Fusogenic Conformational Changes Research Articles

The Viral Class II Membrane Fusion Machinery: Divergent Evolution from an Ancestral Heterodimer.

A key step during the entry of enveloped viruses into cells is the merger of viral and cell lipid bilayers. This process is driven by a dedicated membrane fusion protein (MFP) present at the virion surface, which undergoes a membrane–fusogenic conformational change triggered by interactions with the target cell. Viral MFPs have been extensively studied structurally, and are divided into three classes depending on their three-dimensional fold. Because MFPs of the same class are found in otherwise unrelated viruses, their intra-class structural homology indicates horizontal gene exchange. We focus this review on the class II fusion machinery, which is composed of two glycoproteins that associate as heterodimers. They fold together in the ER of infected cells such that the MFP adopts a conformation primed to react to specific clues only upon contact with a target cell, avoiding premature fusion in the producer cell. We show that, despite having diverged in their 3D fold during evolution much more than the actual MFP, the class II accompanying proteins (AP) also derive from a distant common ancestor, displaying an invariant core formed by a β-ribbon and a C-terminal immunoglobulin-like domain playing different functional roles—heterotypic interactions with the MFP, and homotypic AP/AP contacts to form spikes, respectively. Our analysis shows that class II APs are easily identifiable with modern structural prediction algorithms, providing useful information in devising immunogens for vaccine design.

Species-specific gamete recognition initiates fusion-driving trimer formation by conserved fusogen HAP2

Recognition and fusion between gametes during fertilization is an ancient process. Protein HAP2, recognized as the primordial eukaryotic gamete fusogen, is a structural homolog of viral class II fusion proteins. The mechanisms that regulate HAP2 function, and whether virus-fusion-like conformational changes are involved, however, have not been investigated. We report here that fusion between plus and minus gametes of the green alga Chlamydomonas indeed requires an obligate conformational rearrangement of HAP2 on minus gametes from a labile, prefusion form into the stable homotrimers observed in structural studies. Activation of HAP2 to undergo its fusogenic conformational change occurs only upon species-specific adhesion between the two gamete membranes. Following a molecular mechanism akin to fusion of enveloped viruses, the membrane insertion capacity of the fusion loop is required to couple formation of trimers to gamete fusion. Thus, species-specific membrane attachment is the gateway to fusion-driving HAP2 rearrangement into stable trimers.

Structural basis for human coronavirus attachment to sialic acid receptors.

Coronaviruses cause respiratory tract infections in humans and outbreaks of deadly pneumonia worldwide. Infections are initiated by the transmembrane spike (S) glycoprotein, which binds to host receptors and fuses the viral and cellular membranes. To understand the molecular basis of coronavirus attachment to oligosaccharide receptors, we determined cryo-EM structures of coronavirus OC43 S glycoprotein trimer in isolation and in complex with a 9-O-acetylated sialic acid. We show that the ligand binds with fast kinetics to a surface-exposed groove and that interactions at the identified site are essential for S-mediated viral entry into host cells, but free monosaccharide does not trigger fusogenic conformational changes. The receptor-interacting site is conserved in all coronavirus S glycoproteins that engage 9-O-acetyl-sialogycans, with an architecture similar to those of the ligand-binding pockets of coronavirus hemagglutinin esterases and influenza virus C/D hemagglutinin-esterase fusion glycoproteins. Our results demonstrate these viruses evolved similar strategies to engage sialoglycans at the surface of target cells.

Go go gadget glycoprotein!: HSV-1 draws on its sizeable glycoprotein tool kit to customize its diverse entry routes.

All viruses must enter cells to replicate [1]. Entry is thus the first hurdle a virus must overcome for a successful infection. Given the astonishing diversity of viruses that infect mammals alone—hundreds of thousands of different viruses according to some estimates [2]—it is unsurprising that their entry routes into cells are just as diverse. A major structural distinction that dictates the entry mode is the presence or absence of a lipid bilayer surrounding the viral nucleocapsid, which defines a virus as enveloped or nonenveloped, respectively. Nonenveloped viruses enter cells by endocytosis and subsequently penetrate the endosomal membrane by a variety of mechanisms including pore formation and endosomal fragmentation due to disruptive changes in membrane curvature [3], whereas all enveloped viruses must fuse their envelope with a host cell membrane: either the plasma membrane or the membrane of the endosomal vesicle following cellular uptake [4]. Regardless of the entry route, all viruses initially attach to the surface of the host cell by binding a cellular receptor. After attachment, enveloped viruses must employ fusogens—specialized viral surface glycoproteins that mediate the merger of the viral and host membranes by bringing them together as they undergo large, energetically favorable conformational changes. To do this, a spring-loaded fusogen must be triggered once the virus arrives at the right cell and/or the right intracellular compartment (such as an endosome, for example), either by binding a receptor (or a coreceptor) or by sensing the acidic pH of the endosome [4]. In many enveloped viruses, the receptor-binding and the fusogenic functions are mediated by different domains of a single glycoprotein. For example, the human immunodeficiency virus (HIV) envelope protein, Env, the sole glycoprotein encoded by HIV, binds the cellular glycoprotein cluster of differentiation 4 (CD4) and a coreceptor, C-X-C chemokine receptor 4 (CXCR4) or C-C chemokine receptor 5 (CCR5), on the surface of CD4+ T cells and also serves as the fusogen [5]. The influenza virus glycoprotein hemagglutinin binds an attachment receptor, sialic acid, and undergoes low-pH-triggered fusogenic conformational changes upon endocytosis [6]. In some cases, for example, in paramyxoviruses, the receptor-binding and the fusogenic functions are mediated by separate glycoproteins, and the fusogen receives the triggering signal from the receptor-binding viral protein [7]. Most enveloped viruses thus contain multiple copies of only one or two glycoproteins, which mediate viral attachment and entry into target cells [5–15]. Yet, entry of herpesviruses—large enveloped viruses that infect a wide variety of cells—is more complex, as it requires multiple viral glycoproteins (typically, at least three) and diverse host receptors [16]. Moreover, the coordinated activity of these multiple viral glycoproteins permits entry into different cell types by different routes. Whereas in some herpesviruses, such as human cytomegalovirus (HCMV) or Epstein–Barr virus (EBV), the use of particular entry routes correlates with the involvement of specific viral glycoprotein complexes [17, 18], in other herpesviruses, notably, herpes simplex virus type 1 (HSV-1), the picture is less clear [19]. Nonetheless, the entry mechanisms of all herpesviruses into a given cell, and particularly, the selection of the entry route, are complex and incompletely understood. The HSV-1 replication cycle in humans necessitates the infection of different cell types, chiefly, epithelial and neuronal cells. Although it is known that HSV-1 enters these cells by different mechanisms—endocytosis (epithelial cells) and fusion at the plasma membrane (neurons) [20, 21]—knowledge regarding HSV-1 glycoprotein involvement in the entry route–selection process is minimal. This raises the following question: How does HSV-1 select a particular route to enter different cell types? Although the answer remains elusive, this Pearl will summarize the current understanding of HSV-1 entry strategies and the players involved.

Unexpected Receptor Functional Mimicry Elucidates Activation of Coronavirus Fusion

Recent outbreaks of severe acute respiratory syndrome and Middle East respiratory syndrome, along with the threat of a future coronavirus-mediated pandemic, underscore the importance of finding ways to combat these viruses. The trimeric spike transmembrane glycoprotein S mediates entry into host cells and is the major target of neutralizing antibodies. To understand the humoral immune response elicited upon natural infections with coronaviruses, we structurally characterized the SARS-CoV and MERS-CoV S glycoproteins in complex with neutralizing antibodies isolated from human survivors. Although the two antibodies studied blocked attachment to the host cell receptor, only the anti-SARS-CoV S antibody triggered fusogenic conformational changes via receptor functional mimicry. These results provide a structural framework for understanding coronavirus neutralization by human antibodies and shed light on activation of coronavirus membrane fusion, which takes place through a receptor-driven ratcheting mechanism.

Species-Specific Functional Regions of the Green Alga Gamete Fusion Protein HAP2 Revealed by Structural Studies

SummaryThe cellular fusion protein HAP2, which is structurally homologous to viral class II fusion proteins, drives gamete fusion across several eukaryotic kingdoms. Gamete fusion is a highly controlled process in eukaryotes, and is allowed only between same species gametes. In spite of a conserved architecture, HAP2 displays several species-specific functional regions that were not resolved in the available X-ray structure of the green alga Chlamydomonas reinhardtii HAP2 ectodomain. Here we present an X-ray structure resolving these regions, showing a target membrane interaction surface made by three amphipathic helices in a horseshoe-shaped arrangement. HAP2 from green algae also features additional species-specific motifs inserted in regions that in viral class II proteins are critical for the fusogenic conformational change. Such insertions include a cystine ladder-like module evocative of EGF-like motifs responsible for extracellular protein-protein interactions in animals, and a mucin-like region. These features suggest potential HAP2 interaction sites involved in gamete fusion control.

Extensive Mutagenesis of the HSV-1 gB Ectodomain Reveals Remarkable Stability of Its Postfusion Form

Viral fusogens mediate the merger of the viral envelope and cellular membrane during viral entry. These proteins share little sequence similarity but all are thought to act by refolding through a series of conformational intermediates from the metastable prefusion form to the stable postfusion form. Crystal structures of both prefusion and postfusion forms have illuminated the conformational pathways of several viral fusogens. By contrast, only the structure of the postfusion form is available for glycoprotein B (gB), the conserved fusogen of herpesviruses. To gain insight into the nature of the fusogenic conformational changes in gB, we used several approaches aimed at engineering the prefusion form of the herpes simplex virus type 1 gB ectodomain, including modifications intended to stabilize the prefusion form and novel mutations aimed at destabilizing the postfusion form. We found that the postfusion conformation of gB is remarkably stable and resistant to perturbations. Several mutations successfully destabilized the gB trimer, identifying regions that are critical for the stability of the postfusion form. Yet, none of the constructs adopted the prefusion conformation. We propose that the soluble ectodomain of gB folds into the postfusion form without first adopting the prefusion intermediate. These results suggest that other regions of gB, including the transmembrane region and the cytoplasmic domain, may be necessary to establish and maintain the metastable prefusion conformation.

SnapShot: Viral and Eukaryotic Protein Fusogens

Viral Fusion Effectors Viral fusogens are anchored in the viral membrane, and the initial fusogenic conformational change allows them to insert into the cell membrane. This transition is triggered by interactions of the virus particle with the host cell—either binding a cell surface receptor or protons in the acidic endosomal environment. During the fusogenic conformational change, the fusion protein initially adopts an intermediate extended conformation in which a “fusion peptide” projects away from the virus particle and inserts into the target membrane. The fusion protein subsequently collapses into a “hairpin” conformation in which the fusion peptide becomes juxtaposed to the viral transmembrane (TM) segment, thereby juxtaposing the two membranes. The structures of the postfusion hairpin conformation for a number of viruses are presented, highlighting common structural features of the observed hairpins. The overall process of virus-cell fusion and the accompanying conformational changes of the effector proteins have been reviewed, see for example Harrison (2008). The viral fusion proteins analyzed so far fall into three structural classes in which the postfusion form is a trimer of hairpins with different architectures. The predicted location of the fused membrane is outlined above the trimers. The class I motif is characterized by a 7 residue periodicity of nonpolar amino acids (i.e.,“heptad repeats”) that give rise to a central parallel trimeric a-helical coiled coil along the long axis of a rod-shaped molecule (blue in the ribbon diagrams). The N and C termini (labeled in blue and cyan) pack against each other at the membrane proximal end. A “stutter,” a region where the coiled helix unwinds and alters the nonpolar repeat pattern (in red), permits the structural alignment of the various hairpin trimers (Igonet et al., 2011). The heptad repeats are also interrupted by hydrophilic layers (indicated in magenta, with horizontal arrows). Class II proteins are folded essentially as b sheets with no long coiled a helix, and the trimer of hairpins is formed by the parallel interactions of domains I and II (red and yellow). The trimer is further clamped in place by the lateral interactions of domain III (in blue), which stabilizes the hairpin conformation. A stem region (only partially present in the available structures) connects to the TM segment. The fusion peptide is internal, situated in the loop between two b strands, and is therefore termed “fusion loop” (FL). Class III proteins appear to be intermediate between classes I and II: they have a central parallel coiled coil (blue), but they have an elongated, b-sheet-rich fusion domain N terminal to it (yellow) instead of a fusion peptide as in class I. Although this fusion domain is superficially similar to its counterpart in class II proteins, the topological b-strand organization is unrelated, suggesting convergent rather than divergent evolution. The central parallel coiled coil also has a stutter, allowing a close alignment to the class I fusion proteins. The fusion domain of class III proteins has two fusion loops labeled FL1 and FL2. Although there is no amino acid sequence conservation across virus families, the structures show clear homology within classes II and III. However, the simple heptad repeat pattern of class I fusogens is in several cases not sufficient to distinguish between divergent or convergent evolution and therefore, only for a subset of families displayed in the figure do the fusion proteins appear as clearly homologous. Fusion of Intracellular Vesicles A variety of different proteins control the fusion of intracellular vesicles, but the actual fusion effectors are believed to be the SNARE proteins, as reviewed by Sudhof and Rothman (2009). The prefusion form of the SNAREs appears to be largely unstructured, and the postfusion form consists of a hetero-oligomeric complex formed by SNARE subunits that were anchored in the two opposing membranes before their fusion. The SNAREs in their postfusion conformation share with viral proteins of classes I and III an elongated, a-helical, parallel oligomeric coiled-coil organization in which the C-terminal TM segments are juxtaposed at the same end, making a stable protein rod termed “SNAREpin” by analogy to the viral hairpin. The SNAREpin organization differs from the viral proteins because it is a four-stranded coiled coil in which the amino acid sequence of each a helix is different. At the center, there is a hydrophilic, or “ionic,” layer consisting of a central arginine (R) and three glutamine (Q) residues that hydrogen bond the guanidinium group of the arginine. This feature has allowed the classification of the SNAREs into four different categories—R-SNAREs and Qa-, Qb-, and Qc-SNAREs—with one representative of each being necessary for formation of a functional SNAREpin, as displayed in the figure.

Computational Design of Proteins which Broadly Neutralize Influenza

Design of protein interactions is a key challenge in molecular biology and would open new routes for biomedical research and biotechnology. We developed a general computational method for designing proteins that bind a surface patch of interest on a target macromolecule. Favorable interactions between disembodied amino acid residues and the target surface are identified and used to anchor de novo designed interfaces. The method was used to design proteins that bind a conserved surface patch on the stem of the influenza hemagglutinin (HA) from the 1918 H1N1 pandemic virus. After affinity maturation, two of the designed proteins, HB36 and HB80, bind H1 (Spanish influenza) and H5 (avian influenza) HAs with picomolar affinity. Further, HB80 inhibits the HA fusogenic conformational changes induced at low pH. The crystal structure of HB36 in complex with 1918/H1 HA revealed that the actual binding interface is nearly identical to that in the computational design model. Affinity-increasing mutations isolated through experimental affinity maturation helped shed light on crucial elements which are missing in computational design calculations, such as long-range electrostatics. These have been incorporated in design calculations to improve the computational method's ability to generate de novo designed binders and inhibitors. Such designed binding proteins may be useful as diagnostics, therapeutics, and molecular probes.

X-ray structure of the arenavirus glycoprotein GP2 in its postfusion hairpin conformation

Arenaviruses are important agents of zoonotic disease worldwide. The virions expose a tripartite envelope glycoprotein complex at their surface, formed by the glycoprotein subunits GP1, GP2 and the stable signal peptide. This complex is responsible for binding to target cells and for the subsequent fusion of viral and host-cell membranes for entry. During this process, the acidic environment of the endosome triggers a fusogenic conformational change in the transmembrane GP2 subunit of the complex. We report here the crystal structure of the recombinant GP2 ectodomain of the lymphocytic choriomeningitis virus, the arenavirus type species, at 1.8-Å resolution. The structure shows the characteristic trimeric coiled coil present in class I viral fusion proteins, with a central stutter that allows a close structural alignment with most of the available structures of class I and III viral fusion proteins. The structure further shows a number of intrachain salt bridges stabilizing the postfusion hairpin conformation, one of which involves an aspartic acid that appears released from a critical interaction with the stable signal peptide upon low pH activation.

The domain I-domain III linker plays an important role in the fusogenic conformational change of the alphavirus membrane fusion protein.

The alphavirus Semliki Forest virus (SFV) infects cells through a low-pH-dependent membrane fusion reaction mediated by the virus fusion protein E1. Acidic pH initiates a series of E1 conformational changes that culminate in membrane fusion and include dissociation of the E1/E2 heterodimer, insertion of the E1 fusion loop into the target membrane, and refolding of E1 to a stable trimeric hairpin conformation. A highly conserved histidine (H3) on the E1 protein was previously shown to promote low-pH-dependent E1 refolding. An SFV mutant with an alanine substitution at this position (H3A) has a lower pH threshold and reduced efficiency of virus fusion and E1 trimer formation than wild-type SFV. Here we addressed the mechanism by which H3 promotes E1 refolding and membrane fusion. We identified E1 mutations that rescue the H3A defect. These revertants implicated a network of interactions that connect the domain I-domain III (DI-DIII) linker region with the E1 core trimer, including H3. In support of the importance of these interactions, mutation of residues in the network resulted in more acidic pH thresholds and reduced efficiencies of membrane fusion. In vitro studies of truncated E1 proteins demonstrated that the DI-DIII linker was required for production of a stable E1 core trimer on target membranes. Together, our results suggest a critical and previously unidentified role for the DI-DIII linker region during the low-pH-dependent refolding of E1 that drives membrane fusion.

Structural Basis of Local, pH-Dependent Conformational Changes in Glycoprotein B from Herpes Simplex Virus Type 1

Herpesviruses enter cells by membrane fusion either at the plasma membrane or in endosomes, depending on the cell type. Glycoprotein B (gB) is a conserved component of the multiprotein herpesvirus fusion machinery and functions as a fusion protein, with two internal fusion loops, FL1 and FL2. We determined the crystal structures of the ectodomains of two FL1 mutants of herpes simplex virus type 1 (HSV-1) gB to clarify whether their fusion-null phenotypes were due to global or local effects of the mutations on the structure of the gB ectodomain. Each mutant has a single point mutation of a hydrophobic residue in FL1 that eliminates the hydrophobic side chain. We found that neither mutation affected the conformation of FL1, although one mutation slightly altered the conformation of FL2, and we conclude that the fusion-null phenotype is due to the absence of a hydrophobic side chain at the mutated position. Because the ectodomains of the wild-type and the mutant forms of gB crystallized at both low and neutral pH, we were able to determine the effect of pH on gB conformation at the atomic level. For viruses that enter cells by endocytosis, the low pH of the endosome effects major conformational changes in their fusion proteins, thereby promoting fusion of the viral envelope with the endosomal membrane. We show here that upon exposure of gB to low pH, FL2 undergoes a major relocation, probably driven by protonation of a key histidine residue. Relocation of FL2, as well as additional small conformational changes in the gB ectodomain, helps explain previously noted changes in its antigenic and biochemical properties. However, no global pH-dependent changes in gB structure were detected in either the wild-type or the mutant forms of gB. Thus, low pH causes local conformational changes in gB that are very different from the large-scale fusogenic conformational changes in other viral fusion proteins. We propose that these conformational changes, albeit modest, play an important functional role during endocytic entry of HSV.

The Disulfide Bonds in Glycoprotein E2 of Hepatitis C Virus Reveal the Tertiary Organization of the Molecule

Hepatitis C virus (HCV), a major cause of chronic liver disease in humans, is the focus of intense research efforts worldwide. Yet structural data on the viral envelope glycoproteins E1 and E2 are scarce, in spite of their essential role in the viral life cycle. To obtain more information, we developed an efficient production system of recombinant E2 ectodomain (E2e), truncated immediately upstream its trans-membrane (TM) region, using Drosophila melanogaster cells. This system yields a majority of monomeric protein, which can be readily separated chromatographically from contaminating disulfide-linked aggregates. The isolated monomeric E2e reacts with a number of conformation-sensitive monoclonal antibodies, binds the soluble CD81 large external loop and efficiently inhibits infection of Huh7.5 cells by infectious HCV particles (HCVcc) in a dose-dependent manner, suggesting that it adopts a native conformation. These properties of E2e led us to experimentally determine the connectivity of its 9 disulfide bonds, which are strictly conserved across HCV genotypes. Furthermore, circular dichroism combined with infrared spectroscopy analyses revealed the secondary structure contents of E2e, indicating in particular about 28% β-sheet, in agreement with the consensus secondary structure predictions. The disulfide connectivity pattern, together with data on the CD81 binding site and reported E2 deletion mutants, enabled the threading of the E2e polypeptide chain onto the structural template of class II fusion proteins of related flavi- and alphaviruses. The resulting model of the tertiary organization of E2 gives key information on the antigenicity determinants of the virus, maps the receptor binding site to the interface of domains I and III, and provides insight into the nature of a putative fusogenic conformational change.

A Rotavirus Spike Protein Conformational Intermediate Binds Lipid Bilayers

During rotavirus entry, a virion penetrates a host cell membrane, sheds its outer capsid proteins, and releases a transcriptionally active subviral particle into the cytoplasm. VP5, the rotavirus protein believed to interact with the membrane bilayer, is a tryptic cleavage product of the outer capsid spike protein, VP4. When a rotavirus particle uncoats, VP5 folds back, in a rearrangement that resembles the fusogenic conformational changes in enveloped-virus fusion proteins. We present direct experimental evidence that this rearrangement leads to membrane binding. VP5 does not associate with liposomes when mounted as part of the trypsin-primed spikes on intact virions, nor does it do so after it has folded back into a stably trimeric, low-energy state. But it does bind liposomes when they are added to virions before uncoating, and VP5 rearrangement is then triggered by addition of EDTA. The presence of liposomes during the rearrangement enhances the otherwise inefficient VP5 conformational change. A VP5 fragment, VP5CT, produced from monomeric recombinant VP4 by successive treatments with chymotrypsin and trypsin, also binds liposomes only when the proteolysis proceeds in their presence. A monoclonal antibody that neutralizes infectivity by blocking a postattachment entry event also blocks VP5 liposome association. We propose that VP5 binds lipid bilayers in an intermediate conformational state, analogous to the extended intermediate conformation of enveloped-virus fusion proteins.

Crystal Structure of Dengue Virus Type 1 Envelope Protein in the Postfusion Conformation and Its Implications for Membrane Fusion

Dengue virus relies on a conformational change in its envelope protein, E, to fuse the viral lipid membrane with the endosomal membrane and thereby deliver the viral genome into the cytosol. We have determined the crystal structure of a soluble fragment E (sE) of dengue virus type 1 (DEN-1). The protein is in the postfusion conformation even though it was not exposed to a lipid membrane or detergent. At the domain I-domain III interface, 4 polar residues form a tight cluster that is absent in other flaviviral postfusion structures. Two of these residues, His-282 and His-317, are conserved in flaviviruses and are part of the "pH sensor" that triggers the fusogenic conformational change in E, at the reduced pH of the endosome. In the fusion loop, Phe-108 adopts a distinct conformation, forming additional trimer contacts and filling the bowl-shaped concavity observed at the tip of the DEN-2 sE trimer.