Understanding Immune Recognition: Understanding Biology Through Structures Course Work 2006

Understanding biology through structures Course work 2006
Understanding Immune Recognition

Antigen Recognition
B cells can recognise antigens via their surface Ig molecules

T cells can only recognise antigen in association with a Major
Histocompatibility Complex (MHC) molecule.

Antigen Recognition
B cells can recognise antigens via their
surface Ig molecules

T cells can only recognise antigen in
association with a Major Histocompatibility
Complex (MHC) molecule.

The Immunoglobin Fold
Immunoglobin Fold
V and C domains share the basic Ig fold

Differences between the two domains

C domain is built of seven b-strands
arranged so that four strands form one
sheet and three strands form a second
sheet.

The strands are closely packed together and
joined by a single disulphide bond

Most of the invariant residues of the
constant domain are in the sheets

Overall structure of the V domain very
similar but there are nine strands instead of
seven. The two additional strands harbour
CDR2
Structure of antibody
Complementarity Determining Regions in Ig
Six loops of the VH (H1, H2 and H3) and VL (L1, L2 and L3) domains create a
great variety of surfaces

Deep binding cavities: such as those seen in some antibody-hapten complexes

Wide pockets : seen in certain antibody-peptide complexes

Flat surfaces : seen in antibody-protein interactions

H3 is the most variable of the loops and in all crystallographically solved
antibody-antigen complexes makes several contacts with antigen
The Complementarity Determining Regions
What Do Antibodies Recognize?
1. Proteins (conformational determinants, denatured or proteolyzed
determinants)
2. Nucleic acids
3. Polysaccharides
4. Some lipids
5. Small chemicals (haptens)

Antibodies bind to antigens by
recognizing a large surface, and
through surface complementarity.

Thus, these complexes have a very
high affinity for each other.
Antigen:Antibody complex
The interaction between an antigen and antibody can be very strong, and yet all
of the forces involved are considered to be relatively weak. How can weak
hydrogen bonds, electrostatic attractions, hydrophobic forces, and van der Waals
contacts lead to a high affinity?

Contact between antigen and antibody occurs over a wide surface area, allowing
multiple weak interactions that give a strong affinity

Hydrogen bonds join the antibody and antigen over a wide surface area. Other
weak forces, including van der Waals forces, electrostatic attractions and
hydrophobic forces, add to the strength and specificity of antibody/antigen
binding

Weak forces vs high affinity
Haptens, having a limited total surface area, deeply embed themselves into the VL/VH
dimer interface

Hapten binding antibodies frequently show a deep central cavity, long CDR L1 loops and a
CDR H3 loop with an "open" conformation, allowing the hapten to bind as much as 80%
of its total surface in the interaction.

Antibody-Hapten Complex
Intimate interaction between Ab and Hapten
Peptide Antibody Complex
In contrast, proteins preferentially to a relatively flat binding surface

In a "closed" CDR H3 conformation, the CDR H3 loop packs down onto the
central cavity, and the protein antigen binds on top of it.
Protein Antibody Complex
Effector response is mediated via Ig-FcR
complex formation
Antibodies not only must recognize antigen, but also must
invoke responses effector functions that will remove the
antigen and kill the pathogen.
Variable regions of antibody are the sole agents of binding to
antigen.
The heavy chain constant region (C
H
) is responsible for
interactions with other proteins (e.g. complement), cells
(elements of innate immune system), and tissues that result in the
effector functions of the humoral response.
FcR recognize the Fc portion of antibodies not antigens
The Fc-Fc Receptor complex
FcR plays important role in antibody mediated immune responses

Ig and FcR binding activates effector functions

Fc Receptor interacts with the CH2 and CH3 domains of Immunoglobulins
Mode of
interaction of
FcR with
difference Ig
molecules
Immune Recognition :
MHC and TCR interactions
Antigen Recognition
B cells can recognise antigens via their
surface Ig molecules

T cells can only recognise antigen in
association with a Major Histocompatibility
Complex (MHC) molecule.

T cells
T cells display TCR as their antigen recognition protein

When stimulated they become Cytotoxic or Helper T cells

Secrete cytokines that recruit other cells of the IS

TCRs only recognise short peptides.
MHC & T cells
T cells have a requirement to recognise both the ANTIGEN and the
MHC molecule. This is because the molecular structure of the MHC-
Antigen complex is arranged so that some of the polymorphic amino
acids of the MHC molecule are in direct contact with the TCR
Therefore T cell recognition of antigen is said to be MHC restricted.
Antigen Processing and
Presentation
Fragmentation of protein into peptides
Association of peptide with an MHC molecule
Transport to cell surface for expression
Different cellular pathways for association of peptide with MHC class I
and class II molecules
MHC & Antigens
MHC Class I
present endogenously
derived peptides.
these can be either self or
derived from viruses
because MHC Class I is
present on all cells any cell
can interact with T cells if
infected by a virus
MHC Class II
present exogenous
antigen which has been
phagocytosed and
processed.eg. Bacteria
This is performed by
professional antigen
presenting cells eg
macrophages

MHC
MHC Class I
detected on all
nucleated cells
very highly polymorphic
Tight fit for peptides of
only about 9 aa
consists of an a-chain
of 3 domains associated
with b-2 microglobulin

MHC Class II
seen only on the
professional antigen
processing cells e.g
macrophage
slightly less
polymorphic
accepts peptides of up
to 15 aa acids

a
b
CD4 T-CELL
TCR ab
CD4
CD3
9 aa
peptide
15 aa
peptide
CD8 T-CELL
CD8
a
b
TCR ab
CD3
a
b
ANTIGEN PRESENTING CELL
MHC
CLASS II
a1
b1
b2
a2
Major histocompatibility complex (MHC); human=Human Leukocyte Antigen (HLA); mouse=H-2
Gorer and Snell identified a genetic basis for graft rejection and Snell named it histocompatibility 2
(H-2). Nobel prize awarded to Snell.
Highly polymorphic genes organized in a complex on chromosome 6 (human) and 17 (mouse).
Glycoproteins expressed on the surface of cells. MHC class I is composed of one polypeptide, non-
covalently associated with b2microglobulin. MHC class II is composed of two polypeptides, referred
to as a and b.
MOLECULES OF T LYMPHOCYTE RECOGNITION
CLASS I
MHC
b
2
m
a2 a1
a3
ANTIGEN PRESENTING CELL
MHC Class I and Class II Proteins
Class I
Alpha Chain
3 External domains
1 Transmembrane
1 Cytoplasmic tail
Encoded in MHC
Beta-2 Microglobulin
1 External domain
No transmembrane
No Cytoplasmic tail
Not encoded in MHC
Class II
Alpha Chain
2 External domains
1 Transmembrane
1 Cytoplasmic Tail
Encoded in MHC
Beta Chain
2 External domains
1 Transmembrane
1 Cytoplasmic Tail
Encoded in MHC
MHC Class I and Class II Proteins
Peptides bind to MHC molecules in a polyproline II conformation
Class I:Peptide Binding
MHC-II Structure
Peptide Binding by Major Histocompatibility Complex (MHC)
Antigen-presenting Proteins
Peptides of intracellular origin
Peptides 9-10 residues long
Deep pockets bind peptide
sidechains
Deep pockets bind peptide N-
and C-termini
Peptides of extracellular origin

Peptides 15 residues or longer
Shallow pockets bind peptide
sidechains
Peptide termini free
H-bonds to peptide backbone

MHC I MHC II
Both Class I and Class II genes are highly
polymorphic
Most polymorphic residues of Class I are in
the alpha 1 and alpha 2 domains
Most polymorphic residues of Class II are in
the alpha 1 and beta 1 domains
MHC Polymorphism
Location of Polymorphic Residues
Location of Polymorphic Residues
Allelic variation in MHC occurs at the
peptide binding site and on the top/sides
of the binding cleft
T-cell Receptor
The T cell receptor (TCR) is a complex of integral membrane proteins that
participates in the activation of T cells in response to the presentation of antigen.
Specific recognition and binding by the clonotype-specific a/b heterodimer leads to
activation of transcription and commitment of the T cell to CD4+ or CD8+ fate. This
activation involves other subunits of the receptor complex as well as other membrane-
associated molecules that couple the extracellular liganding event to downstream
signaling pathways such as protein phosphorylation, the release of inositol phosphates
and the elevation of intracellular calcium levels.
TCR binds peptide/MHC with a
restricted (but variable) orientation
peptide binding interface: 21-34%
proportion of TCR contacts with the peptide:26-47%
contact are different between TCR-MHC complex

-the contribution to the binding energy is still uncleared!
Bandovich and Garcia. 2003. Immunity 18,7-11
-CDR1 and CDR2 interact with MHC molecules
(a helices)
-CDR3 interacts with the peptide
-interaction always in the same orientation
-45 to 70 degrees angle related to peptide
-Va see N-ter of the peptide
-Vb see C-ter of the peptide
TRI-MOLECULAR COMPLEX
CHARACTERISTICS
TRI-MOLECULAR COMPLEX
CHARACTERISTICS
- most of the binding interface is between the TCR
and MHC helices

- conformational change in the TCR CDR loops
enhances TCR crossreactivity

- no conformational change in the TCR constant region
(except in one complex out of ten)
Recognition of the Super Antigens
Antigen Recognition by Antibodies (Ab)
and T-cell Receptors (TCR)
Surface area ~ 2x750
2
Epitope discontinuous in
antigen (Ag) sequence
Surface area ~ 2x1000
2
Ag peptide contributes
only 40% of surface area
Epitope continuous in Ag
sequence
Otherwise similar to Ab -
Ag recognition

Ab - Ag TCR MHC/peptide
PARADOX
-TCR-MHC interaction has a weak affinity
-affinity ~ 10 mM
-half-life ~10s

-restricted numbers of ligands (~100) are displayed at the surface
of antigen presenting cells
-T cell activation requires a long interaction with antigen presenting
cells (>2h)

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Understanding Immune Recognition

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