Biochemical studies of MHC molecules culminated in the solution of the crystal structures for the extracellular portions of human MHC-I and MHC-II molecules. Subsequently, many MHC molecules with bound peptides have been crystallized and analyzed in detail. Because of these advances, we now understand how MHC molecules bind and display peptides. In this section, we first summarize the functionally important biochemical features that are common to MHC-I and MHC-II molecules. We then describe the structures of class I and class II proteins, pointing out their main similarities and differences (Table 1).
Table1. Features of Major Histocompatibility Complex (MHC) Class I and Class II Molecules
General Properties of MHC Molecules
All MHC molecules share certain structural characteristics that are critical for their role in peptide display and antigen recognition by T lymphocytes.
• Each MHC molecule consists of an extracellular peptide binding cleft, an immunoglobulin (Ig)-like domain, and transmembrane and cytoplasmic domains. MHC-I molecules are composed of one polypeptide chain encoded in the MHC and a second, non–MHC-encoded chain, whereas MHC-II molecules are made up of two MHC-encoded poly peptide chains. Despite this difference, the overall three dimensional structures of class I and class II molecules are similar.
• The polymorphic amino acid residues of MHC molecules are located in and adjacent to the peptide-binding cleft. This cleft (also called a groove) is formed by the folding of the amino termini of the MHC-encoded proteins and is composed of paired α helices forming the two walls of the cleft, and a floor made up of an eight-stranded β-pleated sheet. The polymorphic residues, which are the amino acids that vary among different MHC alleles, are located in the floor and walls of this cleft. This portion of the MHC molecule binds peptides for display to T cells, and the antigen receptors of T cells interact with the displayed peptide and also with the α helices of the MHC molecules (see Fig. 1). Because of amino acid variability in this region, different MHC molecules bind and display different peptides and are recognized by the antigen receptors of different T cells.
• The nonpolymorphic Ig-like domains of MHC-II and MHC-I molecules contain binding sites for the T-cell molecules CD4 and CD8, respectively. CD4 and CD8 are expressed on distinct classes of mature T lymphocytes and participate, together with antigen receptors, in responses to peptide-MHC complexes. For this reason, CD4 and CD8 are called T-cell coreceptors. CD4 binds selectively to MHC-II molecules, and CD8 binds to MHC-I molecules. Therefore, CD4+ helper T cells recognize MHC-II molecules displaying peptides, whereas CD8+ T cells recognize MHC-I molecules with bound peptides. Stated differently, CD4+ T cells are MHC-II restricted and CD8+ T cells are MHC-I restricted.
Fig1. A model for T-cell recognition of a peptide-major histocompatibility complex (MHC). This illustration shows an MHC molecule binding and displaying a peptide and a T-cell receptor recognizing the complex of peptide and MHC molecule. As discussed later in the text, MHC-associated peptides contain some residues that anchor them into pockets in the cleft of the MHC molecule and other residues that are recognized by T-cell antigen receptors. MHC residues that may vary among individuals (polymorphic residues) are also recognized by the T-cell receptor. Thus, T cells simultaneously see both peptide antigens and the MHC molecules that present the antigens.
MHC Class I Molecules
MHC-I molecules consist of two noncovalently linked polypeptide chains, an MHC-encoded 44- to 47-kD α chain (or heavy chain) and a non–MHC-encoded 12-kD subunit called β2 microglobulin (Fig. 2). About three-quarters of the α chain polypeptide is extracellular; a short hydrophobic segment spans the plasma membrane, and the carboxy-terminal residues are located in the cytoplasm. The amino-terminal α1 and α2 segments of the α chain, each approximately 90 residues long, interact to form a platform of an eight-stranded, antiparallel β-pleated sheet supporting two parallel strands of α helix. This forms the peptide-binding cleft of MHC-I molecules. Its size is large enough (∼25 × 10 × 11 Å) to bind peptides usually of 8 to 11 amino acids in a flexible, extended conformation. The ends of the class I peptide–binding cleft are closed so that larger pep tides cannot be accommodated. Therefore, native globular proteins have to be converted into fragments that are small enough and in an extended linear shape so they can bind to MHC molecules and be recognized by T cells. The polymorphic residues of MHC-I molecules are confined to the α1 and α2 domains, where they contribute to variations among different class I alleles in peptide binding and T-cell recognition (Fig. 3). The α3 segment of the α chain folds into an Ig domain whose amino acid sequence is conserved among all MHC-I molecules. This segment contains most of the binding site for CD8, but β2-microglobulin and a small part of the non polymorphic C-terminal portion of the α2 domain also contribute. At the carboxy-terminal end of the α3 segment is a stretch of approximately 25 hydrophobic amino acids that traverses the lipid bilayer of the plasma membrane. Immediately after this are approximately 30 residues located in the cytoplasm, which include a cluster of basic amino acids that interact with phospholipid head groups of the inner leaflet of the lipid bilayer and anchor the MHC molecule in the plasma membrane.
Fig2. Structure of a major histocompatibility complex (MHC) class I molecule. The schematic diagram (left) illustrates the different regions of the MHC molecule (not drawn to scale). MHC-I molecules are composed of a polymorphic α chain noncovalently attached to the nonpolymorphic β2-microglobulin (β2m). The α chain is glycosylated; carbohydrate residues are not shown. The ribbon diagram (right) shows the structure of the extracellular portion of the HLA-B27 molecule with a bound peptide, resolved by x-ray crystallography. HLA, Human leukocyte antigen; Ig, immunoglobulin. (Courtesy Dr. P. Bjorkman, California Institute of Technology, Pasadena, CA.)
Fig3. Polymorphic residues of major histocompatibility complex (MHC) molecules. The polymorphic residues of MHC class I and class II molecules are located in the peptide-binding clefts and the α helices around the clefts. The regions of greatest variability among different human leukocyte antigens (HLAs) alleles are indicated in red, of intermediate variability in green, and of the lowest variability in blue. (From Margulies DH, Natarajan K, Rossjohn J, McCluskey J. Major histocompatibility complex [MHC] molecules: structure, function, and genetics. In: Paul WE, ed. Fundamental Immunology. 6th ed. Lippincott Williams & Wilkins; 2008.)
β2-Microglobulin, the light chain of MHC-I molecules, is encoded by a gene outside the MHC and is named for its electrophoretic mobility (β2), small size (micro), and solubility (globulin). It interacts noncovalently with the α3 domain of the α chain. Like the α3 segment, β2-microglobulin is structurally homologous to an Ig domain and is invariant among all MHC-I molecules. β2-microglobulin is also associated with several other proteins that are homologous to the MHC-I α chain but have different functions in the immune system, such as the neo natal Fc receptor.
The fully assembled MHC-I molecule is a trimeric complex consisting of an α chain, β2-microglobulin, and bound pep tide, and stable expression of MHC-I molecules on cell surfaces requires the presence of all three components of the complex.
The reason for this is that the interaction of the α chain with β2-microglobulin is stabilized by binding of peptide antigens to the cleft formed by the α1 and α2 segments, and, conversely, the binding of peptide is strengthened by the interaction of β2 microglobulin with the α chain. Because peptides are needed to stabilize the MHC molecules and unstable complexes are degraded, only potentially useful peptide-loaded MHC molecules are expressed on cell surfaces.
Most individuals are heterozygous for MHC genes and therefore express six different MHC-I molecules on every cell, containing α chains encoded by the two inherited alleles of HLA-A, B, and C genes.
MHC Class II Molecules
MHC-II molecules are composed of two noncovalently associated polypeptide chains, a 32- to 34-kD α chain, and a 29- to 32-kD β chain (Fig. 4). Unlike MHC-I molecules, the genes encoding both chains of MHC-II molecules are polymorphic and located in the MHC locus.
Fig4. Structure of a major histocompatibility complex (MHC) class II molecule. The schematic diagram (left) illustrates the different regions of the MHC molecule (not drawn to scale). MHC-II molecules are composed of a polymorphic α chain noncovalently attached to a polymorphic β chain. Both chains are glycosylated; carbohydrate residues are not shown. The ribbon diagram (right) shows the structure of the extracellular portion of the HLA-DR1 molecule with a bound pep tide, resolved by x-ray crystallography. HLA, Human leukocyte antigen; Ig, immunoglobulin. (Courtesy Dr. P. Bjorkman, California Institute of Technology, Pasadena, CA.)
The amino-terminal α1 and β1 segments of the MHC-II chains interact to form the peptide-binding cleft, which is structurally similar to the cleft of MHC-I molecules. Four strands of the floor of the cleft and one of the α-helical walls are formed by the α1 segment, and the other four strands of the floor and the second wall are formed by the β1 segment. The polymorphic residues are located in the α1 and β1 segments, in and around the peptide-binding cleft, as in MHC-I molecules (see Fig. 3). In human MHC-II molecules, most of the polymorphism is in the β chain. The ends of the peptide-binding cleft of MHC-II molecules are open, so peptides of 13 to over 25 residues can bind.
The α2 and β2 segments of MHC-II molecules, like MHC-I α3 and β2-microglobulin, are folded into Ig domains and are nonpolymorphic; that is, they do not vary among alleles of a particular class II gene. Both the α2 and β2 domains of MHC-II molecules contribute to a concavity that accommodates a protrusion of the CD4 protein, thus allowing binding to occur. The carboxy-terminal ends of the α2 and β2 segments continue into short connecting regions followed by approximately 25 amino acid stretches of hydrophobic transmembrane residues. In both chains, the transmembrane regions end with clusters of basic amino acid residues, followed by short hydrophilic cytoplasmic tails.
The fully assembled MHC-II molecule is a trimer consisting of one α chain, one β chain, and a bound antigenic peptide, and stable expression of MHC-II molecules on cell surfaces requires the presence of all three components of the complex. As in MHC-I molecules, this ensures that the MHC-II molecules that end up on the cell surface are the molecules that are carrying out their normal function of peptide display.
Humans inherit, from each parent, separate genes encoding the α and β chains of DP and DQ, the gene for DRα, and variable numbers of genes encoding DRβ (typically 1–3). Because of this variation and because the α chain from one chromosome may pair with the β chain derived from the other chromosome, the number of MHC-II molecules expressed is usually 6 to 8, but can be up to 12.
