After the demonstration that the immunogenicity of proteins depends on the ability of their peptides to be displayed by MHC molecules, considerable effort has been devoted to elucidating the molecular basis of peptide-MHC interactions and the characteristics of peptides that allow them to bind to MHC molecules. These studies initially relied on functional assays of helper T cells and CTLs responding to APCs that were incubated with different peptides. Direct binding of MHC molecules and peptides has been studied with purified MHC molecules and radioactively or fluorescently labeled peptides in solution, using methods such as equilibrium dialysis and gel filtration. X-ray crystallographic analysis of peptide-MHC complexes has provided definitive information about how peptides sit in the clefts of MHC molecules and about the residues of each that participate in this binding. This information has been used to generate computer algorithms that can predict peptides of any given protein that are most likely to bind to MHC molecules. This information can be used to develop vaccines specific for microbial proteins or mutated tumor proteins (see Chapter 18). In the section that follows, we summarize the key features of the interactions between peptides and MHC-I or MHC-II molecules.
Characteristics of Peptide–MHC Molecule Interactions
MHC molecules show a broad specificity for peptide binding, in contrast to the fine specificity of antigen recognition by the antigen receptors of lymphocytes. In other words, a single MHC allele (e.g., HLA-A2) can present any one of many different peptides to T cells, but a single T cell will recognize only one of these many possible HLA-A2–peptide complexes. There are several important features of the interactions of MHC molecules and antigenic peptides.
• Each MHC-I and MHC-II molecule has a single peptide binding cleft that binds one peptide at a time, but each MHC molecule can bind many different peptides. One of the earliest lines of evidence supporting this conclusion was the experimental result that different peptides that bind to the same MHC molecule can competitively inhibit one another’s presentation, implying that there is only a single peptide-binding cleft in every MHC molecule. The solution of the crystal structures of MHC-I and MHC-II molecules confirmed the presence of a single peptide-binding cleft in these molecules (see Fig1. and 2). It is not surprising that a single MHC molecule can bind multiple peptides because each individual contains only a few different MHC molecules (six class I and a few more class II molecules in a heterozygous individual), and these must be able to present peptides from the enormous number of protein antigens that one is likely to encounter.
Fig1. 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.)
Fig2. 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 peptides that bind to MHC molecules share structural features that promote this interaction. One of these features is the size of the peptide—MHC-I molecules can accommodate peptides that are 8 to 11 residues long, and MHC-II molecules bind peptides that may be 13 to 25 residues long or even longer, the optimal length for fitting into the MHC-II cleft being 12 to 16 residues. In addition, peptides that bind to a particular MHC molecule contain amino acid residues that allow complementary interactions between the peptide and that MHC molecule. Some of the amino acid residues that promote binding to MHC molecules are described later, when we discuss the structural basis of peptide-MHC inter actions. The residues of a peptide that bind to MHC molecules are distinct from those that are recognized by T cells.
• MHC molecules acquire their peptide cargo during their biosynthesis and assembly inside cells. Therefore, MHC molecules display peptides derived from microbial antigens that are inside host cells, and this is why MHC-restricted T cells are able to recognize microbes that infect or are ingested into cells. The mechanisms and significance of these processes are discussed later in this chapter.
• The association of peptides and MHC molecules is a saturable interaction with a slow off-rate. In a cell, several chaperones and enzymes facilitate the binding of peptides to MHC molecules. Once formed, most peptide MHC complexes are stable, and kinetic dissociation constants are indicative of long half-lives that range from hours to many days. This slow off-rate of peptide dissociation from MHC molecules ensures that after an MHC molecule has acquired a peptide, it will display the peptide long enough to maximize the chance that a particular T cell will find the peptide it can recognize and initiate a response.
• Very small numbers of peptide-MHC complexes are capable of activating specific T lymphocytes. Because APCs continuously present peptides derived from all the proteins they encounter, only a very small fraction of cell surface peptide MHC complexes will contain the same peptide. It has been estimated that as few as 100 complexes of a particular pep tide with an MHC-II molecule on the surface of an APC can initiate a specific T-cell response. This represents less than 0.1% of the total number of class II molecules likely to be present on the surface of the APC.
• The MHC molecules of an individual can bind and dis play foreign peptides (e.g., those derived from microbial proteins) and peptides derived from the proteins of that individual (self antigens). In fact, most of the peptides being displayed normally by APCs are derived from self proteins. The inability of MHC molecules to discriminate between self and foreign peptides raises the question of why we normally do not develop autoimmune responses against self proteins. The answer is that T cells specific for self peptide-MHC complexes are killed or inactivated. In fact, T cells with receptors for self antigens must recognize self peptides displayed by self MHC molecules in order to be eliminated or made unresponsive. These processes ensure that T cells are normally tolerant to self antigens.
Structural Basis of Peptide Binding to MHC Molecules The binding of peptides to MHC molecules is a noncovalent interaction mediated by residues both in the peptides and in the clefts of the MHC molecules. As we will discuss later, pro tein antigens are proteolytically cleaved in APCs to generate the peptides that will be bound and displayed by MHC molecules. These peptides bind to the clefts of MHC molecules in an extended conformation. Once bound, the peptides and their associated water molecules fill the clefts, making extensive contacts with the amino acid residues that form the β strands of the floor and the α helices of the walls of the cleft (Fig. 3).
Fig3. Peptide binding to major histocompatibility complex (MHC) molecules. (A) These top views of the crystal structures of MHC molecules show how peptides lie in the peptide-binding clefts. The MHC-I molecule shown is HLA-A2, and the MHC-II molecule is HLA-DR1. (B) The side view of a cutout of a peptide bound to an MHC-II molecule shows how anchor residues of the peptide hold it in the pockets in the cleft of the MHC molecule. HLA, Human leukocyte antigen. (A, Courtesy Dr. P. Bjorkman, California Institute of Technology, Pasadena. B, From Scott CA, Peterson PA, Teyton L, Wilson IA. Crystal structures of two I-Ad–peptide complexes reveal that high affinity can be achieved without large anchor residues. Immunity. 1998;8:319–329.)
In most MHC molecules, the β strands in the floor of the cleft contain pockets where side chains of amino acid residues of peptides bind. Many MHC-I molecules have a hydrophobic pocket that recognizes one of the following hydrophobic amino acids—valine, isoleucine, leucine, or methionine—at the C-terminal end of the peptide. Some MHC-I molecules have a predilection for peptides with a basic residue (lysine or arginine) at the C terminus. In addition, other amino acid residues of a peptide may contain side chains that fit into specific pockets and bind to complementary amino acids in the MHC molecule through electrostatic interactions (salt bridges), hydrogen bonding, or van der Waals interactions. The residues of the peptide that fit into the MHC pockets are called anchor residues because they contribute most to the binding—or anchoring—of the peptide in the cleft of the MHC molecule. Each MHC-binding peptide usually contains only one or two anchor residues, and this presumably allows greater variability in the other residues of the pep tide, which are the residues that are recognized by specific T cells. In the case of some peptides binding to MHC molecules, especially MHC-II molecules, specific interactions of peptides with the α-helical sides of the MHC cleft also contribute to peptide binding by forming hydrogen bonds or charge interactions.
Because many of the residues in and around the peptide binding cleft of MHC molecules are polymorphic (i.e., they differ among various MHC alleles), different alleles permit the binding of different peptides. This is the structural basis for the function of MHC genes as immune response genes; only individuals whose MHC molecules can bind a particular peptide and display it to T cells can respond to that peptide.
The antigen receptors of T cells recognize both the anti genic peptides and the MHC molecules, with the peptide being responsible for the fine specificity of antigen recognition and the MHC residues accounting for the MHC restriction of the T cells. A portion of the bound peptide is exposed from the open top of the cleft of the MHC molecule, and the amino acid side chains of this portion of the peptide are recognized by the antigen receptors of specific T cells. The same T-cell receptor also interacts with polymorphic residues of the α helices of the MHC molecule itself. Predictably, variations in either the peptide antigen or the peptide-binding cleft of the MHC molecule will alter the presentation of that peptide or its recognition by T cells.
Because MHC molecules can bind only short linear peptides but microbial and other protein antigens are large molecules made up of long polypeptides in various folded conformations, there must be a mechanism by which these proteins are converted into peptides that can bind to MHC molecules.
