Antigen Presentation to T Cells

What is the key difference bw CD4 and CD8 T cells? Explain the utility of this

CD8 respond to intracellular infections, CD4 to extracellular The expression of MHC class I versus class II molecules on tissue cells is reflective of this divergence in function. During an extracellular infection, a tissue becomes infected by a pathogen, but not the individual cells in the tissue. As a result, CD4 T cells do not need to scan for extracellular-derived pathogen antigens on every cell in the body. Consistent with this, MHC class II molecules are constitutively expressed by only three types of cell: dendritic cells, macrophages, and B cells. These three cell types, which evolved to be adept and specialized in presenting antigens to CD4 T cells, are known as professional antigenpresenting cells. They also are highly phagocytic and have the primary function of engulfing and killing extracellular pathogens. The relative expression levels of MHC class I and class II molecules on a few representative human cell types are presented in Table 1. (Page 9).

Describe the concept of anchor amino acids

Figure 18B presents two sets of peptides eluted from different MHC class I alleles. Two amino acid positions are "anchor" amino acids in each allelic set (shown in green circles). One of these anchor positions is the carboxyl terminal amino acid position. As shown, all of the peptides in each allele set have hydrophobic side chains (valine, isoleucine, or leucine) at the carboxy terminal position. (Page 17). As discussed above, this reflects the TAP transport's specificity for a carboxy terminal amino acid that is either hydrophobic or basic for transfer into the ER, based on the compatibility of such peptides for binding with an MHC class I molecule (see discussion around Figure 8, above). The positions of so-called "anchor" amino acids in the peptides are also quite distinct between the two allelic MHC class I peptide sets shown in Figure 18B. One allele binds peptides that have anchor locations at amino acid 5 and 8 from the amino terminus, and the other allele binds peptides that have anchor amino acids at positions 2 and 9. Anchor amino acids are the portions of the peptide that are tightly bound by "pockets" or depressions in the beta pleated sheet "floor" of the binding site. The anchor amino acids are typically hydrophobic and 3D structural analyses of the MHC-peptide complex have determined that these positions typically involve the extension of a hydrophobic amino acid side chain into a highly hydrophobic depression in the MHC class I structure. These anchor amino acids are thought to be the primary binding elements for peptides in each MHC class I molecule. Figure 18C provides a side-by-side comparison of the peptides that are bound by two different alleles of MHC class I in the mouse. The top space filling model of two peptides bound by the individual alleles reveals how different the spacing and orientation of anchor "pockets" can be between two allelic forms of an MHC class I molecule. (Page 18).

Description of how the peptides bound by MHC class II differs from that of MHC class I

Figure 19 presents a collection of peptides eluted from a single MHC class II allele together with a ribbon model of the MHC class II binding site containing a bound peptide. The data clearly illustrate that the peptides bound by MHC class II molecules are quite distinct from those bound by class I molecules. (Page 18). Figure 19A presents a ribbon model of the MHC class II peptide binding site containing a peptide. As shown, the peptide extends out the open ends on both sides of the binding site, which is quite different from the MHC class I model shown in Figure 18. This illustrates the manner in which MHC class II molecules bind peptides. As discussed above, the peptides bound by MHC class II can vary in length from as short as 10 to more than 24 amino acids in length. This length variation is clear in the set of peptides derived from a single MHC class II allele that are shown in Figure 19B. Note that the peptides in this array vary in length from 12 to 22 and that the location of the 4 anchor amino acids are not at a fixed distance from either end of the peptide. Instead, they are spaced at fixed distances from each other and the length of peptide extending out either side varies. Further, the anchor amino acids, although consistently within a single chemical type of side chain, are more variable then anchor amino acids in MHC class I peptides. Overall, the peptides loaded into MHC class II molecules are much more variable than those in MHC class I. (Page 19).

Describe the mechanisms of alloreactivity

Figure 20 provides schematic models that illustrate the underlying issues that lead to the alloresponse. Three different pathways to alloreactivity are presented in Figure 20B. First, the cells in the grafted tissue will be displaying peptides derived from the donor cell cytoplasm on the donor's HLA class I molecules. Similarly, any professional APC that were included in the grafted tissue (often called "passenger leukocytes") will be presenting peptides from the donor and from the recipient on HLA class II molecules of the donor. As shown in Fig. 20B left, this results in interactions between the recipient's T cell compartment and APC from the donor expressing HLA class I and class II molecules and peptides that are different from those of the recipient. This mismatch between the HLA molecules of the tissue donor and the HLA molecules used to tolerize the recipients T cell compartment during thymic differentiation is the root cause of a massive alloreactivity. As shown, two other pathways also contribute to the alloresponse, which are recipient APC presenting donor-derived peptides and recipient APC presenting donor peptides displayed on donor HLA molecules. (Page 20).

What are the 6 MHC class I isotypes? What is the function of each?

HLA-A - HLA-C: to present pathogen-derived peptide antigens to CD8 T cells HLA-E - HLA-G: ligands for NK cell inhibitory receptors

Description of the two topological compartments of human cells and their significance in bacterial and viral infection

Human cells consist of two topological compartments defined by their cellular membranes. One compartment comprises the nucleus and the cytosol (also called cytoplasm), which are connected by nuclear pores. The other compartment, called the vesicular system, is contiguous with the outside of the cell and comprises the endoplasmic reticulum, the Golgi apparatus, the lysosomes, and a variety of smaller endocytic and exocytic vesicles. Both cellular compartments are subject to infection, but by different types of pathogens. Viruses usually exploit the cytoplasm, whereas bacteria exploit the vesicular system. The evolution of two types of MHC molecule was probably driven by the need to provide immune defense against infections in these two cellular compartments. Thus, MHC class I protects the nucleus and the cytoplasm against intracellular infection, while MHC class II protects the vesicular system against extracellular infection. (Page 5).

Summary statement of alloreactivity

In summary, alloreactivity is a massive activation of the T cell compartment due to the extensive allelic variability of HLA class I and class II molecules. Clinically, alloreactivity impedes the general use of transplantation and necessitates the use of strong immunosuppressants in recipients of mismatched tissue grafts. Although the use of family members as graft donors can allow a complete match of HLA alleles and typically avoid an acute rejection, the presentation of divergent donor proteins by recipient HLA (middle model of Fig. 20B) will still commonly result in the activation of a much smaller set of recipient T cells that can cause graft rejection over time. Clearly, the recognition of foreign antigen by T cells, although good for fighting pathogens, is a major clinical issue in transplantation! (Page 20).

Generally describe the antigen presentation pathway of MHC class II

Like MHC class I heavy chains and β2-microglobulin, MHC class II α and β chains are synthesized on membrane-associated ribosomes and translocated into the endoplasmic reticulum. In the endoplasmic reticulum, the class II α and β chains assemble with a chaperone protein that prevents them from binding a peptide. These heterotrimers move through the Golgi apparatus to a site of intersection between the exocytic and endocytic pathways of membrane transport (Figure 10) This compartment is rich in peptides, because of the degradation of extracellular proteins brought into the cell by endocytosis or phagocytosis. In this environment, the chaperone allows peptides to bind to MHC class II and then move to the cell surface to interact with CD4 T-cell receptors. In the absence of infection, the peptides bound by MHC class II derive from self proteins. In the presence of infection, some MHC class II molecules will bind peptides derived from extracellular pathogens (such as bacteria) that were phagocytosed by the cells. Circulating CD4 T cells ignore the presentation of selfpeptides by MHC class II but respond to the presentation of pathogen-derived peptides. One form of response is the secretion of cytokines that activate macrophages, improving their phagocytosis and recruitment of other effector cells. (Page 10).

Generally describe the human MHC/HLA region

MHC class I and class II molecules together with several other proteins involved in antigen processing and presentation (such as TAP, tapasin, and immunoproteasome components) are encoded in a cluster of genes located on human chromosome 6. (Page 14).

Describe MHC class II molecules

MHC class II molecules are expressed on antigen presenting cells in the immune system and present antigen to the CD4 T cell compartment. MHC class II molecules are composed of two polypeptide chains, termed alpha and beta, both encoded in the MHC complex on human chromosome 6. When assembled with peptide, they form a heterodimer on the cell surface. Each MHC class II chain has two structural domains (Fig. 4B right) and the α1 and β1 domains form the peptide binding site. The β2 domain of the beta chain contains the binding site for the CD4 co-receptor. (Page 4).

How is the presentation of MHC class II molecules on activated dendritic cells extended?

Peptides-MHC class II complexes are continuously recycled from the surface and degraded in APC by ubiquitination. As shown in Figure 13, an E3 ligase named membrane associated ring finger (C3HC4) 1 or MARCH-1, is responsible for the ubiquitination of MHC class II.

Describe the allelic diversity of HLA class I and II genes

Polymorphisms of the HLA class I (HLA-A, - B, and -C) and class II (HLA-DR, -DQ, -DP) genes have been extensively characterized for decades due to the role they play in transplantation compatibility. Decades of study have found that these are the most polymorphic genes in the human genome. The current number of alleles (allotypes) based only on variations in the protein coding regions for all the expressed HLA class I and class II loci are presented in Figure 16. More recently, genetic analyses based on extensive DNA sequencing studies are providing data indicating that regulatory regions that control the expression of the HLA class I and class II genes are also highly diversified and that this diversity leads to allelic variations in expression levels of several HLA Class I and Class II genes. Several features of these data are remarkable. First, the number of allelic forms of these genes is unparalleled in the human genome. Further, many of these alleles have highly divergent sequences and encode peptide binding sites with very different structures. This reflects the ancient origins of several allelic lineages of the HLA Class I and Class II genes in human populations. With respect to the HLA class II genes, the B genes (encoding the class II β chain) are highly polymorphic, while the A genes (α chain) are not. Interestingly, the HLA-E, -F, and -G genes, which encode class I molecules that serve as ligands for the NK cell inhibitory receptors, are much less polymorphic than the HLA-A, -B, -C genes which are responsible for antigen presentation. Similarly, the HLA class II DM and DO genes, which participate in peptide loading (see Figure 11B), also have limited diversity. This result suggests that diversity is specifically focused on HLA genes that are directly responsible for presenting antigenic peptides to T cells. (Page 15).

Specifically describe the HLA-DR gene

The HLA class II genes have continued to evolve by gene duplications and the number of expressed HLA class II genes varies within the human population. As shown in Figure 15 for the HLADR gene, a single HLA-DRA gene (encodes the α chain) is accompanied by a variable number of functional and nonfunctional HLA-DRB genes (encodes the β chain). Of the four functional HLADRB genes—DRB1, DRB3, DRB4, and DRB5—only DRB1 is present on every chromosome 6 (Figure 15). (Page 15).

Describe MHC class I molecules

The MHC class I molecules (Fig. 4A and B, left side) are expressed on all nucleated cells in the body and present antigens to CD8 T cells. MHC class I molecules consist of two polypeptide chains, the alpha chain, which is encoded in the MHC complex on human chromosome 6 and the β2 microglobulin chain, which is encoded outside the MHC on human chromosome 15. As labeled in Figure 4B, the alpha chain has a three-domain structure in which the α1 and α2 domains encode the peptide binding site of the MHC class I molecule, while the membrane proximal α3 domain is associated with β2 microglobulin and forms the binding site for the CD8 co-receptor molecule. (Page 4).

Description of T cells binding to antigen

The antigens that T cells bind and the way they bind to them is completely different than B cells. As shown in Figure 1B(right), the T cell receptor for antigen binds to a short, linear peptide antigen that is embedded in a second molecule, which is a molecule encoded in the major histocompatibility complex (MHC). The function of antigen presenting MHC molecules is to bind selected, short, peptides and display them on the cell surface. The picture in Fig. 1B(left) depicts the binding of a T cell receptor on the surface of a T cell to antigen being presented by an MHC molecule on the surface of an antigen presenting cell. Thus, this binding occurs between two cells in close proximity and essentially results in their adhesion, at least transiently, depending on the affinity of the TCR antigen receptor for the presented peptide-MHC complex. If the binding strength is sufficient to form a stable adhesion, then an activation synapse may form around the TCR-peptideMHC binding triad. This is the first step in the process of T cell activation. (Page 2).

Describe the specific function of tapasin

The chaperone protein tapasin plays a key role in regulating the loading of peptides into MHC class I molecules. Unlike calnexin, calreticulin, and ERp57, which chaperone a range of different proteins, tapasin is dedicated to the assembly of MHC class I molecules and is encoded in the MHC. Tapasin has two extracellular domains, one binds to the α2 domain of MHC class I and the other binds to the α3 domain. The interaction of tapasin with the α2 domain of an empty MHC class I molecule causes a conformational change in the amino-terminal part of the α2 helix and a widening of the peptide-binding groove. This is schematically diagramed in Figure 9. (Page 8). The wider groove is more accessible to peptides and has the overall effect of reducing the affinity of all peptides for MHC class I. This creates a dynamic situation in which most peptides that bind to MHC class I are quickly released. Thus many different peptides can be tested for their strength of binding. When a peptide binds with high affinity, a conformational change is induced that narrows the groove and reduces the affinity of the interaction between tapasin and MHC class I. This causes tapasin to dissociate from MHC class I, which releases it from the peptide-loading complex. In this way, the affinity of tapasin for MHC class I sets the bar that a peptide's affinity must exceed before it can be loaded by MHC class I. This function of tapasin, in which one peptide is selected from many that were tested, is called peptide editing. (Page 8).

Part III of peptide loading by MHC class II

The endosomes contain cathepsin S and other proteases that selectively degrade the invariant chain. This degradation leaves a 24-residue fragment called the class II-associated invariant-chain peptide (CLIP) that fills the MHC class II groove (Figure 11B). Replacement of CLIP by another peptide is achieved by an editing process like that used by tapasin to load peptides onto MHC class I (see Figure 9). The peptide editor for MHC class II is DM, a form of MHC class II molecule that lacks a peptidebinding groove, is absent from the cell surface, and is concentrated in the MIIC. Whereas tapasin binds MHC class I to widen the binding groove in the region around the carboxy terminus of the bound peptide, DM binding to MHC class II opens up the part of the binding site around the amino-terminal residue of CLIP, facilitating dissociation of CLIP. While remaining bound to DM, the MHC class II molecule samples a succession of peptides until one binds with sufficient affinity to induce the conformational change that closes the groove and causes DM to dissociate. Once loaded with peptide, MHC class II molecules are delivered to the plasma membrane (Figure 11B). (Page 12).

Summary statement for this section

The major histocompatibility complex (MHC) encodes many genes that impact the functional properties of the immune system. Among them, the genes encoding the MHC class I and class II molecules function to select and present antigens to the T lymphocyte lineage. MHC class I molecules present antigen to CD8+ T cells, which differentiate into cytotoxic T lymphocytes (CTLs) with the effector function of lysing abnormal or virally infected cells. MHC class II molecules present antigen to CD4+ T cells, which differentiate into T helper cells with the effector function of regulating the activation of the B cell compartment and secreting cytokines to amplify or suppress ongoing adaptive immune responses. MHC class I molecules predominantly present antigens derived from the cytoplasm and MHC class II molecules present antigens derived from endosomal vesicles. MHC class I molecules can also present antigens derived from endosomal vesicles using the "cross" presentation pathway. The pathways by which MHC class I and class II molecules are loaded with peptides are different and involve interactions with several unique chaperone proteins and ancillary molecules. MHC genes are highly polymorphic, and the diversity is localized predominantly to the peptide binding regions of MHC class I and class II. The functional consequences of this diversity are that individual alleles of MHC class I and class II molecules bind and present very different peptides to T cells. As a result, MHC incompatibility of a donor-recipient transplantation combinations results in a potent activation of the recipient's T cells due to extensive changes in the peptide-MHC complexes displayed on the graft tissue. (Page 1).

Describe the process of peptide processing and loading for MHC class I

The principal source of peptides for MHC class I molecules is the cytoplasm. Proteins in the cytosol that are damaged, misfolded, or no longer needed are marked for destruction by covalent attachment of multiple copies of the protein ubiquitin. These ubiquitinated proteins are digested by proteasomes, which are large, barrelshaped protein complexes that make up 1% of all cellular protein. The peptides produced are actively transported into the endoplasmic reticulum by a specialized transport system encoded by the TAP1 and TAP2 genes, which are located within the MHC. Peptides that have the right length and sequence are loaded into MHC class I molecules by a specialized complex of protein chaperones and ancillary molecules. These peptide-MHC class I complexes then move through the Golgi apparatus to the plasma membrane. (Page 6).

Describe the alloimmune response

When a tissue donor- recipient pair have different HLA class I and class II alleles (almost always the case when genetically unrelated, see Figure 16), then the T cells of the recipient were found to be massively activated against the tissues of the graft, typically resulting in antigen-driven activation of 1% -10% of the recipient's T cells. This massive response is called an alloimmune response and was shown experimentally to be due to an allelic mismatch of HLA genes between the donor and the recipient. (Page 19).

Generally describe the MHC class II region What are the 5 MHC class II isotypes? What does each encode?

a segment containing one alpha-chain gene (called A) and one beta-chain gene (called by) that has undergone successive duplications to give rise to 5 expressed genes HLA-DR HLA-DQ HLA-DP these all encode for the MHC class II molecules that present antigen to CD4 T cells HLA-DM HLA-DO these participate in peptide editing during peptide loading The HLA complex contains more than 200 genes, many of which are important for the immune system. Notably, the HLA class II region is largely dedicated to genes encoding proteins involved in the processing of antigens and their presentation to T cells (Figure 14B). In addition to genes encoding the α and β chains of the five HLA class II isotypes, the class II region contains genes encoding the two polypeptides of the TAP peptide transporter, the tapasin gene, and genes encoding two of the three proteolytic subunits, β1i and β5i, that are specific to the immunoproteasome (Figure 14B). (Page 15).

Why are APCs often unable to process cytosolic proteins from viral pathogens? Why is this a problem? How is this avoided?

bc many viral pathogens have restricted cellular tropism and are unable to infect the professional APCs that initiate the primary CD8 responses Presentation of these viral peptides by dendritic cells is especially critical since DC presentation in draining lymph nodes is an essential event in the initiation of a robust T cell adaptive immune response. An alternative pathway (cross-presentation) for the presentation of extracellular material on MHC class I molecules resolves this problem. (Page 12).

Why is the timing of peptide loading of MHC class II critical to their ability to effectively present peptides derived from extracellular material?

bc when they are first synthesized, only a small selection of cytosol-derived peptides are present in the ER and binding of these would impede future binding of extracellular peptides

What is the length of peptides that MHC class I can bind to? Class II? What is the cause and impact of this difference?

class I - 8-9 AAs class II - 10-25 AAs As a result, MHC class II molecules bind a more heterogeneous collection of peptides. Schematic diagrams of the peptide binding sites of MHC class I and class II molecules are provided in Figure 6. As shown, the binding sites of both molecules are formed by a beta-pleated sheet floor section bounded on both sides by alpha helix segments. As shown in Figure 6, peptides are bound between the two alpha helix segments in the pocket formed on the beta pleated sheet floor. The difference in length of the peptides bound by the two molecules predominantly reflects an open-end format for the class II molecules (lower panel, Figure 6) in comparison to the more tightly closed ends of an MHC class I molecule (upper panel, Figure 6). (Page 6).

What are the 3 regions of the human HLA complex? What does each encode for?

class I - MHC class I genes class II - MHC class II genes class III - several key components of the complement system

What is the main advantage conferred by having multiple HLA class I and II genes? Explain

each gene contributes different peptide-binding specificities, this allowing for a greater number of pathogen-derived peptides to be presented during infection Figure 21A provides a model to conceptualize the value of greater peptide presentation. The grey circle in each panel represents the entire universe of peptides that could be derived and presented to the T cell compartment by an HLA allele. The small yellow circles represent the proportion of peptides that are presented by any single HLA. Thus, if an individual is homozygous for HLA, then they would be able to present only those peptides that are bound by that single HLA, In contrast, if an individual is heterozygous for HLA, then they will present all of the peptides bound by both alleles. This would represent an advantage for HLA heterozygotes with respect to their capacity to respond to pathogens. Evolutionarily, selective pressures favoring heterozygosity is termed balancing selection. Also, if the two HLAs have highly divergent peptide binding sites that present completely different peptides, then the individual will be able to respond to more peptides than a heterozygote who has two closely related HLA alleles with more structurally similar binding sites (compare bottom two panels, selection is termed divergent allele advantage). (Page 21). The biology underlying the biological advantage of being heterozygous for divergent HLA alleles is that increased numbers of activated pathogen-specific T cells will improve the strength of the anti-pathogen immune response and be beneficial for general health. Evidence supporting this possibility is provided in Figure 21B. This graph plots the number of years between infection with HIV (human immunodeficiency virus, causative virus of AIDS) and the development of terminal acquired immunodeficiency syndrome (AIDS). The graph plots the length of time that patients remained free of AIDS in years post infection and compares this value for patients that are HLA homozygous (one HLA haplotype), or partially heterozygous (expressing two HLA alleles for some HLA genes but not all), or fully heterozygous for HLA (two divergent HLA haplotypes. As shown, individuals with two divergent HLA haplotypes were able to resist the development of AIDS for the longest period, demonstrating that HLA heterozygotes were more resistant to the deleterious end stage of infection with HIV. These data support the evolutionary advantage of carrying two divergent versions of the HLA complex. (Page 22).

What does the completion of T cell activation require? Describe this phenomenon

formation of an immunological synapse around the TCR-peptide-MHC binding triad this requires multiple binding events bw specific ligand-receptor pairs on the interacting cells Figure 2A illustrates what multiple interacting receptor-ligand pairs would look like using space filling models for several molecules that participate in the T cell immunologic synapse. Figure 2B provides a schematic diagram of the interacting molecules (Fig. 2B left) and a model defining the aggregation distribution of these molecules in a synapse. As shown, the TCR-peptide-MHC triad is at the center of the assembly, consistent with the crucial role that this binding has on maintaining the antigen specificity of the initiation of an activation process for the T cell. (Page 3).

What is the main site of genetic variation of the HLA class I and II genes? What does this suggest?

in the exons that encode the alpha2 and alpha3 domains of HLA class I and the beta1 domain of HLA class II - the peptide binding sites that the extensive polymorphisms exhibited by these molecules does not represent a random collection of sequence changes, but instead reflects the selected retention of MHC class I and II alleles that have different peptide binding site structures

What is the size of the peptides recognized by TCRs? How are they produced?

8-25 AAs long degradation of pathogens and their products - antigen processing

Compare and contrast the functions of TAP, ERAP-1, and ERAP-2

A small fraction of the peptides produced by the proteasome are transported out of the cytosol and into the endoplasmic reticulum by TAP, which is the transporter associated with antigen processing. TAP preferentially transports peptides that bind MHC class I molecules, which are peptides with eight or more amino acids and either hydrophobic or basic residues at the carboxy terminus. Most peptides that TAP delivers to the endoplasmic reticulum have a carboxy-terminal amino acid compatible with binding to MHC class I. But many of these peptides are longer than nonamers and have amino-terminal ends that are incompatible with binding to MHC class I. Two structurally related endoplasmic reticulum aminopeptidases, ERAP-1 and ERAP-2, convert these longer peptides into octamers or nonamers by sequentially removing the superfluous residues from the amino-terminal end of the peptides (Figure 8). (Page 7).

Describe the cross-presentation pathway

As diagramed in Figure 12, a "cross presentation" pathway allows the presentation of extracellular materials (such as viral particles phagocytized by the professional APC) in MHC class I molecules on their surface. As shown, partially digested and degraded proteins from phagosomes are transported into the cytosol where they can be processed by the proteasome and enter the peptide loading process for MHC class I molecules. The peptides and protein fragments produced in the endosomes, lysosomes, or phagosomes are actively transported into the cytosol by TAP where they become subject to degradation by the proteasome and immunoproteasome, giving rise to peptides that are transported into the endoplasmic reticulum by TAP and delivered to the peptide-loading complex. This process is called MHC class I-restricted crosspresentation, or just cross-presentation, because the viral antigens are brought into the antigenpresenting cell by the MHC class II pathway, but they then cross over to the MHC class I pathway of antigen presentation. Although cross-presentation occurs in many cell types, it is of crucial importance in dendritic cells, because only they can initiate antigen activation of naïve T cells. (Page 13).

Explain why self-peptides displayed by donor HLA will be perceived as foreign even tho they are self peptides

As discussed with Figures 17-19 above, the extensive allelic diversity of the HLA Class I and Class II genes significantly effects the peptides that they bind in their antigen binding groove. Thus, for example, when a simple protein like ovalbumin is processed for presentation by different HLA alleles, they will typically present peptides from completely different segments of the protein (see Figure 18). Thus, most of the self-peptides from the donor's tissue that are being displayed on the donor's HLA molecules will be completely different from the same self-peptides being presented on the recipient's HLA molecules. Since the recipient's T cell compartment was tolerized to self-peptides during thymic differentiation using the recipient's HLA and not the donor's HLA, most of the donor's HLA molecules will be presenting peptides that appear foreign to the recipient's T cells, leading to their activation. (Page 20).

Why can structural differences bw donor and recipient HLA class I and II molecules contribute to alloreactivity?

As shown in Fig. 20A, some of the amino acids in the surface of the MHC molecule are included in the interface of the T cell receptor with the MHC. These are also divergent between HLA alleles and will impact the interaction, potentially leading to increased binding affinity with some TCR and further activation. (Page 20).

Part I of peptide loading by MHC class II

As shown in Figure 11A, early-stage endosomes containing extracellular material have a neutral pH. As these vesicles travel inward from the plasma membrane, the fluid in their lumen becomes acidified by the action of proton pumps in the vesicle membrane. The endosomes then fuse with other vesicles containing proteases and hydrolases that are active in acidic conditions. A gradient is created in which the early endosomes near the plasma membrane are least acidic, the late endosomes have intermediate acidity, and the lysosomes deep in the cell are most acidic (Figure 11A). As the vesicles get more acidic, their capacity for proteolytic degradation increases. (Page 11).

Part II of peptide loading by MHC class II

As shown in Figure 11B, the invariant chain is a chaperone that prevents MHC class II αβ heterodimers from binding peptides in the endoplasmic reticulum, while maintaining them in a stable conformation until they find a peptide antigen. The functional form of the invariant chain is a homotrimer that binds and fills the peptide-binding sites of three nascent MHC class II molecules. The resulting complex of three MHC class II molecules and three invariant chains leaves the endoplasmic reticulum and is taken by the invariant chains to a particular region of the cell where exocytic vesicles carrying MHC class II fuse with endosomes. The late endosomes that fuse with vesicles carrying nascent MHC class II molecules have conditions that favor the production of peptides that can bind to MHC class II. These vesicles are collectively called MIIC, for MHC class II compartment. However, before a peptide antigen can bind to the MHC class II molecule, the invariant chain must be removed. (Page 11).

Description of how B cells bind to antigen

As shown in Figure 1A, an antibody molecule on the surface of a naïve B cell interacts directly with a small portion (termed and epitope) of an antigen with its variable region antigen binding site. The epitope bound by the antibody is part of the antigen in its native form and its configuration is impacted by both the conformation and the primary structure of the antigen. The antigen can be a protein, a carbohydrate, or a small chemical compound. This system results in the selection of antibodies that can bind directly to a pathogenic organism or its products (toxins) in their native form as they appear in an infection. (Page 2).

Describe the coreceptors for MHC class I and II

As shown in Figure 5, CD4 and CD8 co-receptors, which are expressed on T cells, assemble with the TCR during TCR binding of the MHC peptide complex. On CD8 T cells, the CD8 co-receptor binds to a site on the α3 domain of the MHC class I molecule on the antigen presenting cell and forms a complex with the TCR-peptide-MHC class I triad. Similarly, CD4 on CD4 T cells, binds to the β2 domain of the MHC class II molecule on the antigen presenting cell and forms a complex with the TCR-peptide-MHC class II triad. This association is consistent throughout the binding and immune synapse formation by T cells recognizing antigens. As shown in Figure 5B, cytolytic CD8 T cells bind to virally infected epithelial cells in this fashion and kill them, while CD4 T cells bind to macrophages or B cells in this fashion to increase their activation and drive their differentiation into effector cells. (Page 5).

Describe antigen processing

As shown, a pathogen protein in a human cell is first broken down into a collection of short peptides, and then an MHC molecule binds with one of these peptides and cycles it to the cell surface, where it binds with the T cell receptor of a T cell that is actively scanning the cell for antigens in the MHC.

Describe the peptide-loading complex (PLC)

At this stage, two heterotrimers of calreticulin, MHC class I heavy chain, and β2-microglobulin become incorporated into a larger structure, the peptide-loading complex (PLC), which assembles around one of the TAP peptide transporters. In this structure, each of the 'empty' MHC class I molecules is aided by calreticulin and two other chaperones, tapasin and ERp57. (Page 7). All together these chaperones form a scaffold that promotes the binding of peptides delivered by TAP to MHC Class I