Bioinformática Inmunológica Grupo 5

The Mammalian Immune System A complex and adaptive learning system Evolved to defend an individual against foreign invaders Operates at multiple levels: from molecule to cell, organ, organism and community

ANTIGENO Sustancia genética y estructuralmente extraña para el organismo receptor Molécula que genera una respuesta inmune: Inmunógeno (contraparte Tolerógeno) Molécula que reacciona con receptores específicos de células T o B (anticuerpos libres)

INMUNÒGENO Molécula que desencadena una respuesta inmune con producción de anticuerpos. Ej: Microorganismos enteros, aislados, productos metabólicos; otras sustancias Características Alto PM Químicamente compleja

Moléculas complejas y mucho más inmunogénicos que los polisacáridos Formado por cientos de Aa Tienen muchos epítopes de diferente especificidad. Proteínas conjugadas: glicoproteinas, lipoproteínas, nucleoproteínas PROTEINAS

RECEPTOR DE CELULA B - RECEPTOR DE CELULAS T

What Are Epitopes Antigenic determinants or Epitopes are the portions of the antigen molecules which are responsible for specificity of the antigens in antigen-antibody (Ag-Ab) reactions and that combine with the antigen binding site of Ab, to which they are complementary.

Properties of Epitopes They occur on the surface of the protein and are more flexible than the rest of the protein. They have high degree of exposure to the solvent. The amino acids making the epitope are usually charged and hydrophilic.

Epitopes In protein antigens epitopes can be defined in terms of: – Amino acid composition – Protein location – Length (5-15 amino acids) Immunodominant epitopes: – Epitopes bound by a greater proportion of antibodies than others in a normal in vivo immune response. – Also known as Major Antigenic Sites. Epitopes can be divided into 2 classes: – Discontinuous epitopes – Continuous (linear) epitopes

Discontinuous Epitopes Constitutive residues are non-sequential in the primary sequence. Highly conformational dependant. Account for approx. 90% of epitopes on a given antigenic (globular) protein.

Linear (continuous) Epitopes Constitutive residues are sequential in the primary sequence of the protein. Fewer conformational constraints on Ab recognition. Often contain residues that are not implicated in antibody interaction.

Epitopes Sequential Conformational Ab-binding sites

Types of Epitopes Conformational / Discontinuous epitopes: recognized by B cells non-linear discrete amino acid sequences, come together due to folding. Sequential / Continuous epitopes: recognized by T cells & B cells linear peptide fragments

Types of Peptide Epitope Linear B cell Epitope T cell Epitope Antibody or “B cell” Epitope Conformational Non- Conformational Class II MHCs Professional Antigen Presenting cells Foreign proteins 8-20 amino acids Class I MHCs all cells Foreign and self proteins 8-10 amino acids

B cells can recognize linear or conformational epitopes on cell surfaces, of proteins, of carbohydrates or of lipids. The B cell antigen receptor is a form of membrane Ig. T cells recognize linear peptide fragments bound to MHC class I or class II molecules. T cells and B cells use Distinct Antigen Receptors to Recognize Fundamentally Different Forms of Antigen

). Sperm whale myoglobin (1vxg) contains five sequential epitopes (red, green, magenta, blue, orange) and two conformational epitopes (yellow, pink).

T cell epitope Denatured antigen Linear peptide 8-30 ac Internal (often) Binding to T cell receptor: K d – M (low affinity) Slow on-rate, slow off-rate (once bound, peptide may stay associated for hours to many days) B cell epitope Native or denatured (rare) antigen Sequential or conformational Accessible, hydrophilic, mobile, usually on the surface or could be exposed as a result of physicochemical change Binding to antibody: K d – M (high affinity) Rapid on-rate, variable off-rate B cells and T cells recognize different epitopes of the same protein antigen

Why is the knowledge of antibody epitopes is so important? Vaccine design (immunogenicity, i.e. ability of vaccine to elicit in the naïve individual the production of pathogen neutralizing antibodies, is required):  Purified antigen (subunit) vaccines: Inactivated toxins “toxoids”: tetanus toxoid, diphteria toxoid Vaccines composed of bacterial polysaccharide antigens: flu, pneumococcus  Synthetic antigen vaccines: hepatitus B (recombinant protein), herpes simplex virus Diagnostic design (antigenicity, i.e. ability of synthetic antigen to be recognized by the original antibody, is required): Autoimmune diseases: lupus, rheumatoid arthritis Allergic reactions Basic knowledge of antigenicity.

Respuesta Inmune

The humoral response involves interaction of B cells with antigen (Ag) and their differentiation into antibody- secreting plasma cells. The secreted antibody (Ab) binds to the antigen and facilitates its clearance from the body. The cell-mediated responses involve various subpopulations of T cells that recognize antigen presented on self- cells. Helper T cells respond to antigen by producing cytokines. Cytotoxic T cells respond to antigen by developing into cytotoxic T lymphocytes (CTLs), which mediate killing of altered self- cells (e.g., virus-infected cells). The Immune Response

Complejo Mayor Histocompatibilidad I

MHC Molécula de reconocimiento de lo propio y extraño. Involucrada en la respuesta inmune adquirida. Importante en la presentación de antígenos. No es exclusiva de humanos.

The genetic organization of the major histocompatibility complex (MHC) in human

CaracterísticaMHC IMHC II Cadenas peptídicas α (44-47 kD) β 2 -microglobulina(12kD) α (32-34kD) β (29-32kD ) Localización de residuos polimorfos Dominio α 1 y α 2Dominio α 1 y β 1 Punto de unión al receptor de linfocito T Región α 3 se une al CD8Región β 2 se une al CD4 Tamaño de la hendidura de unión a peptidos 8-11 a.a10-30 a.a Genes que codf.HLA A, HLA B, HLA CHLA DR HLA DP, HLA DQ Carracteristícas de las moleculas de las MHC clase I y II

The structure of an MHC class I molecule determined by X-ray crystallography

The MHC class I pathway Antigen Presenting Cell Proteasome Antigen Peptides ER MHC I T CD8+ T-cell epitope

MHC class I molecules present antigen derived from proteins in the cytosol

MHC class I molecules do not leave the endoplasmic reticulum unless they bind peptides

Reconocimiento del linfocito T de un complejo péptido -MHC

TCR-Class I MHC peptide complex

Complejo Mayor de Histocompatibilidad II

MHC II La generación de péptidos antigénicos y su asociación con las MHC requiere acción concertada de moléculas accesorias como chaperonas, transportadores de péptidos y proteasas encargadas de degradar los Ags. Los péptidos se originan por vía endógena o exógena. Las MHCI, presentan péptidos de vía endógena, degradados por el proteasoma y presentados al LTCD8+. Las MHCII, presentan péptidos de vía exógena fagocitadas por una APC, son presentados al LTCD4+. En circunstancias especiales péptidos de la vía endógena son presentados por MHCII y viceversa.

MHC class I MHC class II

Peptide binding to MHC class I -8 to 10 amino acids long -importance of N and C term -two or more anchor residues Peptide binding to MHC class II -up to 20 amino acids long -importance of backbone contacts -two or more anchor residues Peptide recognition by MHC molecules

MHC molecules present antigen from 3 main sources

The immunoglobulin fold Common Structures - Both the antibodies of the humoral response and the molecules involved in the cellular response (antibody, TCR, most CD [cell surface molecules expressed on various cell types in the immune system]) contain elements of common structure. The domains in these molecules are built on a common motif, called the immunoglobulin fold, in which two anti-parallel sheets lie face to face. This structure probably represents the primitive structural element in the evolution of the immune response. The immunoglobulin fold is also found in a number of other proteins.