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Analysis of Conformational B-Cell Epitopes in the Antibody-Antigen Complex Using the Depth Function and the Convex Hull.

Zheng W, Ruan J, Hu G, Wang K, Hanlon M, Gao J - PLoS ONE (2015)

Bottom Line: We found that conformational b-cell epitopes are rich in charged residues Asp, Glu, Lys, Arg, His; aliphatic residues Gly, Pro; non-charged residues Asn, Gln; and aromatic residue Tyr.Conservation of epitopes is not significantly lower than that of exposed non-epitopes.The average depths (obtained by four methods) for epitopes are significantly lower than that of non-epitopes on the surface using the Wilcoxon rank sum test.

View Article: PubMed Central - PubMed

Affiliation: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, People's Republic of China.

ABSTRACT
The prediction of conformational b-cell epitopes plays an important role in immunoinformatics. Several computational methods are proposed on the basis of discrimination determined by the solvent-accessible surface between epitopes and non-epitopes, but the performance of existing methods is far from satisfying. In this paper, depth functions and the k-th surface convex hull are used to analyze epitopes and exposed non-epitopes. On each layer of the protein, we compute relative solvent accessibility and four different types of depth functions, i.e., Chakravarty depth, DPX, half-sphere exposure and half space depth, to analyze the location of epitopes on different layers of the proteins. We found that conformational b-cell epitopes are rich in charged residues Asp, Glu, Lys, Arg, His; aliphatic residues Gly, Pro; non-charged residues Asn, Gln; and aromatic residue Tyr. Conformational b-cell epitopes are rich in coils. Conservation of epitopes is not significantly lower than that of exposed non-epitopes. The average depths (obtained by four methods) for epitopes are significantly lower than that of non-epitopes on the surface using the Wilcoxon rank sum test. Epitopes are more likely to be located in the outer layer of the convex hull of a protein. On the benchmark dataset, the cumulate 10th convex hull covers 84.6% of exposed residues on the protein surface area, and nearly 95% of epitope sites. These findings may be helpful in building a predictor for epitopes.

No MeSH data available.


Related in: MedlinePlus

Different depth functions according to the k-th convex hull layers CHk (k = 1, 2,…, 15).(A)DPX (B) Chakravarty Depth.
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pone.0134835.g007: Different depth functions according to the k-th convex hull layers CHk (k = 1, 2,…, 15).(A)DPX (B) Chakravarty Depth.

Mentions: We also analyzed the influence of the depth function according to the k-th convex hull. Fig 7 shows these results. For DPX (Fig 7A), the values for epitopes are smaller than the values for non-epitopes, except on CH2. For Chakravarty depth (Fig 7B), all values for epitopes are smaller than the values for non-epitopes. There are two types of HSE, i.e. HSEA, HSEB. There is no significant rule for the HSEA down sphere (HSEAD) (See S2 Fig), but all values of HSEAU for epitopes are smaller than the values of HSEAU for non-epitopes, except CH4. On the other hand, there is no significant rule for the HSEB down sphere (HSEBD), all values of HSEBU for epitopes are smaller than the values of HSEBU for non-epitopes (S3 Fig). This indicates that the DPX, Chakravarty depth and HSEAU, HSEBU may be useful to classify epitopes and non-epitopes on the surface.


Analysis of Conformational B-Cell Epitopes in the Antibody-Antigen Complex Using the Depth Function and the Convex Hull.

Zheng W, Ruan J, Hu G, Wang K, Hanlon M, Gao J - PLoS ONE (2015)

Different depth functions according to the k-th convex hull layers CHk (k = 1, 2,…, 15).(A)DPX (B) Chakravarty Depth.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4526569&req=5

pone.0134835.g007: Different depth functions according to the k-th convex hull layers CHk (k = 1, 2,…, 15).(A)DPX (B) Chakravarty Depth.
Mentions: We also analyzed the influence of the depth function according to the k-th convex hull. Fig 7 shows these results. For DPX (Fig 7A), the values for epitopes are smaller than the values for non-epitopes, except on CH2. For Chakravarty depth (Fig 7B), all values for epitopes are smaller than the values for non-epitopes. There are two types of HSE, i.e. HSEA, HSEB. There is no significant rule for the HSEA down sphere (HSEAD) (See S2 Fig), but all values of HSEAU for epitopes are smaller than the values of HSEAU for non-epitopes, except CH4. On the other hand, there is no significant rule for the HSEB down sphere (HSEBD), all values of HSEBU for epitopes are smaller than the values of HSEBU for non-epitopes (S3 Fig). This indicates that the DPX, Chakravarty depth and HSEAU, HSEBU may be useful to classify epitopes and non-epitopes on the surface.

Bottom Line: We found that conformational b-cell epitopes are rich in charged residues Asp, Glu, Lys, Arg, His; aliphatic residues Gly, Pro; non-charged residues Asn, Gln; and aromatic residue Tyr.Conservation of epitopes is not significantly lower than that of exposed non-epitopes.The average depths (obtained by four methods) for epitopes are significantly lower than that of non-epitopes on the surface using the Wilcoxon rank sum test.

View Article: PubMed Central - PubMed

Affiliation: School of Mathematical Sciences and LPMC, Nankai University, Tianjin, People's Republic of China.

ABSTRACT
The prediction of conformational b-cell epitopes plays an important role in immunoinformatics. Several computational methods are proposed on the basis of discrimination determined by the solvent-accessible surface between epitopes and non-epitopes, but the performance of existing methods is far from satisfying. In this paper, depth functions and the k-th surface convex hull are used to analyze epitopes and exposed non-epitopes. On each layer of the protein, we compute relative solvent accessibility and four different types of depth functions, i.e., Chakravarty depth, DPX, half-sphere exposure and half space depth, to analyze the location of epitopes on different layers of the proteins. We found that conformational b-cell epitopes are rich in charged residues Asp, Glu, Lys, Arg, His; aliphatic residues Gly, Pro; non-charged residues Asn, Gln; and aromatic residue Tyr. Conformational b-cell epitopes are rich in coils. Conservation of epitopes is not significantly lower than that of exposed non-epitopes. The average depths (obtained by four methods) for epitopes are significantly lower than that of non-epitopes on the surface using the Wilcoxon rank sum test. Epitopes are more likely to be located in the outer layer of the convex hull of a protein. On the benchmark dataset, the cumulate 10th convex hull covers 84.6% of exposed residues on the protein surface area, and nearly 95% of epitope sites. These findings may be helpful in building a predictor for epitopes.

No MeSH data available.


Related in: MedlinePlus