Erratum: Transplanting supersites of HIV-1 vulnerability (PLoS ONE (2014) 9, 7 (e99881) DOI: 10.1371/journal.pone.0099881);Transplanting supersites of HIV-1 vulnerability

PLoS ONE

Volumn 9, Issue 7, 2014, Pages

  Zhou, Tongqing ^a   Zhu, Jiang ^a   Yang, Yongping ^a   Gorman, Jason ^a   Ofek, Gilad ^a   Srivatsan, Sanjay ^a   Druz, Aliaksandr ^a   Lees, Christopher R ^a   Lu, Gabriel ^a   Soto, Cinque ^a   Stuckey, Jonathan ^a   Burton, Dennis R ^b,c   Koff, Wayne C ^d   Connors, Mark ^a   Kwon, Peter D ^a  

^a NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d INTERNATIONAL AIDS VACCINE INITIATIVE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY 10E8; ANTIBODY PG9; ANTIBODY PGT128; EPITOPE; GLYCAN; NANOPARTICLE; NEUTRALIZING ANTIBODY; SCAFFOLD PROTEIN; UNCLASSIFIED DRUG; GLYCOPROTEIN GP 120; GLYCOPROTEIN GP 41; GP120 PROTEIN, HUMAN IMMUNODEFICIENCY VIRUS 1; GP41 PROTEIN, HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS ANTIBODY;

ALGORITHM; ANTIGEN BINDING; ANTIGEN RECOGNITION; ANTIGENICITY; ARTICLE; BINDING AFFINITY; CONTROLLED STUDY; HUMAN IMMUNODEFICIENCY VIRUS 1; IMMUNE EVASION; SEQUENCE ALIGNMENT; SUPERSITE TRANSPLANT; TRANSPLANTATION; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; IMMUNOLOGY;

ANTIBODIES, NEUTRALIZING; HIV ANTIBODIES; HIV ENVELOPE PROTEIN GP120; HIV ENVELOPE PROTEIN GP41; HIV-1; HUMANS; MODELS, MOLECULAR;

EID: 84903757787     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0105659     Document Type: Erratum

References (71)

1. Klein F, Mouquet H, Dosenovic P, Scheid JF, Scharf L, et al. (2013) Antibodies in HIV-1 vaccine development and therapy. Science 341: 1199-1204.
2. Burton DR, Desrosiers RC, Doms RW, Koff WC, Kwong PD, et al. (2004) HIV vaccine design and the neutralizing antibody problem. Nat Immunol 5: 233-236. (Pubitemid 38332116)
3. Starcich BR, Hahn BH, Shaw GM, McNeely PD, Modrow S, et al. (1986) Identification and characterization of conserved and variable regions in the envelope gene of HTLV-III/LAV, the retrovirus of AIDS. Cell 45: 637-648. (Pubitemid 16063128)
4. Wyatt R, Kwong PD, Desjardins E, Sweet RW, Robinson J, et al. (1998) The antigenic structure of the HIV gp120 envelope glycoprotein. Nature 393: 705-711. (Pubitemid 28289663)
5. Kwong PD, Doyle ML, Casper DJ, Cicala C, Leavitt SA, et al. (2002) HIV-1 evades antibody-mediated neutralization through conformational masking of receptor-binding sites. Nature 420: 678-682. (Pubitemid 36764500)
6. Wei X, Decker JM, Wang S, Hui H, Kappes JC, et al. (2003) Antibody neutralization and escape by HIV-1. Nature 422: 307-312. (Pubitemid 36378357)
7. Julien JP, Cupo A, Sok D, Stanfield RL, Lyumkis D, et al. (2013) Crystal structure of a soluble cleaved HIV-1 envelope trimer. Science 342: 1477-1483.
8. Lyumkis D, Julien JP, de Val N, Cupo A, Potter CS, et al. (2013) Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. Science 342: 1484-1490.
9. Gray ES, Moody MA, Wibmer CK, Chen X, Marshall D, et al. (2011) Isolation of a monoclonal antibody that targets the alpha-2 helix of gp120 and represents the initial autologous neutralizing-antibody response in an HIV-1 subtype C-infected individual. J Virol 85: 7719-7729.
10. Mikell I, Sather DN, Kalams SA, Altfeld M, Alter G, et al. (2011) Characteristics of the earliest cross-neutralizing antibody response to HIV-1. PLoS Pathog 7: e1001251.
11. Li Y, Migueles SA, Welcher B, Svehla K, Phogat A, et al. (2007) Broad HIV-1 neutralization mediated by CD4-binding site antibodies. Nat Med 13: 1032-1034. (Pubitemid 47517505)
12. Binley JM, Lybarger EA, Crooks ET, Seaman MS, Gray E, et al. (2008) Profiling the specificity of neutralizing antibodies in a large panel of plasmas from patients chronically infected with human immunodeficiency virus type 1 subtypes B and C. J Virol 82: 11651-11668.
13. Sather DN, Armann J, Ching LK, Mavrantoni A, Sellhorn G, et al. (2009) Factors associated with the development of cross-reactive neutralizing antibodies during human immunodeficiency virus type 1 infection. J Virol 83: 757-769.
14. Simek MD, Rida W, Priddy FH, Pung P, Carrow E, et al. (2009) Human immunodeficiency virus type 1 elite neutralizers: individuals with broad and potent neutralizing activity identified by using a high-throughput neutralization assay together with an analytical selection algorithm. J Virol 83: 7337-7348.
15. Stamatatos L, Morris L, Burton DR, Mascola JR (2009) Neutralizing antibodies generated during natural HIV-1 infection: good news for an HIV-1 vaccine? Nat Med 15: 866-870.
16. Hraber P, Seaman MS, Bailer RT, Mascola JR, Montefiori DC, et al. (2014) Prevalence of broadly neutralizing antibody responses during chronic HIV-1 infection. AIDS 28: 163-169.
17. Ofek G, Guenaga FJ, Schief WR, Skinner J, Baker D, et al. (2010) Elicitation of structure-specific antibodies by epitope scaffolds. Proc Natl Acad Sci U S A 107: 17880-17887.
18. Correia BE, Ban YE, Holmes MA, Xu H, Ellingson K, et al. (2010) Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope. Structure 18: 1116-1126.
19. Azoitei ML, Correia BE, Ban YE, Carrico C, Kalyuzhniy O, et al. (2011) Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Science 334: 373-376.
20. McLellan JS, Correia BE, Chen M, Yang Y, Graham BS, et al. (2011) Design and characterization of epitope-scaffold immunogens that present the motavizumab epitope from respiratory syncytial virus. J Mol Biol 409: 853-866.
21. Stanfield RL, Julien JP, Pejchal R, Gach JS, Zwick MB, et al. (2011) Structure-Based Design of a Protein Immunogen that Displays an HIV-1 gp41 Neutralizing Epitope. Journal of molecular biology 414: 460-476.
22. Azoitei ML, Ban YE, Julien JP, Bryson S, Schroeter A, et al. (2012) Computational design of high-affinity epitope scaffolds by backbone grafting of a linear epitope. J Mol Biol 415: 175-192.
23. Correia BE, Bates JT, Loomis RJ, Baneyx G, Carrico C, et al. (2014) Proof of principle for epitope-focused vaccine design. Nature 507: 201-206.
24. Kwong PD, Mascola JR (2012) Human antibodies that neutralize HIV-1: identification, structures, and B cell ontogenies. Immunity 37: 412-425.
25. Kong L, Lee JH, Doores KJ, Murin CD, Julien JP, et al. (2013) Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120. Nat Struct Mol Biol 20: 796-803.
26. Zhang Y, Skolnick J (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33: 2302-2309. (Pubitemid 41439897)
27. Jakuschev S, Hoffmann D (2009) A novel algorithm for macromolecular epitope matching. Algorithms 2: 498-517.
28. Hasegawa H, Holm L (2009) Advances and pitfalls of protein structural alignment. Curr Opin Struct Biol 19: 341-348.
29. Zhou H, Zhou Y (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 11: 2714-2726. (Pubitemid 35191145)
30. Muster T, Guinea R, Trkola A, Purtscher M, Klima A, et al. (1994) Cross-neutralizing activity against divergent human immunodeficiency virus type 1 isolates induced by the gp41 sequence ELDKWAS. J Virol 68: 4031-4034. (Pubitemid 24177431)
31. Stiegler G, Kunert R, Purtscher M, Wolbank S, Voglauer R, et al. (2001) A potent cross-clade neutralizing human monoclonal antibody against a novel epitope on gp41 of human immunodeficiency virus type 1. AIDS Res Hum Retroviruses 17: 1757-1765. (Pubitemid 34114213)
32. Muster T, Steindl F, Purtscher M, Trkola A, Klima A, et al. (1993) A conserved neutralizing epitope on gp41 of human immunodeficiency virus type 1. J Virol 67: 6642-6647. (Pubitemid 23309131)
33. Huang J, Ofek G, Laub L, Louder MK, Doria-Rose NA, et al. (2012) Broad and potent neutralization of HIV-1 by a gp41-specific human antibody. Nature 491: 406-412.
34. Cardoso RM, Zwick MB, Stanfield RL, Kunert R, Binley JM, et al. (2005) Broadly neutralizing anti-HIV antibody 4E10 recognizes a helical conformation of a highly conserved fusion-associated motif in gp41. Immunity 22: 163-173. (Pubitemid 40255708)
35. Pejchal R, Gach JS, Brunel FM, Cardoso RM, Stanfield RL, et al. (2009) A conformational switch in human immunodeficiency virus gp41 revealed by the structures of overlapping epitopes recognized by neutralizing antibodies. J Virol 83: 8451-8462.
36. Morris L, Chen X, Alam M, Tomaras G, Zhang R, et al. (2011) Isolation of a human anti-HIV gp41 membrane proximal region neutralizing antibody by antigen-specific single B cell sorting. PLoS One 6(9): e23532.
37. Samara NL, Datta AB, Berndsen CE, Zhang XB, Yao TT, et al. (2010) Structural Insights into the Assembly and Function of the SAGA Deubiquitinating Module. Science 328: 1025-1029.
38. Kobayashi K, Kikuno I, Kuroha K, Saito K, Ito K, et al. (2010) Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1alpha complex. Proc Natl Acad Sci U S A 107: 17575-17579.
39. Zwick MB, Labrijn AF, Wang M, Spenlehauer C, Saphire EO, et al. (2001) Broadly neutralizing antibodies targeted to the membrane-proximal external region of human immunodeficiency virus type 1 glycoprotein gp41. J Virol 75: 10892-10905. (Pubitemid 33034579)
40. Walker LM, Phogat SK, Chan-Hui PY, Wagner D, Phung P, et al. (2009) Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target. Science 326: 285-289.
41. Bonsignori M, Hwang KK, Chen X, Tsao CY, Morris L, et al. (2011) Analysis of a clonal lineage of HIV-1 envelope V2/V3 conformational epitope-specific broadly neutralizing antibodies and their inferred unmutated common ancestors. J Virol 85: 9998-10009.
42. Walker LM, Huber M, Doores KJ, Falkowska E, Pejchal R, et al. (2011) Broad neutralization coverage of HIV by multiple highly potent antibodies. Nature 477: 466-470.
43. McLellan JS, Pancera M, Carrico C, Gorman J, Julien JP, et al. (2011) Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9. Nature 480: 336-343.
44. Pancera M, Shahzad-Ul-Hussan S, Doria-Rose NA, McLellan JS, Bailer RT, et al. (2013) Structural basis for diverse N-glycan recognition by HIV-1-neutralizing V1-V2-directed antibody PG16. Nat Struct Mol Biol 20: 804-813.
45. Julien JP, Lee JH, Cupo A, Murin CD, Derking R, et al. (2013) Asymmetric recognition of the HIV-1 trimer by broadly neutralizing antibody PG9. Proc Natl Acad Sci U S A 110: 4351-4356.
46. Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, et al. (2008) Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin. Mol Cell 30: 26-38. (Pubitemid 351470144)
47. Gerhardt S, Abbott WM, Hargreaves D, Pauptit RA, Davies RA, et al. (2009) Structure of IL-17A in complex with a potent, fully human neutralizing antibody. J Mol Biol 394: 905-921.
48. Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, et al. (2005) Structural analysis of a set of proteins resulting from a bacterial genomics project. Proteins 60: 787-796. (Pubitemid 41266436)
49. Stieglitz B, Bee C, Schwarz D, Yildiz O, Moshnikova A, et al. (2008) Novel type of Ras effector interaction established between tumour suppressor NORE1A and Ras switch II. EMBO J 27: 1995-2005.
50. Saikrishnan K, Manjunath GP, Singh P, Jeyakanthan J, Dauter Z, et al. (2005) Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary association. Acta Crystallogr D Biol Crystallogr 61: 1140-1148. (Pubitemid 43951496)
51. Trkola A, Purtscher M, Muster T, Ballaun C, Buchacher A, et al. (1996) Human monoclonal antibody 2G12 defines a distinctive neutralization epitope on the gp120 glycoprotein of human immunodeficiency virus type 1. J Virol 70: 1100-1108. (Pubitemid 26029030)
52. Mouquet H, Scharf L, Euler Z, Liu Y, Eden C, et al. (2012) Complex-type N-glycan recognition by potent broadly neutralizing HIV antibodies. Proc Natl Acad Sci U S A 109: E3268-3277.
53. Georgiev IS, Doria-Rose NA, Zhou T, Kwon YD, Staupe RP, et al. (2013) Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization. Science 340: 751-756.
54. Pejchal R, Doores KJ, Walker LM, Khayat R, Huang PS, et al. (2011) A potent and broad neutralizing antibody recognizes and penetrates the HIV glycan shield. Science 334: 1097-1103.
55. Sanders RW, Venturi M, Schiffner L, Kalyanaraman R, Katinger H, et al. (2002) The mannose-dependent epitope for neutralizing antibody 2G12 on human immunodeficiency virus type 1 glycoprotein gp120. J Virol 76: 7293-7305.
56. Scanlan CN, Pantophlet R, Wormald MR, Ollmann Saphire E, Stanfield R, et al. (2002) The broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2G12 recognizes a cluster of alpha1->2 mannose residues on the outer face of gp120. J Virol 76: 7306-7321.
57. Kanekiyo M, Wei CJ, Yassine HM, McTamney PM, Boyington JC, et al. (2013) Self-assembling influenza nanoparticle vaccines elicit broadly neutralizing H1N1 antibodies. Nature 499: 102-106.
58. Roldao A, Mellado MC, Castilho LR, Carrondo MJ, Alves PM (2010) Virus-like particles in vaccine development. Expert Rev Vaccines 9: 1149-1176.
59. Chakraborty K, Durani V, Miranda ER, Citron M, Liang X, et al. (2006) Design of immunogens that present the crown of the HIV-1 V3 loop in a conformation competent to generate 447-52D-like antibodies. Biochem J 399: 483-491. (Pubitemid 44672639)
60. Moseri A, Tantry S, Sagi Y, Arshava B, Naider F, et al. (2010) An optimally constrained V3 peptide is a better immunogen than its linear homolog or HIV-1 gp120. Virology 401: 293-304.
61. Totrov M, Jiang X, Kong XP, Cohen S, Krachmarov C, et al. (2010) Structure-guided design and immunological characterization of immunogens presenting the HIV-1 gp120 V3 loop on a CTB scaffold. Virology 405: 513-523.
62. McLellan JS, Chen M, Joyce MG, Sastry M, Stewart-Jones GB, et al. (2013) Structure-based design of a fusion glycoprotein vaccine for respiratory syncytial virus. Science 342: 592-598.
63. Bhattacharyya S, Singh P, Rathore U, Purwar M, Wagner D, et al. (2013) Design of an Escherichia coli expressed HIV-1 gp120 fragment immunogen that binds to b12 and induces broad and potent neutralizing antibodies. J Biol Chem 288: 9815-9825.
64. Calarese DA, Scanlan CN, Zwick MB, Deechongkit S, Mimura Y, et al. (2003) Antibody domain exchange is an immunological solution to carbohydrate cluster recognition. Science 300: 2065-2071. (Pubitemid 36760127)
65. Wang G, Dunbrack RL Jr (2003) PISCES: a protein sequence culling server. Bioinformatics 19: 1589-1591. (Pubitemid 37038881)
66. Zhu J, Fan H, Periole X, Honig B, Mark AE (2008) Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins 72: 1171-1188.
67. Xiang Z, Honig B (2001) Extending the accuracy limits of prediction for sidechain conformations. J Mol Biol 311: 421-430. (Pubitemid 32744551)
68. Desmet J, Spriet J, Lasters I (2002) Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization. Proteins 48: 31-43. (Pubitemid 34595046)
69. Xu J, Zhang Y (2010) How significant is a protein structure similarity with TM-score =0.5? Bioinformatics 26: 889-895.
70. DeLano WL (2002) The PyMOL Molecular Graphics System. San Carlos, CA: DeLano Scientific.
71. Krissinel E, Henrick K (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol 372: 774-797. (Pubitemid 47321791)