Dataset Information

Phosphosite-dependent presentation of dual phosphorylated peptides by MHC class I molecules.

ABSTRACT: Phosphopeptides presented by major histocompatibility complex (MHC) class I have been regarded as a pivotal type of cancer neoantigens that are recognized by T cells. The structural basis of single-phosphorylated peptide presentation has been well studied. Diphosphorylation with one interval between two sites is one of the prevalent forms of multisite-phosphorylated peptides. Herein, we determined the molecular basis of presentation of two P4/P6 double pS-containing peptides by HLA-B27 and compared them with unmodified and single-phosphorylated peptide complexes. These data clarified not only the HLA allele-specific presentation of phosphopeptides by MHC class I molecules but also the cooperativity of peptide conformation within P4 and P6 phosphorylation sites. The phosphorylation of P6 site can influence the binding mode of P4 phosphorylated site to HLA-B27. And we found the diphospho-dependent attenuated effect of peptide binding affinity. This study provides insights into the MHC presentation features of diphosphopeptides, which is different from monophosphopeptides.

SUBMITTER: Zhao Y

PROVIDER: S-EPMC8931367 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

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Phosphosite-dependent presentation of dual phosphorylated peptides by MHC class I molecules.

Zhao Yingze Y Sun Mingwei M Zhang Nan N Liu Xueyuan X Yue Can C Feng Lei L Ji Shushen S Liu Xiao X Qi Jianxun J Wong Catherine C L CCL Gao George F GF Liu William J WJ

iScience 20220301 4

Phosphopeptides presented by major histocompatibility complex (MHC) class I have been regarded as a pivotal type of cancer neoantigens that are recognized by T cells. The structural basis of single-phosphorylated peptide presentation has been well studied. Diphosphorylation with one interval between two sites is one of the prevalent forms of multisite-phosphorylated peptides. Herein, we determined the molecular basis of presentation of two P4/P6 double pS-containing peptides by HLA-B27 and compa ...[more]

PMID: 35310951

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Project description:BackgroundPeptides binding to Major Histocompatibility Complex (MHC) class II molecules are crucial for initiation and regulation of immune responses. Predicting peptides that bind to a specific MHC molecule plays an important role in determining potential candidates for vaccines. The binding groove in class II MHC is open at both ends, allowing peptides longer than 9-mer to bind. Finding the consensus motif facilitating the binding of peptides to a MHC class II molecule is difficult because of different lengths of binding peptides and varying location of 9-mer binding core. The level of difficulty increases when the molecule is promiscuous and binds to a large number of low affinity peptides. In this paper, we propose two approaches using multi-objective evolutionary algorithms (MOEA) for predicting peptides binding to MHC class II molecules. One uses the information from both binders and non-binders for self-discovery of motifs. The other, in addition, uses information from experimentally determined motifs for guided-discovery of motifs.ResultsThe proposed methods are intended for finding peptides binding to MHC class II I-Ag7 molecule - a promiscuous binder to a large number of low affinity peptides. Cross-validation results across experiments on two motifs derived for I-Ag7 datasets demonstrate better generalization abilities and accuracies of the present method over earlier approaches. Further, the proposed method was validated and compared on two publicly available benchmark datasets: (1) an ensemble of qualitative HLA-DRB1*0401 peptide data obtained from five different sources, and (2) quantitative peptide data obtained for sixteen different alleles comprising of three mouse alleles and thirteen HLA alleles. The proposed method outperformed earlier methods on most datasets, indicating that it is well suited for finding peptides binding to MHC class II molecules.ConclusionWe present two MOEA-based algorithms for finding motifs, one for self-discovery and the other for guided-discovery by experimentally determined motifs, and thereby predicting binding peptides to I-Ag7 molecule. Our experiments show that the proposed MOEA-based algorithms are better than earlier methods in predicting binding sites not only on I-Ag7 but also on most alleles of class II MHC benchmark datasets. This shows that our methods could be applicable to find binding motifs in a wide range of alleles.

Dataset Information

Phosphosite-dependent presentation of dual phosphorylated peptides by MHC class I molecules.

Publications

Phosphosite-dependent presentation of dual phosphorylated peptides by MHC class I molecules.

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