Please elaborate with some examples and any valid references if one has.
Dear Muhammad Attique
A peptide is a short chain of amino acids, for example, two bound amino acids called a dipeptide, three amino acids triple peptide, and so on.
An epitope is the part of an antigen that interacts with the antigen-specific receptor or antigen-specific antibody (the epitope is a small section of the antigen).
An antigen is every foreign body in relation to the immune system, that enters the body, it may be a bacteria, virus, protein, or others.. and this antigen consists of a number of epitopes.
A neoantigen is newly formed antigens that have not been previously recognized by the immune system. It can arise from altered tumor proteins formed as a result of tumor mutations or from new viral strains.
An antigen is operationally defined as something recognized by a given antibody (and by extension by T cell receptors in the case of T cell antigens). An antigen can be small or large, self or non-self. Non-self antigens are those foreign substances or particles that enter the body (bacteria, virus, injected proteins and others) and tend to induce antibody responses (sometimes very strong) that protect the body from them. Self-antigens are molecules (proteins and other classes) normally present in the body. There are also antibody responses against them, but these responses are tightly regulated under normal conditions to guarantee homeostasis. Exacerbated responses to self-antigens are typical of autoimmune diseases.
Sometimes self-antigens change, for instance a normal body protein is replaced by a mutated variant with amino acid substitutions at some positions due to genetic instability of tumors, or aberrant glycosylation under certain circumstances changes the surface of otherwise normal body molecules. Modified versions of self-antigens are often called neoantigens. Even if the original antigen is tolerated by the immune system, the neoantigen derived from it can behave as non-self and induce a strong antibody (or T cell receptor) response. This property of neoantigens is exploited to produce anti-cancer vaccines.
An antigen can be a very small chemical compound that accomodates into the binding pocket of the antibody or other receptor. In this case the whole antigen is in contact with the antibody. But more often antigens are large proteins, carbohydrates, or larger particles like bacteria and viruses. Only a small group of atoms from them are in close contact with each antibody. This small portion of the antigen directly interacting with the antibody is called epitope. An antigen can have multiple epitopes, as many as different antibodies can recognize it.
As a peptide is a small chain of amino acids connected by peptide bonds, some epitopes of protein antigens can coincide with segments of the amino acid sequence of the same protein. If so, a small peptide an be equivalent to the epitope. Other epitopes comprise amino acids separated in the primary sequence of the proteins, but close in its tri-dimensional structure. These conformational epitopes are more difficult to define using short peptides. Epitopes can be totally or partially made of non-protein material (sugars, lipids, nucleic acids and other molecule). Such epitopes do not correpond to any peptide.
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