Epitope predictions indicate the presence of two distinct types of epitope-antibody-reactivities determined by epitope profiling of intravenous immunoglobulins

PLoS One. 2013 Nov 11;8(11):e78605. doi: 10.1371/journal.pone.0078605. eCollection 2013.

Abstract

Epitope-antibody-reactivities (EAR) of intravenous immunoglobulins (IVIGs) determined for 75,534 peptides by microarray analysis demonstrate that roughly 9% of peptides derived from 870 different human protein sequences react with antibodies present in IVIG. Computational prediction of linear B cell epitopes was conducted using machine learning with an ensemble of classifiers in combination with position weight matrix (PWM) analysis. Machine learning slightly outperformed PWM with area under the curve (AUC) of 0.884 vs. 0.849. Two different types of epitope-antibody recognition-modes (Type I EAR and Type II EAR) were found. Peptides of Type I EAR are high in tyrosine, tryptophan and phenylalanine, and low in asparagine, glutamine and glutamic acid residues, whereas for peptides of Type II EAR it is the other way around. Representative crystal structures present in the Protein Data Bank (PDB) of Type I EAR are PDB 1TZI and PDB 2DD8, while PDB 2FD6 and 2J4W are typical for Type II EAR. Type I EAR peptides share predicted propensities for being presented by MHC class I and class II complexes. The latter interaction possibly favors T cell-dependent antibody responses including IgG class switching. Peptides of Type II EAR are predicted not to be preferentially presented by MHC complexes, thus implying the involvement of T cell-independent IgG class switch mechanisms. The high extent of IgG immunoglobulin reactivity with human peptides implies that circulating IgG molecules are prone to bind to human protein/peptide structures under non-pathological, non-inflammatory conditions. A webserver for predicting EAR of peptide sequences is available at www.sysmed-immun.eu/EAR.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Epitopes / chemistry*
  • Humans
  • Immunoglobulin G / chemistry*
  • Immunoglobulins, Intravenous / chemistry*
  • Peptides / chemistry*
  • Protein Array Analysis*
  • Sequence Analysis, Protein*

Substances

  • Epitopes
  • Immunoglobulin G
  • Immunoglobulins, Intravenous
  • Peptides

Grant support

EU funded Autorome (LSHM-CT-2004-005264) and E-RARE (01GM0803); BMBF support through Med-Sys (0315450D), and funding by the State of Mecklenburg-Vorpommern MV-Excellence: (UR08051 und UR09012). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.