Lecture 3 - Antigens and Immunogenicity Flashcards
What molecules are the model immunogens/antigens used in immunology research? Why?
Proteins because most is known about the immune response to this class of molecule
What animals are the model immunogens/antigens used in immunology research?
Mice
What is the difference between antigens and immunogens? What to note?
- Antigens: molecules that can be recognized (bound) by antigen receptors of B cells (BCR) and T cells (TCR), but do not necessarily induce them
- Immunogens: molecules that can induce an immune response de novo and contain Pathogen-Associated Molecular Patterns (PAMPS) or DAMPS
Note: all immunogens are antigens, but not all antigens are immunogens
How can TCRs recognize antigens? Is this true for BCRs?
Antigens must be presented bound to (in the context of) a Major HistoCompatibility (MHC) molecule
NOPE - BCRs can bind antigens directly
What is immunogenicity?
Measure of how effective a substance is at provoking an immune response against it
Are all vaccines immunogens?
Not all, but some:
- Whole bacteria and viruses vaccines are
- Sub-unit vaccines (i.e. purified components) may not be (e.g. tetanus)
What is the immunoglobulin super-gene family? What does this mean?
Gene family including:
- BCR
- TCR
- MHC
Means they have structural similarities:
- Domain-like structure
- Form a 3D structure that is complimentary to the ligand at the N-terminus = paratope that binds the epitope/antigenic determinant
What does signaling through BCRs and TCRs require?
Requires the co-operation of additional molecules to transduce the signal to the interior of the cell:
- BCRs: Igβ and Igα with cytoplasmic tails (ITAMs)
- TCR: CD3 and ζ chain with cytoplasmic tails (ITAMs)
What is a BCR exactly?
Cell membrane form of an antibody
8 differences between BCRs and TCRs?
- BCR is membrane-bound and secreted/TCR is only membrane-bound
- TCR has the same structure as one of the arms of BCR
- BCR recognizes epitopes on the solvent exposed surface of a protein/TCR binds to epitopes presented by MHC molecules
- BCR can recognize conformational and linear epitopes/TCR can recognize linear epitopes
- BCR involves binary complex of membrane Ig and antigen/TCR involves ternary complex of TCR, antigen, and MHC molecule
- BCR binds soluble antigen/TCR binds particulate antigen
- BCR recognizes proteins, polysaccharides, lipids, glycolipids, glycoproteins, etc./TCR recognizes mostly proteins, but also some lipids, oligosaccharides, and glycolopids presented on MHC like molecules
- No somatic mutations possible for TCRs
Do BCRs and TCRs have a cytoplasmic component/tail? What does this mean?
NOPE
They cannot transduce signals to the inside of the cell
What are ITAMs?
Immunoreceptor tyrosine-based activation motifs
Form of CD3?
Heterodimer
Other name for paratope of antibody?
Variable domain
Structure of BCR?
- Two long chains = heavy chains
2. Two short chains = light chains
Form of TCR?
Heterodimer
Form of MHC molecules?
Heterodimers
Structure of MHC Class I molecules?
- α chain with 3 α domains: 1, 2, and 3, with 1 and 2 forming a cleft together to bind a peptide
- β2-microgobulin domain non-covalently bound
Other name of peptide binding cleft of MCH?
Peptide binding groove
What do MHC I bind?
Peptides generated in the cytoplasm of the cell, which may derive from:
- Aging self protein molecules that are replaced as a normal housekeeping function of the cell
- Pathogens in the cytosol
- As a result of the cell undergoing malignant transformation
What do MHC II bind?
Peptides derived from pathogens that have been taken up from outside the cell by the process of phagocytosis and been broken down inside the phagolysosome of professional APCs
Where does loading of MHC I occur?
In the ER
Where does loading of MHC II occur?
Late endosome/phagolysome
Structure of MHC Class II molecules?
- α chain with 2 α domains: 1 and 2
- β chain with 2 β domains: 1 and 2
β1 and α1 form a cleft together to bind a peptide
2 types of antigens/immunogens?
- Foreign: dangerous or innocuous
2. Self
What are the 9 properties of antigens i.e. the factors that influence their immunogenecity?
- Foreignness
- Molecular Size
- Chemical nature and composition
- Physical form
- Genetic factors
- Age
- Degradability
- Dose of the antigen
- Route of administration
How does foreignness of an antigen affect its immunogenicity?
The greater the phylogenetic distance the more immunogenic
How does molecular size of an antigen affect its immunogenicity?
- Antigens are generally 14 kDa to 600 kDa
- Molecules < 5-10 kDa are poor immunogens
- Small molecules below about 1 kD are not antigenic
- Some polysaccharides must be > 1,000 kD to be antigenic because they lack structural complexity
How do chemical nature and composition of an antigen affect its immunogenicity?
Generally, the more chemically complex the more immunogenic (e.g. with disulfide bonds, with 3D folded structure)
How does physical form of an antigen affect its immunogenicity? Why?
- Particulate antigens are more immunogenic than soluble ones because dendritic cells have an easier time taking up particulate antigens
- Denatured antigens are more immunogenic than the native form
How do genetic factors of individuals affect the immunogenicity of an antigen? Why?
Some substances are immunogenic in one species but not in another and some substances are immunogenic in one individual but not in another
Reason: the MHCs’ affinity to peptides is genetically determined
How does age of individual affect the immunogenicity of an antigen? Why?
Usually the very young and the very old have reduced ability to elicit an immune response to an immunogen
Reason: immune system is suboptimal
How does degradability of an antigen affect its immunogenicity? Why?
Antigens that are easily phagocytosed and degraded are generally more immunogenic
Reason: if it cannot be degraded it cannot be loaded onto an MHC
How does dose of an antigen affect its immunogenicity? Why?
There is a dose of antigen above or below which the immune response will be suboptimal
Reason: not enough antigen to trigger the dendritic cell or too much and saturates it/paralyzes it
How does route of administration of an antigen affect its immunogenicity? Why?
It can alter the nature of the response
Reason: given later in the course
Which APC is designed to take up soluble antigens? Why?
B cells because they have cell-associated Igs
What are adjuvants?
Any substance that enhances immunogenicity => molecules that contain pathogen-associated molecular patterns (PAMPS) or DAMPS (danger-associated molecular patterns)
Some convert soluble antigens to particulate antigens
4 effects of PAMPS binding to PPRs?
- Signal transduction
- Cytokine release
- Chemokine release
- Upregulation of various other molecules
What is an example of an antigen that requires an adjuvant to be immunogenic?
Tetanus toxoid vaccine
Do adjuvants form stable linkages with the immunogen?
NOPE
What is an example of a human adjuvant that convert soluble antigens to particulate antigens?
Al(OH)3
Modes of action of Al(OH)3 adjuvant?
- Delayed release of antigen
2. Enhanced uptake of antigen by APCs by converting soluble antigens to particulate antigens
Mode of action of complete Freund’s adjuvant?
Activates Th1 cells through TLR2 and TLR4
Composition of complete Freund’s adjuvant?
Oil-in-water emulsion with dead mycobacteria
Toxicity of complete Freund’s adjuvant?
High
Toxicity of Al(OH)3 adjuvant?
Very low
What are immune stimulatory complexes (ISCOMs)?
Adjuvants
Composition ISCOM adjuvant?
Matrix of Quil A (saponin = amphiphatic glycoside) containing viral proteins
Toxicity of ISCOM adjuvant?
Low
Mode of action of ISCOM adjuvant?
- Delivers antigens to cytosol
2. Allows induction of cytotoxic T cells
Do BCRs and TCRs recognize the entire antigen?
NOPE
Length of B cell epitope? What is this comparable to?
15-22 AAs
Length of peptides bound by MHC II
How many H bonds between epitope and paratope?
75-120 H bonds
Which are longer: peptides bound by MHC I or MHC II?
MHC II
18-20 vs 9-12 AAs
How can the number of epitopes affect the immune response? What do we call these antigens?
The immune response is more likely to be successful if the antigen contains a large number of different epitopes =
- Multivalant antigens with multiple epitopes that are identical or different
- Multideterminant antigens with multiple structurally different epitopes
3 types of epitopes? Which is most potent?
- ***Immunodominant
- Subdominant
- Cryptic
Differences between BCR and TCR epitopes?
- B-cell epitopes are generally accessible, mobile, hydrophilic and can be derived from native or denatured proteins
- T-cell epitopes are generally hydrophobic and are derived from the interior of the folded protein
What is a cryptic epitope? Example?
Epitope exposed by conformational change of the antigen
Example: HIV binding on receptor on CD4 T cell changes its conformation prior to entry into the cell
Other name for conformational epitope?
Discontinous epitope
What is a neoantigenic epitope?
Epitope created by proteolysis
What is a hapten? Example?
Small organic molecule of simple structure that does not provoke antibodies when injected by themselves
Example: urushiol = skin-sensitizing agent in poisoin ivy
How can antibodies against haptens be raised? What is this called? What to note?
If haptens are covalently attached to a protein carrier (does not need to be an immunogen) that is used in priming and challenge => carrier effect
Note: anti-carrier protein and anti-protein-hapten complex (neoepitope) antibodies will also be formed (minor though)
Why are anti-hapten antibodies important medically?
They mediate allergic reactions to penicillin and other compounds that elicit antibody responses when they attach to self-proteins in the blood
Other name for linear epitope?
Sequential epitope
What is the paratope formed by?
3D structure of the variable domain of the heavy and light chains
What does the strength of the binding between the epitope and the paratope depend on? What is this called?
Depends on the goodness of fit (complementarity) between paratope and epitope = hand in glove concept
What are the 4 different types of binding between an epitope and a paratope? Provide an example for each.
- Pocket: ferrocene (small hapten) with the complementaritydetermining regions (CDRs) of a Fab fragment
- Groove: HIV peptide
- Extended surface: hen egg-white lysozyme and the Fab fragment of its corresponding antibody (HyHel5) (all six CDRs of the antigen-binding site are involved in the binding)
- Protruding surface: antibody against HIV gp120 antigen has an elongated CDR3 loop that protrudes into a recess on the side of the antigen
Describe the binding between MHC I and peptides.
Peptide is bound in an elongated conformation with both ends tightly bound at either end of the cleft
Describe the binding between MHC II and peptides.
Peptide is also bound in an elongated conformation but the ends of the peptide are not tightly bound and the peptide extends beyond the cleft
What exactly is recognized by T cells?
The upper surface of the peptide:MHC complex composed of residues of the MHC molecule and the peptide
Why do MHC II bind longer peptides than MHC I?
Because with MHC II the ends of the peptide are not tightly bound and the peptide extends beyond the cleft
Can one paratope bind multiple epitopes?
YUP
What is a cross-reacting paratope?
Paratope that can bind multiple epitopes
What forces bind paratope to epitope? What does it mean?
Noncovalent forces:
- Electrostatic forces between opposite charges
- Hydrogen bonds
- Van der Waals forces
- Hydrophobic forces
=> REVERSIBLE binding
Do covalent bonds occur between antigens and naturally produced antibodies?
NOPE
What is intrinsic affinity between paratope and epitope?
The goodness of fit between a single epitope and paratope aka the degree of complementarity
What is functional affinity between paratope and epitope?
The increase of affinity resulting from valency, i.e., 2 or more epitope-paratope interactions
What is avidity between paratope and epitope?
The average function affinity of a population of antibodies recognizing epitopes on an antigen
This is what happens in a normal polyclonal humoral immune response
By how much is affinity increasing by bivalency?
x10,000 increase
What is a multivalant antibody?
Antibody molecules that have either two, four or ten paratopes
What are mitogens? Which cells can they activate?
Antigens that trigger signal transduction pathways in which mitogen-activated protein kinase (MAPK) is involved, leading to mitosis
They have the capacity to activate ALL B cells or ALL T cells and some can activate both B and T cells
What are superantigens? Which cells can they activate?
Antigens from some bacteria and viruses that can bind independently to MHC class II molecules outside the peptide-binding site and to TCRs (Vβ domain = variable domain) away from the complementarity determining regions, regardless of their specificity
They can activate any CD4 T cell that has the appropriate binding site on the Vβ domain.
What are T-independent antigens? What are they important for? What to note? Which cells can they activate?
Antigens with repeating epitopes that can activate B cells without the need for T cell help
This ability is important early in the adaptive immune response to generate IgM antibodies
Note: however, without T cell help, B cells cannot make other types of antibody such as IgG or IgA
Difference between particulate and soluble antigens?
- Soluble antigens: molecules that dissolve in a solvent in the human body, the solvent being tissue fluid, lymph, blood, etc.
- Particulate antigens: microorganisms (bacteria, fungi, virus particles, etc.)
The importance difference between the two is the ease with which antigen-presenting cells (APCs) take them up. Only the B-cell takes up soluble antigens efficiently. The DC and macrophage (MO) use pinocytosis which is less efficient.
