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

• Autores: Barazorda-Ccahuana H.L., Valencia D.E., Aguilar-Pineda J.A., Gómez B.
• Formato: artículo
• Fecha de Publicación: 2018
• Institución: Consejo Nacional de Ciencia Tecnología e Innovación
• Repositorio: CONCYTEC-Institucional
• Lenguaje: inglés
• OAI Identifier: oai:repositorio.concytec.gob.pe:20.500.12390/2760
• Enlace del recurso: https://hdl.handle.net/20.500.12390/2760; https://doi.org/10.1021/acsomega.8b02288
• Nivel de acceso: acceso abierto
• Materia: General Chemistry; General Chemical Engineering; http://purl.org/pe-repo/ocde/ford#3.04.03

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.