The major histocompatibility complex (MHC) is present in all vertebrates, and is encoded by a group of genes called HLA in humans and H-2 in mice. Products of these genes are mostly cell surface glycoproteins involved in antigen presentation. MHC molecules must be bound to a peptide (it does not even have to be pathogenic) in order to be brought to the cell surface by the endoplasmic reticulum. The peptide-binding residues within the MHC determine what kinds of peptides it can bind. While B cells interact with free antigens, T cells interact only with antigens that are associated with a major histocompatibility complex, thus limiting T cells to interaction with antigens at cell surfaces.

Class I Major Histocompatibility Complex

Class I MHC molecules bind peptides and present them to cytotoxic T cells. A mammalian cell can express all Class I MHC alleles (up to six) at a time. Class I MHC molecules contain a 45kD transmembrane glyocoprotein α chain associated noncovalently with a 12kD β₂-microglobulin. The three Class I MHC genes — A, B and C in humans; K, D and L in mice — are polymorphic and each encode a different α chain (although be clear that each chain contains α1, α2 and α3 subunits). α chains contain α1, α2 and α3 domains; the α3 region contains a cytoplasmic tail that goes through the lipid bilayer and into the cytoplasm. To summarize, the Class I region of HLA contains HLA-A, HLA-B and HLA-C, which each encode different α chains. Lastly, the noncovalently bound β-2 microglobulin is not encoded within the MHC, but is critical for getting the MHC protein to the cell surface.

Between the α1 and α2 regions is the peptide binding groove (aka antigen binding groove), which presents antigenic peptides to CD8 (cytotoxic) T cells. Antigenic peptides — usually about nine amino acids — anchor into the groove at both ends via hydrogen bonds; without this anchoring, the Class I MHC glycoprotein is not brought to the cell surface. Longer peptides bulge out in the middle, while shorter peptides are taught. The middle of the peptide makes negligible contact with the MHC molecule, and is instead available for direct T cell receptor contact.

In the absence of β₂-microglobulin, Class I MHC molecules are not expressed on the cell surface. A cell that does not express β₂-microglobulin will have Class I MHC molecules floating in the cytoplasm but completely absent from the cell surface; if these same cells are transfected with a functional β₂-microglobulin gene, then they begin to express Class I MHC molecules on their cell surface. The enzyme papain cleaves Class I MHC molecules near the transmembrane domain, thus releasing just the extracellular portion (α1, α2, α3 and β₂-microglobulin).

Class II Major Histocompatibility Complex

Class II MHC molecules bind peptides and present them to helper T cells. Encoded by the centromeric end of HLA, the Class II MHC protein is (under normal conditions) found on macrophages, dendritic cells, B cells and activated T cells; however, in inflamed tissue, other cells can also express Class II MHC proteins. Class II MHC genes encode 32kD α and 27kD β transmembrane chains, and an intracellular invariant and non-polymorphic Ii chain. The α chain consists of α₁ and α₂ domains; the β chain consists of β₁ and β₂ domains. Just as with Class I MHC molecules, the α chain and β chain are noncovalently bound transmembrane glycoproteins with a cytoplasmic anchor.

Between the α₁ and β₁ domains is the peptide-binding cleft. Just as with the Class I cleft, the Class II cleft presents a peptide antigen; however, the Class II cleft binds antigens of at least 13 peptides (sometimes much longer) that are held in place along their backbone (instead of anchored at the ends) by interactions between cleft residues and the amino acids of the antigen. CD4 (helper) T cells recognize antigens presented by the Class II MHC protein.

The Class II region of HLA contains three genes (HLA-DR, HLA-DP and HLA-DQ) which each encode multiple different α and β chains. This allows a single translation of the HLA Class II genes to produce multiple different Class II MHC complexes. HLA-DR encodes three β chains and a single α chain; HLA-DP encodes one each of β1, β2, α1 and α2; HLA-DQ encodes one each of β1, β2, β3, α1 and α2. Please note, however, that α and β chains from different genes never mix; individual MHCs are always all HLA-DP, HLA-DR or HLA-DQ. Also, mice carry just two Class II Genes (IA, or AαAβ, and IE, or EαEβ).

Cell-surface peptide-bound MHCs bind to T Cell Receptors (TCRs). TCRs have a combining site which interacts the the α helices of α1 and α2, as well as the bound peptide. The center of the MHC-bound peptide nestles into a hydrophobic pocket between the CDR3α and CDR3β regions of the TCR. CDRs 1 and 2 of the Vα domain interact with the NH₂-terminus of the MHC-bound peptide; CDR2 1 and 2 of the Vβ domain interact with the C-terminus of the MHC-bound peptide, as well as some of the MHC helices.

Peptide Binding Cleft Detail

The binding of a peptide to an MHC molecule is very stable under physiologic conditions. Thus, most MHC molecules on a cell surface are associated with a peptide. Each cell expresses ∼10⁵ copies of each Class I molecule, with 2,000 different peptides being presented 100 to 4,000 times on each cell.

There are three different Class I MHC molecules — A, B and C in humans; K, D and L in mice — which each bind a different kind of peptide; within each gene, each allele delivers more specificity. Class I MHC molecules usually bind hydrophobic nonameric (nine amino acid) peptides, with specificity defined by same or similar amino acids at certain positions. Different alleles encode different peptide binding cleft residues at these positions.

Class II MHC molecules bind longer peptides than Class I MHC molecules, but only the central 13 amino acids actually interact with the molecule. These central 13 amino acids are conserved, meaning that certain patterns will specifically bind to certain Class II MHC molecule alleles. Peptides binding to Class I MHC molecules are bound primarily at their ends, while peptides binding to Class II MHC molecules are hydrogen-bound along their core amino acids (as opposed to being anchored at their ends).

Major Histocompatibility Complex Diversity

Class I and Class II MHC genes — present on Chromosome 6 in humans (Chromosome 17 in mice) — are polygenic, polymorphic and codominant. Polygenic DNA encodes multiple proteins with similar structure and function. A polymorphic gene has many different alleles which are all common within a population. Codominance means that both alleles of a gene — the maternal and the paternal copy — are equally expressed.

Antibodies and T Cell Receptors (TCRs) use mutation, recombination and other techniques to generate diversity. However, MHC Class I and II molecules just use promiscuity to bind the vast population of peptides. Class I and Class II molecules have low specificity, allowing a single molecule to bind many different kinds of peptide. In addition, Class I and Class II genes are highly polymorphic; for some genes there are over 100 common alleles. Within these alleles, the region encoding the peptide binding cleft has the highest variability.

With so many alleles, most individuals are heterozygous for MHC Class I and MHC Class II genes. However, inbred populations sometimes are homozygous for alleles that encode MHCs able to bind no protein. Although rare, this condition drives home the point that MHC diversity is at the population level, not the individual level (unlike with antibodies and TCRs, whose diversity is generated during hematopoiesis).

Class I genes are expressed co-dominantly. This means that all six alleles (three on each chromosome) are expressed together. As a result, a single cell can have up to six different types of Class I MHCs on its surface. Class II genes are expressed only on proliferating antigen-presenting cells (macrophages, dendritic cells, B cells and activated T cells. Because each class II molecule consists of two proteins encoded by two genes, an individual not only has combinations of individual α and β alleles, but also hybrid Class II MHCs contain maternal and paternal α and β chains (heterozygote complementation).

Major Histocompatiblity Complex Genetics

The major histocompatibility complex is encoded by HLA genes in humans and H-2 genes in mice. HLA and H-2 genes encoding the MHC itself are classical genes; HLA and H-2 genes which do not encode the MHC are non-classical genes). Non-classical genes are described in the table below, with non-classical genes without important immune functions are marked with a degree symbol. Although most non-classical genes have mysterious functions, it is suspected that some have MHC-like function.

Each region is highly polymorphic, meaning that it can have one of many different alleles. There are several common mouse strains, and for the sake of efficiency their haplotypes (their set of K, IA, IE, S and D alleles) have been compressed into shorthand. For example, H-2^k mice have all k alleles, H-2^d mice have all d alleles and H-2^b mice have all b alleles. Mice obviously have two chromosomes, so a H-2^k/k mouse is one whose two chromosomes have both have all k alleles, and a H-2^k/b is a heterozygote with one all-k-allele and one all-b-allele chromosome. Haplotypes are closely linked and new recombinant haplotypes rarely arise. If a patient receives an organ transplant from a donor with a different MHC haplotype (for example, H-2^b/b vs H-2^k/k) then that organ is rejected as non-self; the only exception is if a heterozygote (for example, H-2^b/k) receives an organ homozygous for one of its haplotypes (for example, H-2^b/b or H-2^k/k) because it recognizes that haplotype as self. Also, note that the alleles of individual regions can be described — for example, an H-2^k/b mouse has K^k and K^b regions.

The Class I region is ∼2,000kb long and contains ∼20 genes. In humans, the Class I region is at the telomeric end of the HLA complex. In mice, the Class I region is split in two, with Class II and III genes in the middle. The Class I region contains HLA-A, HLA-B and HLA-B in humans, and H-2K, H-2D and sometimes H-2L in mice. In humans, there is a litany of Class I non-classical proteins: HLA-E, -F and -G; HFE; HLA-J and -X; and MICA, B, C, D and E. In mice, Class I non-classical proteins are encoded in H-2Q, -T and M regions.

Located on the centromeric end of the MHC region, the Class II MHC region is broken into HLA-DR, -DP and -DQ in humans and H-2IA and H-2IE in mice. Each region encodes multiple Class II α and β chains — for example, HLA-DR encodes as many as four functional β chains. The multiple α and β chains combine, thereby increasing the diversity of Class II MHC molecules. There are also several non-classical Class II genes, all of which have limited polymorphism. Examples of murine non-classical Class II genes are Oα, Oβ, Mα and Mβ; and two human non-classical Class II genes have been identified, DM and DO.

Class III genes are located between Class I and Class II genes, and encode a variety of proteins. Although not encoding proteins directly related to the major histocompatibility complex itself, Class III genes are present in all vertebrates. Mutations in Class III genes frequently lead to disease.

Antibody-Dependent Cell Mediated Cytotoxicity (ADCC) is when leukocytes bearing F(c) receptors bind to and destroy antibody-coated cells.

Cells of the innate immune system recognize non-self cells by detecting structures unique to microbial pathogens and not present in mammalian cells. This non-adaptive recognition is performed by cell-surface pattern-recognition receptors. Pattern-recognition receptors detect repetitive pathogen-associated molecular patterns (PAMPs). Common PAMPs include nucleic acids, proteins, lipids and carbohydrates, as shown in the table below.

Pattern-recognition receptors are: encoded by the genome; expressed by all cells of a particular type (as opposed to clonal expansion); immediately responsive once bound to their ligand; and optimized for a broad range of pathogens. The two tables below chronicle the four steps in which pattern-recognition receptors operate, and the different types of pattern-recognition receptors.

The complement cascade (aka complement system or just complement) has seven functions — shown in the table below — all of which are essential to the immune system. Complements consists of three different simultaneous pathways of activating the membrane attack complex: the classical pathway, part of adaptive immunity; and alternative and lectin pathways, part of innate immunity. Three different pathways are involved in complement activation: classical pathway, which is stimulate by antigen-antibody complexes; alternative pathway, which spontaneously activates on contact with pathogenic cell surfaces; and mannose-binding lectin pathway, which recognizes mannose sugars which are usually present only on pathogenic cell surfaces.

Classical Pathway

In the classical pathway of complement, the F(c) of an antigen-antibody complex binds to the C1q component of C1. The F(c) must be immobilized as part of an antigen-antibody complex — an antibody enough is not alone to bind C1q and activate C1q’s two protease components (C1r and C1s). C1q has low affinity for F(c), so multiple F(c)s must be bound to C1q before C1r and C1s are activated. Once these proteases are activated, they cleave C4 and then C2. Two of the cleavage products — C4b and C2a — form a new protease (C3 convertase, aka C4b2a) which cleaves C3 into C3a and C3b. C3 convertase binds to C3b to form a new protease (C5 convertase, aka C4b2a3b) that cleaves C5 into C5a and C5b. C5b is the first protein of the membrane attack complex (MAC).

Because IgM has multiple F(c)s, it is more effective than other antibodies at activating complement. However, IgM must first change its conformation to expose its C1q binding sites. Also, please note that C3a and C5a just float away.

Lectin Pathway

The lectin pathway of complement is identical to the classical pathway, except the lectin pathway begins with mannose-binding protein instead of C1. Mannose-binding protein (aka MBP, mannose-binding lectin or MBL) is a primitive and non-clonal form of humoral immunity (immunity mediated by antibodies). Mannose-binding protein binds carbohydrate antigens frequently found on pathogen cell surfaces, but infrequently expressed by host cells. MBP is structurally similar to C1, with a binding region and two proteases, mannan-binding lectin associated proteases (or MASPs for short). Once MBP binds its carbohydrate antigen, the MASPs are activated to cleave C4 and then C2, with subsequent events identical to the classical pathway.

Alternative Pathway

There are two concepts behind the alternative pathway of complement: what occurs when a non-self cell is absent; and what occurs when a non-self cell is present. When a non-self cell is absent (meaning the tissue is healthy) then there is fluid-phase activation. Fluid-phase activation occurs continuously, spontaneously and very slowly. In fluid-phase activation, C3 spontaneously activates via hydrolysis to form C3_H2O — since it is unstable, C3_H2O usually reverts to C3. However, if C3_H2O encounters Factor B, then the two molecules bind to form a more stable C3_H2OB molecule. Factor D then cleaves C3_H2OB molecule to yield the enzyme C3_H2OBb (aka fluid-phase C3 convertase). C3_H2OBb has an active site on Bb; to culminate fluid-phase activation, this active site cleaves C3 into C3a and C3b. Fluid-phase activation is depicted in the figure to the left.

When a non-self cell is present, then a much faster process occurs. C3b binds to the surface of the non-self cell, then Factor B binds to the C3b. This cell-surface C3b-B complex is cleaved by Factor D to form C3b-Bb, a potent C3 convertase which begins cleaving C3 at an enormous rate to yield lots of C3a and C3b. The C3b eventually smothers the cell-surface, marking it for phagocytosis by macrophages, and granulocytes with C3b receptors. As the concentration of Factor B is depleted, a C3b-Bb begins to bind C3b to form the enzyme C3b-Bb-C3b (C5 convertase). This C5 convertase cleaves C5 into C5a and C5b: as in the classical pathway of complement, C3a and C5a just float away; C5b, already stuck to the cell surface, binds other proteins to form the membrane attack complex.

Membrane Attack Complex

The membrane attack complex (MAC) is an extremely potent agent of cell lysis. After cleavage of C5 into C5a and C5b, C5b binds one molecule each of C6, C7 and C8. After this, C5b binds an additional 6-10 molecules of C9 to form the complete membrane attack complex. The large multi-subunit membrane attack complex inserts into the lipid bilayer, allowing fluid to rush into the cell and kill the cell. Just one membrane attack complex per cell is enough to destroy the cell.

Peptides of Complement

Discovery of Complement

Cell lysis — a function of complement — was identified in the early 1900s as critical to the immune system yet independent of antibodies. An experiment was devised to identify the agents of complement.

Circulating white blood cells are stimulated to cross out of blood circulation (extravasation) by sets of adhesion molecules present on both white blood cells and the vascular endothelium of post-capilarry venules (or PCVs, located downstream of every blood capillary). Extravasation only occurs when adhesion molecules are expressed in both white blood cells and the vascular endothelium. Adhesion molecules on white blood cells are selectins, while adhesion molecules on PCVs are addressins. The table below describes the steps of extravasation to the site of an infection.

Similarly, virgin lymphocytes must extravasate to specific organs to complete their maturation. These lymphocytes express selectin-like molecules specific for addressins presented on PVCs adjacent to the target tissue. For example, virgin T cells migrating from the bone marrow express selectin-like molecules which bind specifically to addressins expressed only at the thymus (but not at lymph nodes or in the bone marrow). Similarly, virgin B cells migrating from the bone marrow express selectin-like molecules specific for addressins only at lymph nodes and the spleen.

The table above lists some addressins, when during an infection they are expressed and their affinity for the selectins they bind.

Bound pathogen is surrounded by a membrane, forming the phagosome which becomes acidified. Lycososomes containing enzymes, proteins and peptides fuse with the phagosome to form the phagolysosome. Upon phagocytosis, macrophages and neutrophils produce toxic products which are directly toxic to bacteria. Pathogenic microbes must either avoid engulfment, grow inside the phagosome (as do mycobacteria) or grow a thick polysaccharide capsule not recognized by any phagocyte receptor.

1. Foreign microbe attaches to pseudopods on the surface of a phagocyte. Pseudopods are long extensions of the cell, like arms.
2. The phagocyte’s cellular membrane engulfs the microbe to forma phagosome organelle which floats into the cytoplasm.
3. The phagosome fuses with a lysosome organelle which contains the toxic chemical and enzymes (such as H₂O₂, O₂^- and NO).
4. Lysosomal contents digest the captured microbe; the phagolysosome refuses with the phagocyte cellular membrane to release its contents into surrounding tissue.

Type 1: Allergy

Type I hypersensitivity (most commonly allergies) stem from overproduction of IgE. Thus, it requires an initial encounter so that isotype switching can occur — in secondary responses, the IgE crosslinks the antigen (and F(c)εRI and causes mast-cell and basophil degranulation. Atopic allergies and asthmatics are becoming more common in economically developed nations due to changes in exposure to childhood infectious disease (atopy is negatively associated with measles, hepatitis A or tuberculosis infections), environmental pollution (diesel exhaust enhances T_H2 responses, leading to higher IgE production), allergen levels (crazy cat ladies) and dietary changes.

IL-4 is pivotal in regulating the IgE response: IgG1 and IgE account ∼2% of all antibodies secreted by splenic B cells incubated with LPS; IgG1 accounts for ∼50% and IgE accounts for ∼20% of all antibodies secreted by B cells incubated with LPS and IL-4. IL-4 knockout mice cannot mount an IgE response to parasites. IL-4 stimulates isotype switching by activating the promoters for Iε, and Iγ1 (the I regions for ε and γ1 isotype genes). T_H1 cells enhance response to IL-3, IL-4 and IL-10. T_H2 cells reduce response to IFN-γ.

Type 4: Delayed-Type Hypersensitivity

Delayed-type hypersensitivity (DTH) is a T_H1-mediated localized inflammatory reaction that effectively clears intracellular pathogens (such as viruses) and contact allergens (such as poison oak and poison ivy). DTH is characterized by large influxes of inflammatory cells (like mφs), tissue damage and delayed onset. DTH reactions functional antibodies and a functional complement system; it cannot occur without B1 cells nor C5. There are two phases related to delayed-type hypersensitivity:

Contact allergens (such as poison oak) are usually small molecules which complex with skin proteins; these complexes are internalized by Langerhans cells (APCs found in skin) and then presented to T_H cells. Also, when DTH is continuously activated, normal tissue is damaged due to a continuous assault of lytic enzymes. This can occur in the lungs of Mycobacterium tuberculosis patients, as well as lesions in Mycobacterium leprae patients.