Lecture 7 Flashcards
what are the 2 major differences between TCRs and BCRs?
- antibodies have 2 antigen binding sites, TCR has 1
- BCR can be on membrane or secreted
3 similar parts of BCR and TCR structures
- 2 chains
- variable regions (Ag-binding)
- constant regions
describe the structure of TCR
1 alpha chain, 1 beta chain joined by disulfide bond
both chains glycosylated
what does the TCR recognize?
antigenic peptides presented by MHC
how does the TCR only recognize antigenic peptides, rather than the whole antigen?
MHC presents the epitope but the epitope is buried within the antigen so antigen is processed
what does the TCR interact with?
MHC and antigen
what does MHC I present? and to which type of T cell?
MHC I presents ENDOGENOUS antigens to cytotoxic T cells
what does MHC II present? and to which type of T cell?
MHC II presents EXOGENOUS antigens to helper T cells
describe the structure of MHC I
3 alpha subunits (1 tethered to membrane) and a beta-microglobulin subunit
describe the structure of MHC II
2 beta subunits, with 1 tethered to membrane
2 alpha subunits, with 1 tethered to membrane
which part of MHC I and II determines what type of peptides they can have?
peptide binding cleft
what size of peptides does MHC I present? why?
short peptides
helices in binding cleft almost touch, so the cleft is closed and can accommodate smaller peptides only –> N and C termini of peptide are involved in binding to MHC I
what size of peptides does MHC II present? why?
longer, more variable sizes
the binding cleft is more open on either end and can accommodate larger peptides –> N and C termini of peptide are NOT involved in binding to MHC II
what are anchor residues?
anchor residues are on MHC I/II and bind specific residues on the peptide to allow the peptide to bind
are anchor residues similar or different from peptides that bind the same MHC?
SIMILAR
what is the difference btwn anchor residues that bind MHC I vs MHC II? why?
anchor residues that bind MHC I are in same position in the peptide bc the N and C termini are important for binding
anchor residues that bind MHC II are in diff positions in the peptide bc it can bind a wide range of peptide sizes, so the N and C termini don’t line up bc they’re not involved
why are there specific peptide residues on the peptide antigen?
so it can specifically bind the MHC and TCR
why is the TCR-MHC-peptide interaction important?
important during T cell development for +/- selection
what do TCR co-receptors bind?
co-receptors bind MHC
are TCR co-receptors involved in peptide interaction?
no
what are the 2 TCR co-receptors? which recognizes MHC I, which recognizes MHC II?
CD8+ –> MHC I
CD4+ –> MHC II
what type of cell is the main MHC-expressing cell?
dendritic cells
what type of MHC do brain cells have?
small amount of MHC I
why do brain cells only have a small amount of MHC I?
usually viruses cannot enter the brain bc of BBB but if they do get in, don’t want the T cell response to start killing brain cells
CYTOSOLIC PATHOGENS
- Degraded in:
- MHC:
- Presented to:
- Effect on presenting cell:
CYTOSOLIC PATHOGENS
- Degraded in cytosol
- MHC I
- Presented to CD8 T cell
- Causes cell death
INTRAVESICULAR PATHOGENS
- Degraded in:
- MHC:
- Presented to:
- Effect on presenting cell:
INTRAVESICULAR PATHOGENS
- Degraded in acidic endocytic vesicles
- MHC II
- Presented to CD4 T cell
- APC activated to kill intravesicular bacteria + proteins
EXTRACELLULAR PATHOGENS AND TOXINS
- Degraded in:
- MHC:
- Presented to:
- Effect on presenting cell:
- EXTRACELLULAR PATHOGENS AND TOXINS
- Degraded in acidic endocytic vesicles
- MHC II
- Presented to CD4 T cells
- B cell activated to secrete Ig to kill extracellular pathogen
general 4 steps of processing and presentation of intracellular antigen
peptide fragments of intracellular antigen is bound by MHC I in ER
then bound peptide transported by MHC I to cell surface
describe the specific steps of intracellular antigen processing in the ER with MHC I
what is calnexin?
chaperone involved in the folding of many proteins in ER
why does MHC processing occur in ER
ER is the site of membrane protein folding
what proteins are processed for MHC I?
DRiPs (any misfolded proteins, 30% of all protein) and viral proteins
what is TRiC protein?
prevents the peptide fragments from being further degraded into aa to allow specific size to work with MHC I
What type of enzyme is ERAAP? Why?
ERAAP is an aminopeptidase which trims the peptide at N terminus to make the N terminus compatible with binding to MHC I
when is the MHC I fully stabilized?
once the peptide binds
describe the structure of the proteasome
cylinder with two 19S rings on the outside and a catalytic 20S ring in the center
what is the role of the outside 19S rings on the proteasome?
polyubiquitinated proteins are bound by the 19S ring and then degraded in the center
describe the expression of protein subunits in the proteasome
NORMALLY: constitutively expressed
INDUCTION OF IMMUNE RESPONSE: via production of IFN (for ex) the constitutive subunits will change to LMP2/LMP7
why are the constitutive subunits changed to LMP2/LMP7 upon immune induction? (3)
- peptides become better at binding to MHC I
- peptides can be more efficiently transported by TAP
ultimately allows for better antigen presentation
what does DRiP stand for?
defective ribosomal products
where are LMP2/LMP7 encoded?
at the MHC locus
what is the role of TAP?
uses active transport to move cytosolic peptide fragments into ER
structure of TAP + domains
heterodimer
each subunit has hydrophobic transmembrane domain on ER membrane and ATP-binding cassette domain in cytosol
what is the size of peptides that can pass thru TAP? and specific characteristic of the peptide
8-16 aa peptide with hydrophobic or basic residues at C terminus
where is TAP encoded?
in MHC locus
where are peptides presented by MHC II generated?
in endocytic compartments
what types of cells express MHC II? (1 main type and 3 examples + 1 more)
APC cells with lymphoid origin
1. B cells
2. Macrophages
3. DCs
Non-lymphoid
4. Epithelial cells in thymus
why do epithelial cells in thymus express MHC II if they are not of lymphoid origin?
allows T cells to differentiate btwn self and non-self
where is MHC II made?
in ER
what is the issue with both MHC I and II being made in the ER? and how is it fixed?
MHC II could bind to endogenous peptides but this is prevented with the INVARIANT CHAIN
What is the role of invariant chain?
- to prevent endogenous peptides from binding but still allows for stabilized MHC II
- directs MHC II to acidic components
what chaperone used in MHC I folding is also used in MHC II folding?
calnexin
structure of invariant chain?
trimer
describe the steps of MHC II presenting antigen
what protein is involved in cleaving the invariant chain?
cathepsins
what is the role of CLIP?
stabilizes MHC II while it waits for exogenous peptides to enter the vesicle
what is HLA-DM structure?
HLA-DM has similar structure to MHC
what is HLA-DM role?
releases CLIP to allow peptides to bind
where is HLA-DM encoded?
encoded at the MHC locus
what happens to MHC II in immature DCs?
in immature DCs, MARCH-1 targets MHC II for degradation
what type of enzyme is MARCH-1?
E3 ubiquitin ligase
what happens to MHC II in absence of antigen?
TLR isn’t binding anything so DCs are immature –> MARCH-1 will trigger degradation of MHC II
how does MARCH-1 target MHC II for degradation?
MARCH-1 ubiquitinates MHC II
what happens to MHC II in presence of antigen?
TLRs are activated to make mature DCs which stops the synthesis of MARCH-1 and any remaining MARCH-1 is degraded –> increased MHC II at cell surface and stability
what is the purpose of the system with MARCH-1 degradation of MHC II?
when the DC becomes activated and there’s no MARCH-1, the MHC II will last longer and allow more time to get to T cells to activate them, ultimately allowing better presentation of antigens
if MHC II was short-lived and there was constant turnover, once it brought the antigen to T cells, the MHC would no longer be there
what is MHC I cross-presentation? how does it work?
MHC I presents exogenous peptides
- DCs and other cells that can phagocytose/endocytose will take up proteins which are then degraded by the proteasome
what is MHC II cross-presentation? how does it work?
MHC II presents endogenous peptides
- autophagy allows phagosomes to take up part of the cytoplasm with endogenous peptides
benefit of cross-presentation
viruses may downregulate MHC I so this gives immune cells another pathway to fight viral infection
what is a common strategy for immune invasion by viruses?
often alter antigen presentation by MHC I
what is special about large viruses in affecting MHC I presentation?
large viruses have larger genomes which have genes dedicated to evading MHC I presentation
what part of the MHC I presentation pathway can viral proteins target?
almost every component
what is the one part of the MHC I presentation pathway that viral proteins do not target? why?
CALNEXIN usually not targeted bc calnexin is important for folding many other proteins in ER which virus may need
what is CMV and describe infection?
very large virus that can evade immune system
CMV by itself has no impact on healthy ppl but bad in immunocompromised ppl and can lead to secondary infection by other viruses that don’t have the evasion strategy
why is it helpful to study viral evasion by CMV?
help us learn about normal cell function
how did we learn about transport of proteins from ER to cytosol in protein synthesis?
studying CMV immune evasion proteins US2 and US11
how did they find the role of US2 and US11?
Co-IP –> infect cell with virus and MHC I or peptide loading complex will by physically associated with US2 and US11
what does US11 do specifically?
US11 dislocates MHC I heavy chains from ER to cytosol
how did US11 show that degraded cellular proteins are taken from ER to cytosol?
with US11 –> MHC I is degraded by ER-associated degradation
with US11 + proteasome inhibitors –> MHC I accumulated, therefore must normally be proteasome degradation and since proteasome degradation occurs in cytosol, must be a way to translocate the proteins from ER to cytosol
