Major Histocompatibility Complex

&
Antigen Processing and Presentation

Sreeraj E
BPS051318
PlantScience
 MHC molecules
• Major Histocompatibility Complex
– Cluster of genes found in all mammals
– Its products play role in discriminating self/non-self
– Participant in both humoral and cell-mediated immunity
• Act as antigen presenting structures
• Polymorphic (genetically diverse) glycoproteins
• Cross over rate is low (0.5 %)
• Alleles are co-dominantly expressed
• Promiscous binding to peptides
• In Humans - Chromosome 6 & referred to as HLA complex
• In Mice - Chromosome 17 & referred to as H-2 complex
Structure of MHC class I molecules

MHC-encoded -chain of 43kDa

-chain anchored to the cell membrane

Peptide antigen in a groove formed

from a pair of -helicies on a floor of anti-
parallel  strands

2-microglobulin, 12kDa, non-MHC encoded, non-

transmembrane, non covalently bound to -chain

3 Highly Conserved Among MHC I Molecules Interacts

with CD8+ TCyt cell
3 domain & 2m have structural & amino acid sequence
homology with Ig C domains Ig GENE SUPERFAMILY
 MHC Class I

• The α3 segment of the MHC

I serves as a binding site for
CD8.
• The β2-microglobulin
interacts with the α3 non-
covalently.
• Class I MHC is found in
almost all nucleated cell.
• Presents endogenous
antigen.
 Structure of MHC class I molecules
• The α chains forms a platform of 8-stranded anti-parallel β pleated
sheet supporting two parallel strands of α-helix.
• The formed cleft can bind peptides of 8 -10 amino acids in a flexible
extended conformation.

Chains Structures
Properties of the inner faces of the helices and floor of the cleft determine
which peptides bind to the MHC molecule
Structure of MHC class II molecules

• MHC-encoded, -chain of 34kDa

• A -chain of 29kDa
•  and  chains anchored to the cell
membrane
• NO -2 microglobulin
• Peptide antigen in a groove formed from a
pair of -helicies on a floor of anti-parallel 
strands
• Found in APCs,presents exogenous antigen.
• 2 & 2 domains have structural & amino
acid sequence homology with Ig C domains
Ig GENE SUPERFAMILY
 Cleft geometry

MHC class I

MHC class II

Peptide is held in the cleft by non-covalent forces

 Cleft geometry

-chain -chain

Peptide
Peptide -chain
2-M

MHC class I accommodate MHC class II accommodate

peptides of 8-10 amino acids peptides of >13 amino acids
 Anchor residues and T cell antigen receptor
contact residues

Anchor residue: The peptide residue that anchor the antigenic

peptide into the MHC groove.

MHC class I
Cell Sliced between
surface -helicies to reveal
peptide

MHC anchor residue T cell antigen receptor contact

side-chains point down residue side-chains point up
MHC molecules can bind peptides of different length

Arched
peptide

P S S
I
S A K A K S I P S
Y Y
I I

MHC molecule MHC molecule

Complementary anchor residues & pockets provide the broad specificity of a

particular type of MHC molecule for peptides
Peptide sequence between anchors can vary
Number of amino acids between anchors can vary
 A flexible binding site?
A binding site that is flexible at an early, intracellular stage of maturation Formed by folding
the MHC molecules around the peptide.

Floppy Compact

Allows a single type of MHC molecule to

• bind many different peptides
• bind peptides with high affinity
• form stable complexes at the cell surface
• Export only molecules that have captured a
peptide to the cell surface
Peptides can be eluted from MHC molecules

Purify stable MHC- Fractionate and

peptide complexes microsequence
peptides

Acid elute
peptides
 Eluted peptides from MHC molecules have different sequences
but contain motifs
Peptides bound to a particular type of MHC class I molecule have conserved patterns of
amino acids

A common sequence in a peptide antigen

that binds to an MHC molecule is called a N T Y Q R T R L V C
MOTIF
S Y F P E I H I
Amino acids common to many peptides
tether the peptide to structural features of K Y Q A V T T L
the MHC molecule S Y I P S A K I
ANCHOR RESIDUES
Tethering amino acids need not be identical R G Y V Y Q Q L
but must be related
Y & F are aromatic
S I I N F E K L
V, L & I are hydrophobic A P G N Y P A L
Side chains of anchor residues bind into
POCKETS in the MHC molecule
Different types of MHC molecule bind peptides with different patterns of conserved
amino acids
 Genetic map of MHC

Human Leukocyte Antigen (HLA)

• In humans, there are three MHC Class I α-chain genes, called:
HLA -A, HLA-B, and HLA-C

• There are also three pairs of MHC Class II α- and β-chain genes,
called :HLA-DR, HLA-DP, and HLA-DQ.
The genes of the MHC locus
 Other genes in the MHC
MHC Class 1b genes
Encoding MHC class I-like proteins that associate with -2 microglobulin:
HLA-G binds to CD94, an NK-cell receptor. Inhibits NK attack of foetus/ tumours
HLA-E binds conserved leader peptides from HLA-A, B, C. Interacts with CD94
HLA-F function unknown

MHC Class II genes

Encoding several antigen processing genes:
HLA-DM and , proteasome components LMP-2 & 7, peptide transporters
TAP-1 & 2, HLA-DO and DO
Many pseudogenes

MHC Class III genes

Encoding complement proteins C4A and C4B, C2 and FACTOR B
TUMOUR NECROSIS FACTORS  AND 

Immunologically irrelevant genes

Genes encoding 21-hydroxylase, RNA Helicase, Caesin kinase
Heat shock protein 70, Sialidase
 Diversity of MHC molecules in the individual
DP DQ DR B C A
    1 
Polygeny

DP DQ DR B C A
    1 
Variant alleles
HAPLOTYPE 1 polymorphism

DP DQ DR B C A
    1 
Additional set of
HAPLOTYPE 2 variant alleles on
second chromosome

MHC molecules are CODOMINANTLY expressed

Two of each of the six types of MHC molecule are expressed

Genes in the MHC are tightly LINKED and usually inherited in a unit called an MHC
HAPLOTYPE
 Populations need to express variants
of each type of MHC molecule

• Populations of microorganisms reproduce faster than humans

• Mutations that change MHC-binding antigens or MHC molecules can only be
introduced to populations after reproduction
• The ability of microorganisms to mutate in order to evade MHC molecules will always
outpace counter evasion measures that involve mutations in the MHC
• The number of types of MHC molecules are limited

To counteract the superior flexibility of pathogens:

Human populations possess many variants of each type of MHC molecule
Variant MHC may not protect every individual from every pathogen.
However, the existence of a large number of variants means that the population is
prevented from extinction
Limited diversity in HLA gene polymorphism due to breeding bottle-neck in recent
past leaves cheetahs exceptionally susceptible to viral infections. (6th Ed. P. 206)
 MHC Expression
• Expression is increased by cytokines such as IFN, IFN, IFN and TNF

• Transcription factors like CIITA (Transactivator), RFX (Transactivator) increase MHC

gene expression

• Some viruses (CMV, HBV, Ad12) decrease MHC expression

• Reduction of MHC may allow for immune system evasion

HLA vs. Transplantation
• HLA matching between the donor and recipient - a predictor of graft survival
in the kidney allograft patient

• HLA mis-matches may cause chronic pathologies in the allograft

• It is clear that a negative HLA-A2 recipient receiving an allograft expressing

HLA-A2 will have a much higher risk of humoral rejection of the vascular
endothelium.

IMMUNE GRAFT REJECTION

Molecular basis of transplant rejection

TcR TcR TcR

MHC A MHC B MHC C

Normal peptide Indirect peptide Direct peptide

recognition recognition recognition
 Differential distribution of MHC molecules
Cell activation affects the level
of MHC expression.
Tissue MHC class I MHC class II
The pattern of expression
T cells +++ +/- reflects the function of MHC
molecules:
• Class I is involved in the
B cells +++ +++
regulation of anti-viral
Macrophages +++ ++ immune responses
Other APC +++ +++ • Class II involved in regulation
of the cells of the immune
Thymus epithelium + +++ system

Neutrophils +++ - Anucleate erythrocytes can not

Hepatocytes + - support virus replication -
hence no MHC class I.
Kidney + -
Some pathogens exploit this -
Brain + - e.g. Plasmodium species.
Erythrocytes - -
 Bacterial superantigens
Superantigens act by binding to both
the MHC protein and
the TCR at positions
outside the normal
binding site

superantigens can
interact with large
numbers of cells,
stimulating massive T-
cell activation,
cytokine release and
systemic inflammation
Conventional Antigen Superantigen
Antigen presenting cell

CHO α2 β2 CHO α2 β2
MHC Class II
CHO α1 β1 CHO CHO α1 β1 CHO
Super
Antigen antigen
CHO CHO CHO CHO
αV βV αV βV
T cell receptor
CHO CHO CHO CHO
αC βC αC βC

T lymphocyte
Antigen Processing and Presentation
 MHC-restricted antigen recognition by T cells

• Any T cell can recognize an antigen on an APC only if that antigen is

displayed by MHC molecules
– Antigen receptors of T cells have dual specificities:
1. for peptide antigen (responsible for specificity of immune response)
and
2. for MHC molecules (responsible for MHC restriction)
– During maturation in the thymus, T cells whose antigen receptors see
MHC are selected to survive and mature; therefore, mature T cells are
“MHC-restricted”
 Antigen processing

• Conversion of native antigen (large globular protein) into

peptides capable of binding to MHC molecules

• Occurs in cellular compartments where MHC molecules

are synthesized and assembled (ER)
– Determines how antigen in different cellular
compartments generates peptides that are displayed by
class I or class II MHC molecules
 What Does the αβ T Cell Receptor (TCR) Recognize?

1. Only fragments of proteins (peptides) associated with MHC

molecules on surface of cells
• Helper T cells CD4+(Th) recognize peptide associated with
MHC class II molecules
• Cytotoxic T cells CD8+ (Tcyt) recognize peptide associated
with MHC class I molecules.
Antigen-presenting cells

Dendritic cells
 Pathways of antigen processing

Protein antigen in cytosol (cytoplasm) --> class I MHC pathway

Protein antigen in vesicles --> class II MHC pathway
 Class I MHC molecules
Endogenous Antigens: The Cytosolic Pathway

• Cytotoxic T lymphocytes need to kill cells containing cytoplasmic microbes, and

tumor cells (which contain tumor antigens in the cytoplasm)

• Cytosolic proteins are processed into peptides that are presented in association with
class I molecules

• Most cytosolic peptides are derived from endogenously synthesized (e.g. viral,
tumor) proteins

• All nucleated cells (which are capable of being infected by viruses or transformed)
express class I
 The class I MHC pathway of processing
of endogenous cytosolic protein antigens

Cytoplasmic peptides are actively transported into the ER;

class I MHC molecules are available to bind peptides in the ER
 Cytosolic proteolytic system for degradation of intracellular
proteins.
• Proteins to be degraded are often covalently linked to a small protein called
ubiquitin.
• A ubiquinating enzyme complex links several ubiquitin molecules to a lysine-amino
group near the amino terminus of the protein.
• Degradation of ubiquitin-protein complexes occurs within the central channel of
proteasomes, Proteasomes are large cylindrical particles whose subunits catalyze
cleavage of peptide bonds.
• In the cytosol,association of LMP2, LMP7, and LMP10 with a proteasome changes
its catalytic specificity to favor production of peptides that bind to class I MHC
molecules. All three are induced by increased levels of the T-cell cytokine IFN-γ
• Peptides generated in the cytosol by the proteasome are translocated by
TAP (transporter associated with antigen processing )into the RER by a
process that requires the hydrolysis of ATP.
• TAP has the highest affinity for peptides containing 8–10 amino acids,
which is the optimal peptide length for class I MHC binding.
• Within the RER membrane, a newly synthesized class I chain associates
with calnexin until β2-microglobulin binds to the chain.
• The class I αchain/β2-microglobulin heterodimer then binds to calreticulin
and the TAP-associated protein tapasin.
• When a peptide delivered by TAP is bound to the class I molecule, folding
of MHC class I is complete and it is released from the RER and transported
through the Golgi to the surface of the cell.
 Assembly and stabilization of class I MHC molecules.

• Newly formed class I chains associate with calnexin, a molecular

chaperone, in the RER membrane.
• Subsequent binding to β2-microglobulin releases calnexin and allows
binding to the chaperonin calreticulin and to tapasin, which is associated
with the peptide transporter TAP.
• This association promotes binding of an antigenic peptide, which stabilizes
the class I molecule–peptide complex, allowing its release from the RER
 Class I MHC Pathway
Peptide is presented
by MHC-I to CD8
cytotoxic T cell Viral protein is made
Plasma membrane on cytoplasmic
ribosomes

Globular viral
protein - intact
Peptide passes
with MHC from Golgi Proteasome
body to surface rER degrades
Peptide associates protein to
with MHC-I complex peptides
Peptide transporter
protein moves
peptide into ER
MHC class I alpha
Golgi body Peptide with MHC
and beta proteins
goes to Golgi body
are made on the rER
CD8 CTL

Tumour cell
Exogenous Antigens: The Endocytic Pathway
Loading of antigen to MHC class II
 Generation of antigenic peptides in the endocytic
processing pathway.
• Internalized exogenous antigen moves through several acidic
compartments, in which it is degraded into peptides that ultimately
associate with class II MHC molecules transported in vesicles from the
Golgi complex.
 Assembly of class II MHC molecules

• Within the rough endoplasmic reticulum, a newly synthesized class II MHC

molecule binds an invariant chain.
• The bound invariant chain prevents premature binding of peptides to the
class II molecule and helps to direct the complex to endocytic
compartments containing peptides derived from exogenous antigens.
• Digestion of the invariant chain leaves CLIP, a small fragment remaining in
the binding groove of the class II MHC molecule.
• HLA-DM, a nonclassical MHC class II molecule expressed within
endosomal compartments, mediates exchange of antigenic peptides for
CLIP.
How class I- and class II-associated antigen presentation
influence the nature of the host T cell response
Thank you