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 polisacáridosFormado por cientos de AaTienen 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

Epitopes could be -

contiguous (when Ab binds to a contiguous sequence of amino acids)

non-contiguous (when Ab binds to non-contiguous residues, brought together by folding).

Sequential epitopes are contiguous epitopes.

Conformational epitopes are non-contiguous antigenic determinants.

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

LinearB cell

Epitope

T cell Epitope

Antibody or “B cell”

EpitopeConformational

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 Receptorsto 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:

Kd 10-5 – 10-7 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 conformationalSequential or conformational

Accessible, hydrophilic, mobile, usually on the surface or could be exposed as a result of physicochemical change

Binding to antibody:

Kd 10-7 – 10-11 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

Característica MHC I MHC II

Cadenas peptídicas α (44-47 kD)

β2-microglobulina(12kD)

α (32-34kD)

β (29-32kD)

Localización de residuos polimorfos

Dominio α1 y α2 Dominio α1 y β1

Punto de unión al receptor de linfocito T

Región α3 se une al CD8 Región β2

se une al CD4

Tamaño de la hendidura de unión a peptidos

8-11 a.a 10-30 a.a

Genes que codf. HLA A, HLA B, HLA C HLA 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 TCD8+

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.

•

MHCclass I

MHCclass II

http://www.bio.us.es/Departamentos/INMUNOLOGIA/Nueva%20carpeta/Bolsilloi.htm

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.