Asymmetric recognition of HIV-1 Envelope trimer by V1V2 loop-targeting antibodies

Wang, Haoqing; Gristick, Harry B.; Scharf, Louise; West, Anthony P.; Galimidi, Rachel P.; Seaman, Michael S.; Freund, Natalia T.; Nussenzweig, Michel C.; Björkman, Pamela J.

doi:10.7554/elife.27389

Cited by 54 publications

(62 citation statements)

References 73 publications

(172 reference statements)

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“…We sought to develop a general computational method for generating de novo protein nanoparticles with geometries tailored to display specific antigens of interest, focusing in particular on the challenge of displaying the pre-fusion conformations of the trimeric viral glycoproteins HIV-1 Env (BG505 SOSIP) 23,24 , influenza hemagglutinin (H1 HA) 25 , and respiratory syncytial virus (RSV) F (DS-Cav1) 7 . To make the tailored nanoparticle design problem computationally tractable, we used a hierarchical approach.…”

Section: Methods Overviewmentioning

confidence: 99%

Tailored Design of Protein Nanoparticle Scaffolds for Multivalent Presentation of Viral Glycoprotein Antigens

Ueda

Antanasijevic

Fallas

et al. 2020

Preprint

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The adaptive immune system is highly sensitive to arrayed antigens, and multivalent display of viral glycoproteins on symmetric scaffolds has been found to substantially increase the elicitation of antigen-specific antibodies. Motivated by the considerable promise of this strategy for next-generation anti-viral vaccines, we set out to design new self-assembling protein nanoparticles with geometries specifically tailored to scaffold ectodomains of different viral glycoproteins. We first designed and characterized homo-trimers from designed repeat proteins with N-terminal helices positioned to match the C termini of several viral glycoprotein trimers. Oligomers found to experimentally adopt the designed configuration were then used to generate nanoparticles with tetrahedral, octahedral, or icosahedral symmetry. Examples of all three target symmetries were experimentally validated by cryo-electron microscopy and several were assessed for their ability to display viral glycoproteins via genetic fusion. Electron microscopy and antibody binding experiments demonstrated that the designed nanoparticles display conformationally intact native-like HIV-1 Env, influenza hemagglutinin, and prefusion RSV F trimers in the predicted geometries. This work demonstrates that novel nanoparticle immunogens can be designed from the bottom up with atomic-level accuracy and provides a general strategy for precisely controlling epitope presentation and accessibility.

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Section: Methods Overviewmentioning

confidence: 99%

Tailored Design of Protein Nanoparticle Scaffolds for Multivalent Presentation of Viral Glycoprotein Antigens

Ueda

Antanasijevic

Fallas

et al. 2020

Preprint

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“…Bivalent binding to single Env trimer (intra-spike crosslinking) is another way to utilize avidity effects to counteract the low spike density of HIV-1. Although the architecture of Env trimers prohibits this mode of binding for conventional, host-derived IgGs (29,30), we analyzed how synthetic diFabs (Fabs from a neutralizing anti-HIV-1 IgG joined by a linker containing rigid dsDNA flanked by flexible ssDNA shown in Fig. 1B) could be designed to achieve optimal intraspike crosslinking.…”

Section: Discussionmentioning

confidence: 99%

“…(B) Schematics of a Fab, an IgG, a diFab composed of two Fabs joined together by d bp dsDNA and two segments of s ssDNA bases, and a triFab made up of three Fabs. spike mutations is supported by independent biochemical and EM studies demonstrating that HIV-1 has an unusually low number of spikes that are not clustered (23)(24)(25)(26)31), and that bivalent IgG forms of anti-HIV-1 NAbs are only modestly more effective than monovalent Fabs, by contrast to bivalent IgGs against other viruses, which can be 100s-to 1000s-fold more potent than counterpart monovalent Fabs (21,22,29,30).…”

Section: Introductionmentioning

confidence: 94%

Harnessing Avidity: Quantifying Entropic and Energetic Effects of Linker Length and Rigidity Required for Multivalent Binding of Antibodies to HIV-1 Spikes

Galimidi

Einav

Gnanapragasam

et al. 2018

Preprint

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Due to the low density of envelope (Env) spikes on the surface of HIV-1, neutralizing IgG antibodies rarely bind bivalently using both antigen-binding arms (Fabs) to crosslink between spikes (inter-spike crosslinking), instead resorting to weaker monovalent binding that is more sensitive to Env mutations. Synthetic antibodies designed to bivalently bind a single Env trimer (intra-spike crosslinking) were previously shown to exhibit increased neutralization potencies. In initial work, diFabs joined by varying lengths of rigid double-stranded DNA (dsDNA) were considered. Anticipating future experiments to improve synthetic antibodies, we investigate whether linkers with different rigidities could enhance diFab potency by modeling DNA-Fabs containing different combinations of rigid dsDNA and flexible single-stranded DNA (ssDNA) and characterizing their neutralization potential. Model predictions suggest that while a long flexible polymer may be capable of bivalent binding, it exhibits weak neutralization due to the large loss in entropic degrees of freedom when both Fabs are bound. In contrast, the strongest neutralization potencies are predicted to require a rigid linker that optimally spans the distance between two Fab binding sites on an Env trimer, and avidity can be further boosted by incorporating more Fabs into these constructs. These results inform the design of multivalent anti-HIV-1 therapeutics that utilize avidity effects to remain potent against HIV-1 in the face of the rapid mutation of Env spikes. SignificanceIgG antibodies utilize avidity to increase their apparent affinities through simultaneous binding of two antigen-binding Fabsif one Fab dissociates from an antigen, the other Fab can remain attached, allowing rebinding. HIV-1 foils this strategy by having few, and highly-separated, Envelope spike targets for antibodies, forcing most IgGs to bind monovalently. Here we develop a statistical mechanics model of synthetic diFabs joined by DNA linkers of different lengths and flexibilities. This framework enables us to translate the energetic and entropic effects of the linker into the neutralization potency of a diFab. We demonstrate that the avidity of multivalent binding is enhanced by using rigid linkers or including additional Fabs capable of simultaneous binding, providing the means to quantitatively predict the potencies of other antibody designs.

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“…Our cryo-EM structures of the natively glycosylated Env trimer (Wang et al, 2016(Wang et al, , 2017 were solved at low resolutions (6.2 and 8.9 Å ), precluding the interpretation of glycan conformations. However, densities for N-glycans were apparent and we were able to use glycan coordinates from our higher resolution crystal structures to interpret the lower resolution density maps.…”

Section: Discussionmentioning

confidence: 99%

“…One structure, reconstructed at 8.9 Å resolution, was of a complex between the Env trimer, the host receptor CD4 and Fabs from two different antibodies (Wang et al, 2016). A second structure at 6.2 Å resolution was an asymmetric complex of the Env trimer bound to two, rather than three, apex-binding bNAb Fabs (Wang et al, 2017). Density for ordered N-glycans at some PNGSs was visible in both maps, and coordinates for ordered N-linked glycans from our natively glycosylated Env trimer structure were fitted separately as rigid bodies at PNGSs at which EM density was apparent, and geometric restraints for N-glycans were generated using Privateer (Agirre et al, 2015).…”

Section: Glycans In Cryo-em Mapsmentioning

confidence: 99%

X-ray and EM structures of a natively glycosylated HIV-1 envelope trimer

Gristick

Wang

Björkman

2017

Acta Crystallogr D Struct Biol

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The structural and biochemical characterization of broadly neutralizing anti-HIV-1 antibodies (bNAbs) has been essential in guiding the design of potential vaccines to prevent infection by HIV-1. While these studies have revealed critical mechanisms by which bNAbs recognize and/or accommodate N-glycans on the trimeric envelope glycoprotein (Env), they have been limited to the visualization of high-mannose glycan forms only, since heterogeneity introduced from the presence of complex glycans makes it difficult to obtain high-resolution structures. 3.5 and 3.9 Å resolution crystal structures of the HIV-1 Env trimer with fully processed and native glycosylation were solved, revealing a glycan shield of high-mannose and complex-type N-glycans that were used to define the complete epitopes of two bNAbs. Here, the refinement of the N-glycans in the crystal structures is discussed and comparisons are made with glycan densities in glycosylated Env structures derived by single-particle cryo-electron microscopy.

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Asymmetric recognition of HIV-1 Envelope trimer by V1V2 loop-targeting antibodies

Cited by 54 publications

References 73 publications

Tailored Design of Protein Nanoparticle Scaffolds for Multivalent Presentation of Viral Glycoprotein Antigens

Tailored Design of Protein Nanoparticle Scaffolds for Multivalent Presentation of Viral Glycoprotein Antigens

Harnessing Avidity: Quantifying Entropic and Energetic Effects of Linker Length and Rigidity Required for Multivalent Binding of Antibodies to HIV-1 Spikes

X-ray and EM structures of a natively glycosylated HIV-1 envelope trimer

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