Homology modeling and epitope prediction of Der f 33

Abstract

Dermatophagoides farinae (Der f), one of the main species of house dust mites, produces more than 30 allergens. A recently identified allergen belonging to the alpha-tubulin protein family, Der f 33, has not been characterized in detail. In this study, we used bioinformatics tools to construct the secondary and tertiary structures and predict the B and T cell epitopes of Der f 33. First, protein attribution, protein patterns, and physicochemical properties were predicted. Then, a reasonable tertiary structure was constructed by homology modeling. In addition, six B cell epitopes (amino acid positions 34–45, 63–67, 103–108, 224–230, 308–316, and 365–377) and four T cell epitopes (positions 178–186, 241–249, 335–343, and 402–410) were predicted. These results established a theoretical basis for further studies and eventual epitope-based vaccine design against Der f 33.

Structure/Epitope-Based Immunoinformatics Analysis of Structural Proteins of 2019 Novel Coronavirus

“…The multiple alignment of homologous amino acid sequences was performed using Clustal X 2.1 program [12]. Physicochemical analysis of the protein sequences was predicted by ProtParam (http://web.expasy.org/protparam/), including molecular weight, amino acid composition, negatively charged residues (Asp + Glu), positively charged residues (Arg + Lys), theoretical isoelectric point pI, aliphatic index, grand average of hydropathicity (GRAVY) and instability index of proteins [13].…”