Bioinformática Inmunológica

1. Bioinformática Inmunológica Grupo 5

2. 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

3. 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)

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

5. PROTEINAS 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

6. RECEPTOR DE CELULA B - RECEPTOR DE CELULAS T

7. 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.

8. 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.

9. 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

11. 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.

12. 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.

13. Sequential Conformational Ab-binding sites Epitopes

15. 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

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

17. T cells and B cells use Distinct Antigen Receptorsto Recognize Fundamentally Different Forms of Antigen 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.

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

19. B cells and T cells recognize different epitopes of the same protein antigen 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 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

20. 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.

21. Respuesta Inmune

22. The Immune Response 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).

23. Complejo Mayor Histocompatibilidad I

24. 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.

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

26. Carracteristícas de las moleculas de las MHC clase I y II

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

28. The MHC class I pathway Antigen Proteasome Peptides T-cell epitope ER MHC I TCD8+ Antigen Presenting Cell

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

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

31. Reconocimiento del linfocito T de un complejo péptido -MHC

32. TCR-Class I MHC peptide complex

33. Complejo Mayor de Histocompatibilidad II

34. 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.

37. MHC class I MHC class II

39. Peptide recognition by MHC molecules 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

43. MHC molecules present antigen from 3 main sources

49. 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.