Cryo-EM structure of an antibody that neutralizes dengue virus type 2 by locking E protein dimers

Fibriansah, Guntur; Ibarra, Kristie D.; Ng, Thiam-Seng; Smith, Scott A.; Tan, Joanne L.; Lim, Xin Ni; Ooi, Justin S. G.; Kostyuchenko, V.A.; Wang, Jiaqi; Silva, Aravinda M. de; Harris, Eva; Crowe, James E.; Lok, Shee-Mei

doi:10.1126/science.aaa8651

Cited by 215 publications

(251 citation statements)

References 37 publications

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“…Like E16, MAb CR4354 inhibits WNV at a postattachment step and can inhibit virus fusion with synthetic liposomes (59,170). The structure of the CR4354 Fab bound to WNV revealed a discontinuous epitope that spanned neighboring E proteins, suggesting that this MAb and others that bind complex quaternary epitopes might block fusion by cross-linking E proteins on the virion (61,(170)(171)(172). While the multiple-hit hypothesis assumes that neutralization is a reversible process (181), in some cases, antibody binding results in an irreversible change in virion infectivity that persists upon the reversal of binding.…”

Section: Mechanisms Of Neutralizationmentioning

confidence: 99%

“…More critically, the number of accessible epitopes on the intact infectious virion provides the "denominator" for this relationship, as epitope accessibility ultimately governs the number of antibody molecules capable of binding the virus particle at saturation. Antibodies may bind epitopes defined by amino acid contacts from a single viral structural protein (167) or engage residues found on adjacent proteins or carbohydrates (61,(110)(111)(112)(113)(168)(169)(170)(171)(172). Complex or quaternary epitopes have been defined for many viruses, including flaviviruses (see below).…”

Section: Neutralization By the Numbersmentioning

confidence: 99%

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Deconstructing the Antiviral Neutralizing-Antibody Response: Implications for Vaccine Development and Immunity

VanBlargan

Goo

Pierson

2016

Microbiol Mol Biol Rev

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SUMMARY The antibody response plays a key role in protection against viral infections. While antiviral antibodies may reduce the viral burden via several mechanisms, the ability to directly inhibit (neutralize) infection of cells has been extensively studied. Eliciting a neutralizing-antibody response is a goal of many vaccine development programs and commonly correlates with protection from disease. Considerable insights into the mechanisms of neutralization have been gained from studies of monoclonal antibodies, yet the individual contributions and dynamics of the repertoire of circulating antibody specificities elicited by infection and vaccination are poorly understood on the functional and molecular levels. Neutralizing antibodies with the most protective functionalities may be a rare component of a polyclonal, pathogen-specific antibody response, further complicating efforts to identify the elements of a protective immune response. This review discusses advances in deconstructing polyclonal antibody responses to flavivirus infection or vaccination. Our discussions draw comparisons to HIV-1, a virus with a distinct structure and replication cycle for which the antibody response has been extensively investigated. Progress toward deconstructing and understanding the components of polyclonal antibody responses identifies new targets and challenges for vaccination strategies.

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Section: Mechanisms Of Neutralizationmentioning

confidence: 99%

Section: Neutralization By the Numbersmentioning

confidence: 99%

Deconstructing the Antiviral Neutralizing-Antibody Response: Implications for Vaccine Development and Immunity

VanBlargan

Goo

Pierson

2016

Microbiol Mol Biol Rev

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“…The B-B′ dimer moves to a higher radius and the E proteins dissociate from each other. A study of an antibody, which traps a transitional stage of this motion 11 , suggests that the A-C′ dimer probably moves to a higher radius before the B-B′ dimer 11 . In the ZIKV structure, the possible network of interactions around the five-fold vertex between the five A-C′ dimers may result in tighter packing that prevents this structural transition.…”

mentioning

confidence: 99%

Structure of the thermally stable Zika virus

Kostyuchenko

Lim

Zhang

et al. 2016

Nature

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448

469

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Zika virus (ZIKV), formerly a neglected pathogen, has recently been associated with microcephaly in fetuses 1 , and with Guillian-Barré syndrome in adults 2 . Here we present the 3.7 Å resolution cryoelectron microscopy structure of ZIKV, and show that the overall architecture of the virus is similar to that of other flaviviruses. Sequence and structural comparisons of the ZIKV envelope (E) protein with other flaviviruses show that parts of the E protein closely resemble the neurovirulent West Nile and Japanese encephalitis viruses, while others are similar to dengue virus (DENV). However, the contribution of the E protein to flavivirus pathobiology is currently not understood. The virus particle was observed to be structurally stable even when incubated at 40 °C, in sharp contrast to the less thermally stable DENV 3 . This is also reflected in the infectivity of ZIKV compared to DENV serotypes 2 and 4 (DENV2 and DENV4) at different temperatures. The cryoelectron microscopy structure shows a virus with a more compact surface. This structural stability of the virus may help it to survive in the harsh conditions of semen 4 , saliva 5 and urine 6 . Antibodies or drugs that destabilize the structure may help to reduce the disease outcome or limit the spread of the virus.Zika virus (ZIKV), a flavivirus, is thought to be principally transmitted to humans by the mosquito (Aedes aegypti) vector. Other flaviviriuses include West Nile virus (WNV), Japanese encephalitis virus (JEV), dengue virus (DENV) and yellow fever virus (YFV). ZIKV generally causes a mild disease. However, when pregnant women are infected with ZIKV, there is an increased risk of developing microcephaly in the fetus 1 .Retrospective analysis of data collected from a ZIKV outbreak in French Polynesia in 2013-2014 showed association of the virus with microcephaly 7 . Here we present the 3.7 Å resolution structure of ZIKV strain H/PF/2013 isolated during that outbreak 8 .For cryo-electron microscopy (cryoEM) studies, ZIKV was grown in the mosquito cell line at 28 °C and purified at 4 °C by polyethylene glycol precipitation, a sucrose cushion, followed by a potassium tartrate gradient. The gel analysis of the purified sample suggested it contained mostly mature virus (Extended Data Fig. 1). The ZIKV samples were incubated at 28 °C, 37 °C and 40 °C (mimicking high fever) for 30 min, before imaging by cryoEM (Fig. 1a). At 28 °C, there were broken and shrivelled particles together with some smooth surfaced particles (about 500 Å in diameter), similar to the compact DENV mature particles. Conversely, samples incubated at 37 °C and 40 °C showed many more smooth surfaced particles. The presence of a larger fraction of shrivelled particles at 28 °C could be due to the exposure of particles to high osmolality during purification. We speculate that ZIKV particles may expand into smooth surfaced particles when incubated at higher temperatures, making the lipid envelope more fluid, and allowing the structure to revert to its normal state. Some strains of DENV2 (New G...

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“…4 in (37)). For an IgG Ab, we found that the connectivity between the two Fabs is well approximated by a linker of [16][17][18] residues. The range of p(d 0 ) associated with the N AA values used in our application can be found in the Section F in the Supporting Material.…”

Section: Bivalent Binding Of Igg Absmentioning

confidence: 95%

“…For example, the DENV Ab 1F4 was found to bind exclusively to epitopes along the twofold and fivefold axis of symmetry of the viral envelope, with a total stoichiometry of 120 Abs (17); the DENVAb 2D22 was found to have a maximum stoichiometry of 180 Abs while binding to epitopes along all three axes of symmetry (18); and the DENV Ab 5J7 was found to have a stoichiometry of 60 Abs, binding to epitopes along only the threefold axis of symmetry (19). 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.…”

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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Cryo-EM structure of an antibody that neutralizes dengue virus type 2 by locking E protein dimers

Cited by 215 publications

References 37 publications

Deconstructing the Antiviral Neutralizing-Antibody Response: Implications for Vaccine Development and Immunity

Deconstructing the Antiviral Neutralizing-Antibody Response: Implications for Vaccine Development and Immunity

Structure of the thermally stable Zika virus

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

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