Chapter 5

Question 1

What is the structure of T cell receptors?

Answer 1

• T-cell receptor α chain (TCRα) and T-cell receptor β chain (TCRβ)
• germline organisation (like Ig) -> unique sequence
• V and C regions
  
  • Vα and Vβ domains form antigen-recognition site (only 1 site)
  • composed of CDRs (1, 2, 3)
  • C region member-anchoring
• membrane spanning region (in membrane)
• T cells bind an antigen presented on MHC class II mol

Question 2

How do T cell diversify before binding antigen?

Answer 2

• gene rearrangement
• like immunoglobulins
• assembly of V regions
  
  • α-chain has V and J
  • β-chain V, D, J
  • surrounded by RSSs, RAG complex present for splicing
• for C regions only 1 gene is available per chain
• assembly of 2 chains in ER -> only then receptor expressed on surface
  
  • associate with CD3 complex and ζ chain -> T cell receptor complex
  • proteins transmit the signal

Question 3

What are γδ T-cell receptors?

Answer 3

• similar to αβ
• δ-chain located within α-chain locus -> usually deleted
• less V segments in both -> less diversity than αβ
• in δ 2 D segments can be incorporated

Question 4

What is the difference between αβ and γδ T cells?

Answer 4

• each T cell expresses only one of the receptor types
• αβ: MHC and short peptides -> adaptive immunity
• γδ: wide variety of antigens -> innate immunity (associated with NK cells)

Question 5

How are antigens presented to T cells?

Answer 5

• antigen processing in phagocytes
  
  • degradation of pathogen -> short peptide (antigen) formed for recognition
• brought to cell surface by MHC
  
  • once bound MHC can travel to surface
  • antigen-presenting cells (APCs) formed

Question 6

What are the two types of MHCs?

Answer 6

• MHC class I: presents antigens from intracellular pathogens (such as viruses and some bacteria)
  
  • degradation in cytoplasm -> binding in ER
  • cytotoxic T cells correspond to this molecule
• MHC class II: extracellular pathogens
  
  • degradation in endosomal vesicles -> MHC travels there to bind
  • helper T cells correspond

Question 7

How are helper and cytotoxic T cells distinguished?

Answer 7

• helper T cells express CD4
• cytotoxic CD8
• CD8 and CD4: T-cell co-receptors
  
  • bind to sites on MHCs (separate from antigen binding)

Question 8

What are the modes of action of CD8 and CD4 T cells?

Answer 8

• CD8 T cells kill infected cell
• CD4 T cell secretes cytokines -> activation of macrophages
  
  • cytokines also cause differentiation of B cells -> plasma cells

Question 9

What is the overall structure of MHC molecules?

Answer 9

• 4 domains formed by 2 chains (heterodimers)
• MHC class I: α chain has 3 domains (α1, 2, 3) and β2-microglobulin (β2m)
• MHC class II: α and β chains have 2 domains each
• MHC fold creates peptide-binding site
  
  • class I: α1 and α2
  • class II: α1 and β1
  • α helices and β sheets
  • away from cell surface (easier to access by T cells)
• immunoglobulin-like domains closer to membrane (support)
  
  • class I: α3 and β2m
  • class II: α2 and β2
  • bind CD4 or CD8
• domains separated so T cell co-receptors and receptors cwn bind simultaneously

Question 10

What is the detailed structure of MHC peptide-binding sites?

Answer 10

• barbecue (B sheets) with hot dogs on them (a helices)
• a helices are antiparallel
  
  • between them is a deep groove -> one peptide can bind
  • different peptides can bind = promiscuous binding specificity

Question 11

How do MHCs bind peptides?

Answer 11

• MHC class I (9aa peptides): residue in groove use H bonds and salt bridges to bind to peptide (amino- or carboxy-terminal)
  
  • side chains bind to floor and walls of groove (esp. 2nd and 9th residue) = anchor residues
  • side chains pointing out of the groove bound by T cells
• MHC class II: similar to MHC class I
  
  • ends of peptide groove aren’t blocked off -> can bind longer peptides
  • core (8-10aa) binds to groove, different number of aa overhang depending on peptide
  • 3-4 anchor residues

Question 12

Where in the cell do MHC class I bind?

Answer 12

• intracellular pathogens affect cytoplasm + nucleus
  
  • proteases in cytoplasm degrade damaged / misfolded proteins = ER-associated protein degrad (ERAD)
  • healthy cell: self-proteins (displayed by MHC class I but not recognised by T cells)
  • unhealthy: non-self proteins recognised
• synthesised in membrane-bound ribosomes -> ER
  
  • cannot leave ER until bind a peptide
  • Golgi -> plasma membrane

Question 13

Where in the cell do MHC class II bind peptides?

Answer 13

• extracellular pathogens: vesicular system (ER, Golgi, vesicles)
• in ER α and β chains assemble with chaperone protein to prevent binding
• move to Golgi -> site of intersection between exocytic and endocytic pathway
  
  • chaperone allows binding there

Question 14

How is proteasome response adjusted to infection?

Answer 14

• 2 types: constitutive and immunoproteasome
• immuno- activated by inflammatory cytokine (interferon-γ = IFN-γ = type II interferon)
  
  • cleavage of hydrophobic and basic residues -> favoured by MHC class I
• IFN-γ induces production of PA28 complex which form cap for proteasome
  
  • faster than regular cap

Question 15

How can peptides formed by proteasome be transported from cytosol into ER?

This happens to a small fraction of peptides

Answer 15

• peptides must cross membrane of ER
  
  • mediated by transporter associated with antigen processing (TAP)
• those peptides are essential for MHC class I

Question 16

What happens when proteins transported by TAP into ER are too long for MHC class I to bind?

Answer 16

• modification by aminopeptidases: ERAP-1 and ERAP-2
• nonamers formed -> MHC can bind

Question 17

How is MHC class I assembled and attached to peptide?

Answer 17

• calnexin: membrane-bound chaperone
  
  • binds α chain -> β2m can bind
• calnexin replaced by calreticulin -> with MHC class I α and β2m incorporated to peptide-loading complex (PLC)
  
  • assembles around 1 TAP molecule
  • 2 additional chaperones: tapasin and ERp57
• peptide delivered by TAP bound to MHC class I
• tapasin binds α2 and α3
  
  • conformational change of α2 widens groove for peptide-binding -> easy binding but also easy release
    
    • high affinity peptide binds -> confromational change of groove makes it stay (reduction of tapasin interaction)
      
      • tapasin released -> MHC released from PLC
      • selection of peptide + triming by ERAPs when bound = peptide editing

Question 18

Are MHC expressed on all cell types?

Answer 18

• MHC class I is on all (intracellular pathogen affects all cells)
• MHC class II is on dendritic cells, macrophages, B cells (antigen-presenting cells)
  
  • stimulation can be induced by inflammatory cytokines in epithelial and T cells

Question 19

How is binding by MHC class II blocked?

Answer 19

• invariant chain (Ii) is a heterotrimer
• functional protein is a homotrimer -> binds with 3 MHC class II
• leaves ER in a vesicle -> fuses with endosomes

Question 20

How is Ii detached from MHC class II?

Answer 20

• MIIC (MHC class II compartment) = late endosome + MHC class II molecule
  
  • late endosome more acidic than early -> production of peptide for MHC favoured
• cathepsin S (in endosome) degrade invariant chain -> leaves CLIP (part of invariant chain) in the groove
  
  • DM binds to MHC (functions like tapasin)
    - DM in MIIC
    - opens groove -> CLIP released
    - new peptides go in, until one binds with high affinity
  • DM’s antagonist = DO
    - binds to DM to inhibit
    - balance of DO and DM controlled by IFN-γ
• MHC leaves -> to cell surface

Question 21

How is CD8 T cell response initiated?

Answer 21

• by dendritic cells
  
  • not infected by virus (viruses usually infect one specific kind of cell)
  • DCs phagocytose viral DNA from another cell (activated by MHC class II molecule) -> present it on MHC class I -> CD8 T cells activated
• this is called MHC class I-restricted cross-presentation

Question 22

What is human MHC called?

Answer 22

• human leukocyte antigen complex (HLA complex) -> react with leukocytes
• HLA class I and II

Question 23

What are the sources of variation in MHC?

Answer 23

• no rearrangements
• instead: gene families (set of proteins encoding proteins with similar structure and function)
  
  • 1 gene family -> MHC class I heavy chain
  • MHC class II α chain
  • MHC class II β chain
  • protein products of different members of gene family = isotypes
• genetic polymorphism -> many alternative forms of gene in a population
  
  • alleles: protein encoded = allotype
• MHC diversity from isotypes and allotypes = isoform

Question 24

What are MHC class I isotypes and their roles?

Answer 24

• highly polymorphic (many alleles): HLA-A, HLA-B, HLA-C
  
  • presentation of antigens to CD8 T cells
  • differences: positions in α1 and α2 -> different specificity of binding with antigens
• oligomorphic: HLA-E, HLA-F, and HLA-G
  
  • E expressed in all cells, bind 1 peptide -> nonamer cleaved from leaders binding to A, B, C -> NK cell receptor (monitoring expressions of MHC class I)
  • F binds long, has overhangs
  • G expressed by fetal cells, binds to NK receptors -> formation of placenta (C is also expressed by fetal cells to form placenta)

Question 25

What are MHC class II isotypes and their roles?

Answer 25

• HLA-DM, HLA-DO
  
  • influence other HLA class II molecules (regulation of peptide binding to groove)
• polymorphic: HLA-DP, HLA-DQ, and HLA-DR
  
  • DR has most allotypes for β chain but then α chain is monomorphic
• less allotypes than HLA class I = more specialised

Question 26

What are the components of HLA complex?

Answer 26

• class I region: HLA class I genes
  
  • many class I heavy chain genes
• class II region: HLA class II
• class III region separates I and II (central MHC)
• β2m is on a diff chromosome
• duplications of gene fragments gave rise to variety
• combination of HLA gene and alleles together on chromosome 6 = haplotype
  
  • between individuals subregions (such as HLA-DR) vary in gene content
  • or high diversity in combinations
• low meiotic recombination -> parental HLA complex stays the same

Question 27

What are proteins encoded by class II region?

Answer 27

• TAP, tapasin, two of three proteolytic subunits (for immunoproteasome)
• IFN-α, -β, and -γ control expression
• genes encoding class I and related proteins are on different chromosomes as well
  
  • HLA class II for adaptive immunity only
  • HLA class I wide range of functions

Question 28

Why is diversity of HLA complex important?

Answer 28

• more peptide-binding specificities
  
  • especially since differences tend to be in binding sites of HLA
• for wide range of antigens
• heterozygosity favoured = balancing selection (natural selection)
• selection based on epidemics (towards a certain type of HLA class I and II) = directional selection
  
  • new HLA variants by point mutation or recombination
  • interallelic conversion = small segment of one allele replaced by homologous section of another