319
Views
10
CrossRef citations to date
0
Altmetric
Review

New insights into viral structure and virus–cell interactions through proteomics

, &
Pages 577-588 | Published online: 09 Jan 2014

References

  • Kellam P. Post-genomic virology: the impact of bioinformatics, microarrays and proteomics on investigating host and pathogen interactions. Rev. Med. Virol. 11(5), 313–329 (2001).
  • Korth MJ, Katze MG. Unlocking the mysteries of virus–host interactions: does functional genomics hold the key? Ann. NY Acad. Sci. 975, 160–168 (2002).
  • Misumi S, Fuchigami T, Takamune N, Takahashi I, Takama M, Shoji S. Three isoforms of cyclophilin A associated with human immunodeficiency virus Type 1 were found by proteomics by using two-dimensional gel electrophoresis and matrix-assisted laser desorption ionization-time of flight mass spectrometry. J. Virol. 76(19), 10000–10008 (2002).
  • Johannsen E, Luftig M, Chase MR et al. Proteins of purified Epstein–Barr virus. Proc. Natl Acad. Sci. USA 101(46), 16286–16291 (2004).
  • Kattenhorn LM, Mills R, Wagner M et al. Identification of proteins associated with murine cytomegalovirus virions. J. Virol. 78(20), 11187–11197 (2004).
  • Zhu FX, Chong JM, Wu L, Yuan Y. Virion proteins of Kaposi’s sarcoma-associated herpesvirus. J. Virol. 79(2), 800–811 (2005).
  • Taylor TJ, Knipe DM. Proteomics of herpes simplex virus replication compartments: association of cellular DNA replication, repair, recombination, and chromatin remodeling proteins with ICP8. J. Virol. 78(11), 5856–5866 (2004).
  • Fontaine-Rodriguez EC, Taylor TJ, Olesky M, Knipe DM. Proteomics of herpes simplex virus infected cell protein 27: association with translation initiation factors. Virology 330(2), 487–492 (2004).
  • You J, Croyle JL, Nishimura A, Ozato K, Howley PM. Interaction of the bovine papillomavirus E2 protein with Brd4 tethers the viral DNA to host mitotic chromosomes. Cell 117(3), 349–360 (2004).
  • Brasier AR, Spratt H, Wu Z et al. Nuclear heat shock response and novel nuclear domain 10 reorganization in respiratory syncytial virus-infected a549 cells identified by high-resolution two-dimensional gel electrophoresis. J. Virol. 78(21), 11461–11476 (2004).
  • Liu HL, Hsu JP. Recent developments in structural proteomics for protein structure determination. Proteomics 5(8), 2056–2068 (2005).
  • Randall AZ, Baldi P, Villarreal LP. Structural proteomics of the poxvirus family. Artif. Intell. Med. 31(2), 105–115 (2004).
  • McDonald TP, Pitt AR, Brown G, Rixon HW, Sugrue RJ. Evidence that the respiratory syncytial virus polymerase complex associates with lipid rafts in virus-infected cells: a proteomic analysis. Virology 330(1), 147–157 (2004).
  • Persidsky Y, Gendelman HE. Mononuclear phagocyte immunity and the neuropathogenesis of HIV-1 infection. J. Leukoc. Biol. 74(5), 691–701 (2003).
  • Wojna V, Carlson KA, Luo X et al. Proteomic fingerprinting of human immunodeficiency virus Type 1-associated dementia from patient monocyte-derived macrophages: a case study. J. Neurovirol. 10(1), 74–81 (2004).
  • Yokoyama Y, Kuramitsu Y, Takashima M et al. Proteomic profiling of proteins decreased in hepatocellular carcinoma from patients infected with hepatitis C virus. Proteomics 4(7), 2111–2116 (2004).
  • Takashima M, Kuramitsu Y, Yokoyama Y et al. Proteomic profiling of heat shock protein 70 family members as biomarkers for hepatitis C virus-related hepatocellular carcinoma. Proteomics 3(12), 2487–2493 (2003).
  • Arnaud MC, Gazarian T, Rodriguez YP, Gazarian K, Sakanyan V. Array assessment of phage-displayed peptide mimics of human immunodeficiency virus type 1 gp41 immunodominant epitope: binding to antibodies of infected individuals. Proteomics 4(7), 1959–1964 (2004).
  • Greenberg M, Cammack N, Salgo M, Smiley L. HIV fusion and its inhibition in antiretroviral therapy. Rev. Med. Virol. 14(5), 321–327 (2004).
  • Maeda K, Nakata H, Ogata H, Koh Y, Miyakawa T, Mitsuya H. The current status of, and challenges in, the development of CCR5 inhibitors as therapeutics for HIV-1 infection. Curr. Opin. Pharmacol. 4(5), 447–452 (2004).
  • Kawamura T, Bruse SE, Abraha A et al. PSC-RANTES blocks R5 human immunodeficiency virus infection of Langerhans cells isolated from individuals with a variety of CCR5 diplotypes. J. Virol. 78(14), 7602–7609 (2004).
  • Gingras AC, Aebersold R, Raught B. Advances in protein complex analysis using mass spectrometry. J. Physiol. 563(Pt 1), 11–21 (2005).
  • Zhu H, Bilgin M, Snyder M. Proteomics. Ann. Rev. Biochem. 72, 783–812 (2003).
  • Simpson RJ. Proteins and proteomics. A laboratory manual. (2003).
  • Aebersold R, Mann M. Mass spectrometry-based proteomics. Nature 422(6928), 198–207 (2003).
  • Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75(17), 4646–4658 (2003).
  • Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74(20), 5383–5392 (2002).
  • Eddes JS, Kapp EA, Frecklington DF et al. CHOMPER: a bioinformatic tool for rapid validation of tandem mass spectrometry search results associated with high-throughput proteomic strategies. Proteomics 2(9), 1097–1103 (2002).
  • Xiao X, Wu L, Stantchev TS et al. Constitutive cell surface association between CD4 and CCR5. Proc. Natl Acad. Sci. USA 96(13), 7496–7501 (1999).
  • Gavin AC, Bosche M, Krause R et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415(6868), 141–147 (2002).
  • Graziani-Bowering G, Filion LG, Thibault P, Kozlowski M. CD4 is active as a signaling molecule on the human monocytic cell line Thp-1. Exp. Cell Res. 279(1), 141–152 (2002).
  • Bernhard OK, Cunningham AL, Sheil MM. Analysis of proteins copurifying with the CD4/lck complex using one-dimensional polyacrylamide gel electrophoresis and mass spectrometry: comparison with affinity-tag based protein detection and evaluation of different solubilization methods. J. Am. Soc. Mass Spectrom. 15(4), 558–567 (2004).
  • Bernhard OK, Burgess JA, Hochgrebe T, Sheil MM, Cunningham AL. Mass spectrometry analysis of CD4-associating proteins using affinity chromatography and affinity tag-mediated purification of tryptic peptides. Proteomics 3(2), 139–146 (2003).
  • Husi H, Ward MA, Choudhary JS, Blackstock WP, Grant SG. Proteomic analysis of NMDA receptor–adhesion protein signaling complexes. Nature Neurosci. 3(7), 661–669 (2000).
  • Blagoev B, Ong SE, Kratchmarova I, Mann M. Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nature Biotechnol. 22(9), 1139–1145 (2004).
  • Ranish JA, Yi EC, Leslie DM et al. The study of macromolecular complexes by quantitative proteomics. Nature Genet. 33(3), 349–355 (2003).
  • Dornan S, Sebestyen Z, Gamble J et al. Differential association of CD45 isoforms with CD4 and CD8 regulates the actions of specific pools of p56lck tyrosine kinase in T-cell antigen receptor signal transduction. J. Biol. Chem. 277(3), 1912–1918 (2002).
  • Bernhard OK, Sheil MM, Cunningham AL. Lateral membrane protein associations of CD4 in lymphoid cells detected by cross-linking and mass spectrometry. Biochemistry 43(1), 256–264 (2004).
  • Mitchell DA, Fadden AJ, Drickamer K. A novel mechanism of carbohydrate recognition by the C-type lectins DC-SIGN and DC-SIGNR. Subunit organization and binding to multivalent ligands. J. Biol. Chem. 276(31), 28939–28945 (2001).
  • Call ME, Pyrdol J, Wiedmann M, Wucherpfennig KW. The organizing principle in the formation of the T-cell receptor–D3 complex. Cell 111(7), 967–979 (2002).
  • Bernhard OK, Lai J, Wilkinson J, Sheil MM, Cunningham AL. Proteomic analysis of DC-SIGN on dendritic cells detects tetramers required for ligand binding but no association with CD4. J. Biol. Chem. 279(50), 51828–51835 (2004).
  • Kleymann G. Novel agents and strategies to treat herpes simplex virus infections. Expert Opin. Investig. Drugs 12(2), 165–183 (2003).
  • Kleymann G. New antiviral drugs that target herpesvirus helicase primase enzymes. Herpes 10(2), 46–52 (2003).
  • Kleymann G. Helicase primase: targeting the Achilles heel of herpes simplex viruses. Antivir. Chem. Chemother. 15(3), 135–140 (2004).
  • Visalli RJ, van Zeijl M. DNA encapsidation as a target for antiherpesvirus drug therapy. Antiviral Res. 59(2), 73–87 (2003).
  • Diefenbach RJ, Miranda-Saksena M, Diefenbach E et al. Herpes simplex virus tegument protein US11 interacts with conventional kinesin heavy chain. J. Virol. 76(7), 3282–3291 (2002).
  • Douglas MW, Diefenbach RJ, Homa FL et al. Herpes simplex virus Type 1 capsid protein VP26 interacts with dynein light chains RP3 and Tctex1 and plays a role in retrograde cellular transport. J. Biol. Chem. 279(27), 28522–28530 (2004).
  • Vittone V, Diefenbach E, Triffett D, Douglas MW, Cunningham AL, Diefenbach RJ. Determination of interactions between tegument proteins of herpes simplex virus Type 1. J. Virol. 79(15), 9566–9571 (2005).
  • Fields S, Song O. A novel genetic system to detect protein–protein interactions. Nature 340(6230), 245–246 (1989).
  • Gyuris J, Golemis E, Chertkov H, Brent R. Cdi1, a human G1 and S phase protein phosphatase that associates with Cdk2. Cell 75(4), 791–803 (1993).
  • Causier B. Studying the interactome with the yeast two-hybrid system and mass spectrometry. Mass Spectrom. Rev. 23(5), 350–367 (2004).
  • Mettenleiter TC. Budding events in herpesvirus morphogenesis. Virus Res. 106(2), 167–180 (2004).
  • Klupp BG, Fuchs W, Granzow H, Nixdorf R, Mettenleiter TC. Pseudorabies virus UL36 tegument protein physically interacts with the UL37 protein. J. Virol. 76(6), 3065–3071 (2002).
  • Terpe K. Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems. Appl. Microbiol. Biotechnol. 60(5), 523–533 (2003).
  • Mazzulli T, Low DE, Poutanen SM. Proteomics and severe acute respiratory syndrome (SARS): emerging technology meets emerging pathogen. Clin. Chem. 51(1), 6–7 (2005).
  • Labaer J, Ramachandran N. Protein microarrays as tools for functional proteomics. Curr. Opin. Chem. Biol. 9(1), 14–19 (2005).
  • Sakanyan V. High-throughput and multiplexed protein array technology: protein–DNA and protein–protein interactions. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 815(1–2), 77–95 (2005).
  • Davies DH, Liang X, Hernandez JE et al. Profiling the humoral immune response to infection by using proteome microarrays: high-throughput vaccine and diagnostic antigen discovery. Proc. Natl Acad. Sci. USA 102(3), 547–552 (2005).
  • Yuk CS, Lee HK, Kim HT et al. Development and evaluation of a protein microarray chip for diagnosis of hepatitis C virus. Biotechnol. Lett. 26(20), 1563–1568 (2004).

Websites

  • Expert Protein Analysis System http://au.expasy.org (Viewed July 2005)
  • NCBI – PubMed www.ncbi.nlm.nih.gov/entrez/query. fcgi?db = Protein (Viewed July 2005)
  • MASCOT www.matrixscience.com/search_form_ select.html (Viewed July 2005)
  • SEQUEST http://fields.scripps.edu/sequest/index.html (Viewed July 2005)

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.