Computational analysis of anti-HIV-1 antibody neutralization panel data to identify potential functional epitope residues

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 26, 2013, Pages 10598-10603

  West, Anthony P ^a   Scharf, Louise ^a   Horwitz, Joshua ^b   Klein, Florian ^b   Nussenzweig, Michel C ^b   Bjorkman, Pamela J ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; GLYCOPROTEIN GP 120; HUMAN IMMUNODEFICIENCY VIRUS 1 ANTIBODY; HUMAN IMMUNODEFICIENCY VIRUS ANTIBODY; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; EPITOPE MAPPING; GLYCOSYLATION; HUMAN IMMUNODEFICIENCY VIRUS 1; IC 50; IN VITRO STUDY; MATHEMATICAL ANALYSIS; MOUSE; NONHUMAN; PRIORITY JOURNAL; VIRUS NEUTRALIZATION;

HUMAN IMMUNODEFICIENCY VIRUS 1; MUS;

EID: 84879538530     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1309215110     Document Type: Article

References (38)

1. Wu X, et al. (2010) Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1. Science 329(5993):856-861.
2. Walker LM, et al. (2009) Broad and potent neutralizing antibodies from an African donor reveal a new HIV-1 vaccine target. Science 326(5950):285-289.
3. Scheid JF, et al. (2011) Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding. Science 333(6049):1633-1637.
4. Wu X, et al. (2011) Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. Science 333(6049):1593-1602.
5. Walker LM, et al. (2011) Broad neutralization coverage of HIV by multiple highly potent antibodies. Nature 477(7365):466-470.
6. Corti D, et al. (2011) A neutralizing antibody selected from plasma cells that binds to group 1 and group 2 influenza A hemagglutinins. Science 333(6044):850-856.
7. Ekiert DC, et al. (2012) Cross-neutralization of influenza A viruses mediated by a single antibody loop. Nature 489(7417):526-532.
8. Kwong PD, Mascola JR (2012) Human antibodies that neutralize HIV-1: Identification, structures, and B cell ontogenies. Immunity 37(3):412-425.
9. Gnanakaran S, et al. (2010) Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies. PLoS Comput Biol 6(10):e1000955.
10. Mata-Fink J, et al. (2013) Rapid conformational epitope mapping of anti-gp120 antibodies with a designed mutant panel displayed on yeast. J Mol Biol 425(2):444-456.
11. Rabinowitz M, et al. (2006) Accurate prediction of HIV-1 drug response from the reverse transcriptase and protease amino acid sequences using sparse models created by convex optimization. Bioinformatics 22(5):541-549.
12. Wang K, Jenwitheesuk E, Samudrala R, Mittler JE (2004) Simple linear model provides highly accurate genotypic predictions of HIV-1 drug resistance. Antivir Ther 9(3):343-352.
13. Montefiori DC (2005) Evaluating neutralizing antibodies against HIV, SIV, and SHIV in luciferase reporter gene assays. Curr Protoc Immunol Chapter 12:Unit 12.11.
14. Frey G, et al. (2008) A fusion-intermediate state of HIV-1 gp41 targeted by broadly neutralizing antibodies. Proc Natl Acad Sci USA 105(10):3739-3744.
15. Chakrabarti BK, et al. (2011) Direct antibody access to the HIV-1 membrane-proximal external region positively correlates with neutralization sensitivity. J Virol 85(16):8217-8226.
16. Brünger AT (1992) Free R value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature 355(6359):472-475.
17. Bhattacharya T, et al. (2007) Founder effects in the assessment of HIV polymorphisms and HLA allele associations. Science 315(5818):1583-1586.
18. Muster T, et al. (1993) A conserved neutralizing epitope on gp41 of human immunodeficiency virus type 1. J Virol 67(11):6642-6647.
19. Zwick MB, et al. (2005) Anti-human immunodeficiency virus type 1 (HIV-1) antibodies 2F5 and 4E10 require surprisingly few crucial residues in the membrane-proximal external region of glycoprotein gp41 to neutralize HIV-1. J Virol 79(2):1252-1261.
20. Bryson S, Julien JP, Hynes RC, Pai EF (2009) Crystallographic definition of the epitope promiscuity of the broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2F5: Vaccine design implications. J Virol 83(22):11862-11875.
21. Trkola 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(2):1100-1108.
22. Scanlan CN, 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(14):7306-7321.
23. West AP, Jr., Diskin R, Nussenzweig MC, Bjorkman PJ (2012) Structural basis for germ-line gene usage of a potent class of antibodies targeting the CD4-binding site of HIV-1 gp120. Proc Natl Acad Sci USA 109(30):E2083-E2090.
24. Klein F, et al. (2012) HIV therapy by a combination of broadly neutralizing antibodies in humanized mice. Nature 492(7427):118-122.
25. Mouquet H, et al. (2012) Complex-type N-glycan recognition by potent broadly neutralizing HIV antibodies. Proc Natl Acad Sci USA 109(47):E3268-E3277.
26. Tomiya N, Betenbaugh MJ, Lee YC (2003) Humanization of lepidopteran insect-cellproduced glycoproteins. Acc Chem Res 36(8):613-620.
27. Reeves PJ, Kim JM, Khorana HG (2002) Structure and function in rhodopsin: A tetracyclineinducible system in stable mammalian cell lines for high-level expression of opsin mutants. Proc Natl Acad Sci USA 99(21):13413-13418.
28. Binley JM, et al. (2010) Role of complex carbohydrates in human immunodeficiency virus type 1 infection and resistance to antibody neutralization. J Virol 84(11):5637-5655.
29. Corti D, Lanzavecchia A (2013) Broadly neutralizing antiviral antibodies. Annu Rev Immunol 31:705-742.
30. Georgiev IS, et al. (2013) Delineating antibody recognition in polyclonal sera from patterns of HIV-1 isolate neutralization. Science 340(6133):751-756.
31. Wells JA, de Vos AM (1996) Hematopoietic receptor complexes. Annu Rev Biochem 65:609-634.
32. Myszka DG, et al. (2000) Energetics of the HIV gp120-CD4 binding reaction. Proc Natl Acad Sci USA 97(16):9026-9031.
33. Diskin R, et al. (2013) Restricting HIV-1 pathways for escape using rationally-designed anti-HIV-1 antibodies. J Exp Med, 10.1084/jem.20130221.
34. Huang J, et al. (2012) Broad and potent neutralization of HIV-1 by a gp41-specific human antibody. Nature 491(7424):406-412.
35. Doria-Rose NA, et al. (2012) HIV-1 neutralization coverage is improved by combining monoclonal antibodies that target independent epitopes. J Virol 86(6):3393-3397.
36. Diskin R, et al. (2011) Increasing the potency and breadth of an HIV antibody by using structure-based rational design. Science 334(6060):1289-1293.
37. Durocher Y, Perret S, Kamen A (2002) High-level and high-throughput recombinant protein production by transient transfection of suspension-growing human 293-EBNA1 cells. Nucleic Acids Res 30(2):E9.
38. Mouquet H, et al. (2011) Memory B cell antibodies to HIV-1 gp140 cloned from individuals infected with clade A and B viruses. PLoS One 6(9):e24078.