Bioinform

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Bioinformática Inmunológica

• Grupo 5

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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

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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)

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INMUNÒGENO

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

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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
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RECEPTOR DE CELULA B - RECEPTOR DE CELULAS T
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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.

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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.

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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

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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.

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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.

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Epitopes
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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

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

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Respuesta Inmune
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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).
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Complejo Mayor Histocompatibilidad I
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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.

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The genetic organization of the major
histocompatibility complex (MHC) in human
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Carracteristícas de las moleculas de las MHC
clase I y II
Característica MHC I MHC II
Cadenas peptídicas a (44-47 kD) ß2-microglobulina(12kD) a (32-34kD) ß (29-32kD)
Localización de residuos polimorfos Dominio a1 y a2 Dominio a1 y ß1
Punto de unión al receptor de linfocito T Región a3 se une al CD8 Región ß2 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
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The structure of an MHC class I molecule
determined by X-ray crystallography
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The MHC class I pathway
Antigen
Proteasome
Peptides
T-cell epitope
ER
MHC I
TCD8
Antigen Presenting Cell
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MHC class I molecules present antigen derived
from proteins in the cytosol
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MHC class I molecules do not leave the
endoplasmic reticulum unless they bind peptides
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Reconocimiento del linfocito T de un complejo
péptido -MHC
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TCR-Class I MHC peptide complex
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Complejo Mayor de Histocompatibilidad II
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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.

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MHC class I
MHC class II
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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
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MHC molecules present antigen from 3 main sources
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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.