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Review
. 2017:2017:2680160.
doi: 10.1155/2017/2680160. Epub 2017 Dec 28.

Fundamentals and Methods for T- and B-Cell Epitope Prediction

Jose L Sanchez-Trincado  1 , Marta Gomez-Perosanz  1 , Pedro A Reche  1
Affiliations
Review

Fundamentals and Methods for T- and B-Cell Epitope Prediction

Jose L Sanchez-Trincado et al. J Immunol Res. 2017.

Abstract

Adaptive immunity is mediated by T- and B-cells, which are immune cells capable of developing pathogen-specific memory that confers immunological protection. Memory and effector functions of B- and T-cells are predicated on the recognition through specialized receptors of specific targets (antigens) in pathogens. More specifically, B- and T-cells recognize portions within their cognate antigens known as epitopes. There is great interest in identifying epitopes in antigens for a number of practical reasons, including understanding disease etiology, immune monitoring, developing diagnosis assays, and designing epitope-based vaccines. Epitope identification is costly and time-consuming as it requires experimental screening of large arrays of potential epitope candidates. Fortunately, researchers have developed in silico prediction methods that dramatically reduce the burden associated with epitope mapping by decreasing the list of potential epitope candidates for experimental testing. Here, we analyze aspects of antigen recognition by T- and B-cells that are relevant for epitope prediction. Subsequently, we provide a systematic and inclusive review of the most relevant B- and T-cell epitope prediction methods and tools, paying particular attention to their foundations.

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Figures

Figure 1
Figure 1
B-cell epitope recognition. B-cell epitopes are solvent-exposed portions of the antigen that bind to secreted and cell-bound immunoglobulins. (a) B-cell receptors encompass cell-bound immunoglobulins, consisting of two heavy chains and two light chains. The different chains and regions are annotated. (b) Molecular representation of the interaction between an antibody and the antigen. Antibodies are secreted immunoglobulins of known specificity.
Figure 2
Figure 2
T-cell epitope recognition. T-cell epitopes are peptides derived from antigens and recognized by the T-cell receptor (TCR) when bound to MHC molecules displayed on the cell surface of APCs. (a) CD4 T-cells express the CD4 coreceptor, which binds to MHC II, and recognize peptides presented by MHC II molecules. (b) CD8 T-cells express the CD8 coreceptor, which binds to MHC I, and recognize peptides presented by MHC I molecules.
Figure 3
Figure 3
MHC molecule binding groove. The figure depicts the molecular surface as seen by the TCR of representative MHC I and II molecules. Note how the binding groove of the MHC I molecule is closed but that of MHC II is open. As a result, MHC I molecules bind short peptides (8–11 amino acids), while MHC II molecules bind longer peptides (9–22 amino acids). The figure was prepared from PDB files 1QRN (MHC I) and 1FYT (MHC II) using PyMol.
Figure 4
Figure 4
Class I antigen processing. The figure depicts the major steps involved in antigen presentation by MHC I molecules. Proteins are degraded by the proteasome and peptide fragments transported to the endoplasmic reticulum (ER) by TAP where they are loaded onto nascent MHC I molecules. TAP transports peptides ranging from 8 to 16 amino acids. Long peptides cannot bind MHC I molecules but often become suitable for binding after N-terminal trimming by ERAAP.
Figure 5
Figure 5
Linear and conformational B-cell epitopes. Linear B-cell epitopes (a) are composed of sequential/continuous residues, while conformational B-cell epitopes (b) contain scattered/discontinuous residues along the sequence.
See this image and copyright information in PMC

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