An assembly model of rift valley Fever virus - PubMed (original) (raw)
An assembly model of rift valley Fever virus
Mirabela Rusu et al. Front Microbiol. 2012.
Abstract
Rift Valley fever virus (RVFV) is a bunyavirus endemic to Africa and the Arabian Peninsula that infects humans and livestock. The virus encodes two glycoproteins, Gn and Gc, which represent the major structural antigens and are responsible for host cell receptor binding and fusion. Both glycoproteins are organized on the virus surface as cylindrical hollow spikes that cluster into distinct capsomers with the overall assembly exhibiting an icosahedral symmetry. Currently, no experimental three-dimensional structure for any entire bunyavirus glycoprotein is available. Using fold recognition, we generated molecular models for both RVFV glycoproteins and found significant structural matches between the RVFV Gn protein and the influenza virus hemagglutinin protein and a separate match between RVFV Gc protein and Sindbis virus envelope protein E1. Using these models, the potential interaction and arrangement of both glycoproteins in the RVFV particle was analyzed, by modeling their placement within the cryo-electron microscopy density map of RVFV. We identified four possible arrangements of the glycoproteins in the virion envelope. Each assembly model proposes that the ectodomain of Gn forms the majority of the protruding capsomer and that Gc is involved in formation of the capsomer base. Furthermore, Gc is suggested to facilitate intercapsomer connections. The proposed arrangement of the two glycoproteins on the RVFV surface is similar to that described for the alphavirus E1-E2 proteins. Our models will provide guidance to better understand the assembly process of phleboviruses and such structural studies can also contribute to the design of targeted antivirals.
Keywords: bunyavirus assembly; hybrid modeling; multi-body refinement; multi-resolution registration; protein structure prediction.
Figures
Figure 1
Three-dimensional structure models of RVFV Gn and Gc proteins. (A) Schematic representation of the RVFV M-segment polyprotein. Transmembrane and cytoplasmic tail domains are highlighted in dark gray or white bars, respectively. N-Glycosylation sites are indicated with the position of the respective Asn residue. The regions of the two glycoproteins used for molecular modeling are indicated with N and C. 3D molecular models for RVFV (B) Gn and (C) Gc are shown. Secondary structures are highlighted in blue for β-strands, red for α-helices, and gray for turns. The predicted location of the fusion peptide within Gc is represented in purple. The domain nomenclature in modeled Gc were used in adoption to the alphavirus E1 protein. The molecular graphics in this paper were generated with Sculptor (Birmanns et al., 2011) and Chimera (Pettersen et al., 2004).
Figure 2
Schematic representation of the modeling steps undertaken to create the atomic model of the RVFV envelope. A detailed description of the individual steps is found in the text.
Figure 3
Positioning of the Gn and Gc molecular models into the RVFV cryoEM reconstruction for the top scoring model. (A,B) Show the glycoprotein arrangement within a penton extracted from the cryoEM density. The cryoEM density is represented as a gray transparent capsomer and the glycoprotein monomer models are indicated in red (Gn) and blue (Gc). Gn could only be positioned in the outer caldera of the capsomer and Gc in the skirt region of the capsomer. Two different viewing angles are shown (side-view, and top-view). (C) One structural unit (Gn-Gc heterodimer) and an adjacent Gn monomer have been extracted from the docking results shown in (A). Within the basic structural unit, the head domain of the Gn model (red and yellow) covers domain II of Gc. The predicted location of the fusion peptide shown in domain II of Gc is highlighted in magenta and indicated by the black arrow. (D) Epitopes for three monoclonal antibodies recognizing Gn (Keegan and Collett, 1986) are highlighted. These epitopes are corresponding to the monoclonal antibodies 4-32-8D (gray), 4-D4 (blue), and 3C-10 (green).
Figure 4
Intercapsomer connections for the top scoring model. (A) Top-view of two neighboring capsomers (gray cryoEM density) with two Gc monomers shown in blue. The domain III’s (red) are very well positioned within the ridges connecting adjacent capsomers. The fusion peptide is directed to the capsomer center. (B) Side-view of one capsomer along the tunnel located beneath the connecting ridges. Two Gcs are shown and their proposed position within the cryoEM density. The black arrow indicates the location of the fusion peptide within domain II. The domain IIIs are highlighted in red to indicate their placement within the ridges. (C) CryoEM density of one extracted penton at a very low threshold (0.54). The outer region of the capsomer is indicated in red (representing mainly Gn molecules), the capsomer base in blue (representing mainly Gc molecules), the lipid envelope in green, and the density corresponding to the RNP core is shown in yellow. Densities spanning the gap between the lipid bilayer and the RNP core are representing the glycoprotein cytoplasmic tails. (D) Surface-shaded representation of the central section of the RVFV cryoEM map viewed along the fivefold orientation. The sections show glycoprotein protrusions on virus surface, lipid bilayer, and RNP core. In the lower right corner a blow-up of the boxed area is shown. Red arrows point to clearly defined densities spanning the lipid bilayer. These densities represent glycoprotein transmembrane domains and are located either on the outer edge of the capsomer or directly beneath the connecting channels.
Figure 5
Overview of the RVFV glycoprotein shell. (A) The proposed T = 12 icosahedral protein layer formed by Gn and Gc. Individual subunits are color coded. (B) Tilted representation as shown in (A). The red triangle represents one triangular face. (C) Schematic representation of the Gn and Gc contacts. Drawn is one of the 20 triangular faces of the icosahedrons enclosing the RVFV particle and the distribution of the Gn and Gc glycoproteins [corresponding to red triangle in **(B)**]. Black numbers denote icosahedral two-, three-, and fivefold symmetry axes. Gn monomers are represented as bulb-like structures in yellow, and Gc monomers as a tube-like structure. The individual domains are represented in red (domain I), blue (domain II), and green (domain III). The fusion peptides are indicated as red circles, and are pointing to the capsomer center. (D) Hypothetical model of the RVFV – host cell interaction. The RVFV glycoproteins Gn and Gc are represented according to our model and show similarities to the alphavirus E1 and E2 proteins. (1) Gn is depicted as the receptor binding protein and binds to the host cell receptor (green). (2) After receptor binding the uptake of the RVFV particle is initiated and an acidification step of the endocytic vesicle triggers the dissociation of Gn and Gc. This results in the formation of potentially Gc trimers (in accordance with current models for class II fusion proteins) and insertion of the fusion peptides into the host cell membrane.
Figure A1
Capsomer twofold axis; (A,C) first; (B,D) second; (E,G) third; (F,H) fourth top-scoring model.
Figure A2
Capsomer threefold axis; (A,C) first; (B,D) second; (E,G) third; (F,H) fourth top-scoring model.
Figure A3
Capsomer quasi-threefold axis; (A,C) first; (B,D) second; (E,G) third; (F,H) fourth top-scoring model.
Figure A4
Capsomer fivefold axis; (A,C) first; (B,D) second; (E,G) third; (F,H) fourth top-scoring model.
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