Evolutionary interactions between N-Linked glycosylation sites in the HIV-1 envelope

PLoS Computational Biology

Volumn 3, Issue 1, 2007, Pages 0110-0119

  Poon, Art F Y ^a   Lewis, Fraser I ^b   Kosakovsky Pond, Sergei L ^a   Frost, Simon D W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; ANTIBODIES; DISEASES; GLYCOSYLATION; POLYSACCHARIDES; VIRUSES;

EMPIRICAL DATA; GLYCANS; GLYCOSYLATION SITES; HUMAN IMMUNODEFICIENCY VIRUS; N-LINKED; N-LINKED GLYCOSYLATION; NEUTRALIZING ANTIBODIES; PHYLOGENETICS; POLYSACCHARIDE CHAIN; PROTEIN FOLDINGS;

PHYLOGENETIC;

GLYCAN; GLYCOPROTEIN; POLYSACCHARIDE; VIRUS ENVELOPE PROTEIN;

ARTICLE; BAYES THEOREM; CODON; CONTROLLED STUDY; EVOLUTIONARY HOMOLOGY; GLYCOSYLATION; HUMAN IMMUNODEFICIENCY VIRUS 1; NONHUMAN; PHYLOGENY; PROTEIN LOCALIZATION; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; SEQUENCE ALIGNMENT; VIRUS ENVELOPE; AMINO ACID SEQUENCE; BINDING SITE; GENETICS; METABOLISM; METHODOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN ANALYSIS; PROTEIN BINDING; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

HUMAN IMMUNODEFICIENCY VIRUS 1;

AMINO ACID SEQUENCE; BINDING SITES; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GLYCOSYLATION; HIV-1; MOLECULAR SEQUENCE DATA; POLYSACCHARIDES; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; VIRAL ENVELOPE PROTEINS;

EID: 33846501408     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030011     Document Type: Article

References (53)

1. Weerapana E, Imperiali B (2006) Asparagine-linked protein glycosylation: From eukaryotic to prokaryotic systems. Glycobiology 16: 91R-101R.
2. Gavel Y, von Heijne G (1990) Sequence differences between glycosylated and non-glycosylated Asn-X-Thr/Ser acceptor sites: Implications for protein engineering. Protein Eng 3: 433-442.
3. Chen W, Helenius J, Braakman I, Helenius A (1995) Cotranslational folding and calnexin binding during glycoprotein synthesis. Proc Natl Acad Sci U S A 92: 6229-6233.
4. Meunier JC, Fournillier A, Choukhi A, Cahour A, Cocquerel L, et al. (1999) Analysis of the glycosylation sites of the hepatitis C virus (HCV) glycoprotein E1 and the influence of E1 glycans on the formation of the HCV glycoprotein complex. J Gen Virol 80: 887-896.
5. Goffard A, Callens N, Bartosch B, Wychowski C, Cosset FL, et al. (2005) Role of N-linked glycans in the functions of hepatitis C virus envelope glycoproteins. J Virol 79: 8400-8409.
6. Goffard A, Dubuisson J (2003) Glycosylation of hepatitis C virus envelope proteins. Biochimie 85: 295-301.
7. Zhang M, Gaschen B, Blay W, Foley B, Haigwood N, et al. (2004) Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin. Glycobiology 14: 1229-1246.
8. Allan JS, Coligan JE, Barin F, McLane MF, Sodroski JG, et al. (1985) Major glycoprotein antigens that induce antibodies in AIDS patients are encoded by HTLV-III. Science 228: 1091-1094.
9. Li Y, Luo L, Rasool N, Yong Kang C (1993) Glycosylation is necessary for the correct folding of human immunodeficiency virus gp120 in CD4 binding. J Virol 67: 584-588.
10. Pollakis G, Kang S, Kliphuis A, Chalaby MIM, Goudsmit J, et al. (2001) N-linked glycosylation of the HIV type-1 gp120 envelope glycoprotein as a major determinant of CCR5 and CXCR4 coreceptor utilization. J Biol Chem 276: 13433-13441.
11. Wei X, Decker JM, Wang S, Hui H, Kappes JC, et al. (2003) Antibody neutralization and escape by HIV-1. Nature 422: 307-312.
12. Koch M, Pancera M, Kwong PD, Kolchinsky P, Grundner C, et al. (2003) Structure- based, targeted deglycosylation of HIV-1 gp120 and effects on neutralization sensitivity and antibody recognition. Virology 313: 387-400.
13. Frost SDW, Wrin T, Smith DM, Kosakovsky Pond SL, Liu Y, et al. (2005) Neutralizing anti-body responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection. Proc Natl Acad Sci U S A 102: 18514-18519.
14. 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.
15. Montefiori DC, Altfeld M, Lee PK, Bilska M, Zhou J, et al. (2003) Viremia control despite escape from a rapid and potent autologous neutralizing antibody response after therapy cessation in an HIV-1-infected individual. J Immunol 170: 3906-3914.
16. Choisy M, Woelk CH, Guegan JF, Robertson DL (2004) Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. J Virol 78: 1962-1970.
17. Ohgimoto S, Shioda T, Mori K, Nakayama EE, Hu H, et al. (1998) Location-specific, unequal contribution of the N glycans in simian immunodeficiency virus gp120 to viral infectivity and removal of multiple glycans without disturbing infectivity. J Virol 72: 8365-8370.
18. Korber BTM, Farber RM, Wolpert DH, Lapedes AS (1993) Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: An information theoretic analysis. Proc Natl Acad Sci U S A 90: 7176-7180.
19. Neher E (1994) How frequent are correlated changes in families of protein sequences? Proc Natl Acad Sci U S A 91: 98-102.
20. Pollock DD, Taylor WR (1997) Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng 10: 647-657.
21. Robinson DM, Jones DT, Kishino H, Goldman N, Thorne JL (2003) Protein evolution with dependence among codons due to tertiary structure. Mol Biol Evol 20: 1692-1704.
22. Rodrigue N, Lartillot N, Bryant D, Philippe H (2005) Site interdependence attributed to tertiary structure in amino acid sequence evolution. Gene 347: 207-217.
23. Jensen JL, Pedersen AMK (2000) Probabilistic models of DNA sequence evolution with context dependent rates of substitution. Adv Appl Prob 32: 499-517.
24. Siepel A, Haussler D (2004) Phylogenetic estimation of context-dependent substitution rates by maximum likelihood. Mol Biol Evol 21: 468-488.
25. Lopez P, Casane D, Philippe H (2002) Heterotachy, an important process of protein evolution. Mol Biol Evol 19: 1-7.
26. Tuffley C, Steel M (1998) Modeling the covarion hypothesis of nucleotide substitution. Math Biosci 147: 63-91.
27. Huelsenbeck JP (2002) Testing a covariotide model of DNA substitution. Mol Biol Evol 19: 698-707.
28. Wright S (1921) Correlation and causation. J Agric Res 20: 557-585.
29. Pearl J (1988) Probabilistic reasoning in intelligent systems: Networks of plausible inference. San Mateo (California): Morgan Kaufmann. 552 p.
30. Friedman N, Linial M, Nachman I, Pe'er D (2000) Using Bayesian networks to analyze expression data. J Comp Biol 7: 601-620.
31. Korb KN, Nicholson AE (2003) Bayesian artificial intelligence. Chapman and Hall. 392 p.
32. Venables WN, Ripley BD (2002) Modern applied statistics. New York: Springer.
33. Kwong PD, Wyatt R, Robinson J, Sweet RW, Sodroski J, et al. (1998) Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 393: 648-659.
34. Blay WM, Gnanakaran S, Foley B, Doria-Rose NA, Korber BT, et al. (2006) Consistent patterns of change during the divergence of human immunodeficiency virus type 1 envelope from that of the inoculated virus in simian/human immunodeficiency virus-infected macaques. J Virol 80: 999-1014.
35. Reddy A, Gibbs BS, Liu YL, Coward JK, Changchien LM, et al. (1999) Glycosylation of the overlapping sequons in yeast external invertase: Effect of amino acid variation on site selectivity in vivo and in vitro. Glycobiology 9: 547-555.
36. Derdeyn CA, Decker JM, Bibollet-Ruche F, Mokili JL, Muldoon M, et al. (2004) Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science 303: 2019-2022.
37. Bohne-Lang A, von der Lieth CW (2005) Glyprot: In silico glycosylation of proteins. Nucleic Acids Res 33: W214-W219.
38. Hartley O, Klasse PJ, Sattentau QJ, Moore JP (2005) V3: HIV's switch-hitter. AIDS Res Hum Retrovir 21: 171-178.
39. Overbaugh J, Rudensey LM, Papenhausen MD, Benveniste RE, Morton WR (1991) Variation in simian immunodeficiency virus env is confined to V1 and V4 during progression to simian AIDS. J Virol 65: 7025-7031.
40. Hemming A, Bolmstedt A, Jansson B, Hansen JES, Travis B, et al. (1994) Identification of three N-linked glycans in the V4-V5 region of HIV-1 gp120, dispensable for CD4- binding and fusion activity of gp120. Arch Virol 134: 335-344.
41. Ren X, Sodroski J, Yang X (2005) An unrelated monoclonal antibody neutralizes human immunodeficiency virus type 1 by binding to an artificial epitope engineered in a functionally neutral region of viral envelope glycoproteins. J Virol 79: 5616-5624.
42. Edwards TG, Wyss S, Reeves JD, Zolla-Pazner S, Hoxie JA, et al. (2002) Truncation of the cytoplasmic domain induces exposure of conserved regions in the ectodomain of human immunodeficiency virus type 1 envelope protein. J Virol 76: 2683-2691.
43. Kalia V, Sarkar S, Gupta P, Montelaro RC (2005) Antibody neutralization escape mediated by point mutations in the intracytoplasmic tail of human immunodeficiency virus type 1 gp41. J Virol 79: 2097-2107.
44. Leitner T, Foley B, Hahn B, Marx P, McCutchan F, et al. (2003) HIV Sequence Compendium 2003. Los Alamos (New Mexico): Theoretical Biology and Biophysics Group.
45. Saitou N, Nei M (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
46. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10: 512-526.
47. Kosakovsky Pond SL, Frost SDW, Muse SV (2005) HyPhy: Hypothesis testing using phylogenies. Bioinformatics 21: 676-679.
48. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Royal Stat Soc B 57: 289-300.
49. Heckerman D, Geiger D, Chickering DM (1995) Learning Bayesian networks: The combination of knowledge and statistical data. Mach Learn 20: 197-243.
50. Cooper GF, Herskovits E (1992) A Bayesian method for the induction of probabilistic networks from data. Mach Learn 9: 309-347.
51. Friedman N, Koller D (2003) Being Bayesian about network structure. A Bayesian approach to structure discovery in Bayesian networks. Mach Learn 50: 95-125.
52. Altekar G, Dwarkadas S, Huelsenbeck JP, Ronquist F (2004) Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20: 407-415.
53. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF Chimera - A visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612.