Structural Analysis of a Dengue Cross-Reactive Antibody Complexed with Envelope Domain III Reveals the Molecular Basis of Cross-Reactivity

Midgley, Claire M; Flanagan, Aleksandra; Tran, Hai B.; Dejnirattisai, Wanwisa; Chawansuntati, Kriangkrai; Jumnainsong, Amonrat; Wongwiwat, Wiyada; Duangchinda, Thaneeya; Mongkolsapaya, Juthathip; Grimes, Jonathan M.; Screaton, Gavin

doi:10.4049/jimmunol.1200227

Cited by 87 publications

(89 citation statements)

References 73 publications

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“…His317, the residue implicated in pH sensing 64, 65 , switches electrostatic polarity with respect to Thr315 ( Table 1). Both His317 and Thr315 are conserved in ZIKV/DENV1-4/JEV/WNV ( Figure 2), and are known epitopes 23, 43 . Another pair (Arg286-Arg288) with EPD-R are stereochemically equivalent in ZIKV/DENV1-4/JEV/WNV ( Figure 3), and lie on a putative GAG-binding domain preceding the DI/DIII linker 48, 49 .…”

Section: Resultsmentioning

confidence: 99%

“…Firstly, a quantitative analysis of spatial and electrostatic perturbation in the pre 37 and post-fusion 12 DENV-2 E proteins was done using MEPP 38 . This revealed that highly perturbed residues are overwhelmingly conserved, and also epitopes of known neutralizing antibodies 23, 35, 39– 43 . Characterization of α -helices in E-proteins using techniques (PAGAL 44, 45 ) previously applied to the Ebola virus 46 , revealed that α 1 in ZIKV-E and DENV-E proteins is not conserved in the sequence space.…”

Section: Introductionmentioning

confidence: 99%

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MEPPitope: spatial, electrostatic and secondary structure perturbations in the post-fusion Dengue virus envelope protein highlights known epitopes and conserved residues in the Zika virus

Chakraborty¹

2016

F1000Res

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The dramatic transformation of the Zika virus (ZIKV) from a relatively unknown virus to a pathogen generating global-wide panic has exposed the dearth of detailed knowledge about this virus. Decades of research in the related Dengue virus (DENV), finally culminating in a vaccine registered for use in endemic regions (CYD-TDV), provides key insights in developing strategies for tackling ZIKV. The previously established MEPP methodology compares two conformations of the same protein and identifies residues with significant spatial and electrostatic perturbations. In the current work, MEPP analyzed the pre-and post-fusion DENV type 2 envelope (E) protein, and identified several known epitopes (His317, Tyr299, Glu26, Arg188, etc.) (MEPPitope). These residues are overwhelmingly conserved in ZIKV and all DENV serotypes. Characterization of α-helices in E-proteins show that α1 is not conserved in the sequence space of ZIKV and DENV. Furthermore, perturbation of α1 in the post-fusion DENV structure includes a known epitope Asp215, a residue absent in the pre-fusion α1. A cationic β-sheet in the GAG-binding domain that is stereochemically equivalent in ZIKV and all DENV serotypes is also highlighted due to a residue pair (Arg286-Arg288) that has a significant electrostatic polarity reversal upon fusion. Finally, two highly conserved residues (Thr32 and Thr40), with little emphasis in existing literature, are found to have significant electrostatic perturbation. Thus, a combination of different computational methods enable the rapid and rational detection of critical residues that can be made the target of small drugs, or as epitopes in the search for an elusive therapy or vaccine that neutralizes multiple members of the Flaviviridae family.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

MEPPitope: spatial, electrostatic and secondary structure perturbations in the post-fusion Dengue virus envelope protein highlights known epitopes and conserved residues in the Zika virus

Chakraborty¹

2016

F1000Res

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“…On one hand, anti-DIII antibodies have been shown to bind to epitopes that are not accessible in the known structures of the virus, suggesting that molecular rearrangements are required to expose them (54,55); on the other hand, antibody binding was shown to either alter the virus structure or trap the antigen in an already existing conformation (21).…”

Section: Discussionmentioning

confidence: 99%

“…2). Similarly, the epitopes of all other anti-DIII antibodies with a known structure are partially inaccessible on the virus surface (1A1D-2, 4E11, and 2H12) (20,54,55). Conformational changes causing different degrees of epitope exposure are likely important for the binding, specificity, and neutralization capacities of antibodies against the four different serotypes (20,27,58).…”

Section: Discussionmentioning

confidence: 99%

Antibody Binding Modulates Conformational Exchange in Domain III of Dengue Virus E Protein

Moraes

Simonelli

Pedotti

et al. 2016

J Virol

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Domain III of dengue virus E protein (DIII) participates in the recognition of cell receptors and in structural rearrangements required for membrane fusion and ultimately viral infection; furthermore, it contains epitopes for neutralizing antibodies and has been considered a potential vaccination agent. In this work, we addressed various structural aspects of DIII and their relevance for both the dengue virus infection mechanism and antibody recognition. We provided a dynamic description of DIII at physiological and endosomal pHs and in complex with the neutralizing human antibody DV32.6. We observed conformational exchange in the isolated DIII, in regions important for the packing of E protein dimers on the virus surface. This conformational diversity is likely to facilitate the partial detachment of DIII from the other E protein domains, which is required to achieve fusion to the host cellular membranes and to expose the epitopes of many anti-DIII antibodies. A comparison of DIII of two dengue virus serotypes revealed many common features but also some possibly unexpected differences. Antibody binding to DIII of dengue virus serotype 4 attenuated the conformational exchange in the epitope region but, surprisingly, generated exchange in other parts of DIII through allosteric effects. IMPORTANCEMany studies have provided extensive structural information on the E protein and particularly on DIII, also in complex with antibodies. However, there is very scarce information regarding the molecular dynamics of DIII, and almost nothing is available on the dynamic effect of antibody binding, especially at the quantitative level. This work provides one of the very rare descriptions of the effect of antibody binding on antigen dynamics. D engue virus (DENV) is a member of the Flaviviridae family, which includes yellow fever, West Nile, Japanese tick-borne encephalitis, and other viruses. DENV is responsible for ϳ500,000 hospitalizations and Ͼ20,000 deaths per year (1). The incidence and geographic expansion of the virus are constantly increasing, and no cure or licensed vaccine is currently available for Dengue disease. There are four Dengue virus serotypes, DENV1 to -4, and secondary infection with a different serotype is associated with a severe form of the disease: dengue hemorrhagic fever (2). This is probably facilitated by a process called antibody-dependent enhancement (ADE), where cross-reactive, poorly neutralizing antibodies allow infection of Fc receptor-bearing cells, leading to increased viral loads and infectivity (3).Flaviviruses recognize their target cells via the interaction of glycoprotein E (E protein) with host receptors, which include the extracellular matrix components (4-6). After virus internalization by endocytosis, exposure to the lower endosomal pH leads to alterations of the E protein structure, exposing the fusion peptide and allowing it to interact with the endosome membrane and mediate viral fusion (1, 7-9).The virus surface is formed by 180 units of antiparallel E protein dimers (1...

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“…Reasons for the observed variations in binding stoichiometry and epitope occupancy are typically attributed to relatively small conformational differences between symmetry-related epitopes that interfere with Ab binding or alter epitope accessibility. Although certainly plausible, such explanations seem at odds with evidence that 1) flaviviruses undergo ''breathing'' motions that confer considerable conformational heterogeneity (20), and 2) Ab binding can induce significant conformational changes, exposing previously buried epitopes (21). Furthermore, there are technical limits to the use of cryo-EM structures alone in understanding the mechanisms of antibody-based neutralization of flaviviruses.…”

Section: Introductionmentioning

confidence: 99%

Modeling the Role of Epitope Arrangement on Antibody Binding Stoichiometry in Flaviviruses

Ripoll

Khavrutskii

Wallqvist

et al. 2016

Biophysical Journal

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Cryo-electron-microscopy (cryo-EM) structures of flaviviruses reveal significant variation in epitope occupancy across different monoclonal antibodies that have largely been attributed to epitope-level differences in conformation or accessibility that affect antibody binding. The consequences of these variations for macroscopic properties such as antibody binding and neutralization are the results of the law of mass action-a stochastic process of innumerable binding and unbinding events between antibodies and the multiple binding sites on the flavivirus in equilibrium-that cannot be directly imputed from structure alone. We carried out coarse-grained spatial stochastic binding simulations for nine flavivirus antibodies with epitopes defined by cryo-EM or x-ray crystallography to assess the role of epitope spatial arrangement on antibody-binding stoichiometry, occupancy, and neutralization. In our simulations, all epitopes were equally competent for binding, representing the upper limit of binding stoichiometry that results from epitope spatial arrangement alone. Surprisingly, our simulations closely reproduced the relative occupancy and binding stoichiometry observed in cryo-EM, without having to account for differences in epitope accessibility or conformation, suggesting that epitope spatial arrangement alone may be sufficient to explain differences in binding occupancy and stoichiometry between antibodies. Furthermore, we found that there was significant heterogeneity in binding configurations even at saturating antibody concentrations, and that bivalent antibody binding may be more common than previously thought. Finally, we propose a structure-based explanation for the stoichiometric threshold model of neutralization.

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Structural Analysis of a Dengue Cross-Reactive Antibody Complexed with Envelope Domain III Reveals the Molecular Basis of Cross-Reactivity

Cited by 87 publications

References 73 publications

MEPPitope: spatial, electrostatic and secondary structure perturbations in the post-fusion Dengue virus envelope protein highlights known epitopes and conserved residues in the Zika virus

MEPPitope: spatial, electrostatic and secondary structure perturbations in the post-fusion Dengue virus envelope protein highlights known epitopes and conserved residues in the Zika virus

Antibody Binding Modulates Conformational Exchange in Domain III of Dengue Virus E Protein

Modeling the Role of Epitope Arrangement on Antibody Binding Stoichiometry in Flaviviruses

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