Hiv vaccine mystery and viral shell disorder

Biomolecules

Volumn 9, Issue 5, 2019, Pages

  Goh, Gerard Kian Meng ^a   Dunker, A Keith ^b   Foster, James A ^c   Uversky, Vladimir N ^d,e  

^a Goh's BioComputing   (Singapore)

^b INDIANA UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF IDAHO   (United States)

^d UNIVERSITY OF SOUTH FLORIDA   (United States)

^e INSTITUTE FOR BIOLOGICAL INSTRUMENTATION   (Russian Federation)

Author keywords

Glycoconjugate; Hepatitis; Herpes; HIV; Immune escape; Intrinsic disorder; Polio; Rabies; Smallpox; Unstructured; Yellow fever

Indexed keywords

HUMAN IMMUNODEFICIENCY VIRUS VACCINE; VIRUS GLYCOPROTEIN; INTRINSICALLY DISORDERED PROTEIN; VIRAL PROTEIN;

ANTIBODY DETECTION; ARTICLE; CANCER THERAPY; EQUINE INFECTIOUS ANEMIA VIRUS; HEPATITIS C VIRUS; HERPES SIMPLEX VIRUS; HERPES SIMPLEX VIRUS 2; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; IMMUNE EVASION; INFLUENZA VIRUS; POLIOMYELITIS; RABIES; SEXUAL TRANSMISSION; SMALLPOX; VACCINATION; VIRION; VIROTHERAPY; VIRUS INFECTION; VIRUS NEUTRALIZATION; YELLOW FEVER VIRUS; ANIMAL; CHEMISTRY; HUMAN IMMUNODEFICIENCY VIRUS 1; IMMUNOLOGY; PHYSIOLOGY; VIRUS LATENCY;

AIDS VACCINES; ANIMALS; HIV-1; HUMANS; IMMUNE EVASION; INTRINSICALLY DISORDERED PROTEINS; VIRAL PROTEINS; VIRUS LATENCY;

EID: 85065888886     PISSN: None     EISSN: 2218273X     Source Type: Journal    
DOI: 10.3390/biom9050178     Document Type: Article

References (76)

1. Esparza J. A brief history of the global effort to develop a preventive HIV vaccine. Vaccine. 2013;31:3502-3518.
2. Acheson N.H. Fundamentals of Molecular Virology. Wiley; Hoboken, NJ, USA: 2007.
3. Goh G.K. Viral Shapeshifters: Strange Behaviors of HIV and Other Viruses. 1st ed. Simplicity Research Institute; Singapore: 2017.
4. Levine A.J. Viruses. Henry Holt and Co.; New York, NY, USA: (Scientific American Library).
5. Moelling K. Viruses: More Friends Than Foes. World Scientific; Singapore: 2015.
6. Malmquist W.A., Barnett D., Becvar C.S. Production of equine infectious anemia antigen in a persistently infected cell line. Archiv für die gesamte Virusforschung. 1973;42:361-370.
7. Leroux C., Cadoré J.L., Montelaro R.C. Equine Infectious Anemia Virus (EIAV): What has HIV’s country cousin got to tell us? Vet. Res. 2004;35:485-512.
8. Montelaro R.C., Grund C., Raabe M., Woodson B., Cook R.F., Cook S., Issel C.J. Characterization of protective and enhancing immune responses to equine infectious anemia virus resulting from experimental vaccines. AIDS Res. Hum. Retroviruses. 1996;12:413-415.
9. World Organization for Animal Health (OIE) Terrestrial Manual 2013; OIE 2013:2.5.6, Equine Infectious Anemial. [(accessed on 3 May 2019)]; Available online: Http://www.oie.int/standard-setting/terrestrial-manual/access-online/
10. Wang X.F., Lin Y.Z., Li Q., Liu Q., Zhao W.W., Du C., Chen J., Wang X., Zhou J.H. Genetic Evolution during the development of an attenuated EIAV vaccine. Retrovirology. 2016;13:9.
11. Goh G.K., Dunker A.K., Uversky V.N. A comparative analysis of viral matrix proteins using disorder predictors. Virol. J. 2008;5:126.
12. Goh G.K., Dunker A.K., Uversky V.N. Shell disorder, immune evasion and transmission behaviors among human and animal retroviruses. Mol. Biosyst. 2015;11:2312-2323.
13. Avery O.T., Goebel W.F. Chemo-Immunological Studies on Conjugated Carbohydrate-Proteins: V. The Immunological Specifity of an Antigen Prepared by Combining the Capsular Polysaccharide of Type III Pneumococcus with Foreign Protein. J. Exp. Med. 1931;54:437-447.
14. Avery O.T., Goebel W.F. Chemo-Immunological Studies on Conjugated Carbohydrate-Proteins: II. Immunological Specificity of Synthetic Sugar-Protein Antigens. J. Exp. Med. 1929;50:533-550.
15. Goebel W.F., Avery O.T. Chemo-Immunological Studies on Conjugated Carbohydrate Proteins: I. The Synthesis of p-Aminophenol beta-glycoside, p-Aminophenol beta-Galactoside, and their Coupling with Serum Globulin. J. Exp. Med. 1929;50:521-531.
16. Goh G.K., Dunker A.K., Uversky V.N. Protein intrinsic disorder toolbox for comparative analysis of viral proteins. BMC Genom. 2008;9(Suppl. 2)
17. Goh G.K., Dunker A.K., Uversky V.N. Protein intrinsic disorder and influenza virulence: The 1918 H1N1 and H5N1 viruses. Virol. J. 2009;6:69.
18. Fonseca A.A., Heinemann M.B., Leite R.C., Reis J.K. A comparative analysis of envelope and tegument proteins of suid herpesvirus 1, bovine herpesvirus 1 and bovine herpesvirus 5. Arch. Virol. 2010;155:1687-1692.
19. Xue B., Williams R.W., Oldfield C.J., Meng Goh G.K., Dunker A., Uversky V.N. Viral disorder or disordered viruses: Do viral proteins possess unique features? Protein Pept. Lett. 2010;17:932-951.
20. Goh G.K., Dunker A.K., Uversky V.N. Understanding Viral transmission behavior via protein intrinsic disorder prediction: Coronaviruses. J. Pathog. 2012;2012:738590.
21. Xue B., Mizianty M.J., Kurgan L., Uversky V.N. Protein intrinsic disorder as a flexible armor and a weapon of HIV-1. Cell. Mol. Life Sci. 2012;69:1211-1259.
22. Goh G.K., Dunker A.K., Uversky V.N. Prediction of Intrinsic Disorder in MERS CoV/HCoV-EMC Supports a High Oral-Fecal Transmission. PLoS Curr. 2013;5
23. Fan X., Xue B., Dolan P.T., LaCount D.J., Kurgan L., Uversky V.N. The intrinsic disorder status of the human hepatitis C virus proteome. Mol. Biosyst. 2014;10:1345-1363.
24. Dolan P.T., Roth A.P., Xue B., Sun R., Dunker A.K., Uversky V.N., LaCount D.J. Intrinsic disorder mediates hepatitis C virus core-host cell protein interactions. Protein Sci. 2015;24:221-235.
25. Goh G.K., Dunker A.K., Uversky V.N. Detection of links between Ebola nucleocapsidand virulence using disorder analysis. Mol. Biosyst. 2015;11:2337-2344.
26. Goh G.K., Dunker A.K., Uversky V.N. Correlating Flavivirus virulence and levels of intrinsic disorder in shell proteins: Protective roles vs. immune evasion. Mol. Biosyst. 2016;12:1881-1891.
27. Dunker A.K., Lawson J.D., Brown C.J., Williams R.M., Romero P., Oh J.S., Oldfield C.J., Campen A.M., Ratliff C.M., Hipps K.W., et al. Intrinsically disordered protein. J. Mol. Graph. Model. 2001;19:26-59.
28. Tompa P. Intrinsically unstructured proteins. Trends Biochem. Sci. 2002;27:527-533.
29. Uversky V.N., Gillespie J.R., Fink A.L. Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins. 2000;41:415-427.
30. Wright P.E., Dyson H.J. Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm. J. Mol. Biol. 1999;293:321-331.
31. Romero P., Obradovic Z., Li X., Garner E.C., Brown C.J., Dunker A.K. Sequence complexity of disordered protein. Proteins. 2001;42:38-48.
32. Romero P., Obradovic Z., Kissinger C., Villafranca J.E., Dunker A.K. Identifying disordered regions in proteins from amino acid sequence; Proceedings of the IEEE International Conference on Neural Networks; Houston, TX, USA. 12 June 1997; pp. 90-95.
33. Garner E., Romero P., Dunker A.K., Brown C., Obradovic Z. Predicting Binding Regions within Disordered Proteins. Genome Inf. 1999;10:41-50.
34. Oldfield C.J., Cheng Y., Cortese M.S., Romero P., Uversky V.N., Dunker A.K. Coupled folding and binding with alpha-helix-forming molecular recognition elements. Biochemistry. 2005;44:12454-12470.
35. Cheng Y., Oldfield C.J., Meng J., Romero P., Uversky V.N., Dunker A.K. Mining alpha-helix-forming molecular recognition features with cross species sequence alignments. Biochemistry. 2007;46:13468-13477.
36. Tagmyer T.L., Craigo J.K., Cook S.J., Even D.L., Issel C.J., Montelaro R.C. Envelope determinants of equine infectious anemia virus vaccine protection and the effects of sequence variation on immune recognition. J. Virol. 2008;82:4052-4063.
37. Gelderblom H.R. In: Medical Microbiology. 4th ed. Baron S., editor. University of Texas Medical Branch at Galveston; Galveston, TX, USA: 1996.
38. Walpole G.A. The New British Traveller. Alexander Hogg; London, UK: 1784. p. 365.
39. Ambrose C.T. Osler and the infected letter. Emerg. Infect. Dis. 2005;11:689-693.
40. Razzell P. Smallpox extinction-a note of caution. New Sci. 1976;71:35.
41. Belshe R.B., Leone P.A., Bernstein D.I., Wald A., Levin M.J., Stapleton J.T., Gorfinkel I., Ashley Morrow R.L., Ewell M.G., Stokes-Riner A., et al. Efficacy results of a trial of a herpes simplex vaccine. N. Engl. J. Med. 2012;366:34-43.
42. Guo H., Shen S., Wang L., Deng H. Role of tegument proteins in herpesvirus assembly and egress. Protein Cell. 2010;1:987-998.
43. Lambers F.A., Prins M., Thomas X., Molenkamp R., Kwa D., Brinkman K., Van der Meer J.T., Schinkel J., MOSAIC (MSM Observational Study of Acute Infection with Hepatitis C) Study Group Alarming incidence of hepatitis C virus re-infection after treatment of sexually acquired acute hepatitis C virus infection in HIV-infected MSM. AIDS. 2011;25:F21-F27.
44. Alencar W.K., Duarte P.S., Waldman E.A. Survival analysis of acquired immune deficiency syndrome patients with and without hepatitis C virus infection at a reference center for sexually transmitted diseases/acquired immune deficiency syndrome in Sao Paulo, Brazil. Braz. J. Infect. Dis. 2013;18:150-157.
45. Chan D.P., Sun H.Y., Wong H.T., Lee S.S., Hung C.C. Sexually acquired hepatitis C virus infection: A review. Int. J. Infect. Dis. 2016;49:47-58.
46. Bloch H. Edward Jenner (1749-1823). The history and effects of smallpox, inoculation, and vaccination. Am. J. Dis. Child. 1993;147:772-774.
47. Riedel S. Baylor University Medical Center Proceedings. Volume 18. Taylor & Francis; Abingdon, UK: 2005. Edward Jenner and the history of smallpox and vaccination; pp. 21-25.
48. Berche P. Louis Pasteur, from crystals of life to vaccination. Clin. Microbiol. Infect. 2012;18(Suppl. 5):1-6.
49. John T.J. The golden jubilee of vaccination against poliomyelitis. Indian J. Med. Res. 2004;119:1-17.
50. Norrby E. Yellow fever and Max Theiler: The only Nobel Prize for a virus vaccine. J. Exp. Med. 2007;204:2779-2784.
51. Du J., Wang X., Ma J., Wang J., Qin Y., Zhu C., Liu F., Shao Y., Zhou J., Qiao W., et al. Structural and biochemical insights into the V/I505T mutation found in the EIAV gp45 vaccine strain. Retrovirology. 2014;11:26.
52. Liu Y., Stone S., Harty R.N. Characterization of filovirus protein-protein interactions in mammalian cells using bimolecular complementation. J. Infect. Dis. 2011;204(Suppl. 3):S817-S824.
53. Kato A., Liu Z., Minowa A., Imai T., Tanaka M., Sugimoto K., Nishiyama Y., Arii J., Kawaguchi Y. Herpes simplex virus 1 protein kinase Us3 and major tegument protein UL47 reciprocally regulate their subcellular localization in infected cells. J. Virol. 2011;85:9599-9613.
54. Chauhan A., Khandkar M. Endocytosis of human immunodeficiency virus 1 (HIV-1) in astrocytes: A fiery path to its destination. Microb. Pathog. 2015;78:1-6.
55. Goudsmit J. Viral Sex: The Nature of AIDS. Oxford University Press; New York, NY, USA: 1997.
56. Urdaneta V., Casadesús J. Interactions between bacteria and bile Salts in the gastrointestinal and hepatobiliary Tracts. Front. Med. 2017;4:163.
57. Nieuwenhuis R.F., Van Doornum G.J., Mulder P.G., Neumann H.A., Van der Meijden W.I. Importance of herpes simplex virus type-1 (HSV-1) in primary genital herpes. Acta Derm. Venereol. 2006;86:129-134.
58. Koelle D.M., Norberg P., Fitzgibbon M.P., Russell R.M., Greninger A.L., Huang M., Stensland L., Jing L., Magaret A.S., Diem K., et al. Worldwide circulation of HSV-2 × HSV-1 recombinant strains. Sci. Rep. 2017;7:44084.
59. Ohori Y., Okazaki H., Watanabe S., Tochio N., Arai M., Kigawa T., Nishimura C. Flexible and rigid structures in HIV-1 p17 matrix protein monitored by relaxation and amide proton exchange with NMR. Biochim. Biophys. Acta. 2014;1844:520-526.
60. Caccuri F., Giagulli C., Reichelt J., Martorelli D., Marsico S., Bugatti A., Barone I., Rusnati M., Guzman C.A., Dolcetti R., et al. Simian immunodeficiency virus and human immunodeficiency virus type 1 matrix proteins specify different capabilities to modulate B cell growth. J. Virol. 2014;88:5706-5717.
61. Giagulli C., D’Ursi P., He W., Zorzan S., Caccuri F., Varney K., Orro A., Marsico S., Otjacques B., Laudanna C., et al. A single amino acid substitution confers B-cell clonogenic activity to the HIV-1 matrix protein p17. Sci. Rep. 2017;7:6555.
62. Pandey U., Renner D.W., Thompson R.L., Szpara M.L., Sawtell N.M. Inferred father-to-son transmission of herpes simplex virus results in near-perfect preservation of viral genome identity and in vivo phenotypes. Sci. Rep. 2017;7:13666.
63. Xue B., Dunker A.K., Uversky V.N. Orderly order in protein intrinsic disorder distribution: Disorder in 3500 proteomes from viruses and the three domains of life. J. Biomol. Struct. Dyn. 2012;30:137-149.
64. Nicholson W.L., Krivushin K., Gilichinsky D., Schuerger A.C. Growth of Carnobacterium spp. from permafrost under low pressure, temperature, and anoxic atmosphere has implications for Earth microbes on Mars. Proc. Natl. Acad. Sci. USA. 2013;110:666-671.
65. Burton D.R. Antibodies, viruses and vaccines. Nat. Rev. Immunol. 2002;2:706-713.
66. Vigerust D.J., Shepherd V.L. Virus glycosylation: Role in virulence and immune interactions. Trends Microbiol. 2007;15:211-218.
67. Keen E.C. A century of phage research: Bacteriophages and the shaping of modern biology. Bioessays. 2015;37:6-9.
68. Trigo G., Martins T.G., Fraga A.G., Longatto-Filho A., Castro A.G., Azeredo J., Pedrosa J. Phage therapy is effective against infection by Mycobacterium ulcerans in a murine footpad model. PLoS Negl. Trop. Dis. 2013;7:e2183.
69. Chernajovsky Y., Layward L., Lemoine N. Fighting cancer with oncolytic viruses. BMJ. 2006;332:170-172.
70. Wei D., Xu J., Liu X., Chen Z.N., Bian H. Fighting cancer with viruses: Oncolytic virus therapy in China. Hum. Gene Ther. 2017
71. Chaurasiya S., Chen N.G., Warner S.G. Oncolytic virotherapy versus cancer stem cells: A review of approaches and mechanisms Cancers. 2018;10:E124.
72. Grigg C., Blake Z., Gartrell R., Sacher A., Taback B., Saenger Y. Talimogene laherparepvec (T-Vec) for the treatment of melanoma and other cancers. Semin. Oncol. 2016;43:638-646.
73. Penkett C.J., Redfield C., Dodd I., Hubbard J., McBay D.L., Mossakowska D.E., Smith R.A., Dobson C.M., Smith L.J. NMR analysis of main-chain conformational preferences in an unfolded fibronectin-binding protein. J. Mol. Biol. 1997;274:152-159.
74. Penkett C.J., Redfield C., Jones J.A., Dodd I., Hubbardett J., Smith R.A., Smith L.J., Dobson C.M. Structural and dynamical characterization of a biologically active unfolded fibronectin-binding protein from Staphylococcus aureus. Biochemistry. 1998;37:17054-17067.
75. House-Pompeo K., Xu Y., Joh D., Speziale P., Hook M.J. Conformational Changes in the Fibronectin Binding MSCRAMMs Are Induced by Ligand Binding. J. Biol. Chem. 1996;271:1379-1384.
76. Dunker A.K., Iakoucheva L.M., Brown C.J., Lawson J.D., Obradovic Z. Intrinsic disorder and protein function. Biochemistry. 2002;41:6573-6582.