Viral Fusion Proteins Research Articles

Adaption of a conventional ELISA to a 96-well ELISA-Array for measuring the antibody responses to influenza virus proteins and vaccines

We describe an adaptation of conventional ELISA methods to an ELISA-Array format using non-contact Piezo printing of up to 30 spots of purified recombinant viral fusion proteins and vaccine on 96 well high-protein binding plates. Antigens were printed in 1 nanoliter volumes of protein stabilizing buffer using as little as 0.25 nanograms of protein, 2000-fold less than conventional ELISA. The performance of the ELISA-Array was demonstrated by serially diluting n = 9 human post-flu vaccination plasma samples starting at a 1/1000 dilution and measuring binding to the array of Influenza antigens. Plasma polyclonal antibody levels were detected using a cocktail of biotinylated anti-human kappa and lambda light chain antibodies, followed by a Streptavidin-horseradish peroxidase conjugate and the dose-dependent signal was developed with a precipitable TMB substrate. Intra- and inter-assay precision of absorbance units among the eight donor samples showed mean CVs of 4.8% and 10.8%, respectively. The plasma could be differentiated by donor and antigen with titer sensitivities ranging from 1 × 103 to 4 × 106, IC50 values from 1 × 104 to 9 × 106, and monoclonal antibody sensitivities in the ng/mL range. Equivalent sensitivities of ELISA versus ELISA-Array, compared using plasma and an H1N1 HA trimer, were achieved on the ELISA-Array printed at 0.25 ng per 200um spot and 1000 ng per ELISA 96-well. Vacuum-sealed array plates were shown to be stable when stored for at least 2 days at ambient temperature and up to 1 month at 4–8 °C. By the use of any set of printed antigens and analyte matrices the methods of this multiplexed ELISA-Array format can be broadly applied in translational research.

Structural monitoring of a transient intermediate in the hemagglutinin fusion machinery on influenza virions.

The influenza virus hemagglutinin (HA) fusion protein has long been viewed as a "spring-loaded" fusion machine whereby activation at low pH initiates a rapid and irreversible cascade of conformational changes that drives the membrane fusion reaction. This mechanism has shaped our understanding of how type 1 viral fusion proteins function as a whole. Experimental limitations have hindered efforts to expand our mechanistic and structural understanding of viral membrane fusion. Here, we used pulse-labeling hydrogen/deuterium exchange mass spectrometry and cryo-electron tomography to monitor and characterize the structural dynamics of HA during fusion activation on intact virions. Our data reveal how concurrent reorganizations at the HA1 receptor binding domain interface and HA2 fusion subunit produce a dynamic fusion intermediate ensemble in full-length HA. The soluble HA ectodomain transitions directly to the postfusion state with no observable intermediate.

Accelerated Discovery of Potent Fusion Inhibitors for Respiratory Syncytial Virus.

A series of five benzimidazole-based compounds were identified using a machine learning algorithm as potential inhibitors of the respiratory syncytial virus (RSV) fusion protein. These compounds were synthesized, and compound 2 in particular exhibited excellent in vitro potency with an EC50 value of 5 nM. This new scaffold was then further refined leading to the identification of compound 44, which exhibited a 10-fold improvement in activity with an EC50 value of 0.5 nM.

New Biophysical Approaches Reveal the Dynamics and Mechanics of Type I Viral Fusion Machinery and Their Interplay with Membranes.

Protein-mediated membrane fusion is a highly regulated biological process essential for cellular and organismal functions and infection by enveloped viruses. During viral entry the membrane fusion reaction is catalyzed by specialized protein machinery on the viral surface. These viral fusion proteins undergo a series of dramatic structural changes during membrane fusion where they engage, remodel, and ultimately fuse with the host membrane. The structural and dynamic nature of these conformational changes and their impact on the membranes have long-eluded characterization. Recent advances in structural and biophysical methodologies have enabled researchers to directly observe viral fusion proteins as they carry out their functions during membrane fusion. Here we review the structure and function of type I viral fusion proteins and mechanisms of protein-mediated membrane fusion. We highlight how recent technological advances and new biophysical approaches are providing unprecedented new insight into the membrane fusion reaction.

Design and Synthesis of 2-(1-Alkylaminoalkyl)pyrazolo[1,5-a]pyrimidines as New Respiratory Syncytial Virus Fusion Protein Inhibitors.

Respiratory syncytial virus (RSV) is one of the most common causes of lower respiratory tract infections and a significant pathogen for both adults and children. Although two drugs have been approved for the treatment of RSV infections, the low therapeutic index of these drugs have led pharmaceutical companies to develop safe and effective small-molecule anti-RSV drugs. The pyrazolo[1,5-a]pyrimidine series of compounds containing a piperidine ring at the 2-position of the pyrazolo[1,5-a]pyrimidine scaffold are known as candidate RSV fusion (F) protein inhibitor drugs, such as presatovir and P3. The piperidine ring has been revealed to facilitate the formation of an appropriate dihedral angle between the pyrazolo[1,5-a]pyrimidine scaffold and the plane of the amide bond for exertion of anti-RSV activity. A molecular-dynamic study on newly designed compounds with an acyclic chain instead of the piperidine ring proposed and demonstrated a new series of pyrazolo[1,5-a]pyrimidine derivatives, such as 9c with a 1-methyaminopropyl moiety, showing similar dihedral angle distributions to those in presatovir. Compound 9c exhibited potent anti-RSV activity with an EC50 value of below 1 nM, which was similar to that of presatovir. A subsequent optimization study on the benzene ring of 9c led to the potent RSV F protein inhibitor 14f with an EC50 value of 0.15 nM. The possibility of improving the biological properties of anti-RSV agents by modification at the 7-position of pyrazolo[1,5-a]pyrimidine is also discussed.

Computational design of closely related proteins that adopt two well-defined but structurally divergent folds

The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used for de novo design of proteins that fold to a single state with a deep free-energy minimum [P.-S. Huang, S. E. Boyken, D. Baker, Nature 537, 320-327 (2016)], and to reengineer natural proteins to alter their dynamics [J. A. Davey, A. M. Damry, N. K. Goto, R. A. Chica, Nat. Chem. Biol. 13, 1280-1285 (2017)] or fold [P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan, Proc. Natl. Acad. Sci. U.S.A. 106, 21149-21154 (2009)], the de novo design of closely related sequences which adopt well-defined but structurally divergent structures remains an outstanding challenge. We designed closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations-one short (∼66 Å height) and the other long (∼100 Å height)-reminiscent of the conformational transition of viral fusion proteins. Crystallographic and NMR spectroscopic characterization shows that both the short- and long-state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates either the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large-scale conformational switches between structurally divergent forms.

Correction for Samal et al., "Mutations in the Cytoplasmic Domain of the Newcastle Disease Virus Fusion Protein Confer Hyperfusogenic Phenotypes Modulating Viral Replication and Pathogenicity".

Volume 87, no. 18, p. 10083–10093, 2013, https://doi.org/10.1128/JVI.01446-13. Figure 6A: Due to errors in figure assembly, the rWt and rY527A panels in the E-cadherin column (column 2, rows 2 and 4 from the top) are identical images, and the rWT panel in the DAPI column (column 1, row 2) and the Mock panel in the Merge column (column 4, row 1) are identical images.

Proteomics Computational Analyses Suggest That the Envelope Glycoproteins of Segmented Jingmen Flavi-Like Viruses are Class II Viral Fusion Proteins (b-Penetrenes) with Mucin-Like Domains.

Jingmen viruses are newly described segmented flavi-like viruses that have a worldwide distribution in ticks and have been associated with febrile illnesses in humans. Computational analyses were used to predict that Jingmen flavi-like virus glycoproteins have structural features of class II viral fusion proteins, including an ectodomain consisting of beta-sheets and short alpha-helices, a fusion peptide with interfacial hydrophobicity and a three-domain architecture. Jingmen flavi-like virus glycoproteins have a sequence enriched in serine, threonine, and proline at the amino terminus, which is a feature of mucin-like domains. Several of the serines and threonines are predicted be modified by the addition of O-linked glycans. Some of the glycoproteins are predicted to have an additional mucin-like domain located prior to the transmembrane anchor, whereas others are predicted to have a stem consisting of two alpha-helices. The flavivirus envelope protein and Jingmen flavi-virus glycoproteins may have diverged from a common class II precursor glycoprotein with a mucin-like domain or domains acquired after divergence.

Rational modifications, synthesis and biological evaluation of new potential antivirals for RSV designed to target the M2-1 protein

Respiratory syncytial virus (RSV) is the main cause of lower respiratory tract diseases in infants and young children, with potentially serious and fatal consequences associated with severe infections. Despite extensive research efforts invested in the identification of therapeutic measures, no vaccine is currently available, while treatment options are limited to ribavirin and palivizumab, which both present significant limitations. While clinical and pre-clinical candidates mainly target the viral fusion protein, the nucleocapsid protein or the viral polymerase, our focus has been the identification of new antiviral compounds targeting the viral M2-1 protein, thanks to the presence of a zinc-ejecting group in their chemical structure. Starting from an anti-RSV hit we had previously identified with an in silico structure-based approach, we have designed, synthesised and evaluated a new series of dithiocarbamate analogues, with which we have explored the antiviral activity of this scaffold. The findings presented in this work may provide the basis for the identification of a new antiviral lead to treat RSV infections.

Evaluation of Plasmodium vivax HAP2 as a transmission-blocking vaccine candidate

Transmission-blocking vaccine (TBV) is a promising strategy to interfere with the transmission of malaria. To date, only limited TBV candidate antigens have been identified for Plasmodium vivax. HAP2 is a gamete membrane fusion protein, with homology to the class II viral fusion proteins. Herein we reported the characterization of the PvHAP2 for its potential as a TBV candidate for P. vivax. The HAP2/GCS1 domain of PvHAP2 was expressed in the baculovirus expression system and the recombinant protein was used to raise antibodies in rabbits. Indirect immunofluorescence assays showed that anti-PvHAP2 antibodies reacted only with the male gametocytes on blood smears. Direct membrane feeding assays were conducted using four field P. vivax isolates in Anopheles dirus. At a mean infection intensity of 72.4, 70.7, 51.3, and 15.6 oocysts/midgut with the control antibodies, anti-PvHAP2 antibodies significantly reduced the midgut oocyst intensity by 40.3, 44.4, 61.9, and 89.7%. Whereas the anti-PvHAP2 antibodies were not effective in reducing the infection prevalence at higher parasite exposure (51.3–72.4 oocysts/midgut in the control group), the anti-PvHAP2 antibodies reduced infection prevalence by 50% at a low challenge (15.6 oocysts/midgut). Multiple sequence alignment showed 100% identity among these Thai P. vivax isolates, suggesting that polymorphism may not be an impediment for the utilization of PvHAP2 as a TBV antigen. In conclusion, our results suggest that PvHAP2 could serve as a TBV candidate for P. vivax, and further optimization and evaluation are warranted.

Enhanced Uptake and Endosomal Release of LbL Microcarriers Functionalized with Reversible Fusion Proteins

The efficient application of smart drug-delivery systems requires further improvement of their cellular uptake and in particular their release from endolysosomal compartments into the cytoplasm of target cells. The usage of virus proteins allows for such developments, as viruses have evolved efficient entry mechanisms into the cell, mediated by their fusion proteins. In our investigations, the transferability of the glycoprotein G which is a fusion protein of the vesicular stomatitis virus (VSV-G) onto the surface of a layer-by-layer (LbL) designed microcarrier was investigated. The assembly of VSV-G as a reversible viral fusion protein onto LbL microcarriers indeed induced an enhanced uptake rate on Vero cells as well as a fast and efficient release of the intact carriers from endolysosomes into the cytoplasm. Additionally, neither virus-associated effects on cellular viability nor activation of an interferon response were detected. Our study emphasizes the suitability of VSV-G as an efficient surface functionalization of drug-delivery systems.

SNAREs, tethers and SM proteins: how to overcome the final barriers to membrane fusion?

Physiological membrane vesicles are built to separate reaction spaces in a stable manner, even when they accidentally collide or are kept in apposition by spatial constraints in the cell. This requires a natural resistance to fusion and mixing of their content, which originates from substantial energetic barriers to membrane fusion [1]. To facilitate intracellular membrane fusion reactions in a controlled manner, proteinaceous fusion machineries have evolved. An important open question is whether protein fusion machineries actively pull the fusion reaction over the present free energy barriers, or whether they rather catalyze fusion by lowering those barriers. At first sight, fusion proteins such as SNARE complexes and viral fusion proteins appear to act as nano-machines, which mechanically transduce force to the membranes and thereby overcome the free energy barriers [2,3]. Whether fusion proteins additionally alter the free energy landscape of the fusion reaction via catalytic roles is less obvious. This is a question that we shall discuss in this review, with particular focus on the influence of the eukaryotic SNARE-dependent fusion machinery on the final step of the reaction, the formation and expansion of the fusion pore.

Peptide Inhibitors of Viral Membrane Fusion

Lipid-enveloped viruses, including HIV-1 and SARS-CoV-2, infect their host cells by fusion either directly with the plasma membrane or with the endosome membrane following endocytosis. Biophysical insights into the conformational changes of viral fusion proteins have led to the development of peptide inhibitors of these changes, and hence of membrane fusion. The peptide T-20 (Enfuvirtide) inhibits HIV-1-cell fusion and is being used clinically. The cholesterol-conjugated C34 peptide has an IC50 of 4 pM for inhibiting HIV-1 infectivity, much lower than that of plain C34 and T-20. A peptide (P155-185-chol) corresponding to a segment of the post-fusion structure of influenza virus hemagglutinin, also coupled to cholesterol, inhibits infection by the A/H3N2 subtype with an IC50 of 0.4 μM. Myrcludex B, a myristoylated lipopeptide, inhibits the entry of hepatitis B virus and hepatitis D virus into hepatocytes with an IC50 of 80 pM. Dimer peptides (HRC2 and HRX4) derived from the measles virus F-protein and coupled to cholesterol inhibit measles virus infection at IC50 values of less than 1 nM to 2 nM. Peptides derived from the E protein of Japanese encephalitis virus inhibit infection at nanomolar IC50 values.  The COVID-19 pandemic has prompted numerous studies to design peptide inhibitors of the SARS-CoV-2 spike protein-mediated membrane fusion. The coupling of a lipidic anchor like cholesterol to some of these peptides enhances the antiviral effect of the peptides, lowering the IC50 to low nanomolar concentrations. It is highly likely that peptides against SARS-CoV-2 will soon be evaluated in clinical trials.

Cryo-EM structure of the prefusion state of canine distemper virus fusion protein ectodomain

Measles virus (MeV) and canine distemper virus (CDV), two members of the Morbillivirus genus, are still causing important global diseases of humans and animals, respectively. To enter target cells, morbilliviruses rely on an envelope-anchored machinery, which is composed of two interacting glycoproteins: a tetrameric receptor binding (H) protein and a trimeric fusion (F) protein. To execute membrane fusion, the F protein initially adopts a metastable, prefusion state that refolds into a highly stable postfusion conformation as the result of a finely coordinated activation process mediated by the H protein. Here, we employed cryo-electron microscopy (cryo-EM) and single particle reconstruction to elucidate the structure of the prefusion state of the CDV F protein ectodomain (solF) at 4.3 Å resolution. Stabilization of the prefusion solF trimer was achieved by fusing the GCNt trimerization sequence at the C-terminal protein region, and expressing and purifying the recombinant protein in the presence of a morbilliviral fusion inhibitor class compound. The three-dimensional cryo-EM map of prefusion CDV solF in complex with the inhibitor clearly shows density for the ligand at the protein binding site suggesting common mechanisms of membrane fusion activation and inhibition employed by different morbillivirus members.

Integrating Duodenal Sampling in a Human Mass Balance Study to Quantify the Elimination Pathways of JNJ-53718678, a Respiratory Syncytial Virus Fusion Protein Inhibitor.

The study objective was to characterize the excretion and metabolic profile of the respiratory syncytial virus fusion protein inhibitor, JNJ-53718678. Prior animal and in vitro studies suggested three main elimination pathways: N-glucuronidation to M8; CYP(3A4) metabolism leading to circulating metabolites M5, M12, M19 and M37; and JNJ-53718678 biliary excretion. To gain insight into the relative contribution of JNJ-53718678 and M8 biliary excretion, duodenal fluid sampling was incorporated into this mass balance study. A single oral dose of 500mg 14C-JNJ-53718678 was administered to six healthy male subjects. Four hours after study drug intake, gallbladder contraction was stimulated and duodenal fluid samples were collected. JNJ-53718678, its key circulating metabolites and total radioactivity (TR) were quantified in plasma, feces, urine and duodenal fluid. Safety was monitored throughout. JNJ-53718678 and M12 represented 47.4% and 17.8%, respectively, of TR area under the curve (AUC)∞ in plasma. M37 (9.6%), M19 (5.2%), M5 (4.3%) and M8 (1.4%) were minor metabolites; 70.6% of TR was recovered in feces and 19.9% in urine. Duodenal fluid concentrations (% of TR) were highest for JNJ-53718678 (11.6%) followed by M8 (10.4%), M5 (5.9%) and M12 (1.1%). In feces, 10-16% of TR was JNJ-53718678, 5-8% M5, < 1% M12 and < 1% M8. N-glucuronidation to M8 and direct biliary excretion of JNJ-53718678 represented 7% and 8% of drug clearance, respectively. JNJ-53718678 was safe and well tolerated. JNJ-53718678 is primarily eliminated through CYP3A4-mediated metabolism. By integrating duodenal sampling, N-glucuronidation was confirmed as another metabolic pathway despite the low amount of M8 excreted in urine and feces. Eudract no. 2016-002664-14.

Antiviral activity of phage display-selected peptides against Japanese encephalitis virus infection in vitro and in vivo

Japanese Encephalitis virus (JEV) is a zoonotic flavivirus that is the most significant etiological agent of childhood viral neurological infections. However, no specific antiviral drug is currently available to treat JEV infections. The JEV envelope (E) protein is a class II viral fusion protein that mediates host cell entry, making interference with the interaction between the E protein of JEV and its cognate receptors an attractive strategy for anti-JEV drug development. In this study, we identified a peptide derived from a phage display peptide library against the E protein of JEV, designated P1, that potentially inhibits in vitro and in vivo JEV infections. P1 inhibits JEV infection in BHK-21 cells with 50% inhibitory capacity at a concentration of 35.9 μM. The time-of-addition assay indicates that JEV replication is significantly inhibited during pre-infection and co-infection of P1 with JEV while post-infection treatments with P1 have very little impact on JEV proliferation, showing that P1 inhibits JEV infection at early stages and indicating the potential prophylactic effect of P1. We adapted an in vitro BiFC assay system and demonstrated that P1 interacts with JEV E proteins and blocks their entry into cells. We also evaluated the therapeutic efficacy of P1 in a lethal JEV mouse model exhibiting systemic and brain infections. Interestingly, P1 treatment protected C57BL/6 mice against mortality, markedly reduced the viral loads in blood and brain, and diminished the histopathological lesions in the brain cells. In addition to controlling systemic infection, P1 has a very low level of cytotoxicity and acts in a sequence-specific manner, as scrambled peptide sP1 does not show any antiviral activity. In conclusion, our in vitro and in vivo experimental findings show that P1 possesses antiviral activity against JEV infections, is safe to use, and has potential for further development as an antiviral treatment against JEV infections.

Alphavirus E1 fusion protein: alternative conformations of the post-fusion trimer depending on the alphavirus

Background. Some of the best characterized alphaviruses are chikungunya virus (CHIKV), Semliki Forest virus (SFV) and Sindbis virus (SINV). E1 is a class II fusion protein, containing 3 domains (DI, DII, DIII) folded essentially as β-sheet, plus a stem region connecting DIII to the transmembrane (TM) segment. The fusion loop (FL) is at the tip of the elongated DII. The X-ray structure of the SFV E1 post-fusion trimer, truncated of the stem region, displayed a tripod-shape with the DII legs open and the FLs away from each other, contrary to the class II viral fusion proteins from other viral genera, in which the FLs interact at the tip of the post-fusion trimer. Here, we set to identify if the stem plays a structural role in zippering together the E1 trimer to bring the fusion loops into contact. Methods. We produced the recombinant ectodomains of E1 of CHIKV, SINV and SFV containing or not the stem, crystallized them and determined the X-ray structure. Results. We observed that CHIKV and SINV display E1 in closed conformation, in contrast to SFV, which displays a tripod even with the full stem. We identified a sequence motif in the stem responsible for the conformational difference. Conclusion. Our results point to potential mechanistic differences between alphavirus E1 in driving fusion. Further functional studies are ongoing to pin-point the significance of these new findings, and the reasons for the alternative post-fusion conformations.

2620. Respiratory Syncytial Virus Rapid Antigen Detection Test, Can It Be Trusted?

BackgroundMany emergency departments and urgent care settings use the commonly available Respiratory Syncytial Virus Rapid Antigen Detection Test (RSV RADT) to diagnose children with RSV. We noted discordant results between RADT and definitive testing. Our study looked at the positive predictive value (PPV) and the false discovery rate (FDR) of the RSV RADT at our facility.MethodsWe pro- and retrospectively reviewed all patients with positive RSV RAPD tests from July 1, 2017 through March 31, 2019. The test utilized was the QuickVue® RSV Test Kit (QUIDEL Corp, CA, USA), which detects the viral fusion protein present in RSV. Of the tests performed, we chose patients who had definitive testing with either a direct fluorescent antibody (DFA) or a polymerase chain reaction (PCR). We then calculated the PPV as well as the FDR of the RSV RADT during the total interval period, as well as off-season periods (April 1 through October 31) and in-season periods (November 1 through March 31).ResultsDuring the study period there were 1128 RSV RADT tests performed, of which 232 had definitive testing with either DFA or PCR (Figures 1 and 2). We found the overall PPV during the study period was 63.3%. During the off-season 30 positive RSV RADT received definitive testing, of which 6 were positive, which yields a PPV of only 20%. In season, 202 RSV RADT received additional testing with 141 positive for RSV. The PPV was 69.8%. The FDR correlated with 36.7% throughout the entire studied period, 80% during the off-season and 30.2% during in-season. As expected, the PPV was higher during times of higher prevalence (Figure 3).ConclusionBased on our results, utilization of the RSV RADT during time of low prevalence yields a high false detection rate and should therefore be discouraged. The use during times of high prevalence yields only modest results and is unlikely to aid in clinical decision-making. Our results differ from those published by the manufacturer (PPV 84%), and may reflect differences in sample collection in the acute care setting. Disclosures All authors: No reported disclosures.

High-Affinity DARPin Allows Targeting of MeV to Glioblastoma Multiforme in Combination with Protease Targeting without Loss of Potency

Measles virus (MeV) is naturally cytolytic by extensive cell-to-cell fusion. Vaccine-derived MeV is toxic for cancer cells and is clinically tested as oncolytic virus. To combine the potential of MeV with enhanced safety, different targeting strategies have been described. We generated a receptor-targeted MeV by using receptor-blind viral attachment protein genetically fused to designed ankyrin repeat protein (DARPin) binding domains specific for the epidermal growth factor receptor (EGFR). To reduce on-target toxicity for EGFR+ healthy cells, we used an engineered viral fusion protein activatable by tumor-associated matrix metalloproteases (MMPs) for additional protease targeting. The dual-targeted virus replicated exclusively on EGFR+/MMP+ tumor cells but was safe on healthy EGFR+ target cells, primary human keratinocytes. Nevertheless, glioblastoma and other tumor cells were efficiently killed by all targeted viruses, although replication and oncolysis were slower for protease-targeted MeV. In vivo, efficacy of EGFR-targeted MeV was virtually unimpaired, whereas also dual-targeted MeV showed significant intra-tumoral spread and efficacy and could be armed with a prodrug convertase. The use of DARPin-domains resulted in potent EGFR-targeted MeV and for the first time effective dual retargeting of an oncolytic virus, further enhancing tumor selectivity. Together with powerful cell-toxic genes, the application as highly tumor-specific platform is promising.

Biochemical Analysis of Coronavirus Spike Glycoprotein Conformational Intermediates during Membrane Fusion.

A fusion protein expressed on the surface of enveloped viruses mediates fusion of the viral and cellular membranes to facilitate virus infection. Pre- and postfusion structures of viral fusion proteins have been characterized, but conformational changes between them remain poorly understood. Here, we examined the intermediate conformation of the murine coronavirus fusion protein, called the spike protein, which must be cleaved by a cellular protease following receptor binding. Western blot analysis of protease digestion products revealed that two subunits (67 and 69 kDa) are produced from a single spike protein (180 kDa). These two subunits were considered to be by-products derived from conformational changes and were useful for probing the intermediate conformation of the spike protein. Interaction with a heptad repeat (HR) peptide revealed that these subunits adopt packed and unpacked conformations, respectively, and two-dimensional electrophoresis revealed a trimeric assembly. Based on biochemical observations, we propose an asymmetric trimer model for the intermediate structure of the spike protein. Receptor binding induces the membrane-binding potential of the trimer, in which at least one HR motif forms a packed-hairpin structure, while membrane fusion subunits are covered by the receptor-binding subunit, thereby preventing the spike protein from forming the typical homotrimeric prehairpin structure predicted by the current model of class I viral fusion protein. Subsequent proteolysis induces simultaneous packing of the remaining unpacked HRs upon assembly of three HRs at the central axis to generate a six-helix bundle. Our model proposes a key mechanism for membrane fusion of enveloped viruses.IMPORTANCE Recent studies using single-particle cryo-electron microscopy (cryoEM) revealed the mechanism underlying activation of viral fusion protein at the priming stage. However, characterizing the subsequent triggering stage underpinning transition from pre- to postfusion structures is difficult because single-particle cryoEM excludes unstable structures that appear as heterogeneous shapes. Therefore, population-based biochemical analysis is needed to capture features of unstable proteins. Here, we analyzed protease digestion products of a coronavirus fusion protein during activation; their sizes appear to be affected directly by the conformational state. We propose a model for the viral fusion protein in the intermediate state, which involves a compact structure and conformational changes that overcome steric hindrance within the three fusion protein subunits.