Citation: Klein JS, Bjorkman PJ (2010) Few and Far Between: How HIV May Be Evading Antibody Avidity. PLoS Pathog 6(5): e1000908. doi:10.1371/journal.ppat.1000908
Editor: Glenn F. Rall, The Fox Chase Cancer Center, United States of America
Published: May 27, 2010
Copyright: © 2010 Klein, Bjorkman. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was conducted with support from the Bill & Melinda Gates Foundation Collaboration for AIDS Vaccine Discovery (www.cavd.org) and the Grand Challenges in Global Health Initiative (www.grandchallenges.org). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
HIV-1 Consistently Evades the Humoral Immune Response
More than 25 years have passed since the discovery of HIV type 1, the causative agent of AIDS, and the first vaccine candidate to exhibit evidence for protection against infection was reported only recently . However, the extent and mode of protection are still under debate . Thus, a vaccine that effectively stimulates complete protective immunity by the cellular branch (cytotoxic T lymphocytes) and/or the humoral branch (antibodies) of the immune system has yet to emerge. Among the millions of people who have received treatment for the disease and the many more who have tested HIV positive, there exists no definitive case in which a potent neutralizing antibody response enabled an infected individual to successfully clear or control the infection. In a small percentage of cases, individuals will exhibit a natural ability to suppress viral replication and progression of the disease. However, the explanation for the existence of this rare phenotype has primarily converged on a robust cellular immune response, with evidence generally lacking for a significant contribution to viral control by antibodies –.
Structural features of the HIV envelope spike are critical to its unusual ability to escape neutralizing antibodies. However, many of the identified features are not unique to this virus. Here, we propose another strategy HIV employs to evade antibodies: the low density of envelope spikes, a distinguishing feature when compared with viruses to which protective neutralizing antibody responses are consistently raised, directly impedes bivalent binding by immunoglobulin G (IgG) antibodies. The result is a minimization of avidity, normally used by antibodies to achieve high affinity binding and potent neutralization, thereby expanding the range of mutations that allow HIV to evade antibodies. Understanding limitations to avidity may be essential to the design of anti-HIV vaccines and therapies.
The HIV Spike Structure and Its Rapid Mutation Facilitate Antibody Evasion
Tremendous effort has been devoted to understanding why HIV so effectively evades antibodies. Accepted explanations include rapid mutation of the two glycoproteins that comprise the envelope spike, gp120 and gp41, and structural features that enable the spike to hide conserved epitopes from antibodies. These structural features include a shield of host-derived carbohydrates , conformational masking , steric occlusion , the protection of conserved regions at interfaces by oligomerization or in narrow pockets –, and the presence of highly variable flexible loops that shield conserved epitopes on the envelope spike , . In addition, it was recently hypothesized that a lack of germline genes capable of maturing into potent anti-HIV antibodies may represent holes in the potential antibody repertoire .
While the importance of the envelope spike's structural attributes to limiting antibody potency are well established, they are not unique to HIV. For example, the receptor binding sites of both rhinovirus and influenza are narrow pockets predicted to be inaccessible to antibodies , and mutation, loop decoys, and glycan shielding have all been implicated in antibody evasion by influenza , . Nevertheless, these viruses and many others and/or the vaccines that have been developed against them elicit potent neutralizing antibody responses that significantly contribute to their clearance or provide sterilizing immunity .
What distinguishes HIV from other viruses in relation to antibody-mediated neutralization? Is it simply that HIV is more adept at employing the evasion strategies outlined above? While it is clear that HIV is superbly adapted for evading antibodies based on these strategies (as described in recent reviews , ), we propose an additional contributing factor in its ability to escape neutralization by antibodies , which is based on recent data that describe the spatial arrangement of spikes on its surface. The reasoning is rooted in an inherent limitation to the architecture of an antibody as it relates to avidity, which in this context refers to the ability of a bivalent antibody to simultaneously bind two epitopes tethered to the same surface . We begin with comparisons of available neutralization data and the spatial arrangements of envelope spikes for HIV and other viruses, then present a discussion of avidity and the factors that influence it, and end with speculations on how a greater understanding of the factors that aid or inhibit avidity might be used to further inform vaccine design.
Comparison of Monovalent and Bivalent Binding of Antibodies to Viruses
Most of the neutralizing activity in the sera of HIV-positive individuals can be attributed to antibodies of the IgG subclass , , which represent the predominant class of immunoglobulin in blood. IgG antibodies are composed of an Fc region fused to two identical Fabs (Figure 1). Antigens bind to the tip of each Fab, which present the unique surfaces that define the epitope specificity of the antibody. While the immune system can draw from an almost unlimited sequence library to change the specificity of the Fabs, the antibody architecture is relatively constant, including the range of permissible end-to-end distances between the Fabs. The Fabs are linked to the Fc region by a flexible hinge, which typically allows a 10–15-nm center-to-center separation between the antigen-binding sites of the two Fabs for IgGs.
Red denotes the locations of antigen recognition sites. A longer than typical separation distance (17 nm) was reported for the structure of intact b12 IgG . The longer distance resulted in part from an unusually long CDR3 loop protruding from the antigen-combining site of each Fab. As this loop wraps around the CD4-binding loop on gp120 , the effective separation distance on this IgG and other antibodies with protruding CDR3 loops would be ∼15 nm.
In the context of antibodies, the term avidity refers to their ability to bind two physically linked antigens simultaneously (e.g., to the surface of the same virus). The result of avidity can be a dramatic increase in the strength of the binding as compared to a monovalent 1∶1 interaction such that once bound, the antibody interaction with antigen becomes essentially irreversible over biologically relevant time scales . Antibodies have been shown to bind bivalently to non enveloped viruses such as rhinovirus and poliovirus, which contain a rigid icosahedrally symmetric outer protein shell with closely spaced epitopes. Thus, rhinovirus and poliovirus saturate with 30 IgGs bound via both Fabs to 60 repeating epitopes created by 30 2-fold symmetry axes , . An early demonstration of the importance of avidity in IgG binding to poliovirus revealed that using papain to digest the antibody and create monovalent Fabs led to a substantial increase in the molar concentration required to inhibit infection in vitro . By contrast, a limited role for avidity in neutralization of HIV by some antibodies is suggested by the relatively modest increases in neutralization potencies of IgGs as compared to their corresponding Fabs –. In addition, conversion of the broadly neutralizing anti-HIV antibodies 2F5 and 4E10 from IgGs with two combining sites to dimeric IgA (four Fabs) and/or pentameric IgM (ten Fabs) either did not improve their neutralization efficiencies or abrogated activity altogether , . Similarly, we have observed equivalent neutralization potencies for the anti-HIV antibody b12 when tested as an IgA, IgM, or IgG (P. Gnanapragasm, R. Galimidi, J. Klein, A. West, Jr., and P. Bjorkman, unpublished data).
One way to quantitatively assess the effects of antibody avidity is to compare the neutralization potency values of a Fab and its parental IgG. We define the molar neutralization ratio (MNR) as the concentration in an in vitro neutralization assay at which a Fab achieves 50% inhibition of viral infectivity (IC50) divided by the IC50 for the parental IgG. If an antibody binds only monovalently to the viral surface (i.e., it is incapable of cross-linking epitopes on the virus), it would inhibit at an approximately 2-fold lower concentration than the Fab (MNR = 2) because the IgG has twice the number of antigen-binding sites . MNRs greater than 2 suggest avidity effects resulting from the IgG cross-linking epitopes on the virus. Results from published studies show high MNRs for respiratory syncytial virus (RSV)  and influenza ,  (Figure 2), suggesting that antibodies can take advantage of avidity effects to bind to enveloped viruses. However, a compilation of the highest reported MNRs we could find for antibodies against HIV – shows that neutralizing antibodies, including those that serve as models for the types of antibodies that researchers would most like to elicit with an HIV vaccine, yield relatively low MNRs (Figure 2). This suggests a general limitation to bivalent binding of IgGs to HIV. We propose that the spatial distribution of envelope spikes on HIV, combined with the distribution of protein epitopes on the spike trimer, explains the predominantly monovalent binding of anti-HIV antibodies, which in turn limits the ability of the humoral immune response to prevent viral escape by mutation.
MNRs were reported for monoclonal antibodies against HIV , , , RSV , and influenza , . The MNR for each antibody was calculated as the IC50 of the Fab divided by the IC50 of the IgG derived from in vitro neutralization assays (IC90s were reported for some influenza IgG/Fab comparisons , but IC50 ratios would be nearly the same because the slopes of the inhibition curves were similar). MNRs for a particular IgG/Fab combination can vary with the strain of virus being tested because the degree to which cross-linking can benefit an IgG depends on the affinity of the Fab for its antigen. Differences in size between a Fab and IgG may also influence the MNR if steric factors play a role in the neutralization mechanism of a particular antibody. However, this effect is probably minor, as (Fab)′2 fragments generally exhibit similar neutralization potencies to their parental IgGs , . Not shown are high MNR values (∼70) derived for IgG/Fab comparisons involving HIV virions with a gp41 cytoplasmic tail truncation . The tail deletion, which is rarely observed in vivo, has been suggested to increase the mobility of envelope trimers  and/or increase the number of spikes per virion , so its effects on intra-spike cross-linking are not well understood.
HIV Envelope Spikes Are Present at Low Density
Enveloped viruses such as HIV contain an outer shell composed of a cell-derived lipid membrane displaying embedded antigens that were acquired during budding from the host cell. Consequently, enveloped viruses generally lack the structural elements of non-enveloped viruses that enforce a symmetric arrangement of antigens in non-enveloped viruses. Electron micrographs of enveloped viruses for which antibody-mediated neutralization is known to be critical to the control and/or elimination of infection ,  generally reveal a high density of envelope spikes. For example, influenza type A virus incorporates ∼450 spikes per virus particle spaced at intervals ≤10 nm  (Figure 3A). Similarly, measles, RSV, and hepatitis B virions include large numbers of closely spaced spikes (Figure 3B–3D). Indeed, the high densities of repetitive, identical epitopes on the surfaces of non-enveloped icosahedral viruses and enveloped viruses such as vesticular stomatitis, rabies, influenza, and Sindbis allow induction of T cell–independent B cell activation during the elicitation of the humoral immune response . In striking contrast, biochemical studies and cryo-electron tomography (cryo-ET) reconstructions showed that HIV, although similar in size to influenza type A, has an average of ∼14 spikes per virus particle (the full range from published studies is four to 35 spikes) – (Figure 3E). Despite the dearth of envelope spikes, HIV remains infectious, as it has been shown that as few as four spikes are sufficient for viral attachment , and possibly fewer may be needed to achieve fusion with the target cell membrane , .
(A) Influenza type A virus. Image provided by Drs. Masashi Yamaguchi and Kuniaki Nagayama. (B) Measles virus. Image reproduced with permission from Dr. Shmuel Rozenblatt from http://www.tau.ac.il/lifesci/departments/biotech/members/rozenblatt/figures.html. (C) RSV (image credit: US Centers for Disease Control and Prevention). (D) Hepatitis B virus. Image provided by Drs. Kelly Dryden and Mark Yeager. (E) HIV type 1. Image provided by Drs. Ping Zhu and Kenneth Roux. See also . Many schematic pictures of HIV in textbooks and on Web sites show more spikes per virion. Some of these figures were based on early electron micrographs of a mutant simian immunodeficiency virus containing a higher number of spikes per viral particle . Others were based on the incorrect assumption that HIV exhibits icosahedral symmetry. (F) Distribution of nearest neighbor distances between HIV spikes derived from cryo-ET analyses of 40 HIV virions. Data were taken from . Although some spike clustering was reported , the virions exhibited a large distribution of nearest neighbor distances between spikes (7–80 nm center to center).
Low Spike Density and Spike Structure Impede Bivalent Binding by IgGs to HIV
What are the consequences of the low number of envelope spikes on HIV virions to antibody binding? Cryo-ET studies of HIV particles allowed an analysis of nearest neighbor distances between individual spikes, revealing that the low number of envelope spikes also translates to a low spike surface density. Thus, the majority of nearest neighbor distances fall outside of the range of the two Fabs of an IgG  (Figure 3F) as previously predicted , leaving a minority of HIV envelope spikes available for cross-linking by a bivalent antibody. Inter-spike cross-linking might still be possible if spikes were able to freely diffuse within the viral membrane, but analyses of cryo-ET data  and evidence for interactions between the cytoplasmic tail of gp41 and the matrix protein of HIV ,  suggest that the arrangement of spikes on a virus particle is likely to be static over time periods relevant to neutralization.
Cross-linking within a spike trimer (intra-spike cross-linking) represents another way to achieve bivalent binding of an IgG. However, cryo-ET structures of HIV spike trimers bound to Fabs  and molecular modeling based on crystal structures ,  suggest that bivalent binding within a single trimeric spike is also unlikely, at least for antibodies directed against gp41 or the CD4-binding site of gp120. Therefore, most anti-HIV antibodies probably bind only one epitope per spike. Anti-carbohydrate antibodies may be an interesting exception: since a single spike subunit contains many carbohydrate attachment sites, an anti-carbohydrate antibody can bind using both Fabs to adjacent carbohydrate sites within a spike monomer. Although antibodies that recognize viral carbohydrates are rare because viral carbohydrates are usually non-immunogenic, one broadly neutralizing antibody against HIV, IgG 2G12, presents its two Fabs as a single domain-swapped structure that recognizes a constellation of viral carbohydrates within gp120  and appears to be unusually effective in conferring protection against infection in vivo . A naturally occurring dimeric form of IgG 2G12 composed of four Fabs and two Fcs was recently found to exhibit a 100- to 160-fold average increased molar neutralization potency over its monomeric form, with an increase of ≥500-fold against seven of the 21 strains tested , suggesting an enhanced ability to cross-link carbohydrate epitopes on a single envelope spike. Another exception might be represented by a new class of highly potent and broadly neutralizing anti-HIV antibodies, which include PG9 and PG16 . The location of the proposed epitope for these antibodies, at the top of the envelope spike, might allow both Fabs of a single IgG to bind the same spike trimer.
How Avidity Can Enhance Antibody Potency: A Theoretical Examination
The affinity of a monomeric Fab, given by the equilibrium dissociation constant (KD), is equal to the dissociation rate constant (koff), divided by the association rate constant (kon). Overall, avidity manifests as an increase in the observed affinity of an IgG (a decrease in the KD) when binding two tethered antigens such that saturation of a surface can be achieved at lower concentrations as compared to a monovalent Fab. The affinity increase is mostly due to a reduction in the observed dissociation rate for the IgG such that binding to antigen becomes virtually irreversible over time scales relevant to the lifetime of a pathogen . The effects of avidity on the affinity of an antibody can be modeled as a two-step reaction involving one antibody molecule and two epitopes tethered to the same surface (Figure 4A). After becoming tethered to its target through the first Fab, the small reaction volume of the second forward reaction serves to increase the second reaction rate , but this second binding step can only occur if the second binding site lies within the volume that is accessible to the free Fab arm. A corollary of the model for avidity is that the potency of a neutralizing IgG that can bind bivalently to two epitopes simultaneously on the same surface of a pathogen will primarily depend on the magnitude of kon. In contrast, the potency of a Fab or an IgG that binds monovalently will depend on the magnitudes of both the kon and the koff.
(A) Schematic of the step-wise bivalent binding model of an IgG to two envelope spikes (Ag, antigen) tethered to the same surface (kon, association rate constant; koff, dissociation rate constant; kon*, enhanced association rate constant resulting from the small reaction volume of Reaction 2). (B) Comparison of the effect of the Fab dissociation rate constant (koff) on the neutralization potency of Fab (left) and IgG (right) variants of palivizumab, a monoclonal antibody against RSV. Adapted from Table 1 in . The names of the Fab/IgG pairs were changed to A–G for clarity. A, AFFFd; B, AFFYd; C, AFSFd; D, AFFGd; E, W100F; F, S32A; G, wild type (see  for an explanation of mutant nomenclature). Note that these results suggest that high affinity Fabs with slow dissociation rates (e.g., Fabs selected by techniques such as phage display) may not exhibit increased neutralization potencies, particularly against a densely packed virus, when converted to bivalent IgGs.
The predicted insensitivity of an IgG to changes in koff under conditions permissible to bivalent binding was demonstrated for palivizumab, a monoclonal antibody directed against RSV , an enveloped virus with a high spike density (Figure 3C). A comparison of neutralization potencies of Fabs and their parental IgGs for a library of antibody variants derived from palivizumab demonstrated that mutations that decreased koff did not change the potency of the corresponding IgG but did increase the neutralization potency of the Fab  (Figure 4B). Furthermore, as predicted by avidity effects, mutations that increased kon served to increase the neutralization potencies of both the Fab and the IgG . Thus, for cases in which efficiently cross-linking the surface of a virus is likely (e.g., RSV or influenza), an antibody can maintain a relatively unchanged neutralization potency even as the virus accumulates mutations that increase its koff. However, in cases in which efficient cross-linking is unlikely (e.g., HIV), the virus can escape antibody-mediated neutralization with mutations that weaken either rate constant, resulting in a virus that can more easily escape the humoral immune system during the course of an infection.
How Understanding Limitations to Avidity Can Inform the Design of Anti-HIV Vaccines and Therapies
The vertebrate immune system is remarkable in its ability to respond to and clear infections. Unfortunately, the relatively fixed distance between the two antigen-binding sites of an IgG and a reliance on avidity as a mechanism to achieve higher affinities makes it susceptible to evasion by pathogens that employ high mutation rates coupled with low antigen densities. When compared to the antigen densities present on the surfaces of viruses to which neutralizing antibody responses can be consistently raised (Figure 3A–3D), it seems an unlikely coincidence that HIV—a virus that is among the most adept at evading antibody-mediated neutralization—also stands out as having an unusually high mutation rate and an unusually low density of surface envelope spikes with apparently restricted mobility. Thus, it is tempting to speculate that whereas antibodies evolved to form a bivalent structure that enhances binding to pathogen surfaces through avidity effects, HIV evolved a low spike density designed to specifically thwart bivalent binding by antibodies.
In the initial immune response to a particular variant of HIV, it is likely that IgGs will exhibit sufficiently slow dissociation rates and high enough affinities to exert selective pressure even when binding monovalently, whether by neutralization of virus particles or by recruiting effector functions against infected cells. However, faced with a target to which bivalent binding is predominantly impossible, antibody potency will be susceptible to escape by a wider range of mutations: ones that serve to decrease the rate of association as well as ones that serve to increase the rate of dissociation. The immune system may respond with revisions to the antibody repertoire, but the rate at which new antibodies are made will be easily outpaced by the virus's rate of mutation.
Without the buffering effect against escape by mutation that avidity provides, it is likely that immunogens derived from HIV will need to be specifically tailored to focus the antibody response against only the most conserved epitopes—a key objective that has already been identified by many research groups , . Viewed through the lens of avidity considerations, a general deficiency in bivalent binding will impose the additional requirement that broadly neutralizing antibodies still exhibit high affinities for their epitopes when binding monovalently. An alternative approach, as others have proposed , , may lie in eliciting anti-carbohydrate antibodies, as the high density of glycans on each gp120 monomer should enable efficient bivalent binding to individual envelope spikes. Thus, new immunogens designed to elicit antibodies capable of intra-spike cross-linking—either carbohydrate epitopes within or between spike monomers, or protein epitopes between spike monomers—may prove critical to the induction of a broadly cross-reactive neutralizing antibody response.
Using available crystallographic , – and electron microscopy data , –, , , it might also be possible to engineer novel bivalent and multivalent antibody architectures that are capable of intra-spike cross-linking by increasing the reach between Fabs using insertions in the hinge region of an IgG that adopt extended conformations , although they would need to be administered via passive immunization or gene therapy. Carbohydrate-binding reagents specific for HIV (perhaps based on the anti-carbohydrate antibody 2G12) might be a logical starting point, as multimerization of 2G12 has been shown to significantly enhance its neutralization potency , . These engineering approaches, as well as the design of immunogens able to elicit intra-spike cross-linking antibodies, could hold a significant advantage in that either approach would make the low spike density on HIV irrelevant to neutralization potency.
We thank Kelly Dryden, Ari Helenius, Jürgen Kartenbeck, Roberta Mancini, Kuniaki Nagayama, Kenneth Roux, Masashi Yamaguchi, Mark Yeager, and Ping Zhu for unpublished electron micrographs of viruses. We thank Leo Stamatatos, David Baltimore, Anthony West, and the members of the Bjorkman laboratory for critical reading of the manuscript.
- 1. Rerks-Ngarm S, Pitisuttithum P, Nitayaphan S, Kaewkungwal J, Chiu J, et al. (2009) Vaccination with ALVAC and AIDSVAX to prevent HIV-1 infection in Thailand. N Engl J Med 361: 2209–2220.
- 2. Dolin R (2009) HIV vaccine trial results–an opening for further research. N Engl J Med 361: 2279–2280.
- 3. Koup RA, Safrit JT, Cao Y, Andrews CA, McLeod G, et al. (1994) Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome. J Virol 68: 4650–4655.
- 4. Migueles SA, Sabbaghian MS, Shupert WL, Bettinotti MP, Marincola FM, et al. (2000) HLA B*5701 is highly associated with restriction of virus replication in a subgroup of HIV-infected long term nonprogressors. Proc Natl Acad Sci U S A 97: 2709–2714.
- 5. McMichael AJ, Rowland-Jones SL (2001) Cellular immune responses to HIV. Nature 410: 980–987.
- 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.
- 7. 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.
- 8. Labrijn AF, Poignard P, Raja A, Zwick MB, Delgado K, et al. (2003) Access of antibody molecules to the conserved coreceptor binding site on glycoprotein gp120 is sterically restricted on primary human immunodeficiency virus type 1. J Virol 77: 10557–10565.
- 9. 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.
- 10. Wyatt R, Desjardin E, Olshevsky U, Nixon C, Binley J, et al. (1997) Analysis of the interaction of the human immunodeficiency virus type 1 gp120 envelope glycoprotein with the gp41 transmembrane glycoprotein. J Virol 71: 9722–9731.
- 11. Moore JP, Sodroski J (1996) Antibody cross-competition analysis of the human immunodeficiency virus type 1 gp120 exterior envelope glycoprotein. J Virol 70: 1863–1872.
- 12. 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.
- 13. Xiao X, Chen W, Feng Y, Zhu Z, Prabakaran P, et al. (2009) Germline-like predecessors of broadly neutralizing antibodies lack measurable binding to HIV-1 envelope glycoproteins: implications for evasion of immune responses and design of vaccine immunogens. Biochem Biophys Res Commun 390: 404–409.
- 14. Rossmann MG (1989) The canyon hypothesis. Hiding the host cell receptor attachment site on a viral surface from immune surveillance. J Biol Chem 264: 14587–14590.
- 15. Kwong PD, Wilson IA (2009) HIV-1 and influenza antibodies: seeing antigens in new ways. Nat Immunol 10: 573–578.
- 16. Skehel JJ, Stevens DJ, Daniels RS, Douglas AR, Knossow M, et al. (1984) A carbohydrate side chain on hemagglutinins of Hong Kong influenza viruses inhibits recognition by a monoclonal antibody. Proc Natl Acad Sci U S A 81: 1779–1783.
- 17. Plotkin SA (2008) Vaccines: correlates of vaccine-induced immunity. Clin Infect Dis 47: 401–409.
- 18. Karlsson Hedestam GB, Fouchier RA, Phogat S, Burton DR, Sodroski J, et al. (2008) The challenges of eliciting neutralizing antibodies to HIV-1 and to influenza virus. Nat Rev Microbiol 6: 143–155.
- 19. Klein JS (2009) Investigations in the design and characterization of HIV-1 neutralizing molecules. Pasadena: California Institute of Technology.. 166 p.
- 20. Janeway CA, Travers P, Walport M, Schlomchik MJ (2005) Immunobiology. New York, , NY: Garland Science Publishing.
- 21. Scheid JF, Mouquet H, Feldhahn N, Seaman MS, Velinzon K, et al. (2009) Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals. Nature 458: 636–640.
- 22. Tomaras GD, Yates NL, Liu P, Qin L, Fouda GG, et al. (2008) Initial B-cell responses to transmitted human immunodeficiency virus type 1: virion-binding immunoglobulin M (IgM) and IgG antibodies followed by plasma anti-gp41 antibodies with ineffective control of initial viremia. J Virol 82: 12449–12463.
- 23. Mattes MJ (2005) Binding parameters of antibodies: pseudo-affinity and other misconceptions. Cancer Immunol Immunother 54: 513–516.
- 24. Smith TJ, Olson NH, Cheng RH, Chase ES, Baker TS (1993) Structure of a human rhinovirus-bivalently bound antibody complex: implications for viral neutralization and antibody flexibility. Proc Natl Acad Sci U S A 90: 7015–7018.
- 25. Icenogle J, Shiwen H, Duke G, Gilbert S, Rueckert R, et al. (1983) Neutralization of poliovirus by a monoclonal antibody: kinetics and stoichiometry. Virology 127: 412–425.
- 26. Zhang MY, Xiao X, Sidorov IA, Choudhry V, Cham F, et al. (2004) Identification and characterization of a new cross-reactive human immunodeficiency virus type 1-neutralizing human monoclonal antibody. J Virol 78: 9233–9242.
- 27. Klein JS, Gnanapragasam PN, Galimidi RP, Foglesong CP, West AP Jr, et al. (2009) Examination of the contributions of size and avidity to the neutralization mechanisms of the anti-HIV antibodies b12 and 4E10. Proc Natl Acad Sci U S A 106: 7385–7390.
- 28. Ofek G, Tang M, Sambor A, Katinger H, Mascola JR, et al. (2004) Structure and mechanistic analysis of the anti-human immunodeficiency virus type 1 antibody 2F5 in complex with its gp41 epitope. J Virol 78: 10724–10737.
- 29. Kunert R, Wolbank S, Stiegler G, Weik R, Katinger H (2004) Characterization of molecular features, antigen-binding, and in vitro properties of IgG and IgM variants of 4E10, an anti-HIV type 1 neutralizing monoclonal antibody. AIDS Res Hum Retroviruses 20: 755–762.
- 30. Wolbank S, Kunert R, Stiegler G, Katinger H (2003) Characterization of human class-switched polymeric (immunoglobulin M [IgM] and IgA) anti-human immunodeficiency virus type 1 antibodies 2F5 and 2G12. J Virol 77: 4095–4103.
- 31. Schofield DJ, Stephenson JR, Dimmock NJ (1997) Variations in the neutralizing and haemagglutination-inhibiting activities of five influenza A virus-specific IgGs and their antibody fragments. J Gen Virol 78 (Pt 10): 2431–2439.
- 32. Wu H, Pfarr DS, Tang Y, An LL, Patel NK, et al. (2005) Ultra-potent antibodies against respiratory syncytial virus: effects of binding kinetics and binding valence on viral neutralization. J Mol Biol 350: 126–144.
- 33. Edwards MJ, Dimmock NJ (2001) Hemagglutinin 1-specific immunoglobulin G and Fab molecules mediate postattachment neutralization of influenza A virus by inhibition of an early fusion event. J Virol 75: 10208–10218.
- 34. Pantaleo G, Koup RA (2004) Correlates of immune protection in HIV-1 infection: what we know, what we don't know, what we should know. Nat Med 10: 806–810.
- 35. Yamaguchi M, Danev R, Nishiyama K, Sugawara K, Nagayama K (2008) Zernike phase contrast electron microscopy of ice-embedded influenza A virus. J Struct Biol 162: 271–276.
- 36. Bachmann MF, Zinkernagel RM (1996) The influence of virus structure on antibody responses and virus serotype formation. Immunol Today 17: 553–558.
- 37. Zhu P, Chertova E, Bess J Jr, Lifson JD, Arthur LO, et al. (2003) Electron tomography analysis of envelope glycoprotein trimers on HIV and simian immunodeficiency virus virions. Proc Natl Acad Sci U S A 100: 15812–15817.
- 38. Zhu P, Liu J, Bess J Jr, Chertova E, Lifson JD, et al. (2006) Distribution and three-dimensional structure of AIDS virus envelope spikes. Nature 441: 847–852.
- 39. Liu J, Bartesaghi A, Borgnia MJ, Sapiro G, Subramaniam S (2008) Molecular architecture of native HIV-1 gp120 trimers. Nature 455: 109–113.
- 40. Chertova E, Bess JW Jr, Crise BJ, Sowder IR, Schaden TM, et al. (2002) Envelope glycoprotein incorporation, not shedding of surface envelope glycoprotein (gp120/SU), Is the primary determinant of SU content of purified human immunodeficiency virus type 1 and simian immunodeficiency virus. J Virol 76: 5315–5325.
- 41. Layne SP, Merges MJ, Dembo M, Spouge JL, Conley SR, et al. (1992) Factors underlying spontaneous inactivation and susceptibility to neutralization of human immunodeficiency virus. Virology 189: 695–714.
- 42. Sougrat R, Bartesaghi A, Lifson JD, Bennett AE, Bess JW, et al. (2007) Electron tomography of the contact between T cells and SIV/HIV-1: implications for viral entry. PLoS Pathog 3: e63. doi:10.1371/journal.ppat.0030063.
- 43. Yang X, Kurteva S, Ren X, Lee S, Sodroski J (2005) Stoichiometry of envelope glycoprotein trimers in the entry of human immunodeficiency virus type 1. J Virol 79: 12132–12147.
- 44. Magnus C, Rusert P, Bonhoeffer S, Trkola A, Regoes RR (2009) Estimating the stoichiometry of human immunodeficiency virus entry. J Virol 83: 1523–1531.
- 45. McInerney TL, McLain L, Armstrong SJ, Dimmock NJ (1997) A human IgG1 (b12) specific for the CD4 binding site of HIV-1 neutralizes by inhibiting the virus fusion entry process, but b12 Fab neutralizes by inhibiting a postfusion event. Virology 233: 313–326.
- 46. Yu X, Yuan X, Matsuda Z, Lee TH, Essex M (1992) The matrix protein of human immunodeficiency virus type 1 is required for incorporation of viral envelope protein into mature virions. J Virol 66: 4966–4971.
- 47. Bhatia AK, Kaushik R, Campbell NA, Pontow SE, Ratner L (2009) Mutation of critical serine residues in HIV-1 matrix result in an envelope incorporation defect which can be rescued by truncation of the gp41 cytoplasmic tail. Virology 384: 233–241.
- 48. Luftig MA, Mattu M, Di Giovine P, Geleziunas R, Hrin R, et al. (2006) Structural basis for HIV-1 neutralization by a gp41 fusion intermediate-directed antibody. Nat Struct Mol Biol 13: 740–747.
- 49. 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.
- 50. Hessell AJ, Rakasz EG, Poignard P, Hangartner L, Landucci G, et al. (2009) Broadly neutralizing human anti-HIV antibody 2G12 is effective in protection against mucosal SHIV challenge even at low serum neutralizing titers. PLoS Pathog 5: e1000433. doi:10.1371/journal.ppat.1000433.
- 51. West AP Jr, Galimidi RP, Foglesong CP, Gnanapragasam PN, Huey-Tubman KE, et al. (2009) Design and expression of a dimeric form of human immunodeficiency virus type 1 antibody 2G12 with increased neutralization potency. J Virol 83: 98–104.
- 52. 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.
- 53. Bongini L, Fanelli D, Piazza F, De Los Rios P, Sanner M, et al. (2007) A dynamical study of antibody-antigen encounter reactions. Phys Biol 4: 172–180.
- 54. 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.
- 55. Pantophlet R, Wilson IA, Burton DR (2004) Improved design of an antigen with enhanced specificity for the broadly HIV-neutralizing antibody b12. Protein Eng Des Sel 17: 749–758.
- 56. Burton DR, Stanfield RL, Wilson IA (2005) Antibody vs. HIV in a clash of evolutionary titans. Proc Natl Acad Sci U S A 102: 14943–14948.
- 57. Pantophlet R, Burton DR (2006) GP120: target for neutralizing HIV-1 antibodies. Annu Rev Immunol 24: 739–769.
- 58. Chan DC, Fass D, Berger JM, Kim PS (1997) Core structure of gp41 from the HIV envelope glycoprotein. Cell 89: 263–273.
- 59. Weissenhorn W, Dessen A, Harrison SC, Skehel JJ, Wiley DC (1997) Atomic structure of the ectodomain from HIV-1 gp41. Nature 387: 426–430.
- 60. Kwong PD, Wyatt R, Majeed S, Robinson J, Sweet RW, et al. (2000) Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates. Structure 8: 1329–1339.
- 61. Chen B, Vogan EM, Gong H, Skehel JJ, Wiley DC, et al. (2005) Structure of an unliganded simian immunodeficiency virus gp120 core. Nature 433: 834–841.
- 62. Huang CC, Tang M, Zhang MY, Majeed S, Montabana E, et al. (2005) Structure of a V3-containing HIV-1 gp120 core. Science 310: 1025–1028.
- 63. Huang CC, Lam SN, Acharya P, Tang M, Xiang SH, et al. (2007) Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4. Science 317: 1930–1934.
- 64. Zhou T, Xu L, Dey B, Hessell AJ, Van Ryk D, et al. (2007) Structural definition of a conserved neutralization epitope on HIV-1 gp120. Nature 445: 732–737.
- 65. Chen L, Kwon YD, Zhou T, Wu X, O'Dell S, et al. (2009) Structural basis of immune evasion at the site of CD4 attachment on HIV-1 gp120. Science 326: 1123–1127.
- 66. Diskin R, Marcovecchio PM, Bjorkman PJ (2010) Structure of a clade C HIV-1 gp120 bound to CD4 and CD4-induced antibody reveals anti-CD4 polyreactivity. Nat Struct Mol Biol.. doi:10.1038/nsmb.1796.
- 67. Zanetti G, Briggs JA, Grunewald K, Sattentau QJ, Fuller SD (2006) Cryo-electron tomographic structure of an immunodeficiency virus envelope complex in situ. PLoS Pathog 2: e83. doi:10.1371/journal.ppat.0020083.
- 68. Bennett A, Liu J, Van Ryk D, Bliss D, Arthos J, et al. (2007) Cryoelectron tomographic analysis of an HIV-neutralizing protein and its complex with native viral gp120. J Biol Chem 282: 27754–27759.
- 69. Saphire EO, Parren PW, Pantophlet R, Zwick MB, Morris GM, et al. (2001) Crystal structure of a neutralizing human IGG against HIV-1: a template for vaccine design. Science 293: 1155–1159.
- 70. Crooks ET, Jiang P, Franti M, Wong S, Zwick MB, et al. (2008) Relationship of HIV-1 and SIV envelope glycoprotein trimer occupation and neutralization. Virology 377: 364–378.
- 71. Zingler K, Littman DR (1993) Truncation of the cytoplasmic domain of the simian immunodeficiency virus envelope glycoprotein increases env incorporation into particles and fusogenicity and infectivity. J Virol 67: 2824–2831.
- 72. Johnston PB, Dubay JW, Hunter E (1993) Truncations of the simian immunodeficiency virus transmembrane protein confer expanded virus host range by removing a block to virus entry into cells. J Virol 67: 3077–3086.