Theoretical analysis of the neuraminidase epitope of the Mexican A H1N1 influenza strain, and experimental studies on its interaction with rabbit and human hosts.
The neuraminidase (NA) epitope from the Mexican AH1N1 influenza virus was identified by using sequences registered at the GenBank during the peak of a pandemic (from April 2009 to October 2010). First, NA protein sequences were submitted for multiple alignment analysis, and their three-dimensional models (3-D) were then built by using homology modeling. The most common sequence (denominated wild-type) and its mutants were submitted to linear and nonlinear epitope predictors, which included the major histocompatibility complex type II (MHC II) and B-cell peptides. The epitope prediction was in accordance with evolutionary behavior and some protein structural properties. The latter included a low NA mutation rate, NA 3-D surface exposure, and the presence of high hindrance side chain residues. After selecting the epitope, docking studies and molecular dynamics (MD) simulations were used to explore interactions between the epitope and MHC II. Afterward, several experimental assays were performed to validate the theoretical study by using antibodies from humans (infected by pandemic H1N1) and rabbits (epitope vaccination). The results show 119 complete sequences that were grouped into 28 protein sequences according to their identity (one wild-type and 27 representative mutants (1-5 mutations)). The predictors yielded several epitopes, with the best fit being the one located in the C-terminal region. Theoretical methods demonstrated that the selected epitope reached the P4, P6, P7, and P9 pockets of MHC II, whereas the experimental evidence indicates that the epitope is recognized by human antibodies and also by rabbit antibodies immunized with the peptide.
Laboratorio de Modelado Molecular y Bioinformática de la Escuela Superior de Medicina, Instituto Politécnico Nacional, México, Plan de San Luis Y Diaz Mirón S/N, Mexico city, Mexico. dra.reyes.loyola@gmail.com
Paola Kinara Reyes
PK
Loyola
R
R
Campos-Rodríguez
Martiniano
M
Bello
S
S
Rojas-Hernández
Mirko
M
Zimic
Miguel
M
Quiliano
Verónica
V
Briz
M Angeles
MA
Muñoz-Fernández
Luis
L
Tolentino-López
Jose
J
Correa-Basurto
D000595:Amino Acid Sequence; D000818:Animals; D000914:Antibodies, Viral / Q000378:metabolism; D019295:Computational Biology; D018604:Epitope Mapping / Q000379:methods*; D018985:Epitopes, B-Lymphocyte / Q000235:genetics / Q000276:immunology / Q000378:metabolism*; D000949:Histocompatibility Antigens Class II / Q000378:metabolism; D054884:Host-Pathogen Interactions / Q000276:immunology*; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000276:immunology*; D007251:Influenza, Human / Q000175:diagnosis / Q000276:immunology*; D008800:Mexico; D023421:Models, Animal; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D009439:Neuraminidase / Q000235:genetics / Q000276:immunology / Q000378:metabolism*; D009976:Orthomyxoviridae Infections / Q000276:immunology*; D011485:Protein Binding; D011487:Protein Conformation; D011817:Rabbits; D014611:Vaccination
D000914:Antibodies, Viral; D018985:Epitopes, B-Lymphocyte; D000949:Histocompatibility Antigens Class II; D009439:Neuraminidase