MHC Class I vs. MHC Class II Protein

Every cell in the body is under constant inspection. To catch a virus hiding inside a cell, the immune system cannot wait for the cell to burst open. Instead, each cell continuously displays small fragments of the proteins it is making on its surface, like holding up samples of its internal work for inspection.

A healthy cell shows only normal self fragments and is left alone. A virus-infected cell shows viral fragments and is marked for killing. The molecules that hold up these fragments are the MHC molecules, and there are two classes that solve two different surveillance problems: what is happening inside a cell, and what is floating outside it. This article explains how the two classes differ and why that difference matters.

Major histocompatibility complex (MHC) molecules are tightly linked cluster of genes whose products are associated with intercellular recognition and self-non-self-discrimination. MHCs are present in every mammalian species. The MHC is referred to as the HLA complex in humans and the H-2 complex in mice.

MHC Genes and Functions

It is a collection of genes within a long stretch of DNA on chromosome 6, which codes for three classes of molecules

1. Class I MHC genes: encode glycoproteins expressed on the surface of nearly all nucleated cells; the major function of the class I gene product is presentation of peptide antigens to TC cells.
2. Class II MHC genes encode glycoproteins expressed primarily on APCs, where they present processed antigenic peptides to TH cells.
3. Class III MHC genes encode various secreted proteins that have immune functions, including components of the complement system and molecules involved in inflammation (e.g. TNF, Heat Shock proteins).

The rule of eight: which T cell reads which MHC

Before the details, one rule organizes everything that follows. It links each MHC class to the T cell that reads it, and it is worth memorizing first because every other difference hangs off it.

CD8 T cells read MHC class I. CD4 T cells read MHC class II. The trick to remember which goes with which is that the two numbers always multiply to eight:

CD8 × MHC-I = 8 × 1 = 8
CD4 × MHC-II = 4 × 2 = 8

This is called MHC restriction: each type of T cell is restricted to recognizing antigen only when it is presented by its matching class of MHC. From this single pairing, the rest follows. MHC class I is on all nucleated cells and shows the inside of the cell to CD8 killer T cells. MHC class II is on antigen-presenting cells and shows engulfed outside material to CD4 helper T cells.

MHC I

MHC Class I is found on all nucleated cells. MHC Class I mediates immune responses against endogenous antigens. Usually, these cells expressing MHC class I are viral-infected or tumor cells.

MHC Class I presents peptides that are 8 – 10 amino acids in size, which will then be recognized by the cytotoxic T cells.

Figure: MHC Class I Structure

Structure of MHC Class I

• α chain anchored in plasma membrane by its hydrophobic transmembrane segment & hydrophilic cytoplasmic tail
• α chain has 3 external domains
• Homology between α3, β2-microglobulin & constant regions in immunoglobulins
• Peptide-binding cleft

Class I MHC-Peptide Interaction and Presentation

Single nucleated cell expresses about 10⁵ (100,000) copies of each class I molecule. Class I MHC will express many different peptides simultaneously on the surface. Each type of Class I (A, B, C in humans) bind a unique set of peptides & presents these peptides to CD8+ T-cells.

Endogenous Processing Pathway

- Class I MHC molecules bind peptides derived from endogenous antigens processed in the cytoplasm.

• Proteins enter the cytoplasm of cells either from phagocytosed microbes or from endogenous synthesis by microbes, such as viruses that reside in the cytoplasm of infected cells.
• Cytoplasmic proteins are unfolded, ubiquitinated, and degraded by proteasomes.
• The proteasome breaks these proteins into short peptides, typically 8 to 10 amino acids long. The TAP transporter carries these peptides into the endoplasmic reticulum, where they bind to newly synthesized MHC class I molecules.
• The MHC class-I-antigen complex will migrate towards the cell surface and are presented to CD8+ T cells.
• CD8+ T cells may recognize the MHC-I Antigen complex and further processing takes place.

MHC II

The MHC class II protein is found on Antigen Presenting Cells (APCs). Class II MHC can bind to various peptides and presents these to CD4+ T cells. MHC class II mediates immune responses against exogenous antigens.

MHC class II binds longer peptides, generally 13 to 18 amino acids, and presents them to helper (CD4) T cells. Unlike the tight size limit of class I, the class II groove is open at both ends, so it can hold peptides of more variable length.

Figure: MHC Class II Structure

MHC II Structure

• It contains 2 different polypeptide chains: α chain (33 kDa) & αβ chain (28 kDa)
• Each chain has 2 external domains
• Antigen binding cleft for processed antigens
• αβ heterodimer  “dimer of dimers.”

Class II MHC-Peptide Interaction and Presentation

Class II MHC molecules bind peptides derived from exogenous antigens internalized by phagocytosis or endocytosis & processed within the endocytic pathway. APCs can internalize antigens by phagocytosis &/or endocytosis. Macrophages do both; B cells use receptor-mediated endocytosis.

Exogenous processing pathway

Figure: Exogenous processing pathway (Source: Kuby Immunology)

• Microbial proteins enter intracellular vesicles called endosomes or phagosomes, which may fuse with lysosomes. The internalized antigen is degraded into peptides.
• APCs synthesize class II MHC molecules in the endoplasmic reticulum (ER).
• Each newly synthesized MHC-II carries an invariant chain or CLIP that binds to the peptide binding cleft, thus occupying the peptide binding region.
• This MHC Class II begins its transport to the cell surface in an exocytic vesicle, which then fuses with the endosomal vesicle containing broken-down peptides derived from ingested extracellular proteins.
• Endosomal vesicle contains a protein named DM, which removes CLIP. Thus, the cleft is available to accept peptides.
• Internalized antigen takes 1-3 hours to travel the endocytic pathway & appear on the cell membrane in the form of peptide-class II MHC complexes.
• If the MHC II molecule does not find a suitable peptide to bind, the empty molecule is unstable and is degraded by proteases in the endosomes.
• Once HLA-DM removes CLIP, the class II groove binds a peptide of about 13 to 18 amino acids from the degraded antigen. The stable peptide-MHC II complex then travels to the cell surface, where a CD4 helper T cell recognizes it and triggers the appropriate response.

Target cells vs APCs

Cells displaying MHC class I are often called target cells. Almost every nucleated cell carries MHC class I, and when it displays a foreign fragment (from a virus or a tumor), it becomes a target for CD8 cytotoxic T cells to kill. The word "target" fits because the outcome is destruction of that cell.

Cells displaying MHC class II are called antigen-presenting cells (APCs), and only a few specialized cells qualify: dendritic cells, macrophages, and B cells. These cells engulf outside material and display it to CD4 helper T cells to start a response. The outcome here is not killing the presenting cell but coordinating the immune response.

So the same verb, "present," leads to opposite outcomes: a class I target cell is presenting evidence that gets it killed, while a class II APC is presenting evidence to recruit help.

One exception worth noting: a few sites are immunoprivileged and express little or no MHC class I, such as neurons and cells of the testis, which is why they are relatively protected from CD8 T-cell attack.

Roles of MHC

• Development of humoral and cell-mediated immune response
• Antigen recognition by T cells: T cells recognize antigen only when it is combined with MHC molecule
  T cell receptor (TCR) can only bind to peptides processed from proteins not whole proteins. Peptides which are bound to MHCs are presented to T cells The main two groups of MHC important in adaptive T cell responses are MHC-I and MHC-II. MHC-I presents peptide to CD8 T cells and MHC-II presents peptide to CD4 T cells.
• Determining whether transplanted tissue will be histocompatible or histoincompatible

MHC Polymorphism and Significance

MHC genes are highly polymorphic (presence of multiple alleles at a given genetic locus within a species). The polymorphism is so great that NO two individuals in the usual outbred population have exactly the same MHC genes and molecule.

1. These polymorphic residues determine which peptides are presented by which MHC molecules
2. This evolution of MHC polymorphism ensures that a population will not succumb to a microbe that mutates its proteins because at least some individuals will be able to mount effective immune responses to the peptide antigens of new introduced or mutated microbes.
3. MHC expressed by an individual does not change over time but differ significantly from those expressed by another individual of the same species
4. The different allele combinations make up the identity of the MHC for that person
5. There are lots and lots of alleles and thousands of combinations, which is why finding someone to whose HLA markers match up with another person is so difficult but it’s not impossible, there are thousands of transplants every year.

How to remember

The rule of eight. CD8 × MHC-I = 8; CD4 × MHC-II = 8.

Inside vs outside: "I is for Inside, II is for Ingested." MHC class I shows endogenous (Inside the cell) antigen. MHC class II shows exogenous, Ingested antigen.

Who carries which: class I is on all nucleated cells (every cell can be a suspect); class II is only on the professional APCs (dendritic cells, macrophages, B cells).

Groove shape sets peptide length. Class I groove closed at both ends → short, fixed 8–10. Class II groove open at both ends → longer, variable 13–18.

Processing machinery, one word each: class I uses the proteasome and TAP (cytoplasm to ER). Class II uses the invariant chain and CLIP, removed by DM (in the endosome).

Key exam facts in one table

Where students get confused

"MHC class II is on all cells like class I." No. Class I is on essentially all nucleated cells. Class II is restricted to professional APCs: dendritic cells, macrophages, and B cells. This is one of the most tested distinctions.

"CD8 T cells read MHC class II." Yes. Use the rule of eight: CD4 goes with MHC class II (4 × 2 = 8), and CD8 goes with MHC class I (8 × 1 = 8).

"MHC class I presents antigens that the cell ate from outside." No. Class I presents endogenous antigen, made inside the cell (including viral proteins made by an infected cell). Class II presents exogenous antigen, ingested from outside. The invariant chain exists precisely to block class II from grabbing the inside peptides too early.

"The invariant chain is the final peptide." No. The invariant chain, and the CLIP fragment left from it, is a placeholder that blocks the class II groove until the cell is ready. HLA-DM removes CLIP so a real antigenic peptide can bind.

"MHC polymorphism is a problem the body should fix." No. Polymorphism is a beneficial immunological feature. Because individuals carry different MHC alleles, a pathogen that escapes one person's MHC will still be presented by another's, so the whole population is unlikely to be wiped out by a single mutating microbe. The cost of this benefit is transplant rejection.

References and further reading:

1. Abbas AK, Lichtman AH, Pillai S. Cellular and Molecular Immunology. 10th ed. Elsevier; 2022.
2. Punt J, Stranford SA, Jones PP, Owen JA. Kuby Immunology. 8th ed. W.H. Freeman; 2019.
3. Delves PJ, Martin SJ, Burton DR, Roitt IM. Roitt's Essential Immunology. 13th ed. Wiley-Blackwell; 2017.
4. Wieczorek M, Abualrous ET, Sticht J, et al. Major histocompatibility complex (MHC) class I and MHC class II proteins: conformational plasticity in antigen presentation. Front Immunol. 2017;8:292. https://doi.org/10.3389/fimmu.2017.00292