Abstract
As a major surface glycoprotein of enveloped viruses, the virus spike protein is a primary target for vaccines and anti-viral treatments. Current vaccines aiming at controlling the COVID-19 pandemic are mostly directed against the SARS-CoV-2 spike protein. To promote virus entry and facilitate immune evasion, spikes must be dynamic. Interactions with host receptors and coreceptors trigger a cascade of conformational changes/structural rearrangements in spikes, which bring virus and host membranes in proximity for membrane fusion required for virus entry. Spike-mediated viral membrane fusion is a dynamic, multi-step process, and understanding the structure–function-dynamics paradigm of virus spikes is essential to elucidate viral membrane fusion, with the ultimate goal of interventions. However, our understanding of this process primarily relies on individual structural snapshots of endpoints. How these endpoints are connected in a time-resolved manner, and the order and frequency of conformational events underlying virus entry, remain largely elusive. Single-molecule Förster resonance energy transfer (smFRET) has provided a powerful platform to connect structure–function in motion, revealing dynamic aspects of spikes for several viruses: SARS-CoV-2, HIV-1, influenza, and Ebola. This review focuses on how smFRET imaging has advanced our understanding of virus spikes’ dynamic nature, receptor-binding events, and mechanism of antibody neutralization, thereby informing therapeutic interventions.
Highlights
Virus spikes on the surface of enveloped viruses are often viral fusion proteins that mediate the fusion between viral membranes and cellular membranes (Figure 1) essential for virus entry [1,2,3]
Kinetic analyses deployed in Single-molecule Förster resonance energy transfer (smFRET) include the transition density for state-to-state transition, the hidden Markov modeling for idealizing molecular motions, and dwelling time for estimating transitional rates. Results from these analyses revealed dynamic aspects of S: (1) connecting extant high-resolution structural snapshots in time with the scale ranging from milliseconds to seconds, (2) S exhibiting a defined transition order between four distinct conformations, (3) ligand-free S being in a dynamic equilibrium of four different states, (4) host receptor human angiotensin-converting enzyme 2 (hACE2) re-equilibrating the balance by accelerating transitions into the activated state, and
Scientific observations that support the conclusion of vaccine candidate SOSIP resembling State 2 Env are from several lines of evidence [25]: (1) smFRET reveals that the SOS modification in Env is mostly responsible for the conformational shift of SOSIP.664 towards State 2; (2) multi-dimensional static and dynamic observations of native Env on the viruses validated State 1 Env dominant in ligand-free virus Env; (3) conformational preferences for States 1 and 2 observed in smFRET can be detected using conventional bulk measurement ELISA and flow cytometry; (4) SOSIP-elicited antibodies exhibit a preference for State 2, and the preference is independent of epitopes (CD4 binding site, glycan hole, fusion peptide) and hosts
Summary
Virus spikes on the surface of enveloped viruses are often viral fusion proteins that mediate the fusion between viral membranes and cellular membranes (Figure 1) essential for virus entry [1,2,3]. The genetically encoded copperdyes on unnatural amino acids by copper-free click chemistry [55,56] Both enzymatic and free click chemistry allowstoreading through introduced stop viruses codons amber-click methods(amber-click) have been applied study virus spikes for manyamber enveloped on the protein of interest as unnatural amino acids through amber suppression, followed to reveal dynamic aspects during viral membrane fusion [22,23,24,25,26,27,28,29,30,31]. Both enzymatic and amber-click methods have been applied to study
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