Structural basis for Zika envelope domain III recognition by a germline version of a recurrent neutralizing antibody

Abstract

Recent epidemics demonstrate the global threat of Zika virus (ZIKV), a flavivirus transmitted by mosquitoes. Although infection is usually asymptomatic or mild, newborns of infected mothers can display severe symptoms, including neurodevelopmental abnormalities and microcephaly. Given the large-scale spread, symptom severity, and lack of treatment or prophylaxis, a safe and effective ZIKV vaccine is urgently needed. However, vaccine design is complicated by concern that elicited antibodies (Abs) may cross-react with other flaviviruses that share a similar envelope protein, such as dengue virus, West Nile virus, and yellow fever virus. This cross-reactivity may worsen symptoms of a subsequent infection through Ab-dependent enhancement. To better understand the neutralizing Ab response and risk of Ab-dependent enhancement, further information on germline Ab binding to ZIKV and the maturation process that gives rise to potently neutralizing Abs is needed. Here we use binding and structural studies to compare mature and inferred-germline Ab binding to envelope protein domain III of ZIKV and other flaviviruses. We show that affinity maturation of the light-chain variable domain is important for strong binding of the recurrent VH3-23/VK1-5 neutralizing Abs to ZIKV envelope protein domain III, and identify interacting residues that contribute to weak, cross-reactive binding to West Nile virus. These findings provide insight into the affinity maturation process and potential cross-reactivity of VH3-23/VK1-5 neutralizing Abs, informing precautions for protein-based vaccines designed to elicit germline versions of neutralizing Abs.

How Antibodies Recognize Pathogenic Viruses: Structural Correlates of Antibody Neutralization of HIV-1, SARS-CoV-2, and Zika

“…Truncation has also been used to produce smaller components such as single domains. Examples of truncated domains include gp120 cores of HIV-1 Env, which have the β4 and β26 strands and all flexible loops removed [ 68 , 69 ], coronavirus RBDs truncated at the base where the flexible hinge connects them to the rest of the S1 subunit [ 70 , 71 ], and the individual EDIII truncated from the rest of the ZIKV E protein [ 52 , 53 , 54 , 72 , 73 ]. Truncation of individual domains has been especially powerful for X-ray crystallography as crystallization is hindered by flexible regions such as loops or inter-domain linkers and hinges.…”

“…Truncation of individual domains has been especially powerful for X-ray crystallography as crystallization is hindered by flexible regions such as loops or inter-domain linkers and hinges. Single domains are useful for solving high resolution structures of Fab-domain complexes that provide detail about the Ab interactions that may not be possible using single particle cryo-EM due to flexibility or heterogeneity of larger protein complex structures [ 32 , 52 , 53 , 54 , 72 , 73 , 74 ].…”

“…Given its role in fusion, the E protein is an important target of neutralizing Abs that effectively clear ZIKV, inhibit ZIKV infection in vitro, decrease vertical transmission, and are protective in ZIKV challenge in animal models [ 53 , 54 , 55 , 56 , 72 , 79 , 124 , 125 ] ( Figure 2 C). Structural characterization of Abs that bind the ZIKV E protein have revealed multiple epitopes on the three domains: (1) the conserved FL found on EDII [ 56 , 126 ], (2) EDIII [ 52 , 53 , 54 , 72 , 73 , 127 ], (3) multiple domains of single E protein [ 79 , 80 ], (4) multiple domains spanning an E protein dimer [ 55 , 60 , 79 , 125 , 128 , 129 ], and (5) multiple domains spanning neighboring E dimer pairs [ 61 , 62 , 79 , 129 ]. Abs against the FL in EDII compose a large portion of the response to infection, and because the FL is conserved among flaviviruses, these Abs can cross-react with different flaviviruses [ 56 , 79 , 124 , 125 , 126 , 130 ].…”

“…Abs against the FL in EDII compose a large portion of the response to infection, and because the FL is conserved among flaviviruses, these Abs can cross-react with different flaviviruses [ 56 , 79 , 124 , 125 , 126 , 130 ]. However, many potently-neutralizing Abs target EDIII and these Abs tend to be more specific for ZIKV than other flaviviruses [ 51 , 52 , 53 , 54 , 55 , 56 , 61 , 72 , 124 , 125 , 131 , 132 , 133 , 134 , 135 , 136 , 137 ] ( Figure 2 C).…”

“…EDII contains a conserved fusion loop (FL) peptide that becomes exposed after viral entry into cells and initiates endosomal fusion [ 42 , 43 , 49 , 50 ]. EDIII is thought to be important for receptor binding during infection, and consequently, is an important target for neutralizing Abs [ 51 , 52 , 53 , 54 , 55 , 56 ]. There is not yet a safe and effective vaccine against ZIKV that is universally available.…”