How do you map the epitope?

There are several methods available for mapping antibody epitopes on target antigens:

  1. X-ray co-crystallography and cryogenic electron microscopy (cryo-EM).
  2. Array-based oligo-peptide scanning.
  3. Site-directed mutagenesis mapping.
  4. High-throughput shotgun mutagenesis epitope mapping.
  5. Hydrogen–deuterium exchange (HDX).

What is epitope and Paratope?

An epitope, also known as antigenic determinant, is the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells. The epitope is the specific piece of the antigen to which an antibody binds. The part of an antibody that binds to the epitope is called a paratope.

How IEDB is assisting the epitope mapping?

The IEDB-AR homology mapping tool provides the mapping of a linear epitope from a source protein to the proteins with known 3D structures by sequence similarity search of the epitope source sequence against protein sequences in the Protein Data Bank (PDB) (26).

How do you predict B cell epitopes?

The predicted B-cell epitopes are ranked according to their score obtained by trained recurrent neural network. Higher score of the peptide means the higher probability to be as epitope. All the peptides shown here are above the threshold value chosen. (C) Output in graphical format.

How does a linear epitope differ from a conformational epitope?

conformational epitopes. Linear epitopes consist of continuous residues on a protein sequence. Conformational epitopes consist of residues that are discontinuous in the protein sequence yet come within close proximity to form an antigenic surface on the protein’s three-dimensional structure.

Where is epitope located?

An epitope is the part of the antigen that binds to a specific antigen receptor on the surface of a B cell. Binding between the receptor and epitope occurs only if their structures are complementary.

What are B cell epitopes?

B-cell epitopes can be defined as a surface accessible clusters of amino acids, which are recognized by secreted antibodies or B-cell receptors and are able to elicit cellular or humoral immune response [1].

What is the difference between linear and discontinuous epitopes?

There are two types of epitope; (1) continuous epitope: amino acids are linear in shape and (2) discontinuous epitope: it exists when the protein has folded conformations. The epitope-based vaccine design is an attractive approach that is being used by several researchers with successful outcomes [2, 4, 5].

What is a conformational epitope?

A conformational epitope is a sequence of sub-units (usually amino acids) composing an antigen that come in direct contact with a receptor of the immune system. An antigen is any substance that the immune system can recognize as foreign.

What’s new in epitope mapping?

These days much effort is put on the development of new fast and precise strategies dealing with epitope mapping. An example for a recent tool is the software SPADE that is the first approach predicting IgE epitopes by combining structural and cross-reactivity data and that compared to other prediction tools yields highest specificities [7] .

How to identify all amino acid residues from a conformational epitope?

However, with currently available technologies, the only rational method of identifying all amino acid residues from a conformational – ‘in shape’ – epitope is measuring the crystal structure of an allergen in complex with the corresponding antibody. References 1.

How do B cells recognize conformational epitopes?

Recognition of conformational epitopes by B cells. A conformational epitope is a sequence of sub-units (usually amino acids) composing an antigen that come in direct contact with a receptor of the immune system.