, Gorman J, Ma X, Zhou Z, Arthos J, Burton DR, Koff WC, Courter JR, Smith AB, III, Kwong PD, Blanchard SC, Mothes W. 2014. Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions. Science 346:759-763. http://dx.doi.org/10.1126/science .1254426.
66. Liu J, Bartesaghi A, Borgnia MJ, Sapiro G, Subramaniam S. 2008. Molecular architecture of native HIV-1 gp120 trimers. Nature 455:109-113. http://dx.doi.org/10.1038/nature07159.
67. 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. 2011. 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 USA108:11440-11445. http://dx.doi.org/10.1073/pnas.1101414108.
68. Moore JP, Trkola A, Sattentau QJ, Cao Y, Ho DD. 1994. Studies on the interactions of monoclonal antibodies with HIV-1 isolates from clades A-F, p 151-155. Proceedings of the IX Colloque des Cent Gardes. Fondation Marcel Mérieux, Lyon, France.
69. Moore JP, Cao Y, Qing L, Sattentau QJ, Pyati J, Koduri R, Robinson J, Barbas CF, III, Burton DR, Ho DD. 1995. Primary isolates of human immunodeficiency virus type 1 are relatively resistant to neutralization by monoclonal antibodies to gp120, and their neutralization is not predicted by studies with monomeric gp120. J Virol 69:101-109.
70. Cao J, Sullivan N, Desjardin E, Parolin C, Robinson J, Wyatt R, Sodroski J. 1997. Replication and neutralization of human immunodeficiency virus type 1 lacking the V1 and V2 variable loops of the gp120 envelope glycoprotein. J Virol 71:9808-9812.
71. Stamatatos L, Wiskerchen M, Cheng-Mayer C. 1998. Effect of major deletions in the V1 and V2 loops of a macrophage-tropic HIV type 1 isolate on viral envelope structure, cell entry, and replication. AIDS Res Hum Retroviruses 14:1129-1139. http://dx.doi.org/10.1089/aid.1998.14 .1129.
72. Saunders CJ, McCaffrey RA, Zharkikh I, Kraft Z, Malenbaum SE, Burke B, Cheng-Mayer C, Stamatatos L. 2005. The V1, V2, and V3 regions of the human immunodeficiency virus type 1 envelope differentially affect the viral phenotype in an isolate-dependent manner. J Virol 79:9069-9080. http://dx.doi.org/10.1128/JVI.79.14.9069-9080.2005.
73. Rusert P, Krarup A, Magnus C, Brandenberg OF, Weber J, Ehlert AK, Regoes RR, Gunthard HF, Trkola A. 2011. Interaction of the gp120 V1V2 loop with a neighboring gp120 unit shields the HIV envelope trimer against cross-neutralizing antibodies. J Exp Med 208:1419-1433. http://dx.doi.org/10.1084/jem.20110196.
74. Boyd DF, Peterson D, Haggarty BS, Jordan AP, Hogan MJ, Goo L, Hoxie JA, Overbaugh J. 5 November 2014. Mutations in HIV-1 envelope that enhance entry with the macaque CD4 receptor alter antibody recognition by disrupting quaternary interactions within the trimer. J Virol http://dx.doi.org/10.1128/JVI.02680-14.
75. Brandenberg OF, Rusert P, Magnus C, Weber J, Boni J, Gunthard HF, Regoes RR, Trkola A. 2014. Partial rescue of V1V2 mutant infectivity by HIV-1 cell-cell transmission supports the domain's exceptional capacity for sequence variation. Retrovirology 11:75. http://dx.doi.org/10.1186/s12977-014-0075-y.