lecture 3 Flashcards
3 types of antigen receptors
MHC molecules
T cells
B cells
two major intracellular compartments of a cell
compartmentation if the cell:
separated by membranes: cytosolic compartment VS endosome and secretory compartments
(anything in the endosome can be counted as extracellular)
cytosolic compartment
when cells are infected - virus can bind to cell and be internalised into the cell and hijack the machinery to make more viral particles
any viral proteins in a cell can be found in the cytosol and these proteins will be loaded onto MHC1 molecules
secretory/endosomal pathway allows us to look at pathogens and infections in tissues whereby we can have extracellular fluid that has bacteria and fungi
the cell can take these into the cell’s compartments
antigens taken in through that pathway can be presented on an MHC2 molecules
3 main pathways to recognise an immune response
- cytosolic pathogens will be intracellular. mechanism can degrade this pathogen in cytosol into small peptides to be loaded onto MHC1 (which present antigen CD8+ T cells, which when mature into effector cell that is a cytotoxic T cell, which recognises the antigen presented by mhc1 and lead to cell death). All of our cells can express antigens via MHC1. only some cells express antigens via MHC2, like specialised cells in thymus and gut.
these have peptides in their binding grooves which has come through there endocytic pathway, taken in from the outside by phagocytosis and then broken down within a vesicle and loaded on MHC2. - we have macrophages which play an important response in the innate system to kickstart everything off. they are attracted to inflammatory regions. they taken potential pathogenic material and express it on mhc II.
a dendritic cell will then take that extracellular source of pathogen and will take it to the lymph nodes. - B cell can also express via MHC2, need help from T helper cell, present the 3D protein and break it down through receptor-mediated endocytosis. CD4 helper cell will mature the B cell to B plasma cell for it to release antibodies or the receptors as antibodies
Peptides that bind to MHC class I molecules
Peptides that bind to MHC class I molecules are actively transported from the cytosol to the endoplasmic reticulum via the TAP complex
CYTOSOLIC PATHWAY
CYTOSOLIC PATHWAY (how mhc-1 is made and how it gets loaded with peptides) we can do this because there are many molecules embedded in our endoplasmic reticulum which can feed peptides in from the cytosol into the endoplasmic reticulum where the mhc 1 molecules are being made
TAP1 and TAP2 form a heterodimer TAP.
they transport proteins or peptides through the lumen of the ER from the cytosol
Peptides for transport into the endoplasmic reticulum
Peptides for transport into the endoplasmic reticulum are generated in the cytosol, by proteolytic digestion in the proteosome
proteins when in proteasome
lifespan of a protein (turnover rate) will start to degrade
then will then be flagged with the addition of ubiquitin to get into the proteasome
proteasome has a central catalytic chamber - 4 rings forming a pore in the middle and proteasome activators flagging them. the peptides and proteins will go into the proteasome activators which will open up the route into the catalytic chamber to get broken down into smaller peptides. (viral proteins will go through that same process)
immunoproteasome
if we have infection after a while, the proteasome becomes changed to immunoproteasome
immunoproteasome will changes the carboxyl terminus of that peptide to a particular hydrophobic side chain so that it can fit into the mhc binding groove more easily - becomes much more specific peptides have a slightly altered carboxyl terminal chain so that I can bind to the anchor residues on the mhc binding groove.
HOW DOES THE PROTEIN GET THROUGH?
Newly synthesized MHC class I molecules are retained in the endoplasmic reticulum until they bind a peptide
DIAGRAM AND NOTES IN L3 S7
Many viruses produce immunoevasins that interfere with antigen presentation by MHC class I molecules
TAPasin will form the complex and bring it to the TAP molecule
a neat subversion of our immune responses
most mechanisms by pathogens subvert any of these mechanisms which allow our immune system to see infections (immunosurveillance becomes blind)
our mechanisms developed by adenovirus evolved to produce a protein called E19 which fits in between the mhc complex and the tapasin - it is too close so the mhc molecule cannot get me enough to the tap and will never be able to be loaded with its peptide (so it is hiding the viral particle for the infection to continue for longer)
Peptides presented by MHC class II molecules are generated in acidified endocytic vesicles
anitgen is taken up from the extracellular space into intracellular vesicles
in early endosome of neutral pH, endosomal proteases are inactive
acidifaction of vesicles activates proteases to degrade antigen into peptide fragments
vesicles containing peptides fuse with vesicles containing MHC class II molecules
NOTES IN L3 S9
role of invariant chain
- blocks the binding groove, stops protien that are around in ER from bidning into groove
- signal it as a directional set of instructions, to get to the surface membrane
The invariant chain sits as a trimer bound to 3 Class II αβ molecules in the ER
MHC2 gets cotranslationally inserted into our ER but needs to be signalled to be sent off into a vesicle and reach the outer membrane (to meet up with incoming peptide vesicles)
makes sure nothing will bind on groove of the newly made mhc molecule - done by invariant chain (IC) molecule (trimer), also called Ii
invariant chain has red regions that bind strongly into the binding groove of mhc2
3 of them will cluster and bind together,
IC has a significant portion that passes through the membrane of ER
It acts as a signalling initiator
this targets and direct the complex to be pushed out of the ER into vesicles which will go to the cell surface
The invariant chain directs newly synthesized MHC class II molecules to acidified intracellular vesicles
- invariant chain Ii binds in the groove of MHC2 molecule
- Ii is cleaved initially to leave a fragment bound to the class 2 molecule and to the membrane
- further cleavage leaves a short peptide fragment, CLIP, bound to the class II molecule
it progresses and ph changes in vesicles to nibble away the legs on the binding groove you end up with a blue region that is stuck in there called CLIP (class 2 associated invariant peptide) bound into the class 2 binding groove prevents anything that shouldnt be in there to bind to the binding groove
cell extraction to try to identify invariant chains
MHC Class II molecules are loaded with peptide in a specialised intracellular compartment - MHC Class II Compartment (MIIC).
(B cell section)
it has to be loaded with peptides at some point in their journey
if you do cell extraction and try to identify them at first we couldn’t figure out the density of them or their sizes because invariably there was always something stuck in the binding groove (electron dense material, which is the peptide)
one of the first mechanisms was called immunoblotting where you attach different gold specks on to different antibodies
you have the larger molecule binding to the clip protein and the smaller molecules bound to antibodies which recognises only the mhc
we see that there are certain mhc2 compartments that only have mhc molecules so it lost its CLIP parts
this means that there are specific compartments where the clip is released and antigen is loaded - so specific compartments that are characterised as the mhc2 compartments which is where the clip is lost and the loading occurs
