Skip to main content
SpringerLink
Log in

Hepatitis C Virus Proteins: From Structure to Function

  • Chapter
Hepatitis C Virus: From Molecular Virology to Antiviral Therapy

Part of the book series: Current Topics in Microbiology and Immunology ((CT MICROBIOLOGY,volume 369))

Abstract

Great progress has been made over the past years in elucidating the structure and function of the hepatitis C virus (HCV) proteins, most of which are now actively being pursued as antiviral targets. The structural proteins, which form the viral particle, include the core protein and the envelope glycoproteins E1 and E2. The nonstructural proteins include the p7 viroporin, the NS2 protease, the NS3-4A complex harboring protease and NTPase/RNA helicase activities, the NS4B and NS5A proteins, and the NS5B RNA-dependent RNA polymerase. NS4B is a master organizer of replication complex formation while NS5A is a zinc-containing phosphoprotein involved in the regulation of HCV RNA replication versus particle production. Core to NS2 make up the assembly module while NS3 to NS5B represent the replication module (replicase). However, HCV proteins exert multiple functions during the viral life cycle, and these may be governed by different structural conformations and/or interactions with viral and/or cellular partners. Remarkably, each viral protein is anchored to intracellular membranes via specific determinants that are essential to protein function in the cell. This review summarizes current knowledge of the structure and function of the HCV proteins and highlights recent advances in the field.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Abbreviations

aa:

Amino acid

AH:

Amphipathic α-helix

CHV:

Canine hepacivirus

CK:

Casein kinase

CsA:

Cyclosporin A

CypA:

Cyclophilin A

DHPC:

1,2-diheptanol-sn-glycero-3-phosphocholine

E:

Envelope glycoprotein

ER:

Endoplasmic reticulum

GBV-B:

GB virus B

HCV:

Hepatitis C virus

HVR:

Hypervariable region

igVR:

Intergenotypic variable domain

IRES:

Internal ribosome entry site

ISDR:

Interferon sensitivity determining region

LCS:

Low complexity sequence

LD:

Lipid droplet

MD:

Molecular dynamics

NCR:

Noncoding region

NMR:

Nuclear magnetic resonance

NS:

Nonstructural protein

ORF:

Open reading frame

PI4KIII:

Phosphatidylinositol 4-kinase III

PI4P:

Phosphatidylinositol 4-phosphate

POPC:

1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

RdRp:

RNA-dependent RNA polymerase

SPP:

Signal peptide peptidase

TMD:

Transmembrane domain

References

  • Albecka A, Montserret R, Krey T, Tarr AW, Diesis E, Ball JK, Descamps V, Duverlie G, Rey F, Penin F, Dubuisson J (2011) Identification of new functional regions in hepatitis C virus envelope glycoprotein E2. J Virol 85:1777–1792

    CAS  PubMed  Google Scholar 

  • Angus AG, Loquet A, Stack SJ, Dalrymple D, Gatherer D, Penin F, Patel AH (2012) Conserved glycine 33 residue in flexible domain I of hepatitis C virus core protein is critical for virus infectivity. J Virol 86:679–690

    CAS  PubMed  PubMed Central  Google Scholar 

  • Appel N, Pietschmann T, Bartenschlager R (2005) Mutational analysis of hepatitis C virus nonstructural protein 5A: potential role of differential phosphorylation in RNA replication and identification of a genetically flexible domain. J Virol 79:3187–3194

    CAS  PubMed  PubMed Central  Google Scholar 

  • Appel N, Zayas M, Miller S, Krijnse-Locker J, Schaller T, Friebe P, Kallis S, Engel U, Bartenschlager R (2008) Essential role of domain III of nonstructural protein 5A for hepatitis C virus infectious particle assembly. PLoS Pathog 4:e1000035

    PubMed  PubMed Central  Google Scholar 

  • Assenberg R, Mastrangelo E, Walter TS, Verma A, Milani M, Owens RJ, Stuart DI, Grimes JM, Mancini EJ (2009) Crystal structure of a novel conformational state of the flavivirus NS3 protein: implications for polyprotein processing and viral replication. J Virol 83:12895–12906

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bartenschlager R, Penin F, Lohmann V, André P (2011) Assembly of infectious hepatitis C virus particles. Trends Microbiol 19:95–103

    CAS  PubMed  Google Scholar 

  • Behrens S-E, Tomei L, De Francesco R (1996) Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus. EMBO J 15:12–22

    CAS  PubMed  PubMed Central  Google Scholar 

  • Beran RK, Lindenbach BD, Pyle AM (2009) The NS4A protein of hepatitis C virus promotes RNA-coupled ATP hydrolysis by the NS3 helicase. J Virol 83:3268–3275

    CAS  PubMed  PubMed Central  Google Scholar 

  • Berger KL, Kelly SM, Jordan TX, Tartell MA, Randall G (2011) Hepatitis C virus stimulates the phosphatidylinositol 4-kinase IIIα-dependent phosphatidylinositol 4-phosphate production that is essential for its replication. J Virol 85:8870–8883

    CAS  PubMed  PubMed Central  Google Scholar 

  • Blight KJ, Kolykhalov AA, Rice CM (2000) Efficient initiation of HCV RNA replication in cell culture. Science 290:1972–1974

    CAS  PubMed  Google Scholar 

  • Boson B, Granio O, Bartenschlager R, Cosset FL (2011) A concerted action of hepatitis C virus p7 and nonstructural protein 2 regulates core localization at the endoplasmic reticulum and virus assembly. PLoS Pathog 7:e1002144

    CAS  PubMed  PubMed Central  Google Scholar 

  • Boulant S, Vanbelle C, Ebel C, Penin F, Lavergne JP (2005) Hepatitis C virus core protein is a dimeric α-helical protein exhibiting membrane protein features. J Virol 79:11353–11365

    CAS  PubMed  PubMed Central  Google Scholar 

  • Boulant S, Montserret R, Hope RG, Ratinier M, Targett-Adams P, Lavergne JP, Penin F, McLauchlan J (2006) Structural determinants that target the hepatitis C virus core protein to lipid droplets. J Biol Chem 281:22236–22247

    CAS  PubMed  Google Scholar 

  • Boulant S, Targett-Adams P, McLauchlan J (2007) Disrupting the association of hepatitis C virus core protein with lipid droplets correlates with a loss in production of infectious virus. J Gen Virol 88:2204–2213

    CAS  PubMed  Google Scholar 

  • Branch AD, Stump DD, Gutierrez JA, Eng F, Walewski JL (2005) The hepatitis C virus alternate reading frame and its family of novel products: the alternate reading frame protein/F-protein, the double-frameshift protein, and others. Semin Liver Dis 25:105–117

    CAS  PubMed  Google Scholar 

  • Brass V, Berke JM, Montserret R, Blum HE, Penin F, Moradpour D (2008) Structural determinants for membrane association and dynamic organization of the hepatitis C virus NS3-4A complex. Proc Natl Acad Sci USA 105:14545–14550

    CAS  PubMed  Google Scholar 

  • Brenndörfer ED, Karthe J, Frelin L, Cebula P, Erhardt A, Schulte am Esch J, Hengel H, Bartenschlager R, Sällberg M, Häussinger D, Bode JG (2009) Nonstructural 3/4A protease of hepatitis C virus activates epithelial growth factor-induced signal transduction by cleavage of the T-cell protein tyrosine phosphatase. Hepatology 49:1810–1820

    Google Scholar 

  • Bressanelli S, Tomei L, Rey FA, De Francesco R (2002) Structural analysis of the hepatitis C virus RNA polymerase in complex with ribonucleotides. J Virol 76:3482–3492

    CAS  PubMed  PubMed Central  Google Scholar 

  • Carrère-Kremer S, Montpellier-Pala C, Cocquerel L, Wychowski C, Penin F, Dubuisson J (2002) Subcellular localization and topology of the p7 polypeptide of hepatitis C virus. J Virol 76:3720–3730

    PubMed  PubMed Central  Google Scholar 

  • Chandler DE, Penin F, Schulten K, Chipot C (2012) The p7 protein of hepatitis C virus forms structurally plastic, minimalist ion channels. PLoS Comp Biol 8:e1002702

    Google Scholar 

  • Ciesek S, Steinmann E, Wedemeyer H, Manns MP, Neyts J, Tautz N, Madan V, Bartenschlager R, von Hahn T, Pietschmann T (2009) Cyclosporine A inhibits hepatitis C virus nonstructural protein 2 through cyclophilin A. Hepatology 50:1638–1645

    CAS  PubMed  Google Scholar 

  • Clarke D, Griffin S, Beales L, Gelais CS, Burgess S, Harris M, Rowlands D (2006) Evidence for the formation of a heptameric ion channel complex by the hepatitis C virus p7 protein in vitro. J Biol Chem 281:37057–37068

    CAS  PubMed  Google Scholar 

  • Cocquerel L, Op de Beeck A, Lambot M, Roussel J, Delgrange D, Pillez A, Wychowski C, Penin F, Dubuisson J (2002) Topologic changes in the transmembrane domains of hepatitis C virus envelope glycoproteins. EMBO J 21:2893–2902

    CAS  PubMed  PubMed Central  Google Scholar 

  • Coelmont L, Hanoulle X, Chatterji U, Berger C, Snoeck J, Bobardt M, Lim P, Vliegen I, Paeshuyse J, Vuagniaux G, Vandamme AM, Bartenschlager R, Gallay P, Lippens G, Neyts J (2010) DEB025 (Alisporivir) inhibits hepatitis C virus replication by preventing a cyclophilin A induced cis-trans isomerisation in domain II of NS5A. PLoS ONE 5:e13687

    PubMed  PubMed Central  Google Scholar 

  • Coller KE, Heaton NS, Berger KL, Cooper JD, Saunders JL, Randall G (2012) Molecular determinants and dynamics of hepatitis C virus secretion. PLoS Pathog 8:e1002466

    CAS  PubMed  PubMed Central  Google Scholar 

  • Counihan NA, Rawlinson SM, Lindenbach BD (2011) Trafficking of hepatitis C virus core protein during virus particle assembly. PLoS Pathog 7:e1002302

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cristofari G, Ivanyi-Nagy R, Gabus C, Boulant S, Lavergne JP, Penin F, Darlix JL (2004) The hepatitis C virus core protein is a potent nucleic acid chaperone that directs dimerization of the viral (+) strand RNA in vitro. Nucleic Acids Res 32:2623–2631

    CAS  PubMed  PubMed Central  Google Scholar 

  • de Chassey B, Navratil V, Tafforeau L, Hiet MS, Aublin-Gex A, Agaugue S, Meiffren G, Pradezynski F, Faria BF, Chantier T, Le Breton M, Pellet J, Davoust N, Mangeot PE, Chaboud A, Penin F, Jacob Y, Vidalain PO, Vidal M, André P, Rabourdin-Combe C, Lotteau V (2008) Hepatitis C virus infection protein network. Mol Syst Biol 4:230

    PubMed  PubMed Central  Google Scholar 

  • de Francesco R, Steinkühler C (2000) Structure and function of the hepatitis C virus NS3–NS4A serine protease. Curr Top Microbiol Immunol 242:149–169

    PubMed  Google Scholar 

  • den Boon JA, Diaz A, Ahlquist P (2010) Cytoplasmic viral replication complexes. Cell Host Microbe 8:77–85

    Google Scholar 

  • Ding SC, Kohlway AS, Pyle AM (2011) Unmasking the active helicase conformation of nonstructural protein 3 from hepatitis C virus. J Virol 85:4343–4353

    CAS  PubMed  PubMed Central  Google Scholar 

  • Egger D, Wölk B, Gosert R, Bianchi L, Blum HE, Moradpour D, Bienz K (2002) Expression of hepatitis C virus proteins induces distinct membrane alterations including a candidate viral replication complex. J Virol 76:5974–5984

    CAS  PubMed  PubMed Central  Google Scholar 

  • Einav S, Elazar M, Danieli T, Glenn JS (2004) A nucleotide binding motif in hepatitis C virus (HCV) NS4B mediates HCV RNA replication. J Virol 78:11288–11295

    CAS  PubMed  PubMed Central  Google Scholar 

  • Einav S, Gerber D, Bryson PD, Sklan EH, Elazar M, Maerkl SJ, Glenn JS, Quake SR (2008) Discovery of a hepatitis C target and its pharmacological inhibitors by microfluidic affinity analysis. Nat Biotechnol 26:1019–1027

    CAS  PubMed  PubMed Central  Google Scholar 

  • Eng FJ, Walewski JL, Klepper AL, Fishman SL, Desai SM, McMullan LK, Evans MJ, Rice CM, Branch AD (2009) Internal initiation stimulates production of p8 minicore, a member of a newly discovered family of hepatitis C virus core protein isoforms. J Virol 83:3104–3114

    CAS  PubMed  PubMed Central  Google Scholar 

  • Enomoto N, Sakuma I, Asahina Y, Kurosaki M, Murakami T, Yamamoto C, Ogura Y, Izumi N, Marumo F, Sato C (1996) Mutations in the nonstructural protein 5A gene and response to interferon in patients with chronic hepatitis C virus 1b infection. N Engl J Med 334:77–81

    CAS  PubMed  Google Scholar 

  • Evans MJ, Rice CM, Goff SP (2004) Phosphorylation of hepatitis C virus nonstructural protein 5A modulates its protein interactions and viral RNA replication. Proc Natl Acad Sci USA 101:13038–13043

    CAS  PubMed  Google Scholar 

  • Flisiak R, Feinman SV, Jablkowski M, Horban A, Kryczka W, Pawlowska M, Heathcote JE, Mazzella G, Vandelli C, Nicolas-Metral V, Grosgurin P, Liz JS, Scalfaro P, Porchet H, Crabbe R (2009) The cyclophilin inhibitor Debio 025 combined with PEG IFNalpha2a significantly reduces viral load in treatment-naive hepatitis C patients. Hepatology 49:1460–1468

    CAS  PubMed  Google Scholar 

  • Gao M, Nettles RE, Belema M, Snyder LB, Nguyen VN, Fridell RA, Serrano-Wu MH, Langley DR, Sun JH, O’Boyle DR 2nd, Lemm JA, Wang C, Knipe JO, Chien C, Colonno RJ, Grasela DM, Meanwell NA, Hamann LG (2010) Chemical genetics strategy identifies an HCV NS5A inhibitor with a potent clinical effect. Nature 465:96–100

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gosert R, Egger D, Lohmann V, Bartenschlager R, Blum HE, Bienz K, Moradpour D (2003) Identification of the hepatitis C virus RNA replication complex in Huh-7 cells harboring subgenomic replicons. J Virol 77:5487–5492

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gouklani H, Bull RA, Beyer C, Coulibaly F, Gowans EJ, Drummer HE, Netter HJ, White PA, Haqshenas G (2012) Hepatitis C virus NS5B is involved in virus morphogenesis. J Virol 86:5080–5088

    Google Scholar 

  • Gouttenoire J, Castet V, Montserret R, Arora N, Raussens V, Ruysschaert JM, Diesis E, Blum HE, Penin F, Moradpour D (2009a) Identification of a novel determinant for membrane association in hepatitis C virus nonstructural protein 4B. J Virol 83:6257–6268

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gouttenoire J, Montserret R, Kennel A, Penin F, Moradpour D (2009b) An amphipathic α-helix at the C terminus of NS4B mediates membrane association. J Virol 51:11378–11384

    Google Scholar 

  • Gouttenoire J, Penin F, Moradpour D (2010a) Hepatitis C virus nonstructural protein 4B: a journey into unexplored territory. Rev Med Virol 20:117–129

    CAS  PubMed  Google Scholar 

  • Gouttenoire J, Roingeard P, Penin F, Moradpour D (2010b) Amphipathic α-helix AH2 is a major determinant for the oligomerization of hepatitis C virus nonstructural protein 4B. J Virol 84:12529–12537

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gu M, Rice CM (2010) Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism. Proc Natl Acad Sci USA 107:521–528

    CAS  PubMed  Google Scholar 

  • Halfon P, Locarnini S (2011) Hepatitis C virus resistance to protease inhibitors. J Hepatol 55:192–206

    CAS  PubMed  Google Scholar 

  • Hanoulle X, Badillo A, Wieruszeski JM, Verdegem D, Landrieu I, Bartenschlager R, Penin F, Lippens G (2009) Hepatitis C virus NS5A protein is a substrate for the peptidyl-prolyl cis/trans isomerase activity of cyclophilins A and B. J Biol Chem 284:13589–13601

    CAS  PubMed  PubMed Central  Google Scholar 

  • Harrus D, Ahmed-El-Sayed N, Simister PC, Miller S, Triconnet M, Hagedorn CH, Mahias K, Rey FA, Astier-Gin T, Bressanelli S (2010) Further insights into the roles of GTP and the C terminus of the hepatitis C virus polymerase in the initiation of RNA synthesis. J Biol Chem 285:32906–32918

    CAS  PubMed  PubMed Central  Google Scholar 

  • Herod MR, Jones DM, McLauchlan J, McCormick CJ (2012) Increasing rate of cleavage at boundary between non-structural proteins 4B and 5A inhibits replication of hepatitis C virus. J Biol Chem 287:568–580

    CAS  PubMed  Google Scholar 

  • Horner SM, Liu HM, Park HS, Briley J, Gale M Jr (2011) Mitochondrial-associated endoplasmic reticulum membranes (MAM) form innate immune synapses and are targeted by hepatitis C virus. Proc Natl Acad Sci USA 108:14590–14595

    CAS  PubMed  Google Scholar 

  • Huang Y, Staschke K, De Francesco R, Tan SL (2007) Phosphorylation of hepatitis C virus NS5A nonstructural protein: a new paradigm for phosphorylation-dependent viral RNA replication? Virology 364:1–9

    CAS  PubMed  Google Scholar 

  • Hwang J, Huang L, Cordek DG, Vaughan R, Reynolds SL, Kihara G, Raney KD, Kao CC, Cameron CE (2010) Hepatitis C virus nonstructural protein 5A: biochemical characterization of a novel structural class of RNA-binding proteins. J Virol 84:12480–12491

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jacobson IM, McHutchison JG, Dusheiko G, Di Bisceglie AM, Reddy KR, Bzowej NH, Marcellin P, Muir AJ, Ferenci P, Flisiak R, George J, Rizzetto M, Shouval D, Sola R, Terg RA, Yoshida EM, Adda N, Bengtsson L, Sankoh AJ, Kieffer TL, George S, Kauffman RS, Zeuzem S (2011) Telaprevir for previously untreated chronic hepatitis C virus infection. N Engl J Med 364:2405–2416

    CAS  PubMed  Google Scholar 

  • Jirasko V, Montserret R, Appel N, Janvier A, Eustachi L, Brohm C, Steinmann E, Pietschmann T, Penin F, Bartenschlager R (2008) Structural and functional characterization of nonstructural protein 2 for its role in hepatitis C virus assembly. J Biol Chem 283:28546–28562

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jirasko V, Montserret R, Lee JY, Gouttenoire J, Moradpour D, Penin F, Bartenschlager R (2010) Structural and functional studies of nonstructural protein 2 of the hepatitis C virus reveal its key role as organizer of virion assembly. PLoS Pathog 6:e1001233

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jolivet M, Penin F, Dalbon P, Ladaviere L, Lacoux X (1997) Antigenic structural peptide, antigenic and immunogenic compounds and uses for detecting, preventing and treating an HCV infection. Patent application EP 1015481, WO 98/39360

    Google Scholar 

  • Jones DM, Patel AH, Targett-Adams P, McLauchlan J (2009) The hepatitis C virus NS4B protein can trans-complement viral RNA replication and modulates production of infectious virus. J Virol 83:2163–2177

    CAS  PubMed  Google Scholar 

  • Kapoor A, Simmonds P, Gerold G, Qaisar N, Jain K, Henriquez JA, Firth C, Hirschberg DL, Rice CM, Shields S, Lipkin WI (2011) Characterization of a canine homolog of hepatitis C virus. Proc Natl Acad Sci USA 108:11608–11613

    CAS  PubMed  Google Scholar 

  • Katze MG, Kwieciszewski B, Goodlett DR, Blakely CM, Neddermann P, Tan SL, Aebersold R (2000) Ser(2194) is a highly conserved major phosphorylation site of the hepatitis C virus nonstructural protein NS5A. Virology 278:501–513

    CAS  PubMed  Google Scholar 

  • Kaul A, Stauffer S, Berger C, Pertel T, Schmitt J, Kallis S, Lopez MZ, Lohmann V, Luban J, Bartenschlager R (2009) Essential role of cyclophilin A for hepatitis C virus replication and virus production and possible link to polyprotein cleavage kinetics. PLoS Pathog 5:e1000546

    PubMed  PubMed Central  Google Scholar 

  • Kielian M, Rey FA (2006) Virus membrane-fusion proteins: more than one way to make a hairpin. Nat Rev Microbiol 4:67–76

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kim S, Welsch C, Yi M, Lemon SM (2011) Regulation of the production of infectious genotype 1a hepatitis C virus by NS5A domain III. J Virol 85:6645–6656

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kopp M, Murray CL, Jones CT, Rice CM (2010) Genetic analysis of the carboxy-terminal region of the hepatitis C virus core protein. J Virol 84:1666–1673

    CAS  PubMed  Google Scholar 

  • Krey T, d’Alayer J, Kikuti CM, Saulnier A, Damier-Piolle L, Petitpas I, Johansson DX, Tawar RG, Baron B, Robert B, England P, Persson MA, Martin A, Rey FA (2010) The disulfide bonds in glycoprotein E2 of hepatitis C virus reveal the tertiary organization of the molecule. PLoS Pathog 6:e1000762

    PubMed  PubMed Central  Google Scholar 

  • Kushima Y, Wakita T, Hijikata M (2010) A disulfide-bonded dimer of the core protein of hepatitis C virus is important for virus-like particle production. J Virol 84:9118–9127

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lesburg CA, Cable MB, Ferrari E, Hong Z, Mannarino AF, Weber PC (1999) Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site. Nat Struct Biol 6:937–943

    CAS  PubMed  Google Scholar 

  • Li K, Foy E, Ferreon JC, Nakamura M, Ferreon AC, Ikeda M, Ray SC, Gale M Jr, Lemon SM (2005) Immune evasion by hepatitis C virus NS3/4A protease-mediated cleavage of the Toll-like receptor 3 adaptor protein TRIF. Proc Natl Acad Sci USA 102:2992–2997

    CAS  PubMed  Google Scholar 

  • Liang Y, Ye H, Kang CB, Yoon HS (2007) Domain 2 of nonstructural protein 5A (NS5A) of hepatitis C virus is natively unfolded. Biochemistry 46:11550–11558

    CAS  PubMed  Google Scholar 

  • Lim YS, Hwang SB (2011) Hepatitis C virus NS5A protein interacts with phosphatidylinositol 4-kinase type III alpha and regulates viral propagation. J Biol Chem 286:11290–11298

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lindenbach BD, Pragai BM, Montserret R, Beran RK, Pyle AM, Penin F, Rice CM (2007) The C-terminus of hepatitis C virus NS4A encodes an electrostatic switch that regulates NS5A hyperphosphorylation and viral replication. J Virol 81:8905–8918

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lindenbach BD, Murray CL, Thiel H-J, Rice CM (2013) Flaviviridae: the viruses and their replication. In: Knipe DM et al. (eds) Fields Virology. Lippincott Williams and Wilkins, New York (in press)

    Google Scholar 

  • Liu Z, Yang F, Robotham JM, Tang H (2009) Critical role of cyclophilin A and its prolyl-peptidyl isomerase activity in the structure and function of the hepatitis C virus replication complex. J Virol 83:6554–6565

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lohmann V, Körner F, Herian U, Bartenschlager R (1997) Biochemical properties of hepatitis C virus NS5B RNA-dependent RNA polymerase and identification of amino acid sequence motifs essential for enzymatic activity. J Virol 71:8416–8428

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lorenz IC, Marcotrigiano J, Dentzer TG, Rice CM (2006) Structure of the catalytic domain of the hepatitis C virus NS2-3 protease. Nature 442:831–835

    CAS  PubMed  Google Scholar 

  • Love RA, Brodsky O, Hickey MJ, Wells PA, Cronin CN (2009) Crystal structure of a novel dimeric form of NS5A domain I protein from hepatitis C virus. J Virol 83:4395–4403

    CAS  PubMed  PubMed Central  Google Scholar 

  • Luik P, Chew C, Aittoniemi J, Chang J, Wentworth P Jr, Dwek RA, Biggin PC, Venien-Bryan C, Zitzmann N (2009) The 3-dimensional structure of a hepatitis C virus p7 ion channel by electron microscopy. Proc Natl Acad Sci USA 106:12712–12716

    CAS  PubMed  Google Scholar 

  • Lundin M, Monne M, Widell A, Von Heijne G, Persson MA (2003) Topology of the membrane-associated hepatitis C virus protein NS4B. J Virol 77:5428–5438

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lundin M, Lindstrom H, Gronwall C, Persson MA (2006) Dual topology of the processed hepatitis C virus protein NS4B is influenced by the NS5A protein. J Gen Virol 87:3263–3272

    CAS  PubMed  Google Scholar 

  • Luo D, Wei N, Doan DN, Paradkar PN, Chong Y, Davidson AD, Kotaka M, Lescar J, Vasudevan SG (2010) Flexibility between the protease and helicase domains of the dengue virus NS3 protein conferred by the linker region and its functional implications. J Biol Chem 285:18817–18827

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ma Y, Yates J, Liang Y, Lemon SM, Yi M (2008) NS3 helicase domains involved in infectious intracellular hepatitis C virus particle assembly. J Virol 82:7624–7639

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ma Y, Anantpadma M, Timpe JM, Shanmugam S, Singh SM, Lemon SM, Yi M (2011) Hepatitis C virus NS2 protein serves as a scaffold for virus assembly by interacting with both structural and nonstructural proteins. J Virol 85:86–97

    CAS  PubMed  Google Scholar 

  • Macdonald A, Harris M (2004) Hepatitis C virus NS5A: tales of a promiscuous protein. J Gen Virol 85:2485–2502

    CAS  PubMed  Google Scholar 

  • Masaki T, Suzuki R, Murakami K, Aizaki H, Ishii K, Murayama A, Date T, Matsuura Y, Miyamura T, Wakita T, Suzuki T (2008) Interaction of hepatitis C virus nonstructural protein 5A with core protein is critical for the production of infectious virus particles. J Virol 82:7964–7976

    CAS  PubMed  PubMed Central  Google Scholar 

  • McCaffrey K, Gouklani H, Boo I, Poumbourios P, Drummer HE (2011) The variable regions of hepatitis C virus glycoprotein E2 have an essential structural role in glycoprotein assembly and virion infectivity. J Gen Virol 92:112–121

    CAS  PubMed  Google Scholar 

  • McLauchlan J, Lemberg MK, Hope G, Martoglio B (2002) Intramembrane proteolysis promotes trafficking of hepatitis C virus core protein to lipid droplets. EMBO J 21:3980–3988

    CAS  PubMed  PubMed Central  Google Scholar 

  • Meylan E, Curran J, Hofmann K, Moradpour D, Binder M, Bartenschlager R, Tschopp J (2005) Cardif is an adaptor protein in the RIG-I antiviral pathway and is targeted by hepatitis C virus. Nature 437:1167–1172

    CAS  PubMed  Google Scholar 

  • Miller S, Krijnse-Locker J (2008) Modification of intracellular membrane structures for virus replication. Nat Rev Microbiol 6:363–374

    CAS  PubMed  PubMed Central  Google Scholar 

  • Miyanari Y, Hijikata M, Yamaji M, Hosaka M, Takahashi H, Shimotohno K (2003) Hepatitis C virus non-structural proteins in the probable membranous compartment function in viral RNA replication. J Biol Chem 278:50301–50308

    CAS  PubMed  Google Scholar 

  • Miyanari Y, Atsuzawa K, Usuda N, Watashi K, Hishiki T, Zayas M, Bartenschlager R, Wakita T, Hijikata M, Shimotohno K (2007) The lipid droplet is an important organelle for hepatitis C virus production. Nat Cell Biol 9:1089–1097

    CAS  PubMed  Google Scholar 

  • Montserret R, Saint N, Vanbelle C, Salvay AG, Simorre JP, Ebel C, Sapay N, Renisio JG, Bockmann A, Steinmann E, Pietschmann T, Dubuisson J, Chipot C, Penin F (2010) NMR structure and ion channel activity of the p7 protein from hepatitis C virus. J Biol Chem 285:31446–31461

    CAS  PubMed  PubMed Central  Google Scholar 

  • Moradpour D, Brass V, Bieck E, Friebe P, Gosert R, Blum HE, Bartenschlager R, Penin F, Lohmann V (2004a) Membrane association of the RNA-dependent RNA polymerase is essential for hepatitis C virus RNA replication. J Virol 78:13278–13284

    CAS  PubMed  PubMed Central  Google Scholar 

  • Moradpour D, Evans MJ, Gosert R, Yuan ZH, Blum HE, Goff SP, Lindenbach BD, Rice CM (2004b) Insertion of green fluorescent protein into nonstructural protein 5A allows direct visualization of functional hepatitis C virus replication complexes. J Virol 78:7400–7409

    CAS  PubMed  PubMed Central  Google Scholar 

  • Moradpour D, Brass V, Penin F (2005) Function follows form: the structure of the N-terminal domain of HCV NS5A. Hepatology 42:732–735

    PubMed  Google Scholar 

  • Moradpour D, Penin F, Rice CM (2007) Replication of hepatitis C virus. Nat Rev Microbiol 5:453–463

    CAS  PubMed  Google Scholar 

  • Morikawa K, Lange CM, Gouttenoire J, Meylan E, Brass V, Penin F, Moradpour D (2011) Nonstructural protein 3–4A: the Swiss army knife of hepatitis C virus. J Viral Hepat 18:305–315

    CAS  PubMed  Google Scholar 

  • Mosley RT, Edwards TE, Murakami E, Lama AM, Grice RL, Dua J, Sofiaa MJ, Furman PA, Otto MJ (2012) Structure of hepatitis C virus polymerase in complex with primer-template RNA. J Virol 86:6503–6511

    Google Scholar 

  • Murray CL, Jones CT, Rice CM (2008) Architects of assembly: roles of Flaviviridae non-structural proteins in virion morphogenesis. Nat Rev Microbiol 6:699–708

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nature Outlook: Hepatitis C (2011). Nature 474:S1–S21

    Google Scholar 

  • Neddermann P, Quintavalle M, Di Pietro C, Clementi A, Cerretani M, Altamura S, Bartholomew L, De Francesco R (2004) Reduction of hepatitis C virus NS5A hyperphosphorylation by selective inhibition of cellular kinases activates viral RNA replication in cell culture. J Virol 78:13306–13314

    CAS  PubMed  PubMed Central  Google Scholar 

  • Oehler V, Filipe A, Montserret R, da Costa D, Brown G, Penin F, McLauchlan J (2012) Structural analysis of hepatitis C virus core-E1 signal peptide and requirements for cleavage of the genotype 3a signal sequence by signal peptide peptidase. J Virol 86:7818–7828

    Google Scholar 

  • Okamoto K, Mori Y, Komoda Y, Okamoto T, Okochi M, Takeda M, Suzuki T, Moriishi K, Matsuura Y (2008) Intramembrane processing by signal peptide peptidase regulates the membrane localization of hepatitis C virus core protein and viral propagation. J Virol 82:8349–8361

    CAS  PubMed  PubMed Central  Google Scholar 

  • Paul D, Romero-Brey I, Gouttenoire J, Stoitsova S, Krijnse-Locker J, Moradpour D, Bartenschlager R (2011) NS4B self-interaction through conserved C-terminal elements is required for the establishment of functional hepatitis C virus replication complexes. J Virol 85:6963–6976

    CAS  PubMed  PubMed Central  Google Scholar 

  • Penin F, Combet C, Germanidis G, Frainais PO, Deleage G, Pawlotsky JM (2001) Conservation of the conformation and positive charges of hepatitis C virus E2 envelope glycoprotein hypervariable region 1 points to a role in cell attachment. J Virol 75:5703–5710

    CAS  PubMed  PubMed Central  Google Scholar 

  • Penin F, Brass V, Appel N, Ramboarina S, Montserret R, Ficheux D, Blum HE, Bartenschlager R, Moradpour D (2004) Structure and function of the membrane anchor domain of hepatitis C virus nonstructural protein 5A. J Biol Chem 279:40835–40843

    CAS  PubMed  Google Scholar 

  • Phan T, Kohlway A, Dimberu P, Pyle AM, Lindenbach BD (2011) The acidic domain of hepatitis C virus NS4A contributes to RNA replication and virus particle assembly. J Virol 85:1193–1204

    CAS  PubMed  Google Scholar 

  • Pietschmann T, Lohmann V, Rutter G, Kurpanek K, Bartenschlager R (2001) Characterization of cell lines carrying self-replicating hepatitis C virus RNAs. J Virol 75:1252–1264

    CAS  PubMed  PubMed Central  Google Scholar 

  • Poordad F, McCone J Jr, Bacon BR, Bruno S, Manns MP, Sulkowski MS, Jacobson IM, Reddy KR, Goodman ZD, Boparai N, DiNubile MJ, Sniukiene V, Brass CA, Albrecht JK, Bronowicki JP (2011) Boceprevir for untreated chronic HCV genotype 1 infection. N Engl J Med 364:1195–1206

    CAS  PubMed  PubMed Central  Google Scholar 

  • Popescu C-I, Callens N, Trinel D, Roingeard P, Moradpour D, Descamps V, Duverlie G, Penin F, Héliot L, Rouillé Y, Dubuisson J (2011) NS2 protein of hepatitis C virus interacts with structural and nonstructural proteins towards virus assembly. PLoS Pathog 7:e1001278

    CAS  PubMed  PubMed Central  Google Scholar 

  • Quinkert D, Bartenschlager R, Lohmann V (2005) Quantitative analysis of the hepatitis C virus replication complex. J Virol 79:13594–13605

    CAS  PubMed  PubMed Central  Google Scholar 

  • Quintavalle M, Sambucini S, Summa V, Orsatti L, Talamo F, De Francesco R, Neddermann P (2007) Hepatitis C virus NS5A is a direct substrate of casein kinase I-alpha, a cellular kinase identified by inhibitor affinity chromatography using specific NS5A hyperphosphorylation inhibitors. J Biol Chem 282:5536–5544

    CAS  PubMed  Google Scholar 

  • Rai R, Deval J (2011) New opportunities in anti-hepatitis C virus drug discovery: targeting NS4B. Antiviral Res 90:93–101

    CAS  PubMed  Google Scholar 

  • Raney KD, Sharma SD, Moustafa IM, Cameron CE (2010) Hepatitis C virus non-structural protein 3: a multifunctional antiviral target. J Biol Chem 285:22725–22731

    CAS  PubMed  PubMed Central  Google Scholar 

  • Reed K, Rice CM (1999) Identification of the major phosphorylation site of the hepatitis C virus H strain NS5A protein as serine 2321. J Biol Chem 274:28011–28018

    CAS  PubMed  Google Scholar 

  • Reiss S, Rebhan I, Backes P, Romero-Brey I, Erfle H, Matula P, Kaderali L, Poenisch M, Blankenburg H, Hiet MS, Longerich T, Diehl S, Ramirez F, Balla T, Rohr K, Kaul A, Bühler S, Pepperkok R, Lengauer T, Albrecht M, Eils R, Schirmacher P, Lohmann V, Bartenschlager R (2011) Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host Microbe 9:32–45

    CAS  PubMed  PubMed Central  Google Scholar 

  • Santolini E, Migliaccio G, La Monica N (1994) Biosynthesis and biochemical properties of the hepatitis C virus core protein. J Virol 68:3631–3641

    CAS  PubMed  PubMed Central  Google Scholar 

  • Schaller T, Appel N, Koutsoudakis G, Kallis S, Lohmann V, Pietschmann T, Bartenschlager R (2007) Analysis of hepatitis C virus superinfection exclusion by using novel fluorochrome gene-tagged viral genomes. J Virol 81:4591–4603

    CAS  PubMed  PubMed Central  Google Scholar 

  • Schmidt-Mende J, Bieck E, Hügle T, Penin F, Rice CM, Blum HE, Moradpour D (2001) Determinants for membrane association of the hepatitis C virus RNA-dependent RNA polymerase. J Biol Chem 276:44052–44063

    CAS  PubMed  Google Scholar 

  • Schregel V, Jacobi S, Penin F, Tautz N (2009) Hepatitis C virus NS2 is a protease stimulated by cofactor domains in NS3. Proc Natl Acad Sci USA 106:5342–5347

    CAS  PubMed  Google Scholar 

  • Shavinskaya A, Boulant S, Penin F, McLauchlan J, Bartenschlager R (2007) The lipid droplet binding domain of hepatitis C virus core protein is a major determinant for efficient virus assembly. J Biol Chem 282:37158–37169

    CAS  PubMed  Google Scholar 

  • Simister P, Schmitt M, Geitmann M, Wicht O, Danielson UH, Klein R, Bressanelli S, Lohmann V (2009) Structural and functional analysis of hepatitis C virus strain JFH1 polymerase. J Virol 83:11926–11939

    CAS  PubMed  PubMed Central  Google Scholar 

  • Stapleford KA, Lindenbach BD (2011) Hepatitis C virus NS2 coordinates virus particle assembly through physical interactions with the E1–E2 glycoprotein and NS3–NS4A enzyme complexes. J Virol 85:1706–1717

    CAS  PubMed  Google Scholar 

  • Steinmann E, Pietschmann T (2010) Hepatitis C virus p7-a viroporin crucial for virus assembly and an emerging target for antiviral therapy. Viruses 2:2078–2095

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tellinghuisen TL, Marcotrigiano J, Gorbalenya AE, Rice CM (2004) The NS5A protein of hepatitis C virus is a zinc metalloprotein. J Biol Chem 279:48576–48587

    CAS  PubMed  Google Scholar 

  • Tellinghuisen TL, Marcotrigiano J, Rice CM (2005) Structure of the zinc-binding domain of an essential replicase component of hepatitis C virus reveals a novel fold. Nature 435:375–379

    Google Scholar 

  • Tellinghuisen TL, Foss KL, Treadaway J (2008) Regulation of hepatitis C virion production via phosphorylation of the NS5A protein. PLoS Pathog 4:e1000032

    PubMed  PubMed Central  Google Scholar 

  • Thompson AA, Zou A, Yan J, Duggal R, Hao W, Molina D, Cronin CN, Wells PA (2009) Biochemical characterization of recombinant hepatitis C virus nonstructural protein 4B: evidence for ATP/GTP hydrolysis and adenylate kinase activity. Biochemistry 48:906–916

    CAS  PubMed  Google Scholar 

  • Verdegem D, Badillo A, Wieruszeski JM, Landrieu I, Leroy A, Bartenschlager R, Penin F, Lippens G, Hanoulle X (2011) Domain 3 of NS5A protein from the hepatitis C virus has intrinsic alpha-helical propensity and is a substrate of cyclophilin A. J Biol Chem 286:20441–20454

    CAS  PubMed  PubMed Central  Google Scholar 

  • Vieyres G, Thomas X, Descamps V, Duverlie G, Patel AH, Dubuisson J (2010) Characterization of the envelope glycoproteins associated with infectious hepatitis C virus. J Virol 84:10159–10168

    CAS  PubMed  PubMed Central  Google Scholar 

  • Voisset C, Dubuisson J (2004) Functional hepatitis C virus envelope glycoproteins. Biol Cell 96:413–420

    CAS  PubMed  Google Scholar 

  • Watashi K, Ishii N, Hijikata M, Inoue D, Murata T, Miyanari Y, Shimotohno K (2005) Cyclophilin B is a functional regulator of hepatitis C virus RNA polymerase. Mol Cell 19:111–122

    CAS  PubMed  Google Scholar 

  • Wölk B, Sansonno D, Kräusslich H-G, Dammacco F, Rice CM, Blum HE, Moradpour D (2000) Subcellular localization, stability and trans-cleavage competence of the hepatitis C virus NS3–NS4A complex expressed in tetracycline-regulated cell lines. J Virol 74:2293–2304

    PubMed  PubMed Central  Google Scholar 

  • Wozniak AL, Griffin S, Rowlands D, Harris M, Yi M, Lemon SM, Weinman SA (2010) Intracellular proton conductance of the hepatitis C virus p7 protein and its contribution to infectious virus production. PLoS Pathog 6:e1001087

    PubMed  PubMed Central  Google Scholar 

  • Yao N, Reichert P, Taremi SS, Prosise WW, Weber PC (1999) Molecular views of viral polyprotein processing revealed by the crystal structure of the hepatitis C virus bifunctional protease-helicase. Structure Fold Des 7:1353–1363

    CAS  PubMed  Google Scholar 

  • Yu GY, Lee KJ, Gao L, Lai MM (2006) Palmitoylation and polymerization of hepatitis C virus NS4B protein. J Virol 80:6013–6023

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

Research in the authors’ laboratories is supported by the Swiss National Science Foundation, the French Centre National de la Recherche Scientifique, and the French National Agency for Research on AIDS and Viral Hepatitis.

Author information

Authors and Affiliations

  1. Division of Gastroenterology and Hepatology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011, Lausanne, Switzerland

    Darius Moradpour

  2. Institut de Biologie et Chimie des Protéines, Bases Moléculaires et Structurales des Systèmes Infectieux, UMR 5086, CNRS, University of Lyon, 69367, Lyon, France

    François Penin

Authors
  1. Darius Moradpour
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. François Penin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Darius Moradpour or François Penin .

Editor information

Editors and Affiliations

  1. Department for Infectious Diseases Molecular Virology, University of Heidelberg, Heidelberg, Germany

    Ralf Bartenschlager

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Moradpour, D., Penin, F. (2013). Hepatitis C Virus Proteins: From Structure to Function. In: Bartenschlager, R. (eds) Hepatitis C Virus: From Molecular Virology to Antiviral Therapy. Current Topics in Microbiology and Immunology, vol 369. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-27340-7_5

Download citation

Publish with us

Policies and ethics

Search

Navigation