scholarly journals A trimeric hydrophobic zipper mediates the intramembrane assembly of SARS-CoV-2 spike

2021 ◽  
Author(s):  
Qingshan Fu ◽  
James J Chou
Keyword(s):  
Transmembrane Domain ◽  
Structural Information ◽  
Heptad Repeat ◽  
Host Immune System ◽  
Type I ◽  
Fold Axis ◽  
Viral Fusion ◽  
S Protein ◽  
Viral Fusion Protein ◽  
Exact Function

The S protein of the SARS-CoV-2 is a Type I membrane protein that mediates membrane fusion and viral entry. A vast amount of structural information is available for the ectodomain of S, a primary target by the host immune system, but much less is known regarding its transmembrane domain (TMD) and its membrane-proximal regions. Here, we determined the nuclear magnetic resonance (NMR) structure of the S protein TMD in bicelles that closely mimic a lipid bilayer. The TMD structure is a transmembrane α-helix (TMH) trimer that assembles spontaneously in membrane. The trimer structure shows an extensive hydrophobic core along the 3-fold axis that resembles that of a trimeric leucine/isoleucine zipper, but with tetrad, not heptad, repeat. The trimeric core is strong in bicelles, resisting hydrogen-deuterium exchange for weeks. Although highly stable, structural guided mutagenesis identified single mutations that can completely dissociate the TMD trimer. Multiple studies have shown that the membrane anchor of viral fusion protein can form highly specific oligomers, but the exact function of these oligomers remain unclear. Our findings should guide future experiments to address the above question for SARS coronaviruses.

scholarly journals Genetic Analysis of Determinants for Spike Glycoprotein Assembly into Murine Coronavirus Virions: Distinct Roles for Charge-Rich and Cysteine-Rich Regions of the Endodomain

2004 ◽  
Vol 78 (18) ◽  
pp. 9904-9917 ◽  
Author(s):  
Rong Ye ◽  
Cynthia Montalto-Morrison ◽  
Paul S. Masters
Keyword(s):  
Transmembrane Domain ◽  
Mutational Analysis ◽  
Hepatitis Virus ◽  
Transmembrane Protein ◽  
Terminal Segment ◽  
Type I ◽  
Viral Fusion ◽  
S Protein ◽  
Infected Cells ◽  
Carboxy Terminal

ABSTRACT The coronavirus spike protein (S) forms the distinctive virion surface structures that are characteristic of this viral family, appearing in negatively stained electron microscopy as stems capped with spherical bulbs. These structures are essential for the initiation of infection through attachment of the virus to cellular receptors followed by fusion to host cell membranes. The S protein can also mediate the formation of syncytia in infected cells. The S protein is a type I transmembrane protein that is very large compared to other viral fusion proteins, and all except a short carboxy-terminal segment of the S molecule constitutes the ectodomain. For the prototype coronavirus mouse hepatitis virus (MHV), it has previously been established that S protein assembly into virions is specified by the carboxy-terminal segment, which comprises the transmembrane domain and the endodomain. We have genetically dissected these domains in the MHV S protein to localize the determinants of S incorporation into virions. Our results establish that assembly competence maps to the endodomain of S, which was shown to be sufficient to target a heterologous integral membrane protein for incorporation into MHV virions. In particular, mutational analysis indicated a major role for the charge-rich carboxy-terminal region of the endodomain. Additionally, we found that the adjacent cysteine-rich region of the endodomain is critical for fusion of infected cells, confirming results previously obtained with S protein expression systems.

scholarly journals Efficient Activation of the Severe Acute Respiratory Syndrome Coronavirus Spike Protein by the Transmembrane Protease TMPRSS2

2010 ◽  
Vol 84 (24) ◽  
pp. 12658-12664 ◽  
Author(s):  
Shutoku Matsuyama ◽  
Noriyo Nagata ◽  
Kazuya Shirato ◽  
Miyuki Kawase ◽  
Makoto Takeda ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Viral Entry ◽  
Target Cell ◽  
Influenza A ◽  
Vero Cells ◽  
Heptad Repeat ◽  
Viral Fusion ◽  
Protein Cleavage ◽  
S Protein ◽  
Viral Fusion Protein

ABSTRACT The distribution of the severe acute respiratory syndrome coronavirus (SARS-CoV) receptor, an angiotensin-converting enzyme 2 (ACE2), does not strictly correlate with SARS-CoV cell tropism in lungs; therefore, other cellular factors have been predicted to be required for activation of virus infection. In the present study, we identified transmembrane protease serine 2 (TMPRSS2), whose expression does correlate with SARS-CoV infection in the upper lobe of the lung. In Vero cells expressing TMPRSS2, large syncytia were induced by SARS-CoV infection. Further, the lysosome-tropic reagents failed to inhibit, whereas the heptad repeat peptide efficiently inhibited viral entry into cells, suggesting that TMPRSS2 affects the S protein at the cell surface and induces virus-plasma membrane fusion. On the other hand, production of virus in TMPRSS2-expressing cells did not result in S-protein cleavage or increased infectivity of the resulting virus. Thus, TMPRSS2 affects the entry of virus but not other phases of virus replication. We hypothesized that the spatial orientation of TMPRSS2 vis-a-vis S protein is a key mechanism underling this phenomenon. To test this, the TMPRSS2 and S proteins were expressed in cells labeled with fluorescent probes of different colors, and the cell-cell fusion between these cells was tested. Results indicate that TMPRSS2 needs to be expressed in the opposing (target) cell membrane to activate S protein rather than in the producer cell, as found for influenza A virus and metapneumoviruses. This is the first report of TMPRSS2 being required in the target cell for activation of a viral fusion protein but not for the S protein synthesized in and transported to the surface of cells. Our findings suggest that the TMPRSS2 expressed in lung tissues may be a determinant of viral tropism and pathogenicity at the initial site of SARS-CoV infection.

Virus Membrane Fusion Proteins: Biological Machines that Undergo a Metamorphosis

2000 ◽  
Vol 20 (6) ◽  
pp. 597-612 ◽  
Author(s):  
Rebecca Ellis Dutch ◽  
Theodore S. Jardetzky ◽  
Robert A. Lamb
Keyword(s):  
Fusion Proteins ◽  
Ebola Virus ◽  
Transmembrane Domain ◽  
Coiled Coil ◽  
Fusion Peptide ◽  
Proteolytic Cleavage ◽  
Heptad Repeat ◽  
Viral Fusion ◽  
Hydrophobic Region ◽  
Viral Fusion Proteins

Fusion proteins from a group of widely disparate viruses, including the paramyxovirus F protein, the HIV and SIV gp160 proteins, the retroviral Env protein, the Ebola virus Gp, and the influenza virus haemagglutinin, share a number of common features. All contain multiple glycosylation sites, and must be trimeric and undergo proteolytic cleavage to be fusogenically active. Subsequent to proteolytic cleavage, the subunit containing the transmembrane domain in each case has an extremely hydrophobic region, termed the fusion peptide, or at near its newly generated N-terminus. In addition, all of these viral fusion proteins have 4–3 heptad repeat sequences near both the fusion peptide and the transmembrane domain. These regions have been demonstrated from a tight complex, in which the N-terminal heptad repeat forms a trimeric-coiled coil, with the C-terminal heptad repeat forming helical regions that buttress the coiled-coil in an anti-parallel manner. The significance of each of these structuralelements in the processing and function of these viral fusion proteins is discussed.

scholarly journals Examination of a Fusogenic Hexameric Core from Human Metapneumovirus and Identification of a Potent Synthetic Peptide Inhibitor from the Heptad Repeat 1 Region

2006 ◽  
Vol 81 (1) ◽  
pp. 141-149 ◽  
Author(s):  
Scott A. Miller ◽  
Sharon Tollefson ◽  
James E. Crowe ◽  
John V. Williams ◽  
David W. Wright
Keyword(s):  
Membrane Proteins ◽  
Coiled Coil ◽  
Helical Structure ◽  
Human Metapneumovirus ◽  
Integral Membrane Proteins ◽  
Heptad Repeat ◽  
Type I ◽  
Viral Fusion ◽  
Fusion Inhibitors ◽  
Major Player

ABSTRACT Paramyxoviruses are a leading cause of childhood illness worldwide. A recently discovered paramyxovirus, human metapneumovirus (hMPV), has been studied by our group in order to determine the structural relevance of its fusion (F) protein to other well-characterized viruses utilizing type I integral membrane proteins as fusion aids. Sequence analysis and homology models suggested the presence of requisite heptad repeat (HR) regions. Synthetic peptides from HR regions 1 and 2 (HR-1 and -2, respectively) were induced to form a thermostable (melting temperature, ∼90°C) helical structure consistent in mass with a hexameric coiled coil. Inhibitory studies of hMPV HR-1 and -2 indicated that the synthetic HR-1 peptide was a significant fusion inhibitor with a 50% inhibitory concentration and a 50% effective concentration of ∼50 nM. Many viral fusion proteins are type I integral membrane proteins utilizing the formation of a hexameric coiled coil of HR peptides as a major driving force for fusion. Our studies provide evidence that hMPV also uses a coiled-coil structure as a major player in the fusion process. Additionally, viral HR-1 peptide sequences may need further investigation as potent fusion inhibitors.

scholarly journals A Discrete Stage of Baculovirus GP64-mediated Membrane Fusion

1999 ◽  
Vol 10 (12) ◽  
pp. 4191-4200 ◽  
Author(s):  
David H. Kingsley ◽  
Ali Behbahani ◽  
Afshin Rashtian ◽  
Gary W. Blissard ◽  
Joshua Zimmerberg
Keyword(s):  
Fusion Protein ◽  
Membrane Fusion ◽  
Conformational Changes ◽  
Fusion Proteins ◽  
Critical Role ◽  
Low Ph ◽  
Heptad Repeat ◽  
Viral Fusion ◽  
Viral Fusion Protein ◽  
Heptad Repeats

Viral fusion protein trimers can play a critical role in limiting lipids in membrane fusion. Because the trimeric oligomer of many viral fusion proteins is often stabilized by hydrophobic 4-3 heptad repeats, higher-order oligomers might be stabilized by similar sequences. There is a hydrophobic 4-3 heptad repeat contiguous to a putative oligomerization domain of Autographa californica multicapsid nucleopolyhedrovirus envelope glycoprotein GP64. We performed mutagenesis and peptide inhibition studies to determine if this sequence might play a role in catalysis of membrane fusion. First, leucine-to-alanine mutants within and flanking the amino terminus of the hydrophobic 4-3 heptad repeat motif that oligomerize into trimers and traffic to insect Sf9 cell surfaces were identified. These mutants retained their wild-type conformation at neutral pH and changed conformation in acidic conditions, as judged by the reactivity of a conformationally sensitive mAb. These mutants, however, were defective for membrane fusion. Second, a peptide encoding the portion flanking the GP64 hydrophobic 4-3 heptad repeat was synthesized. Adding peptide led to inhibition of membrane fusion, which occurred only when the peptide was present during low pH application. The presence of peptide during low pH application did not prevent low pH–induced conformational changes, as determined by the loss of a conformationally sensitive epitope. In control experiments, a peptide of identical composition but different sequence, or a peptide encoding a portion of the Ebola GP heptad motif, had no effect on GP64-mediated fusion. Furthermore, when the hemagglutinin (X31 strain) fusion protein of influenza was functionally expressed in Sf9 cells, no effect on hemagglutinin-mediated fusion was observed, suggesting that the peptide does not exert nonspecific effects on other fusion proteins or cell membranes. Collectively, these studies suggest that the specific peptide sequences of GP64 that are adjacent to and include portions of the hydrophobic 4-3 heptad repeat play a dynamic role in membrane fusion at a stage that is downstream of the initiation of protein conformational changes but upstream of lipid mixing.

scholarly journals The Coronavirus Spike Protein Is a Class I Virus Fusion Protein: Structural and Functional Characterization of the Fusion Core Complex

2003 ◽  
Vol 77 (16) ◽  
pp. 8801-8811 ◽  
Author(s):  
Berend Jan Bosch ◽  
Ruurd van der Zee ◽  
Cornelis A. M. de Haan ◽  
Peter J. M. Rottier
Keyword(s):  
Fusion Protein ◽  
Membrane Fusion ◽  
Fusion Proteins ◽  
Limited Proteolysis ◽  
Fusion Peptide ◽  
Spike Protein ◽  
Class I ◽  
Heptad Repeat ◽  
Viral Fusion ◽  
Viral Fusion Protein

ABSTRACT Coronavirus entry is mediated by the viral spike (S) glycoprotein. The 180-kDa oligomeric S protein of the murine coronavirus mouse hepatitis virus strain A59 is posttranslationally cleaved into an S1 receptor binding unit and an S2 membrane fusion unit. The latter is thought to contain an internal fusion peptide and has two 4,3 hydrophobic (heptad) repeat regions designated HR1 and HR2. HR2 is located close to the membrane anchor, and HR1 is some 170 amino acids (aa) upstream of it. Heptad repeat (HR) regions are found in fusion proteins of many different viruses and form an important characteristic of class I viral fusion proteins. We investigated the role of these regions in coronavirus membrane fusion. Peptides HR1 (96 aa) and HR2 (39 aa), corresponding to the HR1 and HR2 regions, were produced in Escherichia coli. When mixed together, the two peptides were found to assemble into an extremely stable oligomeric complex. Both on their own and within the complex, the peptides were highly alpha helical. Electron microscopic analysis of the complex revealed a rod-like structure ∼14.5 nm in length. Limited proteolysis in combination with mass spectrometry indicated that HR1 and HR2 occur in the complex in an antiparallel fashion. In the native protein, such a conformation would bring the proposed fusion peptide, located in the N-terminal domain of HR1, and the transmembrane anchor into close proximity. Using biological assays, the HR2 peptide was shown to be a potent inhibitor of virus entry into the cell, as well as of cell-cell fusion. Both biochemical and functional data show that the coronavirus spike protein is a class I viral fusion protein.

scholarly journals Viral fusion protein transmembrane domain adopts β-strand structure to facilitate membrane topological changes for virus–cell fusion

2015 ◽  
Vol 112 (35) ◽  
pp. 10926-10931 ◽  
Author(s):  
Hongwei Yao ◽  
Michelle W. Lee ◽  
Alan J. Waring ◽  
Gerard C. L. Wong ◽  
Mei Hong
Keyword(s):  
Fusion Protein ◽  
Transmembrane Domain ◽  
Magic Angle Spinning ◽  
Structure Characterization ◽  
Cubic Phase ◽  
Magic Angle ◽  
Viral Fusion ◽  
Virus Envelope ◽  
Viral Fusion Protein ◽  
Topological Changes

The C-terminal transmembrane domain (TMD) of viral fusion proteins such as HIV gp41 and influenza hemagglutinin (HA) is traditionally viewed as a passive α-helical anchor of the protein to the virus envelope during its merger with the cell membrane. The conformation, dynamics, and lipid interaction of these fusion protein TMDs have so far eluded high-resolution structure characterization because of their highly hydrophobic nature. Using magic-angle-spinning solid-state NMR spectroscopy, we show that the TMD of the parainfluenza virus 5 (PIV5) fusion protein adopts lipid-dependent conformations and interactions with the membrane and water. In phosphatidylcholine (PC) and phosphatidylglycerol (PG) membranes, the TMD is predominantly α-helical, but in phosphatidylethanolamine (PE) membranes, the TMD changes significantly to the β-strand conformation. Measured order parameters indicate that the strand segments are immobilized and thus oligomerized. 31P NMR spectra and small-angle X-ray scattering (SAXS) data show that this β-strand–rich conformation converts the PE membrane to a bicontinuous cubic phase, which is rich in negative Gaussian curvature that is characteristic of hemifusion intermediates and fusion pores. 1H-31P 2D correlation spectra and 2H spectra show that the PE membrane with or without the TMD is much less hydrated than PC and PG membranes, suggesting that the TMD works with the natural dehydration tendency of PE to facilitate membrane merger. These results suggest a new viral-fusion model in which the TMD actively promotes membrane topological changes during fusion using the β-strand as the fusogenic conformation.

scholarly journals Proteomics Computational Analyses Suggest that the Antennavirus Glycoprotein Complex Includes a Class I Viral Fusion Protein (α-Penetrene) with an Internal Zinc-Binding Domain and a Stable Signal Peptide

Viruses ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 750 ◽  
Author(s):  
Courtney E. Garry ◽  
Robert F. Garry
Keyword(s):  
Signal Peptide ◽  
Transmembrane Domain ◽  
Binding Domain ◽  
Class I ◽  
Zinc Binding ◽  
Viral Fusion ◽  
Viral Fusion Protein ◽  
Computational Analyses ◽  
Zinc Binding Domain ◽  
Stable Signal

A metatranscriptomic study of RNA viruses in cold-blooded vertebrates identified two related viruses from frogfish (Antennarius striatus) that represent a new genus Antennavirus in the family Arenaviridae (Order: Bunyavirales). Computational analyses were used to identify features common to class I viral fusion proteins (VFPs) in antennavirus glycoproteins, including an N-terminal fusion peptide, two extended alpha-helices, an intrahelical loop, and a carboxyl terminal transmembrane domain. Like mammarenavirus and hartmanivirus glycoproteins, the antennavirus glycoproteins have an intracellular zinc-binding domain and a long virion-associated stable signal peptide (SSP). The glycoproteins of reptarenaviruses are also class I VFPs, but do not contain zinc-binding domains nor do they encode SSPs. Divergent evolution from a common progenitor potentially explains similarities of antennavirus, mammarenavirus, and hartmanivirus glycoproteins, with an ancient recombination event resulting in a divergent reptarenavirus glycoprotein.

scholarly journals Abstract P-14: Molecular Modeling of the Transmembrane Domain of the SARS Cov-2 S-Protein and its Interaction with the Membrane

2021 ◽  
Vol 11 (Suppl_1) ◽  
pp. S17-S17
Author(s):  
Valery Novoseletsky ◽  
Marine Bozdaganyan ◽  
Daniil Litvinov ◽  
Olga Sokolova
Keyword(s):  
Solution Structure ◽  
Structural Model ◽  
Transmembrane Domain ◽  
Coiled Coil ◽  
Bottom Layer ◽  
Dynamics Simulation ◽  
Type I ◽  
Sars Coronavirus ◽  
S Protein ◽  
Tm Domain

Background: The spike glycoprotein of SARS-coronavirus mediates the early events leading to infection of cells, including fusion of the viral and cellular membranes. The spike is a type I membrane glycoprotein that possesses a conserved transmembrane anchor and an unusual cysteine-rich domain that bridges the putative junction of the anchor and the cytoplasmic tail. In this study, we examined the role of these carboxyl-terminal domains in S-protein interaction with membrane. Methods: Structural model of the trimeric TM domain and adjacent fragments of ecto- and endo domains (residues 1157-1256) of the S-protein was built by homology basing on the solution structure of the SARS-coronavirus S-protein HR2 domain (pdb-code 2fxp), the structure of the transmembrane domain of HIV-1 gp41 in bicelle (5jyn), and assumption of generally coiled-coil fold of the considered domain. C-terminus of the domain was left unstructured but fully palmitoylated. Molecular dynamics simulation in heterogeneous lipid bilayer was prepared with CHARMM-GUI and performed with Gromacs during 100 ns. Results: 1. Ectodomain fragment (residues 1157-1212) demonstrates a tilt by the angle of 40-60 degrees from the axis of the TM domain (residues 1213-1237). This tilt is facilitated by glycine residues in position 1204. 2. Cholesterol molecules of the bottom layer tend to localize around protein due to interaction with palmitoyl tails while lipids in the upper layer do not show such tendency. Conclusion: Performed molecular simulations show that both palmitoylation and a large cluster of aromatic residues provide high stability of the S-protein TM domain.

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