PMID- 18621419
OWN - NLM
STAT- MEDLINE
DCOM- 20081022
LR  - 20240312
IS  - 0161-5890 (Print)
IS  - 0161-5890 (Linking)
VI  - 45
IP  - 14
DP  - 2008 Aug
TI  - Comprehensive 3D-modeling of allergenic proteins and amino acid composition of 
      potential conformational IgE epitopes.
PG  - 3740-7
LID - 10.1016/j.molimm.2008.05.026 [doi]
AB  - Similarities in sequences and 3D structures of allergenic proteins provide vital 
      clues to identify clinically relevant immunoglobulin E (IgE) cross-reactivities. 
      However, experimental 3D structures are available in the Protein Data Bank for 
      only 5% (45/829) of all allergens catalogued in the Structural Database of 
      Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP). Here, an automated 
      procedure was used to prepare 3D-models of all allergens where there was no 
      experimentally determined 3D structure or high identity (95%) to another protein 
      of known 3D structure. After a final selection by quality criteria, 433 reliable 
      3D models were retained and are available from our SDAP Website. The new 3D 
      models extensively enhance our knowledge of allergen structures. As an example of 
      their use, experimentally derived "continuous IgE epitopes" were mapped on 3 
      experimentally determined structures and 13 of our 3D-models of allergenic 
      proteins. Large portions of these continuous sequences are not entirely on the 
      surface and therefore cannot interact with IgE or other proteins. Only the 
      surface exposed residues are constituents of "conformational IgE epitopes" which 
      are not in all cases continuous in sequence. The surface exposed parts of the 
      experimental determined continuous IgE epitopes showed a distinct statistical 
      distribution as compared to their presence in typical protein-protein interfaces. 
      The amino acids Ala, Ser, Asn, Gly and particularly Lys have a high propensity to 
      occur in IgE binding sites. The 3D-models will facilitate further analysis of the 
      common properties of IgE binding sites of allergenic proteins.
FAU - Oezguen, Numan
AU  - Oezguen N
AD  - Department of Biochemistry and Molecular Biology and Sealy Center for Structural 
      Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, 
      TX 77555-0857, USA.
FAU - Zhou, Bin
AU  - Zhou B
FAU - Negi, Surendra S
AU  - Negi SS
FAU - Ivanciuc, Ovidiu
AU  - Ivanciuc O
FAU - Schein, Catherine H
AU  - Schein CH
FAU - Labesse, Gilles
AU  - Labesse G
FAU - Braun, Werner
AU  - Braun W
LA  - eng
GR  - R01 AI064913/AI/NIAID NIH HHS/United States
GR  - R01 AI064913-03/AI/NIAID NIH HHS/United States
GR  - R01 AI064913-04/AI/NIAID NIH HHS/United States
GR  - R01 AI 064913/AI/NIAID NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, U.S. Gov't, Non-P.H.S.
PT  - Research Support, U.S. Gov't, P.H.S.
DEP - 20080714
PL  - England
TA  - Mol Immunol
JT  - Molecular immunology
JID - 7905289
RN  - 0 (Allergens)
RN  - 0 (Amino Acids)
RN  - 0 (Epitopes)
RN  - 0 (Proteins)
RN  - 37341-29-0 (Immunoglobulin E)
SB  - IM
MH  - Allergens/*chemistry/classification/genetics/immunology
MH  - Amino Acid Sequence
MH  - Amino Acids/chemistry
MH  - Databases, Protein
MH  - Epitopes/chemistry
MH  - Immunoglobulin E/*chemistry/classification/genetics/immunology
MH  - *Models, Molecular
MH  - Molecular Sequence Data
MH  - Protein Conformation
MH  - Proteins/*chemistry/classification/genetics/immunology
MH  - Sequence Homology, Amino Acid
PMC - PMC2593650
MID - NIHMS66329
EDAT- 2008/07/16 09:00
MHDA- 2008/10/23 09:00
PMCR- 2009/08/01
CRDT- 2008/07/16 09:00
PHST- 2008/04/22 00:00 [received]
PHST- 2008/05/28 00:00 [revised]
PHST- 2008/05/29 00:00 [accepted]
PHST- 2008/07/16 09:00 [pubmed]
PHST- 2008/10/23 09:00 [medline]
PHST- 2008/07/16 09:00 [entrez]
PHST- 2009/08/01 00:00 [pmc-release]
AID - S0161-5890(08)00226-5 [pii]
AID - 10.1016/j.molimm.2008.05.026 [doi]
PST - ppublish
SO  - Mol Immunol. 2008 Aug;45(14):3740-7. doi: 10.1016/j.molimm.2008.05.026. Epub 2008 
      Jul 14.