Validation of in silico prediction by in vitro immunoserological results of fine epitope mapping on citrate synthase specific autoantibodies

Molecular Immunology

Volumn 43, Issue 7, 2006, Pages 830-838

  Nyarady Z ^a   Czompoly T ^a   Bosze, Sz ^b   Nagy, G ^a   Petrohai, A ^c   Pal J ^a   Hudecz, F ^b,d   Berki, T ^a   Nemeth P ^a  

^a UNIVERSITY OF PÉCS   (Hungary)

^b EÖTVÖS LORÁND UNIVERSITY   (Hungary)

^c SEMMELWEIS UNIVERSITY   (Hungary)

^d EÖTVÖS LORÁND UNIVERSITY   (Hungary)

Author keywords

Autoantibody; Autoimmunity; Citrate synthase; Heart transplantation; Immunoserology; In silico epitope prediction; Multipin ELISA

Indexed keywords

AUTOANTIBODY; CITRATE SYNTHASE; CITRATE SYNTHASE ANTIBODY; ENZYME ANTIBODY; EPITOPE; MEMBRANE ANTIGEN; UNCLASSIFIED DRUG;

ADULT; ALGORITHM; ANTIBODY SPECIFICITY; ANTIGEN RECOGNITION; ARTICLE; AUTOIMMUNITY; BIOINFORMATICS; COMPARATIVE STUDY; COMPUTER MODEL; COMPUTER PROGRAM; CONTROLLED STUDY; ENZYME LINKED IMMUNOSORBENT ASSAY; EPITOPE MAPPING; ERROR; HEART TRANSPLANTATION; HUMAN; IMMUNOPATHOLOGY; IN VITRO STUDY; MITOCHONDRIAL MEMBRANE; PEPTIDE SYNTHESIS; PREDICTION; PRIORITY JOURNAL; SEROLOGY; VALIDATION PROCESS;

AMINO ACID SEQUENCE; ANTIGEN-ANTIBODY REACTIONS; AUTOANTIBODIES; CELL MEMBRANE; CITRATE (SI)-SYNTHASE; COMPUTER SIMULATION; EPITOPE MAPPING; EPITOPES, B-LYMPHOCYTE; EPITOPES, T-LYMPHOCYTE; HUMANS; MODELS, IMMUNOLOGICAL; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION;

EID: 29144470376     PISSN: 01615890     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molimm.2005.06.044     Document Type: Article

References (42)

1. S.F. Altschul, L.T. Madden, A.A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acid Res. 25 1997 3389 3402
2. M.H. Andersen, L. Tan, I. Sondergaard, J. Zeuthen, T. Elliott, and J.S. Haurum Poor correspondence between predicted and experimental binding of peptides to class I MHC molecules Tissue Antigens 55 2000 519 531
3. M.Z. Attasi Antigenic structures of proteins. Their determination has revealed important aspects of immune recognition and generated strategies for synthetic mimicking of protein binding sites Eur. J. Biochem. 145 1984 1 20
4. D.C. Benjamin, J.A. Berzofsky, I.J. East, F.R.N. Gurd, C. Hannum, S.J. Leach, E. Margoliash, J.G. Michael, A. Miller, E.M. Prager, M. Reichlin, E.E. Sercaz, S.J. Smith-Gill, P.E. Todd, and A.C. Wilson The antigenic structure of proteins Rev. Immunol. 2 1984 67 101
5. D.A. Benson, M.S. Boguski, D.J. Lipman, J. Ostell, B.F.F. Ouellette, B.A. Rapp, and D.L. Wheeler GenBank Nucleic Acid Res. 27 1999 12 17
6. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne The Protein Data Bank Nucleic Acid Res. 28 2000 235 242
7. P.Y. Chou, and G.D. Fasman Prediction of the secondary structure of proteins from their amino acid sequence Adv. Enzymol. 47 1978 45 148
8. I.R. Cohen, and D.B. Young Autoimmunity, microbial immunity and the immunological homunculus Immunol. Today 12 1991 105 110
9. I.R. Cohen The cognitive paradigm and the immunological homunculus Immunol. Today 13 1992 490 494
10. D. Eisenberg, M. Wesson, and W. Wilcox Hydrophobic moments as tools for analyzing protein sequences and structures G.D. Fasman Prediction of Protein Structure and the Principles of Protein Conformation 1990 Plenum Press New York p. 635
11. H.M. Geysen, R.H. Meloen, and S.J. Barteling Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid Proc. Natl. Acad. Sci. U.S.A. 81 1984 3998 4002
12. M.J. Goldenthal, J. Marin-Garcia, and R. Ananthakrishnan Cloning and molecular analysis of the human citrate synthase gene Genoma 41 1998 733 738
13. A.S. de Groth, and F.G. Rothman In silico predictions; in vivo veritas Nat. Biotechnol. 17 1999 533 534
14. N. Guex, A. Diemand, and M.C. Peitsch Protein modelling for all TIBS 24 1999 364 367
15. J. Hammer, E. Bono, F. Gallazzi, C. Belunis, Z. Nagy, and F. Sinigaglia Precise prediction of major histocompatibility complex calss II peptide interaction based on peptide side chain scanning J. Exp. Med. 180 1994 2353 2358
16. M.C. Honeyman, V. Brusic, N.L. Stone, and L.C. Harrison Neural network-based prediction of candidate T-cell epitopes Nat. Biotechnol. 16 1998 966 969
17. T.P. Hopp, and K.R. Woods Prediction of protein antigenic determinants from amino acid sequences Proc. Natl. Acad. Sci. 78 1981 3428 3824
18. T.P. Hopp Protein surface analysis J. Immunol. Methods 88 1986 1 18
19. B.A. Jameson, and H. Wolf The antigenic index: a novel algorithm for predicting antigenic determinants CABIOS 4 1988 181 186
20. V. Krchnák, J. Vágner, P. Safár, and M. Lebl Noninvasive continuous monitoring of solid-phase peptide synthesis by acid-base indicator Collection Czechslovak Chem. Commun. 53 1988 2542
21. W.G. Laver, M.G. Air, R.G. Webster, and S.J. Smith-Gill Epitopes on protein antigens: misconceptions and realities Cell 61 1990 553 556
22. R.A. Lerner Antibodies of predetermined specificity in biology and medicine Adv. Immunol. 36 1984 1 44
23. R.A. Lerner Tapping the immunological repertoaire to produce antibodies of predetermined specificity Nature 299 1982 592 596
24. N.J. Maeji, A.M. Bray, R.M. Valerio, and W. Wang Larger scale multipin peptide synthesis Pept. Res. 8 1995 33 38
25. V. Masignani, E. Balducci, D. Serruto, D. Veggi, B. Arico, M. Comanducci, M. Pizza, and R. Rappuoli In silico identification of novel bacterial ADP-ribosyltransferases Int. J. Med. Microbiol. 293 2004 471 478
26. P. Németh, T. Czömpöly, G. Nagy, L. Czirják, and T. Berki Fine epitope mapping of circulating - physiological and pathological - autoantibodies using peptide libraries expressed by filamentous and lambda phages Tissue Antigens 64 2004 357 358
27. N.T. Nguyen, R. Maurus, D.J. Stokell, A. Ayed, H.W. Duckworth, and G.D. Brayer Comparative analysis of folding and substrate binding sites between regulated hexameric type II citrate synthases and unregulated dimeric type I enzymes Biochemistry 40 2001 13177 13187
28. M.C. Peitsch Promod and Swiss-Model: internet-based tools for automated comparative protein modeling Biochem. Soc. Trans. 24 1996 274 279
29. M.C. Peitsch About the use of protein models Bioinformatics 18 2002 934 938
30. J.L. Pellequer, E. Westhof, and M.H.V. van Regenmortel Predicting location of continous epitopes in proteins from their primary structure Methods Enzymol. 203 1991 176 201
31. S. Peri, N. Ibarrola, B. Blagolev, M. Mann, and A. Pandey Common pitfalls in bioinformatics-based analyses: look before you leap Trends Genet. 17 2001 541 545
32. Petrohai, Á., Nagy, G., Bsze, Sz., Hudecz, F., Zsíros, E., Paragh, Gy., Nyárády, Z., Németh, P., Berki, T., 2005. Detection of citrate synthase reacting autoantibodies after heart transpalntation: an epitope mapping study. Transplant Int. (PMID: 15711981).
33. P. Prevelige, and G.D. Fasman G.D. Fasman Prediction of Protein Structure and the Principles of Protein Conformation 1990 Plenum Press New York, U.S.A. p. 391
34. M.H.V. van Regenmortel Which structural features determine protein antigenicity? TIBS 11 1986 36 39
35. M.H.V. van Regenmortel, and D.G. de Marcillac An assessment of prediction methods for locating continuous epitopes in proteins Immunol. Lett. 17 1988 95 108
36. M.H.V. van Regenmortel The concept and operational definition of protein epitopes Philos. Trans. R. Soc. Lond. B323 1989 451 466
37. M.H.V. van Regenmortel The recognition of proteins and peptides by antibodies J. Immunoassay 21 2000 85 108
38. M. Schawarz, and I.R. Cohen Autoimmunity can benefit self-maintanance Immunol. Today 21 2000 265 267
39. T. Schwede, A. Diemand, N. Guex, and M.C. Peitsch Protein structure computing in the genomic era Res. Microbiol. 151 2000 107 112
40. D. Serruto, J. Adu-Bobie, B. Capecchi, R. Rappuoli, M. Pizza, and V. Masignani Biotechnology and vaccines: application of functional genomics to Neisseria meningitidis and other bacterial pathogens J. Biotechnol. 113 2004 15 32
41. T. Sturiniolo, E. Bono, J. Ding, L. Raddrizzani, O. Tuereci, U. Sahin, M. Braxenthaler, F. Gallazzi, M.P. Protti, F. Singaglia, and J. Hammer Generation of tissue specific and promiscous HLA ligand databases using DNA microarrays and virtual HLA class II matrices Nat. Biotechnol. 17 1999 555 561
42. J.M. Thornton, M.S. Edwards, W.R. Taylor, and D.J. Barlow Location of 'continous' antigenic determinants in the protruding regions of proteins EMBO J. 5 1986 409 413