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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

Amino acid composition of epitopes and non-epitopes.
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pone.0134835.g002: Amino acid composition of epitopes and non-epitopes.

Mentions: All exposed residues (RSA>0) are considered. In the following sections, the term non-epitopes will refer to non-epitopes with RSA values larger than zero. Amino acid composition is defined as the count of a type of amino acid divided by the length of the antigen protein. Fig 2 shows the average amino acid composition for 57 antigens. It shows that conformational b-cell epitopes are rich in negatively charged residues Asp(D) and Glu(E); positively charged residues Lys(K), Arg(R), and His(H); non-polar, aliphatic residues Gly(G) and Pro(P); polar, non-charged residues Asn(N) and Gln(Q), and the aromatic residue Tyr(Y). Compared to the epitopes, non-epitopes are rich in non-polar, aliphatic residues Ala(A), Leu(L), and Val(V), and the polar, non-charged residue Ser(S). These results are consistent with previous findings that epitopes are rich in polar amino acids and aromatic amino acids but depleted in aliphatic amino acids [33, 50, 51].


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)

Amino acid composition of epitopes and non-epitopes.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134835.g002: Amino acid composition of epitopes and non-epitopes.
Mentions: All exposed residues (RSA>0) are considered. In the following sections, the term non-epitopes will refer to non-epitopes with RSA values larger than zero. Amino acid composition is defined as the count of a type of amino acid divided by the length of the antigen protein. Fig 2 shows the average amino acid composition for 57 antigens. It shows that conformational b-cell epitopes are rich in negatively charged residues Asp(D) and Glu(E); positively charged residues Lys(K), Arg(R), and His(H); non-polar, aliphatic residues Gly(G) and Pro(P); polar, non-charged residues Asn(N) and Gln(Q), and the aromatic residue Tyr(Y). Compared to the epitopes, non-epitopes are rich in non-polar, aliphatic residues Ala(A), Leu(L), and Val(V), and the polar, non-charged residue Ser(S). These results are consistent with previous findings that epitopes are rich in polar amino acids and aromatic amino acids but depleted in aliphatic amino acids [33, 50, 51].

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