Structural analysis and modeling of the Cupin 1 domain in the quinoa 11S globulin

ALEJANDRA RUBINSTEIN; LAURA B LUCAS; OSCAR E PÉREZ

L.A., Estados Unidos

Congreso; 3rd WBSD L.A.: 3rd Women in Bioinformatics & Data Science; 2022

Comunidad de mujeres que trabajan en las áreas de Bioinformática y Ciencia de Datos creada en 2019.

Quinoa (Chenopodium quinoa Willd.) is an ancestral crop of the Andean peoples, which has resurfaced in recent years due to its nutritional properties being "re-discovered" and its resistance to abiotic stress. The seeds of this pseudocereal contain a high amount of protein and an excellent balance of amino acids, which exceeds the standards of the Federal Agriculture Organization (FAO). One of the main reserve proteins is 11S globulin, whose structure is currently not crystallized in the Protein Data Bank (PDB) platform. In this way, in our laboratory, the bioinformatic study was carried out in order to determine structural alignments by homology and the determination of conserved regions, domains and motifs that were similar to other proteins. Using Blastp against the Protein Data Bank (PDB) platform, establishing BLOSUM62 as matrix parameters, gap cost of 11; extension 1 and word size of 6 it was obtained that the crystallized structures of the organisms Bertholletia excelsa, Amaranthus hypochondriacus, Pisum sativum, Prunus dulcis, Cocos nucifera were the best results obtained. The best homology percentage was 43.85% with an e-value of 1.10-115. Through the use of Pfam (Protein family), it was shown that the Cupin 1 domain was the common motif of the set of proteins, with an average bit-score value of 104.3 and an average e-value of 4.5.10-26. Using Clustalω and Jalview, a multiple alignment was performed and it was determined that the most conserved amino acids in the Cupin 1 domain (glycine 63, glycine 86 and proline 92) remain conserved in all proteins. Finally, from VMD it was possible to visualize the secondary structure of the Cupin 1 domain. In conclusion, the bioinformatic results contribute to the characterization of this domain in greater detail, relevant knowledge for the prediction and modeling of the quinoa 11 S protein.