Lecture 10 - Ag Processing Flashcards
What do the MHC polymorphisms affect?
Why?
- The different alleles have different peptide specificities
* Because the MHC binding cleft is affected by polymorphism
Where do peptides bind to the MHC binding cleft?
- Anchor residues / side chains on peptide
* Binding pockets in the binding cleft of MHC
Can one MHC product bind only one peptide?
No
Peptides that are presented in the same MHC product will have the same binding residues
What can be said of non-anchor residues on the peptide?
These are normally involved in the TCR binding
Compare, for example, HLA-A2 and HLA-A3, in terms of the binding pocket
HLA-A2: peptides w/ Leu and Val anchor residues
HLA-A3: peptide binding cleft w/ -ve charge → peptide anchor residue w/ +ve charge: Leu and Lys
Which structure makes up the MHC peptide binding cleft?
- Two alpha helices (on the sides)
* Beta sheet floor
What can be said of the CD4/CD8 binding sites on the various MHC alleles
Largely conserved
- CD4: binds β2 of MHC II
- CD8: binds α3 of MHC I
Compare the MHC class I and II binding clefts
Class I: closed binding cleft
→ peptide tucked in
Class II: open binding cleft
→ peptide hangs out
Describe the process that turns a protein into ‘peptide’ for presentation
- Protein: many antigens
- Proteolysis of protein into several peptides
- Individual peptides presented by MHC
Why does it sometimes occur that there is no T cell response to an antigen?
The antigen could not be bound by MHC
Thus, T cells were not activated by APC’s, and there was no cellular response
Compare the terms ‘polygeny’ and ‘polymorphism’, and describe the effect of them on the immune response
Polygeny: presence of different versions of a gene within a person; e.g. HLA-A, HLA-B, HLA-C
Polymorphism: presence of different alleles in the population
These different versions increase the likelihood that a peptide can be bound by MHC for activation of the cellular response
Compare the types of antigens that Th and CTLs direct their responses against
CTLs
• ‘Endogenous antigens’
• virus, tumour, transplantation antigens
‘Helper’ T cells
• ‘Exogenous antigens’
• bacterial antigens, soluble protein antigens
Outline the MHC Class II antigen processing pathway
- Antigen taken in by endocytosis
- Degradation in endolysosome
- Fuses with vesicle from ER that contains MHC II
- Binding of peptide to MHC II
- Trafficking of MIIC compartment to the cell surface
Outline the MHC Class I antigen processing pathway
- MHC I made in ER, and is retained there until peptide binds
- Intracellular gene (host or virus)
- Intracellular antigen (IA)
- IA degraded by proteosome
- IA enters ER through TAP
- MHC I in ER binds the peptide
What is the MIIC compartment?
Peptide-binding vesicle
How is antigen ‘captured’ for processing in the MHC II pathway?
- Receptors on cell surface
• Surface bound Ab; Antibody-mediated endocytosis
• Ab bound to FcR on cell surface - Simple endocytosis of antigen
What are the benefits of antibody mediated endocytosis of antigen?
Better Th - B cell interaction
- B cell; surface bound Ab binds antigen
- Endocytosis, processing → presentation of antigen on MHC II
- Th cells recognise antigen with TCR
- T cell help for B cell
Which molecules are really important for Ag presentation in MHC II?
- Invariant chain
* HLA-DM
What is HLA-DM?
- A dimeric, MHC II-like molecule
- Present in MIIC compartment
- Important role in loading of peptide into MHC II
- through the removal of CLIP
NB it is not a surface MHC molecule, and thus does not actually present antigen itself
What is Ii and what is its importance?
Invariant Chain
• Binds the peptide binding groove in MHC II in the ER
• Targets the MHC II to the endosomal compartment → MIIC compartment formation
NB In Ii KO mice, there is greatly reduced surface MHC II expression on APC’s
What are MHC II peptide binding grooves predominantly occupied by before the peptide antigen is loaded?
CLIP:
• Class II associated Invariant chain Peptide
• It is the part of Ii that is left in the binding groove of MHC II after degradation of the Ii
What is TAP?
Describe its function and some features
Transporter associated with Antigen Processing
• transports peptides from the cytosol into the ER
• binds ATP
- encoded by gene within MHC I region
- expression of different components upregulated by IFN-γ
What is MHC restriction?
A given T cell will only be able to recognise one of the types of MHC
Compare the length of peptides that are loaded into MHC I and MHC II
MHC I : length fairly uniform
MHC II: length is far more variable
What is different about the different alleles of MHC molecules?
Different binding pockets
Who is polygeny important for?
An individual
What happens to Ii once the MHC II gets into the endosome?
It is degraded.
However, CLIP remains (HLA-DM needed to get rid of CLIP)
Where are proteins degraded in the MHC I processing pathway?
In the cytosol, in a proteasome
Describe some features of the proteasome
What changes occur during viral infection?
- Large, multi-subunit
- In the cytosol
- Highly conserved (also seen in bacteria)
Viral infection:
• There are alternate subunits that are used in immune responses whose expression is upregulated by IFN-γ
• These up-regulated subunits increase the activity of the proteasome, so that there is more antigen presentation
What molecule is required for TAP function?
ATP
Describe how B cells present exogenous antigen
What are the benefits of this?
- Capture antigen w/ surface bound Ig
- Receptor mediated endocytosis
- Degradation of antigen into epitopes
- Combination of MHC II from ER with epitope in MIIC
- Trafficking to surface for presentation
Ig receptor mediated endocytosis facilitates:
• B cell-Th cell interaction
Is HLA-DM a monomer or a dimer?
Dimer
Describe the structure of TAP
Heterodimeric: TAP1 / TAP2
Describe some features of peptides that TAP transports into the ER
- 8-16 aa in length
* Hydrophobic C-terminal residues
Under what conditions is TAP expression upregulated?
IFN-γ
Viral infection
What are Lmp2, Lmp7, MECL1 and PA28?
Alternate proteasome subunits
- Seem to have a role in antigen processing
- Not normally expressed in cells
- Expression upregulated by IFN-γ
• Preferentially generate peptides ideal for transport into ER with TAP:
- 8-16 aa in length
- C-terminal hydrophobic residues
What can interference with antigen processing lead to, in terms of MHC I expression?
MHC I is retained in the ER until peptide is bound to it
If there is interference with antigen processing, peptides are not being loaded onto MHC I, and thus, there is a reduced presence of MHC I on the cell surface
Which pathway of antigen processing is ‘endosomal’ and which is ‘cytosolic’?
MHC class I: cytosolic
MHC class II: endosomal
