title: Three dimensional structure directs T-cell epitope dominance associated with allergy.
abstract: BACKGROUND
  CD4+ T-cell epitope immunodominance is not adequately explained by peptide selectivity in class II major histocompatibility proteins, but it has been correlated with adjacent segments of conformational flexibility in several antigens.
  
  
  METHODS
  The published T-cell responses to two venom allergens and two aeroallergens were used to construct profiles of epitope dominance, which were correlated with the distribution of conformational flexibility, as measured by crystallographic B factors, solvent-accessible surface, COREX residue stability, and sequence entropy.
  
  
  RESULTS
  Epitopes associated with allergy tended to be excluded from and lie adjacent to flexible segments of the allergen.
  
  
  CONCLUSIONS
  During the initiation of allergy, the N- and/or C-terminal ends of proteolytic processing intermediates were preferentially loaded into antigen presenting proteins for the priming of CD4+ T cells.
authors.affiliation: Biomedical Sciences Graduate Program, Tulane University Health Sciences Center, New Orleans, LA, 70112, USA. smelton@tulane.edu.
authors.forename: Scott J
authors.initials: SJ
authors.lastname: Melton
authors.forename: Samuel J
authors.initials: SJ
authors.lastname: Landry
references.citation: J Mol Biol. 2000 Jan 7;295(1):7-16
references.pmid: 10623504
references.citation: J Allergy Clin Immunol. 2007 Apr;119(4):780-91
references.pmid: 17321578
references.citation: Biochemistry. 2003 Mar 25;42(11):3203-13
references.pmid: 12641451
references.citation: J Mol Graph. 1996 Feb;14(1):51-5, 29-32
references.pmid: 8744573
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3497-500
references.pmid: 12824352
references.citation: J Biol Chem. 2002 Jan 4;277(1):155-60
references.pmid: 11673463
references.citation: Annu Rev Immunol. 2005;23:975-1028
references.pmid: 15771591
references.citation: J Immunol. 1998 Oct 15;161(8):4048-57
references.pmid: 9780175
references.citation: J Biol Chem. 2005 Feb 4;280(5):3740-6
references.pmid: 15539389
references.citation: Immunol Today. 1997 Nov;18(11):527-32
references.pmid: 9386348
references.citation: Biochemistry. 2004 Nov 16;43(45):14420-30
references.pmid: 15533047
references.citation: J Immunol. 1993 Apr 15;150(8 Pt 1):3582-91
references.pmid: 7682244
references.citation: Nat Immunol. 2004 Jul;5(7):685-92
references.pmid: 15224094
references.citation: J Immunol. 2002 Sep 1;169(5):2444-50
references.pmid: 12193713
references.citation: Immunity. 1996 Apr;4(4):357-66
references.pmid: 8612130
references.citation: Biochemistry. 1990 Aug 7;29(31):7133-55
references.pmid: 2207096
references.citation: J Infect Dis. 2000 Mar;181(3):1001-9
references.pmid: 10720523
references.citation: Biol Chem. 2006 Oct-Nov;387(10-11):1503-11
references.pmid: 17081125
references.citation: Proc Natl Acad Sci U S A. 1996 Jan 23;93(2):734-8
references.pmid: 8570625
references.citation: J Immunol. 1995 Feb 15;154(4):1932-40
references.pmid: 7530747
references.citation: J Immunol. 2000 Jul 1;165(1):20-3
references.pmid: 10861030
references.citation: Adv Exp Med Biol. 1996;409:141-6
references.pmid: 9095234
references.citation: Trends Immunol. 2008 Mar;29(3):141-7
references.pmid: 18261958
references.citation: Science. 1990 Dec 14;250(4987):1563-6
references.pmid: 2274788
references.citation: J Immunol. 2007 Jun 1;178(11):7181-9
references.pmid: 17513767
references.citation: J Mol Biol. 1996 Oct 11;262(5):756-72
references.pmid: 8876652
references.citation: Biochemistry. 2006 Oct 10;45(40):12325-33
references.pmid: 17014085
references.citation: J Immunol. 2002 Jul 1;169(1):1-4
references.pmid: 12077220
references.citation: Protein Sci. 1994 May;3(5):757-68
references.pmid: 7520312
references.citation: J Biol Chem. 2001 Nov 9;276(45):41913-20
references.pmid: 11551929
references.citation: J Virol. 2008 Feb;82(3):1238-48
references.pmid: 18057238
references.citation: Nat Immunol. 2002 Feb;3(2):169-74
references.pmid: 11812994
references.citation: J Exp Med. 1997 Aug 18;186(4):549-60
references.pmid: 9254653
references.citation: J Mol Biol. 2006 May 5;358(3):882-904
references.pmid: 16542678
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3381-5
references.pmid: 12824332
references.citation: Protein Eng. 1998 May;11(5):349-59
references.pmid: 9681867
references.citation: J Mol Biol. 1999 Jan 15;285(2):627-43
references.pmid: 9878434
references.citation: Eur J Immunol. 2002 Feb;32(2):467-76
references.pmid: 11813165
references.citation: Vaccine. 1997 Feb;15(3):321-4
references.pmid: 9139493
references.citation: J Immunol. 1998 Jul 1;161(1):448-57
references.pmid: 9647255
references.citation: J Biol Chem. 2002 Jan 4;277(1):161-8
references.pmid: 11602571
references.citation: BMC Bioinformatics. 2007 Jul 04;8:238
references.pmid: 17608956
references.citation: Protein Eng Des Sel. 2005 Feb;18(2):59-64
references.pmid: 15788422
references.citation: J Immunol. 1989 Feb 15;142(4):1063-8
references.pmid: 2783704
references.citation: Immunity. 2000 Apr;12(4):391-8
references.pmid: 10795737
references.citation: Proteins. 1989;6(2):87-103
references.pmid: 2695928
references.citation: Eur J Immunol. 2008 May;38(5):1231-7
references.pmid: 18398933
references.citation: Clin Exp Allergy. 2005 Mar;35(3):367-73
references.pmid: 15784117
references.citation: Clin Exp Allergy. 1996 Nov;26(11):1316-28
references.pmid: 8955581
references.citation: Proc Natl Acad Sci U S A. 2005 Mar 29;102(13):4741-6
references.pmid: 15774579
references.citation: Proteins. 1998 Mar 1;30(4):435-41
references.pmid: 9533627
references.citation: Curr Opin Immunol. 2006 Feb;18(1):70-7
references.pmid: 16316750
references.citation: Biopolymers. 2003 Jun;69(2):176-88
references.pmid: 12767121
references.citation: Proteins. 2001 Dec 1;45(4):438-48
references.pmid: 11746691
references.citation: J Immunol. 1998 Apr 1;160(7):3363-73
references.pmid: 9531296