Cleavage site analysis in picornaviral polyproteins: Discovering cellular targets by neural networks

Protein Science

Volumn 5, Issue 11, 1996, Pages 2203-2216

  Blom, Nikolaj ^a   Hansen, Jan ^a   Blaas, Dieter ^b   Brunak, Søren ^a  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b UNIVERSITY OF VIENNA   (Austria)

Author keywords

cleavage site prediction; neural networks; picornavirus; proteinase; surface exposure

Indexed keywords

PROTEINASE; VIRUS PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CATALYSIS; PICORNAVIRUS; POLIOMYELITIS VIRUS; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; TARGET CELL;

MAMMALIA; PICORNAVIRIDAE; POLIOVIRUS;

EID: 0029846866     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560051107     Document Type: Article

References (60)

1. Arnold E, Luo M, Vriend G, Rossmann MG, Palmenberg C, Parks GD, Nicklin MJH, Wimmer E. 1987. Implications of the picornavirus capsid structure for polyprotein processing. Proc Natl Acad Sci USA 84:21-25.
2. Auvinen P, Hyypia T. 1990. Echoviruses include genetically distinct serotypes. J Gen Virol 71:2133-2139.
3. Barco A, Carrasco L. 1995. Poliovirus 2Apro expression inhibits growth of yeast cells. FEBS Lett 371:4-8.
4. Basavappa R, Syed R, Icenogle JP, Filman DJ, Hogle JM. 1994. Role and mechanism of the maturation cleavage of VPO in poliovirus assembly: Structure of the empty capsid assembly intermediate at 2.9 Å resolution. Protein Sci 3:1651-1669.
5. Beck E, Forss S, Strebel K, Cattaneo R, Feil G. 1983. Structure of the FMDV translation initiation site and of the structural proteins. Nucleic Acids Res 11:7873-7885.
6. Berger A, Schechter I. 1970. Mapping the active site of papain with the aid of peptide substrates and inhibitors. Phil Trans R Soc Lond Biol 257:249-264.
7. Bishop NE, Anderson DA. 1993. RNA-dependent cleavage of VP0 capsid protein in provirions of hepatitis A virus. Virology 197:615-623.
8. Brunak S, Engelbrecht J, Knudsen S. 1990a. Cleaning up gene databases. Nature 343:123.
9. Brunak S, Engelbrecht J, Knudsen S. 1990b. Neural network detects errors in the assignment of pre-mRNA splice site. Nucleic Acids Res 18:4797-4801.
10. Brunak S, Engelbrecht J, Knudsen S. 1991. Prediction of human mRNA donor and acceptor sites from the DNA sequence. J Mol Biol 220:49-65.
11. Cao X, Wimmer E. 1996. Genetic variation of the poliovirus genome with two VPg coding units. EMBO J 15:23-33.
12. Chang KH, Auvinen P, Hyypia T, Stanway G. 1989. The nucleotide sequence of coxsackievirus A9; implications for receptor binding and enterovirus classification J Gen Virol 70:3269-3280.
13. Clark ME, Dasgupta A. 1990. A transcriptionally active form of TFIIIC is modified in poliovirus-infected HeLa cells Mol Cell Biol 10:5106-5113.
14. Clark ME, Hammerle T, Wimmer E, Dasgupta A. 1991. Poliovirus proteinase 3C converts an active form of transcription factor IIIC to an inactive form: A mechanism for inhibition of host cell polymerase III transcription by poliovirus. EMBO J 10:2941-2947.
15. Clark ME, Lieberman PM, Berk AJ, Dasgupta A. 1993. Direct cleavage of human TATA-binding protein by poliovirus protease 3C in vivo and in vitro. Mol Cell Biol 13:1232-1237.
16. Conolly ML. 1983. Solvent-accessible surfaces of proteins and nucleic acids. Science 221:709-713.
17. Cordingley MG, Callahan PL, Sardana VV, Garsky VM, Colonno RJ. 1990. Substrate requirements of human rhinovirus 3C protease for peptide cleavage in vitro. J Biol Chem 265:9062-9065.
18. Cordingley MG, Register RB, Callahan PL, Garsky VM, Colonno RJ. 1989. Cleavage of small peptides in vitro by human rhinovirus 14 3C protease expressed in Escherichia coli. J Virol 63:5037-5045.
19. Falk MM, Grigera PR, Bergmann IE, Zibert A, Multhaup G, Beck E. 1990. Foot-and-mouth disease virus protease 3C induces specific proteolytic cleavage of host cell histone H3. J Virol 64:748-756.
20. Harber JJ, Bradley J, Anderson CW, Wimmer E. 1991. Catalysis of poliovirus VPO maturation cleavage is not mediated by senne 10 of VP2. J Virol 65:326-334.
21. Hellen CU, Lee CK, Wimmer E. 1992. Determinants of substrate recognition by poliovirus 2A proteinase J Virol 66:3330-3338.
22. Hellen CUT, Krausslich HG, Wimmer E. 1989. Ptoteolytic processing of polyproteins in the replication of RNA viruses. Biochemistry 28:9881-9890.
23. Hertz J, Krogh A, Palmer R. 1991. Introduction to the theory of neural computation. Redwood City, California. Addison-Wesley.
24. Iizuka N, Kuge S. Nomoto A. 1987. Complete nucleotide sequence of the genome of coxsackievirus B1 Virology 156:64-73.
25. Jenkins O, Booth JD, Minor PD, Almond JW. 1987. The complete nucleotide sequence of coxsackievirus B4 and its comparison to other members of the Picornaviridae. J Gen Virol 68:1835-1848.
26. Joachims M, Etchison D. 1992. Poliovirus infection results in structural alteration of a microtubule-associated protein. J Virol 66:5797-5804.
27. Joachims M, Harris KS, Etchison D. 1995. Poliovirus protease 3C mediates cleavage of microtubule-associated protein 4. Virology 211:451-461.
28. Kitamura N, Semler BL, Rothberg PG, Larsen GR, Adler CJ, Domer AJ, Emini EA, Hanecak R, Lee JJ, vander Werf S, Andersen CW, Wimmer E. 1981. Primary structure, gene organization and polypeptide expression of poliovirus RNA. Nature 291:547-553.
29. Klump H, Auer H, Liebig HD, Kuechler E, Skern T. 1996. Proteolytically active 2A proteinase of human rhinovirus 2 is toxic for Saccharomyces cerevisiae but does not cleave the homologues of eIF-4 gamma in vivo or in vitro. Virology 220:109-118.
30. Korning PG, Hebsgaard SM, Rouzé P, Brunak S. 1996. Cleaning the GenBank Arabidopsis thaliana data set Nucleic Acids Res 24:316-320.
31. Krausslich HG, Wimmer E. 1988. Viral proteinases Annu Rev Biochem 57:701-754.
32. Lamphear BJ, Kirchweger R, Skern T, Rhoads RE. 1995. Mapping of functional domains in eukaryotic protein synthesis initiation factor 4G (eIF4G) with picornaviral proteases. Implications for cap-dependent and cap-independent translational initiation. J Biol Chem 270:21975-21983.
33. Lamphear BJ, Yan R, Yang F, Waters D, Liebig HD, Klump H, Kuechler E, Skern T, Rhoads RE. 1993. Mapping the cleavage site in protein synthesis initiation factor eIF-4 gamma of the 2A proteases from human coxsackievirus and rhinovirus. J Biol Chem 265:19200-19203.
34. Lawson MA, Semler BL. 1990. Picornavirus protein processing - Enzymes, substrates, and genetic regulation. Curr Topics Microbiol Immunol 161:49-88.
35. Lee CK, Wimmer E. 1988. Proteolytic processing of poliovirus polyprotein: Elimination of 2Apro-mediated, alternative cleavage of polypeptide 3CD by in vitro mutagenesis. Virology 166:405-414.
36. Liebig HD, Ziegler E, Yan R, Hartmuth K, Klump H, Kowalski H, Blaas D, Sommergruber W, Frasel L, Lamphear B, Rhoades R, Kuechler E, Skern T. 1993. Purification of two picornaviral 2A proteinases: Interaction with eIF-4 gamma and influence on in vitro translation. Biochemistry 32:7581-7588.
37. Long AC, Orr DC, Cameron JM, Dunn BM, Kay J. 1989. A consensus sequence for substrate hydrolysis by rhinovirus 3C proteinase. FEBS Lett 258:75-78.
38. MacGregor MJ, Flores TP, Sternberg MJE. 1989. Prediction of beta-turns in proteins using neural networks. Protein Eng 2:521-526.
39. Matthews DA, Smith WW, Ferre RA, Condon B, Budahazi G, Sisson W, Villafranca JE, Janson CA, McElroy HE, Gribskov CL, Worland S. 1994. Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein. Cell 77:761-771.
40. McLean C, Matthews TJ, Rueckert RR. 1976. Evidence of ambiguous processing and selective degradation in the noncapsid proteins of rhinovirus 1A. J Virol 19:903-914.
41. Minsky M, Papert S. 1969. Perceptrons Cambridge, Massachusetts: MIT Press.
42. Nomoto A, Omata T, Toyoda H, Kuge S, Horie H, Kataoka Y, Genba Y, Nakano Y, Imura N. 1982. Complete nucleotide sequence of the attenuated poliovirus Sabin 1 strain genome. Proc Natl Acad Sci USA 79:5793-5797.
43. Qian N, Sejnowski TJ. 1988. Predicting the secondary structure of globular proteins using neural network models. J Mol Biol 202:865-884.
44. Robertson BH, Grubman MJ, Weddell GN, Moore DM, Welsh JD, Fischer T, Dowbenko DJ, Yansura DG, Small B, Kleid DG. 1985. Nucleotide and amino acid sequence coding for polypeptides of foot-and-mouth disease virus type A12. J Virol 54:651-660.
45. Rost B, Sander C. 1993. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 232:584-599.
46. Rumelhart DE, Hinton GE, Williams RJ. 1986. Learning internal representations by error propagation. In: Rumelhart D, McClelland J, PDP Research Group, eds Parallel distributed processing: Explorations in the microstructure of cognition, vol I. Foundations. Cambridge, Massachusetts. MIT Press. pp 318-362.
47. Ryan MD, Drew J. 1994. Foot-and-mouth disease virus 2A oligopeptide mediated cleavage of an artificial polyprotein. EMBO J 13:928-933.
48. Ryan MD, Jenkins O, Hughes PJ, Brown A, Knowles NJ, Booth D, Minor PD, Almond JW. 1990. The complete nucleotide sequence of enterovirus type 70: Relationships with other members of the picornaviridae J Gen Virol 71:2291-2299.
49. Schneider TD, Stephens RM. 1990. Sequence logos. A new way to display consensus sequences. Nucleic Acids Res 18:6097-6100.
50. Schultheiss T, Kusov YY, Gauss-Muller V. 1994. Proteinase 3C of hepatitis A virus (HAV) cleaves the HAV polyprotein P2-P3 at all sites including VP1/2A and 2A/2B. Virology 198:275-281.
51. Shannon CE. 1948. A mathematical theory of communication. Bell System Tech J 27:379-423/623-656.
52. Shen Y, Igo M, Yalamanchili P, Berk AJ, Dasgupta A. 1996. DNA binding domain and subunit interactions of transcription factor IIIC revealed by dissection with poliovirus 3C protease. Mol Cell Biol 16:4163-4171.
53. Skern T, Sommergruber W, Blaas D, Gruendler P, Fraundorfer F, Pieler C, Fogy I, Kuechler E. 1985. Human rhinovirus 2: Complete nucleotide sequence and proteolytic processing signals in the capsid protein region. Nucleic Acids Res 13:2111-2126.
54. Sommergruber W, Ahorn H, Klump H, Seipelt J, Zophel A, Fessl F, Krystek E, Blaas D, Kuechler E, Liebig HD, Skern T. 1994. 2A proteinases of coxsackie- and rhinovirus cleave peptides derived from eIF-4gamma via a common recognition motif. Virology 198:741-745.
55. Sommergruber W, Ahorn H, Zophel A, Maurer-Fogy I, Fessl F, Schnorrenberg G, Liebig HD, Blaas D, Kuechler E, Skern T. 1992. Cleavage specificity on synthetic peptide substrates of human rhinovirus 2 proteinase 2A. J Biol Chem 267:22639-22644.
56. Stanway G, Hughes PJ, Mountford RC, Minor PD, Almond JW. 1984. The complete nucleotide sequence of a common cold virus: Human rhinovirus 14. Nucleic Acids Res 12:7859-7875.
57. Supanaranond K, Takeda N, Yamazaki S. 1992. The complete nucleotide sequence of a variant of Coxsackievirus A24, an agent causing acute hemorrhagic conjunctivitis. Virus Genes 6:149-158.
58. Tesar M, Marquardt O. 1990. Foot-and-mouth disease virus protease 3C inhibits cellular transcription and mediates cleavage of histone H3. Virology 174:364-374.
59. Urzanqui A, Carrasco L. 1989. Degradation of cellular proteins during poliovirus infection: Studies by two-dimensional gel electrophoresis. J Virol 63:4729-4735.
60. Ypma-Wong MF, Filman DJ, Hogle JM, Semler BL. 1988. Structural domains of the poliovirus polyprotein are major determinants for proteolytic cleavage at Gln-Gly pairs. J Biol Chem 263:17846-17856.