Computational protocol: Bet v 1 from Birch Pollen Is a Lipocalin-like Protein Acting as Allergen Only When Devoid of Iron by Promoting Th2 Lymphocytes*

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Protocol publication

[…] We employed three different superposition procedures to compare the structure of allergens using (i) the FATCAT (Flexible structure AlignmenT by Chaining Aligned Fragment Pairs) (), which allows flexibility in structurally aligned blocks by introducing a limited number of twists in the superposed structures; (ii) the CE (Combinatorial Extension) algorithm to align structural fragment pairs (); and (iii) the TM (Template Modeling)-align procedure, which uses rotation matrices and dynamic programming to optimize a structure alignment (). Both CE and TM methods yield superpositions referring to the protein structure as a whole, whereas FATCATflex superpositions may give two or more superposed structural blocks if one or more twists are introduced (as it is the case here for Bet v 1: ).For comparisons between crystal structures, FATCATflex and CE superpositions were accomplished by using the j-interface versions of these methods implemented in the PDB Comparison Tool (). For FATCATflex comparisons involving model structures, the FATCAT server () and a version compiled for Linux of the CE program were used instead. TM-align superpositions were carried out in all cases using the TM website (), which allows comparing experimental as well as theoretical structures. Superposed structures with FATCATflex p values < 0.05 are considered significantly similar, CE superpositions with z-scores between 3.0 and 4.0 suggest structural similarity, and TM-align superpositions with TM scores between 0.4 and 0.5 indicate significant structural relationship. Structural comparisons between NGAL (neutrophil gelatinase-associated lipocalin) wild-type protein and the allergen Bet v 1 were studied using the x-ray crystal structures (Protein Data Bank (PDB) code in parentheses) for NGAL (1L6M) and birch Bet v 1 (1BV1). […]

Pipeline specifications

Software tools FATCAT, TM-align
Application Protein structure analysis
Organisms Homo sapiens
Diseases Respiratory Insufficiency
Chemicals Iron