Global mapping of antibody recognition of the hepatitis C virus E2 glycoprotein: Implications for vaccine design

Abstract

The E2 envelope glycoprotein is the primary target of human neutralizing antibody response against hepatitis C virus (HCV), and is thus a major focus of vaccine and immunotherapeutics efforts. There is emerging evidence that E2 is a highly complex, dynamic protein with residues across the protein that are modulating antibody recognition, local and global E2 stability, and viral escape. To comprehensively map these determinants, we performed global E2 alanine scanning with a panel of 16 human monoclonal antibodies (hmAbs), resulting in an unprecedented dataset of the effects of individual alanine substitutions across the E2 protein (355 positions) on antibody recognition. Analysis of shared energetic effects across the antibody panel identified networks of E2 residues involved in antibody recognition and local and global E2 stability, as well as predicted contacts between residues across the entire E2 protein. Further analysis of antibody binding hotspot residues defined groups of residues essential for E2 conformation and recognition for all 14 conformationally dependent E2 antibodies and subsets thereof, as well as residues that enhance antibody recognition when mutated to alanine, providing a potential route to engineer E2 vaccine immunogens. By incorporating E2 sequence variability, we found a number of E2 polymorphic sites that are responsible for loss of neutralizing antibody binding. These data and analyses provide fundamental insights into antibody recognition of E2, highlighting the dynamic and complex nature of this viral envelope glycoprotein, and can serve as a reference for development and rational design of E2-targeting vaccines and immunotherapeutics.

Submission Details

ID: qhWKngVT4

Submitter: Connie Wang

Submission Date: Nov. 15, 2016, 11:50 a.m.

Version: 1

Publication Details
Pierce BG;Keck ZY;Lau P;Fauvelle C;Gowthaman R;Baumert TF;Fuerst TR;Mariuzza RA;Foung SK,Proc Natl Acad Sci U S A (2016) Global mapping of antibody recognition of the hepatitis C virus E2 glycoprotein: Implications for vaccine design. PMID:27791171
Additional Information

Study Summary

Number of data points 5593
Proteins hepatitis C virus E2 glycoprotein
Unique complexes 355
Assays/Quantities/Protocols Experimental Assay: Binding to CBH-4D Antibody ; Experimental Assay: Binding to HC84.20 ; Experimental Assay: Binding to HC33.4 Antibody ; Experimental Assay: Binding to CD81 Antibody ; Experimental Assay: Binding to A27 Antibody ; Experimental Assay: Binding to CBH-4G Antibody ; Experimental Assay: Binding to CBH-4B Antibody ; Experimental Assay: Binding to CBH-20 Antibody ; Experimental Assay: Binding to CBH-21 Antibody ; Experimental Assay: Binding to CBH-22 Antibody ; Experimental Assay: Binding to NH-1 Antibody ; Experimental Assay: Binding to NH-11 Antibody ; Experimental Assay: Binding to CBH-7 Antibody ; Experimental Assay: Binding to CBH-23 Antibody ; Experimental Assay: Binding to HC84.24 ; Experimental Assay: Binding to HC84.26 Antibody ; Experimental Assay: Binding to HC33.1 Antibody
Libraries Alanine scan of HCV E2 glycoprotein

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1R7F 2004-08-10 NMR structure of the membrane anchor domain (1-31) of the nonstructural protein 5A (NS5A) of hepatitis C virus (Ensemble of 43 structures. Sample in 100mM SDS)
2N1P 2016-04-20 Structure of the C-terminal membrane domain of HCV NS5B protein
2JXF 2008-11-25 The solution structure of HCV NS4B(40-69)
1R7D 2004-08-10 NMR structure of the membrane anchor domain (1-31) of the nonstructural protein 5A (NS5A) of hepatitis C virus (Ensemble of 51 structures, sample in 50% tfe)
1R7E 2004-08-10 NMR structure of the membrane anchor domain (1-31) of the nonstructural protein 5A (NS5A) of hepatitis C virus (Minimized average structure. Sample in 100mM SDS).
1ONB 2003-03-11 Solution structure of an engineered arginine-rich subdomain 2 of the hepatitis C virus NS3 RNA helicase
1R7C 2004-08-10 NMR structure of the membrane anchor domain (1-31) of the nonstructural protein 5A (NS5A) of hepatitis C virus (Minimized average structure, Sample in 50% tfe)
1JR6 2002-08-10 Solution Structure of an Engineered Arginine-rich Subdomain 2 of the Hepatitis C Virus NS3 RNA Helicase
2KNU 2010-01-12 Solution structure of the transmembrane proximal region of the hepatis C virus E1 glycoprotein
1CWX 1999-08-30 SOLUTION STRUCTURE OF THE HEPATITIS C VIRUS N-TERMINAL CAPSID PROTEIN 2-45 [C-HCV(2-45)]
1R7G 2004-08-10 NMR structure of the membrane anchor domain (1-31) of the nonstructural protein 5A (NS5A) of hepatitis C virus (Minimized average structure, Sample in 100mM DPC)
2KDR 2009-09-29 Solution structure of HCV NS4B(227-254)
3MRG 2011-05-25 1.3 Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide
5VXR 2018-02-21 1.4 The antigen-binding fragment of MAb24 in complex with a peptide from Hepatitis C Virus E2 epitope I (412-423)
3RC4 2011-05-04 1.5 Molecular mechanisms of viral and host-cell substrate recognition by HCV NS3/4A protease
3HKW 2010-05-26 1.55 HCV NS5B genotype 1a in complex with 1,5 benzodiazepine inhibitor 6
3RC5 2011-05-04 1.6 Molecular mechanisms of viral and host-cell substrate recognition by HCV NS3/4A protease
6BZY 2018-06-20 1.6 Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the 22D11 broadly neutralizing antibody
5FGB 2016-01-20 1.65 Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV) glycoprotein E2 Fab fragment HC33.4
6BQJ 2018-03-21 1.69 CRYSTAL STRUCTURE OF HEPATIS C VIRUS PROTEASE (NS3) COMPLEXED WITH TRIPEPTIDIC ACYL SULFONAMIDE INHIBITOR (COMPOUND 16)
2XI3 2010-08-04 1.7 HCV-H77 NS5B Polymerase Complexed With GTP
4N0Y 2015-04-01 1.75 Structure of the Hepatitis C Envelope Glycoprotein E1 antigenic region 314-324 bound to the cross-neutralizing antibody IGH526
5VOJ 2017-06-21 1.8 Crystal structure of HCV NS3/4A protease in complex with JZ01-15, an analogue of 5172-mcP1P3
4GAG 2012-10-10 1.8 Structure of the broadly neutralizing antibody AP33 in complex with its HCV epitope (E2 residues 412-423)
3QGI 2011-04-20 1.8 Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase genotype 1a complex with N-[(2S)-butan-2-yl]-6-[(3R)-3-{[4-(trifluoromethoxy)benzyl]carbamoyl}-4-{[4-(trifluoromethoxy)phenyl]sulfonyl}piperazin-1-yl]pyridazine-3-carboxamide
2XI2 2010-08-04 1.8 HCV-H77 NS5B Apo Polymerase
5VP9 2017-06-21 1.86 Crystal structure of HCV NS3/4A protease in complex with AM-07, an analogue of 5172-mcP1P3
3MRJ 2011-05-25 1.87 Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide V5M variant
5FGC 2016-01-20 1.9 Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV) glycoprotein E2 Fab fragment HC33.8
6MVO 2019-09-04 1.95 HCV NS5B 1A Y316 bound to Compound 49
6BQK 2018-03-21 1.97 CRYSTAL STRUCTURE OF HEPATIS C VIRUS PROTEASE (NS3) COMPLEXED WITH TRIPEPTIDIC ACYL SULFONAMIDE INHIBITOR (COMPOUND 18)
5EOC 2016-02-10 1.98 Crystal structure of Fab C2 in complex with a Cyclic variant of Hepatitis C Virus E2 epitope I
4Z0X 2016-07-20 2.0 Structure of Hepatitis C Virus Envelope glycoprotein E2 antigenic region 434-446 bound to the broadly neutralizing antibody HC26AM
2O8M 2007-10-09 2.0 Crystal structure of the S139A mutant of Hepatitis C Virus NS3/4A protease
4XVJ 2015-03-11 2.0 STRUCTURE OF THE HEPATITIS C VIRUS ENVELOPE GLYCOPROTEIN E2 ANTIGENIC 2 REGION 412-423 BOUND TO THE BROADLY NEUTRALIZING ANTIBODY HC33.1
5YXN 2018-12-12 2.03 A T cell receptor in complex with HLA-A0201 restricted Hepatitis C virus NS3 peptide (KLVALGINAV)
4JZN 2013-06-05 2.05 Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV) glycoprotein E2 Fab fragment HC84-1
3MRI 2011-05-25 2.1 Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide G4M-V5W variant
1HEI 1998-10-07 2.1 STRUCTURE OF THE HEPATITIS C VIRUS RNA HELICASE DOMAIN
3QGH 2011-04-20 2.14 Crystal structure of the hepatitis C virus NS5B RNA-dependent RNA polymerase genotype 1a complex with N-cyclopropyl-6-[(3R)-3-{[4-(trifluoromethoxy)benzyl]carbamoyl}-4-{[4-(trifluoromethoxy)phenyl]sulfonyl}piperazin-1-yl]pyridazine-3-carboxamide
6BZW 2018-06-20 2.2 Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the GL precursor of the broadly neutralizing antibody AP33
1A1V 1999-01-13 2.2 HEPATITIS C VIRUS NS3 HELICASE DOMAIN COMPLEXED WITH SINGLE STRANDED SDNA
4JZO 2013-06-05 2.22 Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV) glycoprotein E2 Fab fragment HC84-27
3SU4 2012-09-05 2.26 Crystal structure of NS3/4A protease variant R155K in complex with vaniprevir
2HD0 2006-08-01 2.28 Structure of the catalytic domain of hepatitis C virus NS2
6N4N 2019-09-11 2.29 Crystal structure of the designed protein DNCR2/danoprevir/NS3a complex
2OC0 2007-07-31 2.3 Structure of NS3 complexed with a ketoamide inhibitor SCh491762
3KN2 2010-01-19 2.3 HCV NS3 Protease Domain with ketoamide inhibitor
3EYD 2009-02-10 2.3 Structure of HCV NS3-4A Protease with an Inhibitor Derived from a Boronic Acid
2A4R 2006-07-04 2.4 HCV NS3 Protease Domain with a Ketoamide Inhibitor Covalently bound.
3MRH 2011-05-25 2.4 Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide N3S variant
2QV1 2008-08-19 2.4 Crystal structure of HCV NS3-4A V36M mutant
3MRL 2011-05-25 2.41 Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081 nonapeptide C6V variant
2GVF 2007-01-23 2.5 HCV NS3-4A protease domain complexed with a macrocyclic ketoamide inhibitor, SCH419021
1A1R 1998-06-17 2.5 HCV NS3 PROTEASE DOMAIN:NS4A PEPTIDE COMPLEX
2A4G 2006-07-04 2.5 Hepatitis C Protease NS3-4A serine protease with Ketoamide Inhibitor SCH225724 Bound
2OIN 2007-06-05 2.5 crystal structure of HCV NS3-4A R155K muntant
2OBQ 2007-07-31 2.5 Discovery of the HCV NS3/4A Protease Inhibitor SCH503034. Key Steps in Structure-Based Optimization
5JZI 2017-05-31 2.5 Crystal structure of 1406 TCR bound to HLA-A2 with HCV 1406-1415 antigen peptide
1N1L 2003-10-21 2.6 CRYSTAL STRUCTURE OF HCV NS3 PROTEASE DOMAIN:NS4A PEPTIDE COMPLEX WITH COVALENTLY BOUND INHIBITOR (GW472467X)
2F9V 2007-01-09 2.6 HCV NS3 protease domain with NS4a peptide and a ketoamide inhibitor with P1 and P2 cyclopropylalannines
4MWF 2013-12-11 2.64 Structure of Hepatitis C Virus Envelope Glycoprotein E2 core bound to broadly neutralizing antibody AR3C
6BZV 2018-06-20 2.65 Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the GL precursor of the broadly neutralizing antibody 19B3
2OC8 2007-07-31 2.66 Structure of Hepatitis C Viral NS3 protease domain complexed with NS4A peptide and ketoamide SCH503034
6BZU 2018-06-20 2.7 Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody 19B3
2OC1 2007-07-31 2.7 Structure of the HCV NS3/4A Protease Inhibitor CVS4819
2OC7 2007-07-31 2.7 Structure of Hepatitis C Viral NS3 protease domain complexed with NS4A peptide and ketoamide SCH571696
5YXU 2018-12-12 2.7 an affinity enhanced T cell receptor in complex with HLA-A0201 restricted HCV NS3 peptide KLVALGINAV
1RTL 2004-12-14 2.75 CRYSTAL STRUCTURE OF HCV NS3 PROTEASE DOMAIN: NS4A PEPTIDE COMPLEX WITH COVALENTLY BOUND PYRROLIDINE-5,5-TRANSLACTAM INHIBITOR
2P59 2008-02-05 2.9 Crystal Structure of Hepatitis C Virus NS3.4A protease
5ERW 2016-11-16 2.9 Structure of HCV E2 glycoprotein antigenic Epitope II bound to the broadly neutralizing antibody HC84-26
1RGQ 2004-10-19 2.9 M9A HCV Protease complex with pentapeptide keto-amide inhibitor
4Q0X 2014-07-09 2.9 Crystal structure of non-neutralizing antibody in complex with Epitope II of HCV E2
2XNI 2011-08-17 3.3 Protein-ligand complex of a novel macrocyclic HCV NS3 protease inhibitor derived from amino cyclic boronates

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 hepatitis C virus E2 glycoprotein P27958 POLG_HCVH
95.9 hepatitis C virus E2 glycoprotein P26664 POLG_HCV1
95.2 hepatitis C virus E2 glycoprotein Q03463 POLG_HCVJ1
93.4 hepatitis C virus E2 glycoprotein Q5EG65 POLG_HCVGL
92.2 hepatitis C virus E2 glycoprotein P27956 POLG_HCVH8
91.3 hepatitis C virus E2 glycoprotein P27957 POLG_HCVTH
90.3 hepatitis C virus E2 glycoprotein P27955 POLG_HCVH7
96.9 hepatitis C virus E2 glycoprotein P27954 POLG_HCVE1