Publication:
Art v 4 Protein Structure as a Representative Template for Allergen Profilins: Homology Modeling and Molecular Dynamics
Art v 4 Protein Structure as a Representative Template for Allergen Profilins: Homology Modeling and Molecular Dynamics
No Thumbnail Available
Date
2018
Authors
Barazorda-Ccahuana H.L.
Valencia D.E.
Aguilar-Pineda J.A.
Gómez B.
Journal Title
Journal ISSN
Volume Title
Publisher
American Chemical Society
Research Projects
Organizational Units
Journal Issue
Abstract
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. © 2018 American Chemical Society.
Description
Keywords
General Chemistry,
General Chemical Engineering