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. 2019 Mar 11;9(1):35.
doi: 10.1186/s13568-019-0757-x.

In silico analysis as a strategy to identify candidate epitopes with human IgG reactivity to study Porphyromonas gingivalis virulence factors

Ellen Karla Nobre Dos Santos-Lima  1 , Kizzes Araújo Paiva Andrade Cardoso  2 , Patrícia Mares de Miranda  1 , Ana Carla Montino Pimentel  1 , Paulo Cirino de Carvalho-Filho  3 , Yuri Andrade de Oliveira  4 , Lília Ferreira de Moura-Costa  5 , Teresa Olczak  6 , Isaac Suzart Gomes-Filho  7 , Roberto José Meyer  5 , Márcia Tosta Xavier  3 , Soraya Castro Trindade  8
Affiliations

In silico analysis as a strategy to identify candidate epitopes with human IgG reactivity to study Porphyromonas gingivalis virulence factors

Ellen Karla Nobre Dos Santos-Lima et al. AMB Express. .

Abstract

Porphyromonas gingivalis (Pg) is one of the main pathogens in chronic periodontitis (CP). Studies on the immunogenicity of its virulence factors may contribute to understanding the host response to infection. The present study aimed to use in silico analysis as a tool to identify epitopes from Lys-gingipain (Kgp) and neuraminidase virulence factors of the Pg ATCC 33277 strain. Protein sequences were obtained from the NCBI Protein Database and they were scanned for amino acid patterns indicative of MHC II binding using the MHC-II Binding Predictions tool from the Immune Epitope Database (IEDB). Peptides from different regions of the proteins were chemically synthesized and tested by the indirect ELISA method to verify IgG immunoreactivity in serum of subjects with CP and without periodontitis (WP). T cell epitope prediction resulted in 16 peptide sequences from Kgp and 18 peptide sequences from neuraminidase. All tested Kgp peptides exhibited IgG immunoreactivity whereas tested neuraminidase peptides presented low IgG immunoreactivity. Thus, the IgG reactivity to Kgp protein could be reaffirmed and the low IgG reactivity to Pg neuraminidase could be suggested. The novel peptide epitopes from Pg were useful to evaluate its immunoreactivity based on the IgG-mediated host response. In silico analysis was useful for preselecting epitopes for immune response studies in CP.

Keywords: Immune response; Immunoinformatics; Lys-gingipain; Neuraminidase; Periodontitis; Sialidase.

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Figures

Fig. 1
Fig. 1
Coefficients of absorbance between CP sera pool and WP sera pool after checkerboard ELISA analysis of Kgp synthetic peptides. Brazil, 2018. CP: chronic periodontitis; WP: without periodontitis. The coefficient is the difference of the O.D. value between the sera pools, and it expresses the difference of the mean IgG levels between the CP and the WP sera pools. P. gingivalis (Pg) extract and peptides were used as the antigen in the indirect ELISA test. 1:100 and 1:250 serum concentrations are represented. Kgp12 presented a higher coefficient between CP and WP sera pools in 1:250 serum concentration. Checkerboard ELISA best acquired condition: 5 µg/mL Pg extract concentration, 10 µg/mL peptide concentration, 1:250 sera pool concentration and 1:25,000 anti-human IgG peroxidase conjugate concentration. The nature of the data does not allow statistical analysis between the coefficients
Fig. 2
Fig. 2
Kgp peptides. Kgp 1, 6, 11, 12, 15, 16, 17, 18 and 20 are schematically presented in black in their protein region after its modeling. Brazil, 2018
Fig. 3
Fig. 3
Neuraminidase peptides. N5, N6, N10, N11, N15, N16, N17 and N18 are schematically presented in black in the neuraminidase protein after its modeling. Brazil, 2018
Fig. 4
Fig. 4
Neuraminidase peptides. N5, N6, N10, N11, N15, N16, N17 and N18 are schematically presented in blue in the protein structure after its modeling. N18 includes the catalytic site presented in red. Brazil, 2018
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