Lecture 17 - MHC

TCRs recognize peptide fragments
TCR has a single peptide binding site
- the TCR MHC must also contact through two connection points

MHC: major histocompatibility complex (HLA)
- membrane bound glycoproteins split into class I and class II
Class I MHC
- alpha chain with three domains and a non-covalently associated B2 microglobulin
  - microglobulin in a small Ig-like domain
- only the alpha chain forms the binding cleft
Class II MHC
- alpha and beta chain with two domains each, non-identical
- both form the binding cleft
peptide loading versatility and constraints
- MHC have the capacity to bind a wide variety of peptide sequences
- only one peptide can bind to each MHC protein at a time
- peptides fit into binding cleft of MHC molecules

pathogens can be found in the cytosol or in endosomal/phagocytic compartments
- cytosolic — MHC I (all nucleated cells: “I am sick”)
- endosome — MHC II (professional APCs: “I need help”)
if the pathogen escapes into the cytosol, the cell utilizes MHC I

class II expressed by professional APCs
- B cells, macrophages, and dendritic cells
class I expressed by most nucleated cells
- T cells, B cells, macrophages, dendritic cells, neutrophils, hepatocytes, kidney epithelium, and neurons
MHC :: T cell co-receptor interactions
- CD8 — Cytotoxic T cell — MHC I class — cytosol
  - release of perforin and granzymes to induce apoptosis of the infected cell
- CD4 — Helper T cells — MHC II class — phagosome
  - secretion of cytokines to instruct macrophages to enhance killing and B cells to produce antibodies

ribosomes exist freely in the cytoplasm or on the rough ER
both MHC I and II are synthesized within the ER by ribosomes
- inside the ER, they fold and are membrane-bound
- they are packaged into vesicles that are delivered to the G.
depending on the tag, vesicles are shipped to different parts of the cell or to the outside
endocytosis brings in outside material
- the endosome progresses through early to late endosome phase
- phagocytosis generates phagosome which fuse with lysosomes that contain enzymes activated at low pH (get low pH by proton pumps)
cellular compartmentalization
- three broad compartments: nucleus & cytoplasm, endomembrane system, and mitochondria

stage one — degradation of proteins by the proteosome
- cytosolic proteins are tagged by ubiquitination (labels protein to become targeted for degradation)
- the proteins are degraded by proteosome into peptide fragments
  - constitutive proteasome (baseline)
  - immunoproteasome (induced by IFN-gamma expression to generate peptides more suitable for MHC I)
    - increases the rate of degradation
stage two — import of peptides into the ER
- TAP is a transporter associated with antigen processing
- TAP brings peptides from the cytosol into the ER lumen
stage three — binding of peptides to empty MHC class I proteins in the ER
- ERAP trims overlong peptides to appropriate size for the MHC-I groove
- membrane bound calnexin and other proteins hold the MHC I into an inactive configuration
  - TAP recruitment and associated assembly factors displace calnexin and facilitate peptide loading
stage four — transport of loaded MHC to the cell surface
- after peptide loading, MHC-I is packaged in vesicles, passes through Golgi, and traffics to the plasma membrane for presentation to CD8+ T cells

How cells distinguish viral vs. self proteins (rationale for degradation bias)
- Increased error/misfolding under viral-driven ramp-up of protein synthesis leads to misfolded proteins that are ubiquitinated and degraded regardless of origin
- Post-translational modification deficits: viral proteins often lack normal host signals for modifications (e.g., addition of lipids/sugars), flagging them as abnormal
- Trafficking address/tag deficits: viral proteins often lack proper localization signals, making them “missing address” proteins; cells default to degrade and recycle such proteins
- General principle: although amino acid composition overlaps, quality control and signaling deficiencies in viral proteins bias them toward ubiquitination and degradation

stage one — degradation of pathogen in phagolysome
- encounter of antigen and consumption via endocytosis/phagocytosis
- these vesicles fuse with lysosomes to yield fragmented peptides of the antigen
stage two — fusion of endosomal compartment containing MHC class II in the membrane
- MHC class II molecule is made in the rough ER; it has a small fragment invariant chain bound to prevent unnecessary binding
- MHC-II with invariant chain is trafficked via Golgi into vesicles targeted to the endosomal/lysosomal system
stage three — binding of peptides to empty MHC class II
- fusion of MHC-II–containing vesicles with peptide-rich endolysosomal compartments results in removal of the invariant chain and replacement by exogenous peptides processed in the acidic lumen
stage four — transport of loaded MHC to the cell surface
- loaded MHC-II is then presented at the plasma membrane to CD4+ helper T cells

self-peptides are commonly encountered during a T cell’s maturation phase
- undergoes positive and negative selection to ensure there is no response to self cells
to ensure that infection at any location throughout the body can be detected
- phagocytosis and then dendritic cells present antigens on MHC class I to activate CD8+ T cells which kill infected cells

co-dominant expression of all MHC molecules
- many different isotypes with their own promiscuity allow cells to display a large number of peptides
MHC diversity allows for presentation of a wide range of peptides
- binding pocket to accommodate proteins & two amino acids of the peptide interact with the binding cleft
  - those two amino acids must be kept the same but the other resides can be variable
genetic polymorphism within these genes (allotypes
- polymorphisms primarily occur in the peptide-binding groove
diversity protects human population
- MHC genes are linked: crossover limited
- offspring inherit a ‘set’ of alleles either from the mother or father
  - crossover limited events still generate HLA polymorphism