Art v 4 Protein Structure as a Representative Template for Allergen Profilins: Homology Modeling and Molecular Dynamics

Profilins are panallergenic proteins of clinical relevance. We compared three groups of three-dimensional structures from six vegetable profilins. The first group was composed of crystal structures obtained by X-ray diffraction. The second and the third group structures were obtained by homology modeling; the selection criteria of the templates for these were based on the best resolution structure and the highest sequence identity, respectively. All of the structures underwent a 200 ns molecular dynamics simulation. The best template for the second group was Art v 4 and for the third group was the crystal structure corresponding to each profilin, except for Zea m 12. After molecular dynamics simulation, root-mean-square deviation, root-mean-square fluctuation, and radii of gyration values were similar in all groups, except for Amb a 8 (second group) and Zea m 12 (third group). All structures had acceptable conformation quality values, demonstrated in the Ramachandran plot and Z-score. The evaluation of epitopes did not have pertinent alterations of all of the structures. Art v 4 profilin was an acceptable template to model three-dimensional profilin structures of this work. The selection of templates based on their structural resolution and the measure of the quality is a good alternative to homology modeling of proteins of the same family.