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Bioinformatics criteriafor protein study..

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Selection of Immunogenic sites.

(It must be a functional site of the protein called MOTIF)

Check for the Hydophobicity/Hydrophilicity

Antigenicity

Surface Specificity

N-Glycosylation

Homology Study

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Selection of Immunogenic sites

antigenic determinant, is the part of an antigen that is recognized by the immune

system, specifically by antibodies, B cells, or T cells. The part of an antibody that

recognizes the epitope is called a paratope (The paratope is the part of

an antibody which recognizes an antigen, the antigen-binding site of an antibody. It is a

small region (of 1522 amino acids) of the antibody's). Although epitopes are usually

thought to be derived from non-self proteins, sequences derived from the host that can

be recognized are also classified as epitopes.

The epitopes of protein antigens are divided into two categories, conformational

epitopes and linear epitopes, based on their structure and interaction with the

paratope. A conformational epitope is composed of discontinuous sections of the

antigen's amino acid sequence. These epitopes interact with the paratope based on the

3-D surface features and shape or tertiary structure of the antigen. Most epitopes are

conformational.

In contrast linear epitopes interact with the paratope based on their primary structure.

The amino acids that make up a linear epitope are a continuous sequence of amino

acids from the antigen.

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Cross-reactivity (Homology)

Epitopes are sometimes cross-reactive. This property is exploited by the immunesystem in regulation by anti-idiotypic antibodies (originally proposed by Nobel

laureate Niels Kaj Jerne). If an antibody binds to an antigen's epitope, the paratope

could become the epitope for another antibody that will then bind to it. If this

second antibody is of IgM class, its binding can upregulate the immune response; if

the second antibody is of IgG class, its binding can downregulate the immune

response.

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Epitope mapping is the process of identifying the binding sites, orepitopes, ofantibodies on their target antigens

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Antigenicity Plot

The following applet allows to compute the antigenicity plot of a protein sequence.

In this way the Antigenicity index is computed and the antigenicity behaviour of the

amino acids. Beware, this is only a computation based on the algorithm

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Hydophobicity/Hydrophilicity

An amino acid scale is defined by a numerical value assigned to each type of amino

acid. The most frequently used scales are the hydrophobicity or hydrophilicity scales

and the secondary structure conformational parameters scales, but many other scales

exist which are based on different chemical and physical properties of the amino

acids.

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N-glycosylation

Acceptor sites for N-linked glycosylation on protein sequences, are not well

characterised. The consensus sequence, Asn-Xaa-Ser/Thr (where Xaa is not Pro),

is known to be a prerequisite for the modification. However, not all of these

sequons are modified and it is thus not discriminatory between glycosylated and

non-glycosylated asparagines.

Glycosylation is an important post-translational modification, and is known to

influence protein folding, localisation and trafficking, protein solubility,antigenicity, biological activity and half-life, as well as cell-cell interactions

predicted N-glycosylation sites across functional categories of the human

proteome.