antigen presentation to T lymphocytes

how do BCRs recognize antigens

• bind directly to epitopes on proteins, carbs, or lipids

• antigen binding via CDRs in variable regions

• recognize soluble or cell surface antigens

how do TCRs recognize antigen

• recognize peptide fragments bound to MHC

what is the MHC restriction

CD4 T cells = MHC class II (binds 25-30 aa)

CD8 T cells = MHC class I (8-10 aa)

what is combinatorial diversity

random assembly of V, D, J

what does junctional diversity add

variation (P and N nucleotides)

what chain pairing is BCRs

light and heavy

what chain pairing is TCRs

alpha and beta

what are some secondary lymphoid organs

spleen and lymph nodes 

what cells do T cells recognize and respond to

cell-associated antigens (not to soluble, cell-free antigens)

properties of antigens recognized by T cells

• short peptides

• receptors for CD4+ and CD8+ T cells are specific for peptide antigens that are displayed by MHC molecules

what are the two categories of major intracellular compartments

1. cytosol

2. vesicular compartments 

where do peptides from cytosol get transported

ER

what presentation does cytosol peptides have

direct

cytosolic pathogens are degraded, bind to, present to, and experience/do

cytosol, MHC class I, effector CD8 T cells, cell death

intravesicular pathogens are degraded in, bind to, present to, and experience/do

endocytic vesicles (low pH), MHC class II, effector CD4 T cells, activation of macrophage to kill intravesicular bacteria and parasites

extracellular pathogens and toxins are degraded in, bind to, present to, and experience/do

endocytic vesicles (low pH), MHC class II, effector CD4 T cells, activation of B cells to secrete Ig to eliminate extracellular bacteria/toxins/viruses

what is cross presentation of an antigen

ability of certain APCs to take up and process from exogenous sources and load onto MHC I to CD8 T cells

what is the purpose of antigen cross presentation

to activate naive CD8 T cells into activated CD8 T cells (cross priming)

why can’t infected cells present viral peptide on MHC I

they do, but only to activated (primed/effector) CD8 T cells because infected cells lack co-stimulatory molecules (B7) needed to activate naive CD8 T cells

what does autophagy do

moves cytosolic and nuclear proteins into vesicles, which are then degraded in lysosomes, peptides get loaded onto MHC II

what is the outcome of autophagy

CD4 T cells can recognize antigens that would not normally reach MHC II which boosts antimicrobial defense

exceptions in antigen presentation, autophagy: what happens, antigen source, presented on, activates, purpose

• cytosolic/nuclear proteins are shuttled into vesicles and degraded in lysosomes

• self proteins, intracellular pathogens

• MHC II

• CD4 T cells 

• broadens CD4 recognition tolerance and defense

exceptions in antigen presentation, cross-presentation: what happens, antigen source, presented on, activates, purpose

• exogenous antigens (from dead/infected cells) loaded onto MHC I by DCs

• viruses infecting non-APCs, tumors

• MHC I

• CD 8 T cells

• primes naive CD8 T cells (cross-priming)

how does protein degradation occur in the cytosol

multicatalytic protease complex k (as the proteasome)

what is the protease complex k composed of

20S catalytic core and two 19s regulatory caps on each end

what do the 19S caps do

one binds and delivers protein into proteasome and the other prevents premature exit

what tags protein in cytosol for degradation

ubiquitin proteasome system

what is the difference between proteasomes and ubiquitin-proteasome system

proteasomes: enzymes that do the chopping

ubiquitin-proteasome system: tags the proteins for degradation

5 steps of ubiquitin proteasome system

1. ubiquitination

2. proteasome degradation

3. TAP transporter (delivery truck)

4. loading onto MHC I (billboard)

5. immune recognition (surveillance patrol)

step 1 of ubiquitin proteasome system: ubiquitination

• targets cytosolic proteins get tagged with a chain of several ubiquitin molecules 

• ubiquitin K48 linkage= “trash sticker”

what is K48 linkage

ubiquitin (small protein) attaches to other ubiquitins by linking at lysine (K) residues at position 48 (K48)

step 2 of ubiquitin proteasome system: proteasome degradation

• proteasome = large “protein shredder”

• cuts proteins into small peptides (8-10aa)

• during infection, IFN-Y turns proteasome into immunoproteasome which makes peptides better suited for MHC I presentation

step 3 of ubiquitin proteasome system: TAP transporter

• peptides from cytosol are transported by TAP1 and TAP2 (transporters associated with antigen processing) into the ER before binding to MHC I

• TAP transporter= “delivery truck”

step 4 of ubiquitin proteasome system: loading onto MHC class I molecules 

1. retention in the ER: newly synthesized MHC I alpha chain is stabilized by chaperone calnexin which holds the alpha chain until B2 microglobulin binds

2. peptide-loading complex forms: once B2 macroglobulin associates, calnexin is released. partially folded MHC I is stabilized by calreticulin and ERp57, these chaperones form a PLC with tapasin 

3. peptide delivery: TAP delivers peptides (from proteasome) into the ER, tapasin forms a bridge between MHC I and TAP, helping high affinity peptides bind 

4. stabilization and exit: binding of a suitable peptide (right size and fit) stabilizes MHC I complex, peptide: MHC I complex leaves the ER to golgi to cell surface to ready to be recognized by CD8 T cells

what is the peptide loading complex formed of

calreticulin, ERp57, tapasin, and TAP

where does MHC I and MHC II loading happen

• MHC I: loading happens inside ER

• MHC II: loading happens inside vesicle

steps of MHC II peptide binding/fusing/loading in vesicles

1. uptake: antigen taken up from extracellular space into endocytic vesicles

2. acidification: endosomes become more acidic as they move inward, eventually fuse with lysosomes, V-type ATPase pumps H+ to acidify endosomes and lysosomes

3. proteolysis: acidic endosomes and lysosomes contain proteases, which get activated at low pH and break proteins into short peptides

4. peptide loading: fusion event brings together peptide rich vesicles and MHC II containing vesicles, which is the site of peptide loading

what is the purpose of the invariant chain (li)

newly made MHC II class molecules in ER need protection, so invariant chain binds in the groove, to prevent premature peptide binding, invariant chain acts as sorting signal, directing MHC II to endosomal/lysosomal pathway

what is CLIP fragment

class II- associated invariant chain peptide, results from further cleavage of the invariant chain, leaving a short peptide fragment behind (CLIP), bound to the class II molecule (this stays in the peptide binding groove to block)

what is HLA-DM

specialized molecule that removes CLIP and helps load high affinity peptides from degraded pathogens and ensures only stably bound immunogenic peptides make it to surface

how does HLA-DM work (exchange/editing)

• binds to MHC II- CLIP complex and destabilizes CLIP binding and catalyzes CLIP release 

• in the presence of open (peptide receptive) groove, peptides from the pool can try and bind

• HLA-DM is “peptide editor”, weak/low affinity peptides are more easily displaced, while high-affinity, stable peptide MHC-II complexes are preserved

• once a peptide is stably bound, DM disassociates

what are the consequences of appropriate T cells recognizing the bound peptide fragments derived frm pathogens that MHC molecules bound to cell surface 

• virus infected cells are killed

• macrophages activated to ill bacteria living in their vesicles

• B cells activated to make Igs to eliminate or neutralize pathogens

why cant pathogens easily evade MHC presentation

polygeny, polymorphism, co dominance

what does MHC polygeny mean

each person has multiple MHC I and MHC II genes, so different MHC molecules are expressed in cells, so each MHC molecule binds a different set of peptides (wider coverage)

what does MHC polymorphism mean

theres different alleles in us, so there is allele based species level diversity

why does herd immunity occur

there is enough polymorphism to kickstart it

what is haplotype

the set of MHC genes you are going to inherit

how are maternal and paternal MHC alleles expressed

equally on every nucleated cell

what does the equal expression of maternal and paternal MHC cause, and why are both haplotypes expressed

maximizes each persons antigen-presentation capacity, codominance 

where is MHC polymorphism concentrated

peptide binding groove

what 3 properties are altered by MHC polymorphism

1. range of peptides bound: diff alleles create diff binding pockets, determines which antigens can be presented

2. conformation of bound peptide: polymorphic residues influence how peptide sits in the groove, changes shape of peptide MHC surface seen by TCR

3. direct interaction with the TCR: polymorphic residues of MHC also contacts the TCR, affects TCR recognition and thymic selection

what is MHC restriction

TCR recognizing the antigenic peptide and the self MHC molecule

what would happen if the TCR cannot recognize the antigen

no recognition, the TCR does not have the right shape for the peptide

what would happen if the MHC molecule does not match the TCR

no recognition