HPLC chromatogram peaks that were selected for further proteomics analysis. stoichiometry and a high affinity of UKN2b_2.8 E2e for mAb CBH4D.(1.23 MB TIF) ppat.1000762.s003.tif (1.1M) GUID:?1CE6AB14-4ECE-4281-A8B8-008CB5E7D32F Figure S2: Alignment of HCV E2 amino acid sequences from strains H77, JFH-1 and UKN2b_2.8. Given the deamination of Asn residues by PNGase F, they are turned into Asp residues. Predicted trypsin cleavage sites (grey triangles) and N-glycosylation sites (empty diamonds) are indicated, cysteines are boxed and the respective disulfide bridges displayed (-SS-). Peptides identified after tryptic cleavage are shaded, named according to the respective isolate and numbered sequentially following the amino acid sequence of E2.(2.52 MB TIF) ppat.1000762.s004.tif (2.3M) GUID:?1D97BB29-532B-40D3-813E-15C6266C0AF0 Figure S3: Proteomics results for the determination of the disulfide bridges. HPLC chromatogram peaks that were selected for further proteomics analysis. Results of N-terminal sequencing and SELDI-TOF MS for the respective peaks are shown in panels A-G. Scales for the intensity (y-axis) as well as for the molecular weight (x-axis) vary considerably in the different spectra, resulting in a different appearance of the background noise. A) Peaks JFH-1 6-3 and 12-3, leading to the identification of disulfide bridges 2 (peak 6-3) and 8 (peak 12-3) in E2e of JFH-1. B) Peak JFH-1 16-3, leading to the identification of disulfide bridge 4 in E2e of SNX-2112 JFH-1. C) Peaks UKN2b_2.8 13-1 and 20-1, leading to the identification of disulfide bridges 2 (peak 20-1) and 8 (peak 13-1) in E2e of UKN2b_2.8. D) Peaks UKN2b_2.8 42-3 and 19-1, leading to the identification of disulfide bridges 1 (peak 42-3) and 6 (peak 19-1) in E2e of UKN2b_2.8. E) Peaks H77 15-2 and 6-2, leading to the identification of disulfide bridges 2 (peak 6-2) and 8 (peak 15-2) in E2e of H77. F) Peaks H77 26-2, which is the result of disulfide shuffling, and 32-2, leading to the identification of disulfide bridge 3 in E2e of H77. G) Peaks H77 43-2 and 33-2, leading to the identification of disulfide bridges 5 (peak 33-2) and 9 (peak 43-2) in E2e of H77.(6.93 MB TIF) ppat.1000762.s005.tif (6.6M) GUID:?C60C24F2-FB67-4A03-B170-7917B1CE83E7 Abstract Hepatitis C virus (HCV), a major cause of chronic liver disease in Bmp8a 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 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, SNX-2112 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% -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 SNX-2112 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 SNX-2112 the nature of a putative fusogenic conformational change. Author Summary Little is known about the structure of the envelope glycoproteins of the hepatitis C virus (HCV), in spite of their essential role in the viral cycle of this SNX-2112 major human pathogen. Here, we determined the connectivity of the 9 disulfide bonds formed by the strictly conserved 18 cysteines of the ectodomain of HCV glycoprotein E2. We show that this information, together with important functional data available in the literature, impose important restrictions to the possible three-dimensional fold of the molecule. Indeed, these constraints allow the unambiguous threading of the predicted secondary structure elements along the polypeptide chain onto the template provided by the crystal structures of related flavi- and alphavirus class II fusion proteins. The resulting model of the tertiary organization of E2 shows the.