PDBsum entry 2ny3

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Viral protein/immune system PDB id
Protein chains
305 a.a. *
181 a.a. *
214 a.a. *
223 a.a. *
NAG ×13
Waters ×665
* Residue conservation analysis
PDB id:
Name: Viral protein/immune system
Title: HIV-1 gp120 envelope glycoprotein (k231c, t257s, e267c, s334 complexed with cd4 and antibody 17b
Structure: Envelope glycoprotein gp120. Chain: a. Fragment: core. Engineered: yes. Mutation: yes. T-cell surface glycoprotein cd4. Chain: b. Fragment: d1d2, n-terminal two domain fragment. Synonym: t-cell surface antigen t4/leu-3.
Source: Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: hxbc2. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: embryonic cell line 293. Expression_system_organ: kidney. Homo sapiens. Human.
2.00Å     R-factor:   0.205     R-free:   0.243
Authors: T.Zhou,L.Xu,B.Dey,A.J.Hessell,D.Van Ryk,S.H.Xiang,X.Yang,M.Y M.B.Zwick,J.Arthos,D.R.Burton,D.S.Dimitrov,J.Sodroski,R.Wya G.J.Nabel,P.D.Kwong
Key ref:
T.Zhou et al. (2007). Structural definition of a conserved neutralization epitope on HIV-1 gp120. Nature, 445, 732-737. PubMed id: 17301785 DOI: 10.1038/nature05580
20-Nov-06     Release date:   06-Feb-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q993A8  (Q993A8_9HIV1) -  Envelope glycoprotein (Fragment)
588 a.a.
305 a.a.*
Protein chain
Pfam   ArchSchema ?
P01730  (CD4_HUMAN) -  T-cell surface glycoprotein CD4
458 a.a.
181 a.a.
Protein chain
Pfam   ArchSchema ?
Q6P5S8  (Q6P5S8_HUMAN) -  IGK@ protein
236 a.a.
214 a.a.*
Protein chain
Pfam   ArchSchema ?
Q6N030  (Q6N030_HUMAN) -  Putative uncharacterized protein DKFZp686I15212
518 a.a.
223 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 94 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     viral envelope   2 terms 
  Biological process     cell adhesion   1 term 


DOI no: 10.1038/nature05580 Nature 445:732-737 (2007)
PubMed id: 17301785  
Structural definition of a conserved neutralization epitope on HIV-1 gp120.
T.Zhou, L.Xu, B.Dey, A.J.Hessell, D.Van Ryk, S.H.Xiang, X.Yang, M.Y.Zhang, M.B.Zwick, J.Arthos, D.R.Burton, D.S.Dimitrov, J.Sodroski, R.Wyatt, G.J.Nabel, P.D.Kwong.
The remarkable diversity, glycosylation and conformational flexibility of the human immunodeficiency virus type 1 (HIV-1) envelope (Env), including substantial rearrangement of the gp120 glycoprotein upon binding the CD4 receptor, allow it to evade antibody-mediated neutralization. Despite this complexity, the HIV-1 Env must retain conserved determinants that mediate CD4 binding. To evaluate how these determinants might provide opportunities for antibody recognition, we created variants of gp120 stabilized in the CD4-bound state, assessed binding of CD4 and of receptor-binding-site antibodies, and determined the structure at 2.3 A resolution of the broadly neutralizing antibody b12 in complex with gp120. b12 binds to a conformationally invariant surface that overlaps a distinct subset of the CD4-binding site. This surface is involved in the metastable attachment of CD4, before the gp120 rearrangement required for stable engagement. A site of vulnerability, related to a functional requirement for efficient association with CD4, can therefore be targeted by antibody to neutralize HIV-1.
  Selected figure(s)  
Figure 2.
Figure 2: Conformational states of gp120. The unliganded, b12- and CD4-bound conformations of gp120 are depicted, with polypeptide in ribbon representation and disordered regions as dashed lines. Inner domains are grey, outer domains are red and regions that in the CD4-bound state correspond to the bridging sheet are blue. Both b12- and CD4-bound conformations are of the Ds12 F123 variant of HIV-1, whereas the unliganded structure is of simian immunodeficiency virus (SIV). Comparison of these three gp120 conformations highlights not only the structural plasticity of the inner domain and bridging sheet, but also the conformational stability of the outer domain.
Figure 4.
Figure 4: Structural definition of a conformationally invariant, antibody-accessible portion of the CD4-binding site. The b12- and CD4-bound conformations of gp120 are shown in ribbon representation, after superposition of outer domains (red). A semitransparent molecular surface shows the contact surfaces of b12 (green) and CD4 (yellow). Subsets of these surfaces, corresponding to regions of conformational flexibility (for example, of the inner domain (grey) or bridging sheet (blue)), are delineated, as are regions of b12 contact outside of the conserved CD4-binding site. As can be seen, functional analysis serves to transcend the particulars of b12 binding, whereas antibody defines accessibility. Although we have formally shown only the b12 contact surface to be accessible in the context of a functional viral spike, the highly effective neutralization of D1D2-Ig tp and the kinetics of its association with both core and OD1 variants of gp120 suggest that the CD4-binding surface on the outer domain is accessible.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 445, 732-737) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23007571 P.C.Wilson, and S.F.Andrews (2012).
Tools to therapeutically harness the human antibody response.
  Nat Rev Immunol, 12, 709-719.  
22864288 Y.Mao, L.Wang, C.Gu, A.Herschhorn, S.H.Xiang, H.Haim, X.Yang, and J.Sodroski (2012).
Subunit organization of the membrane-bound HIV-1 envelope glycoprotein trimer.
  Nat Struct Mol Biol, 19, 893-899.  
21117239 A.Emileh, and C.F.Abrams (2011).
A mechanism by which binding of the broadly neutralizing antibody b12 unfolds the inner domain α1 helix in an engineered HIV-1 gp120.
  Proteins, 79, 537-546.  
21288305 A.Schön, N.Madani, A.B.Smith, J.M.Lalonde, and E.Freire (2011).
Some binding-related drug properties are dependent on thermodynamic signature.
  Chem Biol Drug Des, 77, 161-165.  
21112250 B.F.Haynes, M.A.Moody, H.X.Liao, L.Verkoczy, and G.D.Tomaras (2011).
B cell responses to HIV-1 infection and vaccination: pathways to preventing infection.
  Trends Mol Med, 17, 108-116.  
21206085 B.Hong, X.T.Song, L.Rollins, L.Berry, X.F.Huang, and S.Y.Chen (2011).
Mucosal and systemic anti-HIV immunity controlled by A20 in mouse dendritic cells.
  J Clin Invest, 121, 739-751.  
21468932 B.Wei, N.Han, H.Z.Liu, A.Rayner, and S.Rayner (2011).
Use of mutual information arrays to predict coevolving sites in the full length HIV gp120 protein for subtypes B and C.
  Virol Sin, 26, 95.  
21357743 C.R.Ruprecht, A.Krarup, L.Reynell, A.M.Mann, O.F.Brandenberg, L.Berlinger, I.A.Abela, R.R.Regoes, H.F.Günthard, P.Rusert, and A.Trkola (2011).
MPER-specific antibodies induce gp120 shedding and irreversibly neutralize HIV-1.
  J Exp Med, 208, 439-454.  
21479208 F.Breden, C.Lepik, N.S.Longo, M.Montero, P.E.Lipsky, and J.K.Scott (2011).
Comparison of antibody repertoires produced by HIV-1 infection, other chronic and acute infections, and systemic autoimmune disease.
  PLoS One, 6, e16857.  
21383973 F.Nawaz, C.Cicala, D.Van Ryk, K.E.Block, K.Jelicic, J.P.McNally, O.Ogundare, M.Pascuccio, N.Patel, D.Wei, A.S.Fauci, and J.Arthos (2011).
The genotype of early-transmitting HIV gp120s promotes α₄β₇-reactivity, revealing α₄β₇CD4+ T cells as key targets in mucosal transmission.
  PLoS Pathog, 7, e1001301.  
21253014 F.Wegmann, G.Krashias, K.Lühn, K.Laamanen, S.Vieira, S.A.Jeffs, R.J.Shattock, and Q.J.Sattentau (2011).
A novel strategy for inducing enhanced mucosal HIV-1 antibody responses in an anti-inflammatory environment.
  PLoS One, 6, e15861.  
21283793 H.Barroso, P.Borrego, I.Bártolo, J.M.Marcelino, C.Família, A.Quintas, and N.Taveira (2011).
Evolutionary and structural features of the C2, V3 and C3 envelope regions underlying the differences in HIV-1 and HIV-2 biology and infection.
  PLoS One, 6, e14548.  
22113616 J.S.McLellan, M.Pancera, C.Carrico, J.Gorman, J.P.Julien, R.Khayat, R.Louder, R.Pejchal, M.Sastry, K.Dai, S.O'Dell, N.Patel, S.Shahzad-ul-Hussan, Y.Yang, B.Zhang, T.Zhou, J.Zhu, J.C.Boyington, G.Y.Chuang, D.Diwanji, I.Georgiev, Y.D.Kwon, D.Lee, M.K.Louder, S.Moquin, S.D.Schmidt, Z.Y.Yang, M.Bonsignori, J.A.Crump, S.H.Kapiga, N.E.Sam, B.F.Haynes, D.R.Burton, W.C.Koff, L.M.Walker, S.Phogat, R.Wyatt, J.Orwenyo, L.X.Wang, J.Arthos, C.A.Bewley, J.R.Mascola, G.J.Nabel, W.R.Schief, A.B.Ward, I.A.Wilson, and P.D.Kwong (2011).
Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9.
  Nature, 480, 336-343.
PDB codes: 3tcl 3u1s 3u2s 3u36 3u46 3u4b 3u4e
  21465559 L.T.Da, J.M.Quan, and Y.D.Wu (2011).
Understanding the binding mode and function of BMS-488043 against HIV-1 viral entry.
  Proteins, 79, 1810-1819.  
21377881 M.Caffrey (2011).
HIV envelope: challenges and opportunities for development of entry inhibitors.
  Trends Microbiol, 19, 191-197.  
22002224 M.Kim, Z.Y.Sun, K.D.Rand, X.Shi, L.Song, Y.Cheng, A.F.Fahmy, S.Majumdar, G.Ofek, Y.Yang, P.D.Kwong, J.H.Wang, J.R.Engen, G.Wagner, and E.L.Reinherz (2011).
Antibody mechanics on a membrane-bound HIV segment essential for GP41-targeted viral neutralization.
  Nat Struct Mol Biol, 18, 1235-1243.  
22139037 S.Moir, A.Malaspina, and A.S.Fauci (2011).
Prospects for an HIV vaccine: leading B cells down the right path.
  Nat Struct Mol Biol, 18, 1317-1321.  
20227370 A.Finzi, S.H.Xiang, B.Pacheco, L.Wang, J.Haight, A.Kassa, B.Danek, M.Pancera, P.D.Kwong, and J.Sodroski (2010).
Topological layers in the HIV-1 gp120 inner domain regulate gp41 interaction and CD4-triggered conformational transitions.
  Mol Cell, 37, 656-667.  
20463957 A.Hinz, D.Lutje Hulsik, A.Forsman, W.W.Koh, H.Belrhali, A.Gorlani, Haard, R.A.Weiss, T.Verrips, and W.Weissenhorn (2010).
Crystal structure of the neutralizing Llama V(HH) D7 and its mode of HIV-1 gp120 interaction.
  PLoS One, 5, e10482.
PDB code: 2xa3
20232097 A.Malik, A.Firoz, V.Jha, E.Sunderasan, and S.Ahmad (2010).
Modeling the three-dimensional structures of an unbound single-chain variable fragment (scFv) and its hypothetical complex with a Corynespora cassiicola toxin, cassiicolin.
  J Mol Model, 16, 1883-1893.  
19922969 A.Nandi, C.L.Lavine, P.Wang, I.Lipchina, P.A.Goepfert, G.M.Shaw, G.D.Tomaras, D.C.Montefiori, B.F.Haynes, P.Easterbrook, J.E.Robinson, J.G.Sodroski, and X.Yang (2010).
Epitopes for broad and potent neutralizing antibody responses during chronic infection with human immunodeficiency virus type 1.
  Virology, 396, 339-348.  
20826338 B.E.Correia, Y.E.Ban, M.A.Holmes, H.Xu, K.Ellingson, Z.Kraft, C.Carrico, E.Boni, D.N.Sather, C.Zenobia, K.Y.Burke, T.Bradley-Hewitt, J.F.Bruhn-Johannsen, O.Kalyuzhniy, D.Baker, R.K.Strong, L.Stamatatos, and W.R.Schief (2010).
Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope.
  Structure, 18, 1116-1126.
PDB codes: 3lef 3lf6 3lf9 3lg7 3lh2 3lhp
19939935 B.Yu, D.P.Fonseca, S.M.O'Rourke, and P.W.Berman (2010).
Protease cleavage sites in HIV-1 gp120 recognized by antigen processing enzymes are conserved and located at receptor binding sites.
  J Virol, 84, 1513-1526.  
20194785 C.F.Abrams, and E.Vanden-Eijnden (2010).
Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics.
  Proc Natl Acad Sci U S A, 107, 4961-4966.  
20059334 D.H.Barouch, and B.Korber (2010).
HIV-1 vaccine development after STEP.
  Annu Rev Med, 61, 153-167.  
20705840 D.R.Burton, and R.A.Weiss (2010).
AIDS/HIV. A boost for HIV vaccine design.
  Science, 329, 770-773.  
19829304 D.S.Nikolic, and V.Piguet (2010).
Vaccines and microbicides preventing HIV-1, HSV-2, and HPV mucosal transmission.
  J Invest Dermatol, 130, 352-361.  
20053822 E.M.Bunnik, M.J.van Gils, M.S.Lobbrecht, L.Pisas, N.M.Nanlohy, D.van Baarle, A.C.van Nuenen, A.J.Hessell, and H.Schuitemaker (2010).
Emergence of monoclonal antibody b12-resistant human immunodeficiency virus type 1 variants during natural infection in the absence of humoral or cellular immune pressure.
  J Gen Virol, 91, 1354-1364.  
20376006 G.F.Schröder, M.Levitt, and A.T.Brunger (2010).
Super-resolution biomolecular crystallography with low-resolution data.
  Nature, 464, 1218-1222.  
20042512 G.Ofek, K.McKee, Y.Yang, Z.Y.Yang, J.Skinner, F.J.Guenaga, R.Wyatt, M.B.Zwick, G.J.Nabel, J.R.Mascola, and P.D.Kwong (2010).
Relationship between antibody 2F5 neutralization of HIV-1 and hydrophobicity of its heavy chain third complementarity-determining region.
  J Virol, 84, 2955-2962.  
20441761 G.Scarabelli, G.Morra, and G.Colombo (2010).
Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping.
  Biophys J, 98, 1966-1975.  
20052405 H.C.Kelker, V.R.Itri, and F.T.Valentine (2010).
A strategy for eliciting antibodies against cryptic, conserved, conformationally dependent epitopes of HIV envelope glycoprotein.
  PLoS One, 5, e8555.  
19955308 I.Douagi, M.N.Forsell, C.Sundling, S.O'Dell, Y.Feng, P.Dosenovic, Y.Li, R.Seder, K.Loré, J.R.Mascola, R.T.Wyatt, and G.B.Karlsson Hedestam (2010).
Influence of novel CD4 binding-defective HIV-1 envelope glycoprotein immunogens on neutralizing antibody and T-cell responses in nonhuman primates.
  J Virol, 84, 1683-1695.  
20718047 I.Shrivastava, and J.M.LaLonde (2010).
Fluctuation dynamics analysis of gp120 envelope protein reveals a topologically based communication network.
  Proteins, 78, 2935-2949.  
19824826 J.A.Hoxie (2010).
Toward an antibody-based HIV-1 vaccine.
  Annu Rev Med, 61, 135-152.  
20888479 J.Liu, E.R.Wright, and H.Winkler (2010).
3D visualization of HIV virions by cryoelectron tomography.
  Methods Enzymol, 483, 267-290.  
20335257 J.M.Binley, Y.E.Ban, E.T.Crooks, D.Eggink, K.Osawa, W.R.Schief, and R.W.Sanders (2010).
Role of complex carbohydrates in human immunodeficiency virus type 1 infection and resistance to antibody neutralization.
  J Virol, 84, 5637-5655.  
20147404 J.P.Julien, N.Huarte, R.Maeso, S.G.Taneva, A.Cunningham, J.L.Nieva, and E.F.Pai (2010).
Ablation of the complementarity-determining region H3 apex of the anti-HIV-1 broadly neutralizing antibody 2F5 abrogates neutralizing capacity without affecting core epitope binding.
  J Virol, 84, 4136-4147.  
20679402 J.Pietzsch, J.F.Scheid, H.Mouquet, F.Klein, M.S.Seaman, M.Jankovic, D.Corti, A.Lanzavecchia, and M.C.Nussenzweig (2010).
Human anti-HIV-neutralizing antibodies frequently target a conserved epitope essential for viral fitness.
  J Exp Med, 207, 1995-2002.  
20192810 J.R.Mascola, and D.C.Montefiori (2010).
The role of antibodies in HIV vaccines.
  Annu Rev Immunol, 28, 413-444.  
20523901 J.S.Klein, and P.J.Bjorkman (2010).
Few and far between: how HIV may be evading antibody avidity.
  PLoS Pathog, 6, e1000908.  
  20981030 K.H.Huang, D.Bonsall, A.Katzourakis, E.C.Thomson, S.J.Fidler, J.Main, D.Muir, J.N.Weber, A.J.Frater, R.E.Phillips, O.G.Pybus, P.J.Goulder, M.O.McClure, G.S.Cooke, and P.Klenerman (2010).
B-cell depletion reveals a role for antibodies in the control of chronic HIV-1 infection.
  Nat Commun, 1, 102.  
20702629 K.J.Doores, Z.Fulton, M.Huber, I.A.Wilson, and D.R.Burton (2010).
Antibody 2G12 recognizes di-mannose equivalently in domain- and nondomain-exchanged forms but only binds the HIV-1 glycan shield if domain exchanged.
  J Virol, 84, 10690-10699.
PDB code: 3oau
20852065 K.J.Doores, Z.Fulton, V.Hong, M.K.Patel, C.N.Scanlan, M.R.Wormald, M.G.Finn, D.R.Burton, I.A.Wilson, and B.G.Davis (2010).
A nonself sugar mimic of the HIV glycan shield shows enhanced antigenicity.
  Proc Natl Acad Sci U S A, 107, 17107-17112.
PDB codes: 3oay 3oaz 3ob0
  21267356 L.J.Gamble, and Q.L.Matthews (2010).
Current progress in the development of a prophylactic vaccine for HIV-1.
  Drug Des Devel Ther, 5, 9.  
20660185 L.Kong, C.C.Huang, S.J.Coales, K.S.Molnar, J.Skinner, Y.Hamuro, and P.D.Kwong (2010).
Local conformational stability of HIV-1 gp120 in unliganded and CD4-bound states as defined by amide hydrogen/deuterium exchange.
  J Virol, 84, 10311-10321.  
20299194 L.M.Walker, and D.R.Burton (2010).
Rational antibody-based HIV-1 vaccine design: current approaches and future directions.
  Curr Opin Immunol, 22, 358-366.  
20018688 L.Verkoczy, M.Diaz, T.M.Holl, Y.B.Ouyang, H.Bouton-Verville, S.M.Alam, H.X.Liao, G.Kelsoe, and B.F.Haynes (2010).
Autoreactivity in an HIV-1 broadly reactive neutralizing antibody variable region heavy chain induces immunologic tolerance.
  Proc Natl Acad Sci U S A, 107, 181-186.  
20845361 M.Hertje, M.Zhou, and U.Dietrich (2010).
Inhibition of HIV-1 entry: multiple keys to close the door.
  ChemMedChem, 5, 1825-1835.  
20610714 M.J.Duenas-Decamp, and P.R.Clapham (2010).
HIV-1 gp120 determinants proximal to the CD4 binding site shift protective glycans that are targeted by monoclonal antibody 2G12.
  J Virol, 84, 9608-9612.  
20210752 M.L.Bellows, and C.A.Floudas (2010).
Computational methods for de novo protein design and its applications to the human immunodeficiency virus 1, purine nucleoside phosphorylase, ubiquitin specific protease 7, and histone demethylases.
  Curr Drug Targets, 11, 264-278.  
20538861 M.Pancera, J.S.McLellan, X.Wu, J.Zhu, A.Changela, S.D.Schmidt, Y.Yang, T.Zhou, S.Phogat, J.R.Mascola, and P.D.Kwong (2010).
Crystal structure of PG16 and chimeric dissection with somatically related PG9: structure-function analysis of two quaternary-specific antibodies that effectively neutralize HIV-1.
  J Virol, 84, 8098-8110.
PDB codes: 3lrs 3mme
20080564 M.Pancera, S.Majeed, Y.E.Ban, L.Chen, C.C.Huang, L.Kong, Y.D.Kwon, J.Stuckey, T.Zhou, J.E.Robinson, W.R.Schief, J.Sodroski, R.Wyatt, and P.D.Kwong (2010).
Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility.
  Proc Natl Acad Sci U S A, 107, 1166-1171.
PDB codes: 3jwd 3jwo
20439465 M.Raska, K.Takahashi, L.Czernekova, K.Zachova, S.Hall, Z.Moldoveanu, M.C.Elliott, L.Wilson, R.Brown, D.Jancova, S.Barnes, J.Vrbkova, M.Tomana, P.D.Smith, J.Mestecky, M.B.Renfrow, and J.Novak (2010).
Glycosylation patterns of HIV-1 gp120 depend on the type of expressing cells and affect antibody recognition.
  J Biol Chem, 285, 20860-20869.  
  20923574 M.Wen, R.Arora, H.Wang, L.Liu, J.T.Kimata, and P.Zhou (2010).
GPI-anchored single chain Fv--an effective way to capture transiently-exposed neutralization epitopes on HIV-1 envelope spike.
  Retrovirology, 7, 79.  
20164234 P.Utachee, S.Nakamura, P.Isarangkura-Na-Ayuthaya, K.Tokunaga, P.Sawanpanyalert, K.Ikuta, W.Auwanit, and M.Kameoka (2010).
Two N-linked glycosylation sites in the V2 and C2 regions of human immunodeficiency virus type 1 CRF01_AE envelope glycoprotein gp120 regulate viral neutralization susceptibility to the human monoclonal antibody specific for the CD4 binding domain.
  J Virol, 84, 4311-4320.  
  20168075 P.W.Hammond (2010).
Accessing the human repertoire for broadly neutralizing HIV antibodies.
  MAbs, 2, 157-164.  
20463081 P.Wang, and X.Yang (2010).
Neutralization efficiency is greatly enhanced by bivalent binding of an antibody to epitopes in the V4 region and the membrane-proximal external region within one trimer of human immunodeficiency virus type 1 glycoproteins.
  J Virol, 84, 7114-7123.  
  21173880 Q.J.Sattentau, and A.J.McMichael (2010).
New templates for HIV-1 antibody-based vaccine design.
  F1000 Biol Rep, 2, 60.  
20357769 R.Diskin, P.M.Marcovecchio, and P.J.Bjorkman (2010).
Structure of a clade C HIV-1 gp120 bound to CD4 and CD4-induced antibody reveals anti-CD4 polyreactivity.
  Nat Struct Mol Biol, 17, 608-613.
PDB codes: 3lmj 3lqa
20534513 R.Pejchal, L.M.Walker, R.L.Stanfield, S.K.Phogat, W.C.Koff, P.Poignard, D.R.Burton, and I.A.Wilson (2010).
Structure and function of broadly reactive antibody PG16 reveal an H3 subdomain that mediates potent neutralization of HIV-1.
  Proc Natl Acad Sci U S A, 107, 11483-11488.
PDB codes: 3mug 3muh
  20860805 R.Ringe, M.Thakar, and J.Bhattacharya (2010).
Variations in autologous neutralization and CD4 dependence of b12 resistant HIV-1 clade C env clones obtained at different time points from antiretroviral naïve Indian patients with recent infection.
  Retrovirology, 7, 76.  
20949103 S.Gnanakaran, M.G.Daniels, T.Bhattacharya, A.S.Lapedes, A.Sethi, M.Li, H.Tang, K.Greene, H.Gao, B.F.Haynes, M.S.Cohen, G.M.Shaw, M.S.Seaman, A.Kumar, F.Gao, D.C.Montefiori, and B.Korber (2010).
Genetic signatures in the envelope glycoproteins of HIV-1 that associate with broadly neutralizing antibodies.
  PLoS Comput Biol, 6, e1000955.  
20089638 S.H.Xiang, A.Finzi, B.Pacheco, K.Alexander, W.Yuan, C.Rizzuto, C.C.Huang, P.D.Kwong, and J.Sodroski (2010).
A V3 loop-dependent gp120 element disrupted by CD4 binding stabilizes the human immunodeficiency virus envelope glycoprotein trimer.
  J Virol, 84, 3147-3161.  
20518719 S.Hearty, P.J.Conroy, B.V.Ayyar, B.Byrne, and R.O'Kennedy (2010).
Surface plasmon resonance for vaccine design and efficacy studies: recent applications and future trends.
  Expert Rev Vaccines, 9, 645-664.  
20822346 S.Paul, S.Planque, Y.Nishiyama, M.Escobar, and C.Hanson (2010).
Back to the future: covalent epitope-based HIV vaccine development.
  Expert Rev Vaccines, 9, 1027-1043.  
20186035 S.Planque, M.Salas, Y.Mitsuda, M.Sienczyk, M.A.Escobar, J.P.Mooney, M.K.Morris, Y.Nishiyama, D.Ghosh, A.Kumar, F.Gao, C.V.Hanson, and S.Paul (2010).
Neutralization of genetically diverse HIV-1 strains by IgA antibodies to the gp120-CD4-binding site from long-term survivors of HIV infection.
  AIDS, 24, 875-884.  
20956336 S.R.Wu, R.Löving, B.Lindqvist, H.Hebert, P.J.Koeck, M.Sjöberg, and H.Garoff (2010).
Single-particle cryoelectron microscopy analysis reveals the HIV-1 spike as a tripod structure.
  Proc Natl Acad Sci U S A, 107, 18844-18849.  
20577269 S.Zolla-Pazner, and T.Cardozo (2010).
Structure-function relationships of HIV-1 envelope sequence-variable regions refocus vaccine design.
  Nat Rev Immunol, 10, 527-535.  
21203482 T.A.White, A.Bartesaghi, M.J.Borgnia, J.R.Meyerson, la Cruz, J.W.Bess, R.Nandwani, J.A.Hoxie, J.D.Lifson, J.L.Milne, and S.Subramaniam (2010).
Molecular architectures of trimeric SIV and HIV-1 envelope glycoproteins on intact viruses: strain-dependent variation in quaternary structure.
  PLoS Pathog, 6, e1001249.  
20616231 T.Zhou, I.Georgiev, X.Wu, Z.Y.Yang, K.Dai, A.Finzi, Y.D.Kwon, J.F.Scheid, W.Shi, L.Xu, Y.Yang, J.Zhu, M.C.Nussenzweig, J.Sodroski, L.Shapiro, G.J.Nabel, J.R.Mascola, and P.D.Kwong (2010).
Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01.
  Science, 329, 811-817.
PDB code: 3ngb
20653424 V.V.Khrustalev (2010).
Levels of HIV1 gp120 3D B-cell epitopes mutability and variability: searching for possible vaccine epitopes.
  Immunol Invest, 39, 551-569.  
20484560 W.W.Koh, A.Forsman, S.Hué, G.J.van der Velden, D.L.Yirrell, A.McKnight, R.A.Weiss, and M.M.Aasa-Chapman (2010).
Novel subtype C human immunodeficiency virus type 1 envelopes cloned directly from plasma: coreceptor usage and neutralization phenotypes.
  J Gen Virol, 91, 2374-2380.  
20400507 W.W.Koh, S.Steffensen, M.Gonzalez-Pajuelo, B.Hoorelbeke, A.Gorlani, A.Szynol, A.Forsman, M.M.Aasa-Chapman, Haard, T.Verrips, and R.A.Weiss (2010).
Generation of a family-specific phage library of llama single chain antibody fragments that neutralize HIV-1.
  J Biol Chem, 285, 19116-19124.  
20622876 X.Jiang, V.Burke, M.Totrov, C.Williams, T.Cardozo, M.K.Gorny, S.Zolla-Pazner, and X.P.Kong (2010).
Conserved structural elements in the V3 crown of HIV-1 gp120.
  Nat Struct Mol Biol, 17, 955-961.
PDB codes: 3go1 3mlr 3mls 3mlt 3mlu 3mlv 3mlw 3mlx 3mly 3mlz
20616233 X.Wu, Z.Y.Yang, Y.Li, C.M.Hogerkorp, W.R.Schief, M.S.Seaman, T.Zhou, S.D.Schmidt, L.Wu, L.Xu, N.S.Longo, K.McKee, S.O'Dell, M.K.Louder, D.L.Wycuff, Y.Feng, M.Nason, N.Doria-Rose, M.Connors, P.D.Kwong, M.Roederer, R.T.Wyatt, G.J.Nabel, and J.R.Mascola (2010).
Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1.
  Science, 329, 856-861.  
19424134 A.Bhattacharya (2009).
Protein structures: Structures of desire.
  Nature, 459, 24-27.  
19412542 A.Cagigi, L.Du, L.V.Dang, S.Grutzmeier, A.Atlas, F.Chiodi, Q.Pan-Hammarström, and A.Nilsson (2009).
CD27(-) B-cells produce class switched and somatically hyper-mutated antibodies during chronic HIV-1 infection.
  PLoS ONE, 4, e5427.  
19525965 A.J.Hessell, P.Poignard, M.Hunter, L.Hangartner, D.M.Tehrani, W.K.Bleeker, P.W.Parren, P.A.Marx, and D.R.Burton (2009).
Effective, low-titer antibody protection against low-dose repeated mucosal SHIV challenge in macaques.
  Nat Med, 15, 951-954.  
19004960 A.Mörner, I.Douagi, M.N.Forsell, C.Sundling, P.Dosenovic, S.O'Dell, B.Dey, P.D.Kwong, G.Voss, R.Thorstensson, J.R.Mascola, R.T.Wyatt, and G.B.Karlsson Hedestam (2009).
Human immunodeficiency virus type 1 env trimer immunization of macaques and impact of priming with viral vector or stabilized core protein.
  J Virol, 83, 540-551.  
19103601 A.Mascioni, B.E.Bentley, R.Camarda, D.A.Dilts, P.Fink, V.Gusarova, S.K.Hoiseth, J.Jacob, S.L.Lin, K.Malakian, L.K.McNeil, T.Mininni, F.Moy, E.Murphy, E.Novikova, S.Sigethy, Y.Wen, G.W.Zlotnick, and D.H.Tsao (2009).
Structural Basis for the Immunogenic Properties of the Meningococcal Vaccine Candidate LP2086.
  J Biol Chem, 284, 8738-8746.
PDB code: 2kdy
19801669 A.Shulla, and T.Gallagher (2009).
Role of spike protein endodomains in regulating coronavirus entry.
  J Biol Chem, 284, 32725-32734.  
19478876 B.Dey, K.Svehla, L.Xu, D.Wycuff, T.Zhou, G.Voss, A.Phogat, B.K.Chakrabarti, Y.Li, G.Shaw, P.D.Kwong, G.J.Nabel, J.R.Mascola, and R.T.Wyatt (2009).
Structure-based stabilization of HIV-1 gp120 enhances humoral immune responses to the induced co-receptor binding site.
  PLoS Pathog, 5, e1000445.  
19729849 C.D.Rinaudo, J.L.Telford, R.Rappuoli, and K.L.Seib (2009).
Vaccinology in the genome era.
  J Clin Invest, 119, 2515-2525.  
19361425 C.E.Leysath, A.F.Monzingo, J.A.Maynard, J.Barnett, G.Georgiou, B.L.Iverson, and J.D.Robertus (2009).
Crystal structure of the engineered neutralizing antibody M18 complexed to domain 4 of the anthrax protective antigen.
  J Mol Biol, 387, 680-693.
PDB codes: 3esu 3esv 3et9 3etb
19251591 D.C.Ekiert, G.Bhabha, M.A.Elsliger, R.H.Friesen, M.Jongeneelen, M.Throsby, J.Goudsmit, and I.A.Wilson (2009).
Antibody recognition of a highly conserved influenza virus epitope.
  Science, 324, 246-251.
PDB codes: 3gbm 3gbn
19610667 E.P.Go, Q.Chang, H.X.Liao, L.L.Sutherland, S.M.Alam, B.F.Haynes, and H.Desaire (2009).
Glycosylation site-specific analysis of clade C HIV-1 envelope proteins.
  J Proteome Res, 8, 4231-4242.  
19553335 E.S.Gray, N.Taylor, D.Wycuff, P.L.Moore, G.D.Tomaras, C.K.Wibmer, A.Puren, A.DeCamp, P.B.Gilbert, B.Wood, D.C.Montefiori, J.M.Binley, G.M.Shaw, B.F.Haynes, J.R.Mascola, and L.Morris (2009).
Antibody specificities associated with neutralization breadth in plasma from human immunodeficiency virus type 1 subtype C-infected blood donors.
  J Virol, 83, 8925-8937.  
  19146663 F.Canducci, M.C.Marinozzi, M.Sampaolo, S.Berre, P.Bagnarelli, M.Degano, G.Gallotta, B.Mazzi, P.Lemey, R.Burioni, and M.Clementi (2009).
Dynamic features of the selective pressure on the human immunodeficiency virus type 1 (HIV-1) gp120 CD4-binding site in a group of long term non progressor (LTNP) subjects.
  Retrovirology, 6, 4.  
19343205 H.Haim, Z.Si, N.Madani, L.Wang, J.R.Courter, A.Princiotto, A.Kassa, M.DeGrace, K.McGee-Estrada, M.Mefford, D.Gabuzda, A.B.Smith, and J.Sodroski (2009).
Soluble CD4 and CD4-mimetic compounds inhibit HIV-1 infection by induction of a short-lived activated state.
  PLoS Pathog, 5, e1000360.  
19414790 H.Li, C.F.Xu, S.Blais, Q.Wan, H.T.Zhang, S.J.Landry, and C.E.Hioe (2009).
Proximal glycans outside of the epitopes regulate the presentation of HIV-1 envelope gp120 helper epitopes.
  J Immunol, 182, 6369-6378.  
18922866 I.Bontjer, A.Land, D.Eggink, E.Verkade, K.Tuin, C.Baldwin, G.Pollakis, W.A.Paxton, I.Braakman, B.Berkhout, and R.W.Sanders (2009).
Optimization of human immunodeficiency virus type 1 envelope glycoproteins with V1/V2 deleted, using virus evolution.
  J Virol, 83, 368-383.  
19287373 J.F.Scheid, H.Mouquet, N.Feldhahn, M.S.Seaman, K.Velinzon, J.Pietzsch, R.G.Ott, R.M.Anthony, H.Zebroski, A.Hurley, A.Phogat, B.Chakrabarti, Y.Li, M.Connors, F.Pereyra, B.D.Walker, H.Wardemann, D.Ho, R.T.Wyatt, J.R.Mascola, J.V.Ravetch, and M.C.Nussenzweig (2009).
Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals.
  Nature, 458, 636-640.  
19019969 K.L.Davis, F.Bibollet-Ruche, H.Li, J.M.Decker, O.Kutsch, L.Morris, A.Salomon, A.Pinter, J.A.Hoxie, B.H.Hahn, P.D.Kwong, and G.M.Shaw (2009).
Human immunodeficiency virus type 2 (HIV-2)/HIV-1 envelope chimeras detect high titers of broadly reactive HIV-1 V3-specific antibodies in human plasma.
  J Virol, 83, 1240-1259.  
19855822 K.L.Seib, G.Dougan, and R.Rappuoli (2009).
The key role of genomics in modern vaccine and drug design for emerging infectious diseases.
  PLoS Genet, 5, e1000612.  
19193800 K.M.Nolan, G.Q.Del Prete, A.P.Jordan, B.Haggarty, J.Romano, G.J.Leslie, and J.A.Hoxie (2009).
Characterization of a human immunodeficiency virus type 1 V3 deletion mutation that confers resistance to CCR5 inhibitors and the ability to use aplaviroc-bound receptor.
  J Virol, 83, 3798-3809.  
19785005 K.R.Clark, and S.T.Walsh (2009).
Crystal structure of a 3B3 variant-A broadly neutralizing HIV-1 scFv antibody.
  Protein Sci, 18, 2429-2441.
PDB code: 3juy
19965434 L.Chen, Y.Do Kwon, T.Zhou, X.Wu, S.O'Dell, L.Cavacini, A.J.Hessell, M.Pancera, M.Tang, L.Xu, Z.Y.Yang, M.Y.Zhang, J.Arthos, D.R.Burton, D.S.Dimitrov, G.J.Nabel, M.R.Posner, J.Sodroski, R.Wyatt, J.R.Mascola, and P.D.Kwong (2009).
Structural Basis of Immune Evasion at the Site of CD4 Attachment on HIV-1 gp120.
  Science, 326, 1123-1127.
PDB codes: 3hi1 3idx 3idy
19264769 L.Wu, T.Zhou, Z.Y.Yang, K.Svehla, S.O'Dell, M.K.Louder, L.Xu, J.R.Mascola, D.R.Burton, J.A.Hoxie, R.W.Doms, P.D.Kwong, and G.J.Nabel (2009).
Enhanced exposure of the CD4-binding site to neutralizing antibodies by structural design of a membrane-anchored human immunodeficiency virus type 1 gp120 domain.
  J Virol, 83, 5077-5086.  
19439467 M.D.Simek, W.Rida, F.H.Priddy, P.Pung, E.Carrow, D.S.Laufer, J.K.Lehrman, M.Boaz, T.Tarragona-Fiol, G.Miiro, J.Birungi, A.Pozniak, D.A.McPhee, O.Manigart, E.Karita, A.Inwoley, W.Jaoko, J.Dehovitz, L.G.Bekker, P.Pitisuttithum, R.Paris, L.M.Walker, P.Poignard, T.Wrin, P.E.Fast, D.R.Burton, and W.C.Koff (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.  
19121325 M.L.Bissonnette, J.E.Donald, W.F.DeGrado, T.S.Jardetzky, and R.A.Lamb (2009).
Functional analysis of the transmembrane domain in paramyxovirus F protein-mediated membrane fusion.
  J Mol Biol, 386, 14-36.  
19019970 N.B.Siddappa, R.Song, V.G.Kramer, A.L.Chenine, V.Velu, H.Ong, R.A.Rasmussen, R.D.Grisson, C.Wood, H.Zhang, C.Kankasa, R.R.Amara, J.G.Else, F.J.Novembre, D.C.Montefiori, and R.M.Ruprecht (2009).
Neutralization-sensitive R5-tropic simian-human immunodeficiency virus SHIV-2873Nip, which carries env isolated from an infant with a recent HIV clade C infection.
  J Virol, 83, 1422-1432.  
19448659 P.D.Kwong, and I.A.Wilson (2009).
HIV-1 and influenza antibodies: seeing antigens in new ways.
  Nat Immunol, 10, 573-578.  
20048698 P.L.Moore, E.S.Gray, and L.Morris (2009).
Specificity of the autologous neutralizing antibody response.
  Curr Opin HIV AIDS, 4, 358-363.  
19216624 P.Prabakaran, Z.Zhu, X.Xiao, A.Biragyn, A.S.Dimitrov, C.C.Broder, and D.S.Dimitrov (2009).
Potent human monoclonal antibodies against SARS CoV, Nipah and Hendra viruses.
  Expert Opin Biol Ther, 9, 355-368.  
  19619305 R.L.Dunfee, E.R.Thomas, and D.Gabuzda (2009).
Enhanced macrophage tropism of HIV in brain and lymphoid tissues is associated with sensitivity to the broadly neutralizing CD4 binding site antibody b12.
  Retrovirology, 6, 69.  
19747994 R.M.Curran, L.Donnelly, R.J.Morrow, C.Fraser, G.Andrews, M.Cranage, R.K.Malcolm, R.J.Shattock, and A.D.Woolfson (2009).
Vaginal delivery of the recombinant HIV-1 clade-C trimeric gp140 envelope protein CN54gp140 within novel rheologically structured vehicles elicits specific immune responses.
  Vaccine, 27, 6791-6798.  
19327047 R.M.Lynch, T.Shen, S.Gnanakaran, and C.A.Derdeyn (2009).
Appreciating HIV type 1 diversity: subtype differences in Env.
  AIDS Res Hum Retroviruses, 25, 237-248.  
19515770 R.Pejchal, J.S.Gach, F.M.Brunel, R.M.Cardoso, R.L.Stanfield, P.E.Dawson, D.R.Burton, M.B.Zwick, and I.A.Wilson (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.
PDB code: 3fn0
19763269 R.Rong, B.Li, R.M.Lynch, R.E.Haaland, M.K.Murphy, J.Mulenga, S.A.Allen, A.Pinter, G.M.Shaw, E.Hunter, J.E.Robinson, S.Gnanakaran, and C.A.Derdeyn (2009).
Escape from autologous neutralizing antibodies in acute/early subtype C HIV-1 infection requires multiple pathways.
  PLoS Pathog, 5, e1000594.  
19740978 S.Bryson, J.P.Julien, R.C.Hynes, and E.F.Pai (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, 11862-11875.
PDB codes: 1u8h 1u8i 1u8j 1u8l 1u8m 1u8n 1u8o 1u8p 1u8q 1u91 1u92 1u93 1u95 2f5a 2f5b 2pw1 2pw2 3idg 3idi 3idj 3idm 3idn
19258452 S.Li, H.Wang, B.Peng, M.Zhang, D.Zhang, S.Hou, Y.Guo, and J.Ding (2009).
Efalizumab binding to the LFA-1 alphaL I domain blocks ICAM-1 binding via steric hindrance.
  Proc Natl Acad Sci U S A, 106, 4349-4354.
PDB codes: 3eo9 3eoa 3eob
19474108 S.M.O'Rourke, B.Schweighardt, W.G.Scott, T.Wrin, D.P.Fonseca, F.Sinangil, and P.W.Berman (2009).
Novel ring structure in the gp41 trimer of human immunodeficiency virus type 1 that modulates sensitivity and resistance to broadly neutralizing antibodies.
  J Virol, 83, 7728-7738.  
19432534 S.Pervaiz, and A.L.Holme (2009).
Resveratrol: its biologic targets and functional activity.
  Antioxid Redox Signal, 11, 2851-2897.  
19167740 S.S.Kulkarni, A.Lapedes, H.Tang, S.Gnanakaran, M.G.Daniels, M.Zhang, T.Bhattacharya, M.Li, V.R.Polonis, F.E.McCutchan, L.Morris, D.Ellenberger, S.T.Butera, R.C.Bollinger, B.T.Korber, R.S.Paranjape, and D.C.Montefiori (2009).
Highly complex neutralization determinants on a monophyletic lineage of newly transmitted subtype C HIV-1 Env clones from India.
  Virology, 385, 505-520.  
  20140073 S.S.Negi, and W.Braun (2009).
Automated detection of conformational epitopes using phage display Peptide sequences.
  Bioinform Biol Insights, 3, 71-81.  
19692465 X.Wu, T.Zhou, S.O'Dell, R.T.Wyatt, P.D.Kwong, and J.R.Mascola (2009).
Mechanism of human immunodeficiency virus type 1 resistance to monoclonal antibody B12 that effectively targets the site of CD4 attachment.
  J Virol, 83, 10892-10907.  
19726674 Y.Nishiyama, S.Planque, Y.Mitsuda, G.Nitti, H.Taguchi, L.Jin, J.Symersky, S.Boivin, M.Sienczyk, M.Salas, C.V.Hanson, and S.Paul (2009).
Toward effective HIV vaccination: induction of binary epitope reactive antibodies with broad HIV neutralizing activity.
  J Biol Chem, 284, 30627-30642.  
18645585 A.E.Armitage, A.J.McMichael, and H.Drakesmith (2008).
Reflecting on a quarter century of HIV research.
  Nat Immunol, 9, 823-826.  
18842738 A.Forsman, E.Beirnaert, M.M.Aasa-Chapman, B.Hoorelbeke, K.Hijazi, W.Koh, V.Tack, A.Szynol, C.Kelly, A.McKnight, T.Verrips, Haard, and R.A.Weiss (2008).
Llama antibody fragments with cross-subtype human immunodeficiency virus type 1 (HIV-1)-neutralizing properties and high affinity for HIV-1 gp120.
  J Virol, 82, 12069-12081.  
18765264 B.M.Chain, M.Noursadeghi, M.Gardener, J.Tsang, and E.Wright (2008).
HIV blocking antibodies following immunisation with chimaeric peptides coding a short N-terminal sequence of the CCR5 receptor.
  Vaccine, 26, 5752-5759.  
18177204 C.A.Blish, M.A.Nguyen, and J.Overbaugh (2008).
Enhancing exposure of HIV-1 neutralization epitopes through mutations in gp41.
  PLoS Med, 5, e9.  
18068724 C.H.Bell, R.Pantophlet, A.Schiefner, L.A.Cavacini, R.L.Stanfield, D.R.Burton, and I.A.Wilson (2008).
Structure of antibody F425-B4e8 in complex with a V3 peptide reveals a new binding mode for HIV-1 neutralization.
  J Mol Biol, 375, 969-978.
PDB code: 2qsc
18833271 D.H.Barouch (2008).
Challenges in the development of an HIV-1 vaccine.
  Nature, 455, 613-619.  
18493671 D.S.Dalpathado, and H.Desaire (2008).
Glycopeptide analysis by mass spectrometry.
  Analyst, 133, 731-738.  
18761662 E.Scherer, D.Douek, and A.McMichael (2008).
25 years of HIV research on virology, virus restriction, immunopathogenesis, genes and vaccines.
  Clin Exp Immunol, 154, 6.  
18539308 E.T.Crooks, P.Jiang, M.Franti, S.Wong, M.B.Zwick, J.A.Hoxie, J.E.Robinson, P.L.Moore, and J.M.Binley (2008).
Relationship of HIV-1 and SIV envelope glycoprotein trimer occupation and neutralization.
  Virology, 377, 364-378.  
18197170 G.B.Karlsson Hedestam, R.A.Fouchier, S.Phogat, D.R.Burton, J.Sodroski, and R.T.Wyatt (2008).
The challenges of eliciting neutralizing antibodies to HIV-1 and to influenza virus.
  Nat Rev Microbiol, 6, 143-155.  
18322015 G.Frey, H.Peng, S.Rits-Volloch, M.Morelli, Y.Cheng, and B.Chen (2008).
A fusion-intermediate state of HIV-1 gp41 targeted by broadly neutralizing antibodies.
  Proc Natl Acad Sci U S A, 105, 3739-3744.  
18835005 G.Martin, Y.Sun, B.Heyd, O.Combes, J.B.Ulmer, A.Descours, S.W.Barnett, I.K.Srivastava, and L.Martin (2008).
A simple one-step method for the preparation of HIV-1 envelope glycoprotein immunogens based on a CD4 mimic peptide.
  Virology, 381, 241-250.  
18796729 H.Chen, X.Xu, H.H.Lin, S.H.Chen, A.Forsman, M.Aasa-Chapman, and I.M.Jones (2008).
Mapping the immune response to the outer domain of a human immunodeficiency virus-1 clade C gp120.
  J Gen Virol, 89, 2597-2604.  
18264102 J.Arthos, C.Cicala, E.Martinelli, K.Macleod, D.Van Ryk, D.Wei, Z.Xiao, T.D.Veenstra, T.P.Conrad, R.A.Lempicki, S.McLaughlin, M.Pascuccio, R.Gopaul, J.McNally, C.C.Cruz, N.Censoplano, E.Chung, K.N.Reitano, S.Kottilil, D.J.Goode, and A.S.Fauci (2008).
HIV-1 envelope protein binds to and signals through integrin alpha4beta7, the gut mucosal homing receptor for peripheral T cells.
  Nat Immunol, 9, 301-309.  
18499210 J.D.Nelson, H.Kinkead, F.M.Brunel, D.Leaman, R.Jensen, J.M.Louis, T.Maruyama, C.A.Bewley, K.Bowdish, G.M.Clore, P.E.Dawson, S.Frederickson, R.G.Mage, D.D.Richman, D.R.Burton, and M.B.Zwick (2008).
Antibody elicited against the gp41 N-heptad repeat (NHR) coiled-coil can neutralize HIV-1 with modest potency but non-neutralizing antibodies also bind to NHR mimetics.
  Virology, 377, 170-183.  
18668044 J.Liu, A.Bartesaghi, M.J.Borgnia, G.Sapiro, and S.Subramaniam (2008).
Molecular architecture of native HIV-1 gp120 trimers.
  Nature, 455, 109-113.
PDB codes: 3dnl 3dnn 3dno
18250627 K.U.Wendt, M.S.Weiss, P.Cramer, and D.W.Heinz (2008).
Structures and diseases.
  Nat Struct Mol Biol, 15, 117-120.  
19081789 M.Humbert, R.A.Rasmussen, H.Ong, F.M.Kaiser, S.L.Hu, and R.M.Ruprecht (2008).
Inducing cross-clade neutralizing antibodies against HIV-1 by immunofocusing.
  PLoS ONE, 3, e3937.  
18385254 M.J.Duenas-Decamp, P.Peters, D.Burton, and P.R.Clapham (2008).
Natural resistance of human immunodeficiency virus type 1 to the CD4bs antibody b12 conferred by a glycan and an arginine residue close to the CD4 binding loop.
  J Virol, 82, 5807-5814.  
18054978 M.L.Visciano, M.Tuen, M.K.Gorny, and C.E.Hioe (2008).
In vivo alteration of humoral responses to HIV-1 envelope glycoprotein gp120 by antibodies to the CD4-binding site of gp120.
  Virology, 372, 409-420.  
  18638381 M.L.Visciano, M.Tuen, P.D.Chen, and C.E.Hioe (2008).
Antibodies to the CD4-binding site of HIV-1 gp120 suppress gp120-specific CD4 T cell response while enhancing antibody response.
  Infect Agent Cancer, 3, 11.  
18577455 M.Law, and L.Hangartner (2008).
Antibodies against viruses: passive and active immunization.
  Curr Opin Immunol, 20, 486-492.  
18322034 M.Montero, N.E.van Houten, X.Wang, and J.K.Scott (2008).
The membrane-proximal external region of the human immunodeficiency virus type 1 envelope: dominant site of antibody neutralization and target for vaccine design.
  Microbiol Mol Biol Rev, 72, 54.  
18495775 M.Vaine, S.Wang, E.T.Crooks, P.Jiang, D.C.Montefiori, J.Binley, and S.Lu (2008).
Improved induction of antibodies against key neutralizing epitopes by human immunodeficiency virus type 1 gp120 DNA prime-protein boost vaccination compared to gp120 protein-only vaccination.
  J Virol, 82, 7369-7378.  
18481899 N.Kaushik-Basu, A.Basu, and D.Harris (2008).
Peptide inhibition of HIV-1: current status and future potential.
  BioDrugs, 22, 161-175.  
  18205925 P.J.Peters, M.J.Duenas-Decamp, W.M.Sullivan, R.Brown, C.Ankghuambom, K.Luzuriaga, J.Robinson, D.R.Burton, J.Bell, P.Simmonds, J.Ball, and P.R.Clapham (2008).
Variation in HIV-1 R5 macrophage-tropism correlates with sensitivity to reagents that block envelope: CD4 interactions but not with sensitivity to other entry inhibitors.
  Retrovirology, 5, 5.  
18057243 P.L.Moore, E.S.Gray, I.A.Choge, N.Ranchobe, K.Mlisana, S.S.Abdool Karim, C.Williamson, and L.Morris (2008).
The c3-v4 region is a major target of autologous neutralizing antibodies in human immunodeficiency virus type 1 subtype C infection.
  J Virol, 82, 1860-1869.  
18923648 R.Burioni, N.Mancini, D.De Marco, N.Clementi, M.Perotti, G.Nitti, M.Sassi, F.Canducci, K.Shvela, P.Bagnarelli, J.R.Mascola, and M.Clementi (2008).
Anti-HIV-1 response elicited in rabbits by anti-idiotype monoclonal antibodies mimicking the CD4-binding site.
  PLoS ONE, 3, e3423.  
18822440 R.Pantophlet, T.Wrin, L.A.Cavacini, J.E.Robinson, and D.R.Burton (2008).
Neutralizing activity of antibodies to the V3 loop region of HIV-1 gp120 relative to their epitope fine specificity.
  Virology, 381, 251-260.  
  18237398 R.W.Sanders, E.van Anken, A.A.Nabatov, I.M.Liscaljet, I.Bontjer, D.Eggink, M.Melchers, E.Busser, M.M.Dankers, F.Groot, I.Braakman, B.Berkhout, and W.A.Paxton (2008).
The carbohydrate at asparagine 386 on HIV-1 gp120 is not essential for protein folding and function but is involved in immune evasion.
  Retrovirology, 5, 10.  
18753405 R.W.Sanders, S.T.Hsu, E.van Anken, I.M.Liscaljet, M.Dankers, I.Bontjer, A.Land, I.Braakman, A.M.Bonvin, and B.Berkhout (2008).
Evolution rescues folding of human immunodeficiency virus-1 envelope glycoprotein GP120 lacking a conserved disulfide bond.
  Mol Biol Cell, 19, 4707-4716.  
18284327 S.Selvarajah, B.A.Puffer, F.H.Lee, P.Zhu, Y.Li, R.Wyatt, K.H.Roux, R.W.Doms, and D.R.Burton (2008).
Focused dampening of antibody response to the immunodominant variable loops by engineered soluble gp140.
  AIDS Res Hum Retroviruses, 24, 301-314.  
18480460 S.Tasca, S.H.Ho, and C.Cheng-Mayer (2008).
R5X4 viruses are evolutionary, functional, and antigenic intermediates in the pathway of a simian-human immunodeficiency virus coreceptor switch.
  J Virol, 82, 7089-7099.  
18964020 S.Willey, and M.M.Aasa-Chapman (2008).
Humoral immunity to HIV-1: neutralisation and antibody effector functions.
  Trends Microbiol, 16, 596-604.  
17805298 A.J.Hessell, L.Hangartner, M.Hunter, C.E.Havenith, F.J.Beurskens, J.M.Bakker, C.M.Lanigan, G.Landucci, D.N.Forthal, P.W.Parren, P.A.Marx, and D.R.Burton (2007).
Fc receptor but not complement binding is important in antibody protection against HIV.
  Nature, 449, 101-104.  
17360741 B.Dey, M.Pancera, K.Svehla, Y.Shu, S.H.Xiang, J.Vainshtein, Y.Li, J.Sodroski, P.D.Kwong, J.R.Mascola, and R.Wyatt (2007).
Characterization of human immunodeficiency virus type 1 monomeric and trimeric gp120 glycoproteins stabilized in the CD4-bound state: antigenicity, biophysics, and immunogenicity.
  J Virol, 81, 5579-5593.  
17931104 C.Maplanka (2007).
AIDS: is there an answer to the global pandemic? The immune system in HIV infection and control.
  Viral Immunol, 20, 331-342.  
17460665 C.N.Scanlan, J.Offer, N.Zitzmann, and R.A.Dwek (2007).
Exploiting the defensive sugars of HIV-1 for drug and vaccine design.
  Nature, 446, 1038-1045.  
17566740 D.Eggink, M.Melchers, and R.W.Sanders (2007).
Antibodies to HIV-1: aiming at the right target.
  Trends Microbiol, 15, 291-294.  
18052607 D.Montefiori, Q.Sattentau, J.Flores, J.Esparza, and J.Mascola (2007).
Antibody-based HIV-1 vaccines: recent developments and future directions.
  PLoS Med, 4, e348.  
17427229 E.M.Bublil, N.T.Freund, I.Mayrose, O.Penn, A.Roitburd-Berman, N.D.Rubinstein, T.Pupko, and J.M.Gershoni (2007).
Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm.
  Proteins, 68, 294-304.  
17634239 E.S.Gray, P.L.Moore, R.A.Pantophlet, and L.Morris (2007).
N-linked glycan modifications in gp120 of human immunodeficiency virus type 1 subtype C render partial sensitivity to 2G12 antibody neutralization.
  J Virol, 81, 10769-10776.  
17571457 G.J.Nabel (2007).
Mapping the future of HIV vaccines.
  Nat Rev Microbiol, 5, 482-484.  
  17509143 H.Chen, X.Xu, and I.M.Jones (2007).
Immunogenicity of the outer domain of a HIV-1 clade C gp120.
  Retrovirology, 4, 33.  
17803292 H.Xie, D.Ng, S.N.Savinov, B.Dey, P.D.Kwong, R.Wyatt, A.B.Smith, and W.A.Hendrickson (2007).
Structure-activity relationships in the binding of chemically derivatized CD4 to gp120 from human immunodeficiency virus.
  J Med Chem, 50, 4898-4908.  
17598811 J.Albert, F.Chiodi, and E.M.Fenyö (2007).
Introduction: HIV neutralizing antibodies: relevance to pathogenesis and vaccines.
  J Intern Med, 262, 2-4.  
  18076768 J.Sterjovski, M.J.Churchill, A.Ellett, L.R.Gray, M.J.Roche, R.L.Dunfee, D.F.Purcell, N.Saksena, B.Wang, S.Sonza, S.L.Wesselingh, I.Karlsson, E.M.Fenyo, D.Gabuzda, A.L.Cunningham, and P.R.Gorry (2007).
Asn 362 in gp120 contributes to enhanced fusogenicity by CCR5-restricted HIV-1 envelope glycoprotein variants from patients with AIDS.
  Retrovirology, 4, 89.  
17786227 K.Honey (2007).
Winning or losing: where are we in the fight against HIV and AIDS?
  J Clin Invest, 117, 2348.  
17722977 M.M.Laakso, F.H.Lee, B.Haggarty, C.Agrawal, K.M.Nolan, M.Biscone, J.Romano, A.P.Jordan, G.J.Leslie, E.G.Meissner, L.Su, J.A.Hoxie, and R.W.Doms (2007).
V3 loop truncations in HIV-1 envelope impart resistance to coreceptor inhibitors and enhanced sensitivity to neutralizing antibodies.
  PLoS Pathog, 3, e117.  
17599380 R.L.Dunfee, E.R.Thomas, J.Wang, K.Kunstman, S.M.Wolinsky, and D.Gabuzda (2007).
Loss of the N-linked glycosylation site at position 386 in the HIV envelope V4 region enhances macrophage tropism and is associated with dementia.
  Virology, 367, 222-234.  
18066025 R.Rappuoli (2007).
Bridging the knowledge gaps in vaccine design.
  Nat Biotechnol, 25, 1361-1366.  
17907342 R.Rappuoli (2007).
An audience with... Rino Rappuoli.
  Nat Rev Drug Discov, 6, 694.  
17542747 S.K.Phogat, S.M.Kaminsky, and W.C.Koff (2007).
HIV-1 rational vaccine design: molecular details of b12-gp120 complex structure.
  Expert Rev Vaccines, 6, 319-321.  
17598813 S.Phogat, R.T.Wyatt, and G.B.Karlsson Hedestam (2007).
Inhibition of HIV-1 entry by antibodies: potential viral and cellular targets.
  J Intern Med, 262, 26-43.  
17517649 S.W.Chi, C.Y.Maeng, S.J.Kim, M.S.Oh, C.J.Ryu, S.J.Kim, K.H.Han, H.J.Hong, and S.E.Ryu (2007).
Broadly neutralizing anti-hepatitis B virus antibody reveals a complementarity determining region H3 lid-opening mechanism.
  Proc Natl Acad Sci U S A, 104, 9230-9235.
PDB codes: 2eh7 2eh8
17721546 Y.Li, S.A.Migueles, B.Welcher, K.Svehla, A.Phogat, M.K.Louder, X.Wu, G.M.Shaw, M.Connors, R.T.Wyatt, and J.R.Mascola (2007).
Broad HIV-1 neutralization mediated by CD4-binding site antibodies.
  Nat Med, 13, 1032-1034.  
17728243 Y.Nishiyama, Y.Mitsuda, H.Taguchi, S.Planque, M.Salas, C.V.Hanson, and S.Paul (2007).
Towards covalent vaccination: improved polyclonal HIV neutralizing antibody response induced by an electrophilic gp120 V3 peptide analog.
  J Biol Chem, 282, 31250-31256.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.