Sanjib Kr Das [Link] Hons. In ZOOLOGY 05.06.

2020
Assistant Professor (WBES) SEM-IV
Dept. of Zoology Paper- CC-10 Immunology
Jhargram Raj College UNIT-5 Major Histocompatibility Complex

Structure & Function of MHC molecules

I n contrast to antibodies or B-cell receptors, which can recognize an antigen alone, T-cell
receptors only recognize pieces of antigen that are positioned on the surface of other cells.
These antigen pieces are held within the binding groove of a cell surface protein called the
major histocompatibility complex (MHC) molecule, encoded by a cluster of genes collectively
called the MHC locus. These fragments are generated inside the cell following antigen digestion,
and the complex of the antigenic peptide plus MHC molecule then appears on the cell surface.
MHC molecules thus act as a cell surface vessel for holding and displaying fragments of antigen
so that approaching T cells can engage with this molecular complex via their T-cell receptors.

The MHC got its name from the fact that the genes in this region encode proteins that
determine whether a tissue transplanted between two individuals will be accepted or rejected.
George Snell introduced the term histocompatibility (H) antigen to describe antigens provoking
graft rejection and demonstrated that, of all the potential H antigens, differences at the H‐2 (i.e.,
antigen II) locus provoked the strongest graft rejection seen between various mouse strains. Far
from representing a single gene locus, H‐2 proved to be a large complex of multiple genes, many
of which were highly polymorphic, hence the term major histocompatibility complex (MHC).

MHC plays a central role in-

1. Determining whether the transplanted tissue will be accepted as self ( histocompatible)
2. Development of both humoral and cell mediated immune response i.e., T cell recognize
antigen when it is associated only with MHC.

The MHC Locus Encodes Three Major Classes of Molecules

The major histocompatibility complex is a collection of genes arrayed within a long continuous
stretch of DNA on chromosome 6 in humans and on chromosome 17 in mice. The MHC is
referred to as the human leukocyte antigen (HLA) complex in humans and as the H-2 complex
in mice, the two species in which these regions have been most studied. Although the
arrangement of genes is somewhat different in the two species, in both cases the MHC genes are
organized into regions encoding three classes of molecules.

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Sanjib Kr Das [Link] Hons. In ZOOLOGY 05.06.2020
Assistant Professor (WBES) SEM-IV
Dept. of Zoology Paper- CC-10 Immunology
Jhargram Raj College UNIT-5 Major Histocompatibility Complex

Comparison of the organization of the major histocompatibility complex (MHC) in mouse and human

 Class I MHC genes encode glycoproteins expressed on the surface of nearly all
nucleated cells; the major function of the class I gene products is presentation of
endogenous peptide antigens to CD8+ T cells.
 Class II MHC genes encode glycoproteins expressed predominantly on APCs
(macrophages, dendritic cells, and B cells), where they primarily present exogenous
antigenic peptides to CD4+ T cells.
 Class III MHC genes encode several different proteins, some with immune functions,
including components of the complement system and molecules involved in
inflammation.

There are two main classes of MHC molecules: class I and class II. Both of these two MHC
molecules are membrane-bound glycoproteins that are closely related in both structure and
function. Both classes of MHC molecule have been isolated and purified, and the three-
dimensional structures of their extracellular domains have been resolved by x-ray
crystallography. These membrane glycoproteins function as highly specialized antigen-
presenting molecules with grooves that form unusually stable complexes with peptide ligands,
displaying them on the cell surface for recognition by T cells via T-cell receptor (TCR)
engagement. In contrast, class III MHC molecules are a group of unrelated proteins that do not
share structural similarity or function with class I and II molecules, although many of them do
participate in other aspects of the immune response.

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Sanjib Kr Das [Link] Hons. In ZOOLOGY 05.06.2020
Assistant Professor (WBES) SEM-IV
Dept. of Zoology Paper- CC-10 Immunology
Jhargram Raj College UNIT-5 Major Histocompatibility Complex

Class I and class II molecules are very similar in their final quaternary structure, although they
differ in how they create these shapes via primary through quaternary protein arrangements.
MHC molecules assemble within the cell, where they associate with short peptide fragments
derived either from proteins being made by the cell or proteins that have been internalized by the
cell through phagocytosis or pinocytosis. So they also differ in terms of which cells express them
and in the source of the antigens they present to T cells. Class I molecules are present on all
nucleated cells in the body and specialize in presenting antigens that originate from the cytosol,
such as viral proteins (MHC class I molecules bind to peptides derived from proteins being
synthesized within the cell). These are presented to CD8+ T cells, which recognize and kill cells
expressing such intracellular antigens. In contrast, class II MHC molecules are expressed almost
exclusively on a subset of leukocytes called antigen-presenting cells (APCs) and specialize in
presenting antigens from extracellular spaces that have been engulfed by these cells, such as
fungi and extracellular bacteria (MHC class II molecules bind to peptides derived from proteins
made external to the cell). Once expressed on the cell surface, the MHC class II molecule
presents the antigenic peptide to CD4+T cells, which then become activated and go on to
stimulate immunity directed primarily toward destroying extracellular invaders.

MHC class I molecules:

Structure:
 A single class I MHC molecule consists of a 45-kilodalton (kDa) α chain associated
noncovalently with a 12-kDa β2-microglobulin molecule.
 The α chain is organized into three external domains (α1, α2, and α3), each approximately
90 amino acids long; a transmembrane domain of about 25 hydrophobic amino acids
followed by a short stretch of charged (hydrophilic) amino acids; and a cytoplasmic
anchor segment of 30 amino acids.
 The α chain is encoded by polymorphic genes, referred to as HLA‐A, HLA‐B, and HLA‐C
within the A, B & C regions of human HLA complex located on chromosome no 6 and
H‐2 K, H‐2D, and H‐2 L genes within K, D/L region of mouse H2 complex located on

chromosome no 17, which can result in the expression of at least three different class I
proteins in every cell.
 Its companion, β2-microglobulin, is similar in size and organization to the α3 domain. β2-
microglobulin does not contain a transmembrane region and is noncovalently bound to
the MHC class I α chain.
 β2-microglobulin is a protein encoded by a highly conserved gene located on a different
chromosome.
 Sequence data reveal strong homology between the α3 domain of MHC class I, β2-
microglobulin, and the constant-region domains found in immunoglobulin molecule,
that’s why MHC class I has been categorized within the immunoglobulin superfamily
proteins.

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Sanjib Kr Das [Link] Hons. In ZOOLOGY 05.06.2020
Assistant Professor (WBES) SEM-IV
Dept. of Zoology Paper- CC-10 Immunology
Jhargram Raj College UNIT-5 Major Histocompatibility Complex

Functions of different domains:

 The α1 and α2 domains interact to form a platform of eight antiparallel β strands spanned
by two long α -helical regions to form a deep groove, or cleft, with the long α helices as
sides and the β strands of the β sheet as the bottom. This peptide-binding groove (-25Å X
10Å X 11Å) is located on the top surface of the class I MHC molecule, and it is large
enough to bind a peptide of 8 to 10 amino acids in a flexible, extended conformation.
 The α3 domain and β2-microglobulin are organized into two β pleated sheets each formed
by antiparallel β strands of amino acids.
 The α3 domain appears to be highly conserved among class I MHC molecules and
contains a sequence that interacts strongly with the CD8 cell surface molecule found on
TC cells.
 All three molecules (class I α chain, β2-microglobulin, and a peptide) are essential for the
proper folding and expression of the MHC-peptide complex on the cell surface. In
absence of the β2-microglobulin, class I MHC α chain is not expressed on the membrane.

Fig: Schematic diagrams of class I and class II MHC molecules showing the external domains, transmembrane segments,
and cytoplasmic tails

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Sanjib Kr Das [Link] Hons. In ZOOLOGY 05.06.2020
Assistant Professor (WBES) SEM-IV
Dept. of Zoology Paper- CC-10 Immunology
Jhargram Raj College UNIT-5 Major Histocompatibility Complex

Fig: Representations of the three-dimensional structure of the external domains of human MHC class I and class II
molecules based on x-ray crystallographic analysis

MHC class II molecules:

Structure:
 Class II MHC molecules contain two different polypeptide chains, a 33-kDa α chain and
a 28-kDa β chain, which associate by noncovalent interactions.
 Like class I α chains, class II MHC molecules are membranebound glycoproteins that
contain external domains, a transmembrane segment, and a cytoplasmic anchor segment.
 Each chain in a class II molecule contains two external domains: α1 and α2 domains in
one chain and β1 and β2 domains in the other.
 The membrane-proximal α2 and β2 domains, like the membrane-proximal α3/β2-
microglobulin domains of class I MHC molecules, bear sequence similarity to the

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Sanjib Kr Das [Link] Hons. In ZOOLOGY 05.06.2020
Assistant Professor (WBES) SEM-IV
Dept. of Zoology Paper- CC-10 Immunology
Jhargram Raj College UNIT-5 Major Histocompatibility Complex

immunoglobulin-fold structure. For this reason, class II MHC molecules are also
classified in the immunoglobulin superfamily.
 The membrane distal portions of class II molecule is composed of α1 and β1 domains and
forms the peptide-binding groove for processed antigen.
 Three different types of MHC class II α‐and β‐chain genes expressed in humans, HLA‐
DQ, HLA-DP, and HLA‐DR, and two pairs in mice, H2‐A (I‐A) and H2‐E (I‐E). Thus,
humans can express a minimum of three different class II molecules.

Functions of different domains:

 The peptide-binding groove of class II molecules, like that found in class I molecules, is
composed of a floor of eight antiparallel β strands and sides of antiparallel α helices,
(Four strands of the floor of the cleft and one of the helices are formed by α1 and the
other four strands of the floor and the second helix is formed by β1) where peptides
typically ranging from 13 to 18 amino acids can bind.
 β2 domain of class II MHC is the binding site for CD4.
 The polymorphic residues are located in α1 and β1, in and around the peptide binding
cleft.
 A nonpolymorphic polypeptide called the invariant chain (Ii) is associated with newly
synthesized class II molecule.

Different Antigen Processing and Presentation Pathways:

The immune system typically uses different pathways to eliminate intracellular and extracellular
antigens. As a general rule, endogenous antigens (those generated within the cell) are processed
in the cytosolic or endogenous pathway and presented on the membrane with class I MHC
molecules. Exogenous antigens (those taken up from the extracellular environment by
endocytosis) are typically processed in the exogenous pathway and presented on the membrane
with class II MHC molecules.

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Sanjib Kr Das [Link] Hons. In ZOOLOGY 05.06.2020
Assistant Professor (WBES) SEM-IV
Dept. of Zoology Paper- CC-10 Immunology
Jhargram Raj College UNIT-5 Major Histocompatibility Complex

Mechanism of Antigen processing & presentation by MHC class I molecule:

Endogenous antigen & cytosolic pathway:

1. Intracellular proteins are degraded into short peptides by a cytosolic proteolytic system
present in all cells, called the proteasome. Many proteins are targeted for proteolysis when a
small protein called ubiquitin is attached to them. These ubiquitin-protein conjugates enter
the proteasome complex for degradation.
2. Each proteasome is composed of 14 subunits arrayed in a barrel-like structure of symmetrical
rings. ubiquitin-protein conjugates enter the proteasome complex, consisting of the 20S base
and an attached 19S regulatory component, through a narrow channel at the 19S end. The
proteasome complex cleaves peptide bonds in an ATP-dependent process. Degradation of
ubiquitin-protein complexes is thought to occur within the central hollow of the proteasome.
3. In addition to the standard 20S proteasomes resident in all cells, a distinct proteasome of the
same size can be found in pAPCs and the cells of infected tissues. This distinct proteasome,
called the immunoproteasome, has some unique components that can be induced by
exposure to interferon-γ or TNF- α. LMP2 and LMP7, genes that are located within the class I
region and are responsive to these cytokines, encode replacement catalytic protein subunits
that convert standard proteasomes into immunoproteasomes, increasing the production of
peptides that bind effi ciently to MHC class I proteins.
4. Peptides generated in the cytosol by the proteasome are translocated by TAP (transporter
associated with antigen processing ) which is a transporter protein, into the RER by a process
that requires the ATP hydrolysis. TAP is a membrane-spanning heterodimer consisting of
two proteins: TAP1 and TAP2. TAP has affinity for peptides containing 8 to 16 amino acids.
The optimal peptide length for class I MHC binding is around 9 amino acids, and longer
peptides are trimmed by enzymes present in the ER, such as ERAP (endoplasmic reticulum
aminopeptidase).
5. The α chain and β2-microglobulin components of the class I MHC molecule are synthesized
on ribosomes on the RER.
6. The assembly of these components into a stable class I MHC molecular complex involves
several steps and includes the participation of molecular chaperones that facilitate the folding
of polypeptides that can exit the RER. I also requires the presence of a peptide in the binding
groove of the class I molecule.
7. The first molecular chaperone involved in class I MHC assembly is calnexin, a resident
membrane protein of the ER. ERp57, a protein with enzymatic activity, and calnexin
associate with the free class I α chain and promote its folding. When β 2-microglobulin binds
to the α chain, calnexin is released and the class I molecule associates with the chaperone
calreticulin and with tapasin.
8. Tapasin (TAPassociated protein) brings the TAP transporter into proximity with the class I
molecule and allows it to acquire an antigenic peptide. The TAP protein promotes peptide
capture by the class I molecule before the peptides are exposed to the luminal environment of
the RER.
9. As a consequence of productive peptide binding, the class I molecule displays increased
stability and can dissociate from the complex with calreticulin, tapasin, and ERp57. The class
I molecule can then exit from the RER and proceed to the cell surface via the Golgi complex.

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Sanjib Kr Das [Link] Hons. In ZOOLOGY 05.06.2020
Assistant Professor (WBES) SEM-IV
Dept. of Zoology Paper- CC-10 Immunology
Jhargram Raj College UNIT-5 Major Histocompatibility Complex

Fig: Cytosolic proteolytic system for degradation of intracellular proteins

Fig: TAP (transporter associated with antigen processing)

Fig: Assembly and stabilization of class I MHC molecules.

Mechanism of Antigen processing & presentation by MHC class II molecule:

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Sanjib Kr Das [Link] Hons. In ZOOLOGY 05.06.2020
Assistant Professor (WBES) SEM-IV
Dept. of Zoology Paper- CC-10 Immunology
Jhargram Raj College UNIT-5 Major Histocompatibility Complex

EXogenous antigen & endocytic pathway:

1. Antigen presenting cells (APCs) can internalize particulate material by simple phagocytosis (also
called “cell eating”), where material is engulfed by pseudopods of the cell membrane, or by
receptor-mediated
2. endocytosis, where the material first binds to specific surface receptors. Macrophages and
dendritic cells internalize antigen by both processes.
3. Once an antigen is internalized, it is degraded into peptides within compartments of the endocytic
processing pathway.
4. The endocytic antigen processing pathway appears to involve several increasingly acidic
compartments, including early endosomes (pH 6.0–6.5); late endosomes, or endolysosomes (pH
4.5–5.0); and lysosomes (pH 4.5). Internalized antigen progresses through these compartments,
encountering hydrolytic enzymes and a lower pH in each compartment.
5. Antigen-presenting cells have a unique form of late endosome, the MHC class II-containing
compartment (MIIC), in which final protein degradation and peptide loading into MHC class II
proteins occurs. Within the compartments of the endocytic pathway, antigen is degraded into
oligopeptides of about 13 to 18 residues that meet up with and bind to class II MHC molecules in
late endosomes.
6. When class II MHC molecules are synthesized within the RER, these class II αβ chains associate
with a protein called the invariant chain (Ii, CD74). This conserved, non-MHC encoded protein
interacts with the class II peptide-binding groove preventing any endogenously derived peptides
from binding while the class II molecule is within the RER.
7. The invariant chain also appears to be involved in the folding of the class II α and β chains, their
exit from the RER, and the subsequent routing of class II molecules to the endocytic processing
pathway from the trans-Golgi network. The invariant chain contains sorting signals in its
cytoplasmic tail that direct the transport of the class II MHC complex from the trans-Golgi
network to the endocytic compartments.
8. Recent experiments indicate that most class II MHC invariant chain complexes are transported
from the RER, where they are formed, through the Golgi complex and trans-Golgi network, and
then through the endocytic pathway, moving from early endosomes to the MIIC late endosomal
compartments, and finally to lysosome.
9. As the proteolytic activity increases in each successive compartment, the invariant chain is
gradually degraded. However, a short fragment of the invariant chain termed CLIP (for class II–
associated invariant chain peptide) remains bound to the class II molecule after the majority of
the invariant chain has been cleaved within the endosomal compartments
10. CLIP physically occupies the peptide-binding groove of the class II MHC molecule, preventing
any premature binding of antigen-derived peptide.
11. A nonclassical class II MHC molecule called HLA-DM is required to catalyze the exchange of
CLIP with antigenic [Link] reaction between HLA-DM and the class II CLIP complex
facilitating exchange of CLIP with another peptide is impaired in the presence of HLA-DO,
which binds to HLA-DM and lessens the efficiency of the exchange reaction.

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Sanjib Kr Das [Link] Hons. In ZOOLOGY 05.06.2020
Assistant Professor (WBES) SEM-IV
Dept. of Zoology Paper- CC-10 Immunology
Jhargram Raj College UNIT-5 Major Histocompatibility Complex

Fig: Generation of antigenic peptides in the exogenous processing pathway.

Fig: Assembly of class II MHC molecules.

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Sanjib Kr Das [Link] Hons. In ZOOLOGY 05.06.2020
Assistant Professor (WBES) SEM-IV
Dept. of Zoology Paper- CC-10 Immunology
Jhargram Raj College UNIT-5 Major Histocompatibility Complex

Fig: Separate antigen-presenting pathways are utilized for endogenous (green) and exogenous (red) antigens

References:
 Kuby Immunology Seventh edition.
 Roitt’s Essential Immunology Thirteenth edition

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