The document discusses immune recognition molecules, focusing on major histocompatibility complex (MHC), T-cell receptors, T-cell epitopes, T-cell markers, B-cell epitopes, and Toll-like receptors. It describes how MHC molecules present antigen peptides to T cells to initiate immune responses. MHC class I molecules present intracellular peptides to CD8+ T cells, while class II molecules present extracellular peptides to CD4+ T cells. MHC molecules bind peptides through their peptide-binding cleft in a polymorphic and promiscuous manner. Very few peptide-MHC complexes are needed to activate antigen-specific T cells.

1. DEPARTMENT OF MICROBIOLOGY AND
IMMUNOLOGY
IMMUNE RECOGNITION MOLECULES (MHC, T-
CELL RECEPTORS, T-CELL EPITOPES, T CELL
MARKERS, B CELL EPITOPES, TOLL LIKE
RECEPTORS)
Facilitator: DR S. S. MASOUD
Presenter: Victoria Shayo
Venue: Microbiology Lab
Date: 29/05/2023
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2. Learning Outcomes
• Describe IMMUNE RECOGNITION MOLECULES
• Explain MHC, T-CELL RECEPTORS, T-CELL EPITOPES, T
CELL MARKERS, B CELL EPITOPES, TOLL LIKE
RECEPTORS
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3. Outlines
• Introduction
• Major Histocompatibility Complex
• T-cell receptors
• T-cell epitopes
• T-cell Markers
• B-cell epitopes
• Toll-like Receptors
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4. Introduction
IMMUNE RECOGNITION MOLECULE(IRM)
These are the major proteins of the
immune system.
Before any immune mechanism can go
into action, there must be a recognition
that something exists for it to act against
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5. Forms of IRM
Soluble molecules including Cytokines,
Interleukins, antibodies, Complements and
metabolites.
Cell membrane associated including
markers (CD), receptors (BCR, TCR,
MHCI, MHCII etc.), co stimulatory
molecules e.g. B7 family on DCs
,adhesion molecules (integrins, selectins,
mucins, etc.) and Tumour markers e.g
CEA 125
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6. The immune recognition and receptors in innate
and adaptive immunity
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9. Major Histocompatibility Complex
• The major histocompatibility complex (MHC) is a large
locus on vertebrate DNA containing a set of closely
linked polymorphic genes that code for cell surface
proteins essential for the adaptive immune system.
• The major histocompatibility complex is located on
chromosome 6 in humans and extends over some 4
centimorgans of DNA, about 4 × 106 base pairs.
• In humans it contains more than 224 genes, and about
half have known immune functions
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10. Major Histocompatibility Complex
• The genes encoding the α chains of MHC class I molecules
and the α and β chains of MHC class II molecules are linked
within the complex.
• In humans these genes are called Human Leukocyte Antigen or
HLA genes, as they were first discovered through antigenic
differences between white blood cells from different individuals.
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11. Expression of MHC Molecules
• Because MHC molecules are required to present
antigens to T lymphocytes, the expression of these
proteins in a cell determines whether foreign antigens in
that cell will be recognized by T cells.
• There are several important features of the expression
of MHC molecules that contribute to their role in
protecting individuals from different microbial infections.
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12. Expression of MHC Molecules
 Class I molecules are expressed on virtually all nucleated cells, whereas
class II molecules are expressed only on dendritic cells, B lymphocytes,
macrophages, thymic epithelial cells, and a few other cell types.
 MHC I displays endogenous antigens, or antigens from within the cell, while
MHC II displays exogenous antigens, or antigens from outside the cell.
These outside antigens are obtained by way of phagocytosis, so only
phagocytes in the body have MHC-2.
 CD8+ CTLs kill cells infected with intracellular microbes, such as viruses,
as well as tumours that express tumor antigens, and any nucleated cell
can harbour a virus or develop into cancer.
 In contrast, class II–restricted CD4+ helper T lymphocytes have a set of
functions that require recognizing antigen presented by a more limited
number of cell types, and class II molecules are expressed mainly on
these cell types, for the following reasons.
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13. Expression of MHC Molecules
 The expression of MHC molecules is increased by cytokines produced
during both innate and adaptive immune responses.
 Although class I molecules are constitutively expressed on nucleated cells, their
expression is increased by the type I interferons IFN-α and IFN-β, which are
produced during the early innate immune response to many viruses.
 The expression of class II molecules is regulated by cytokines and other signals
in different cells. IFN-γ is the principal cytokine involved in stimulating expression
of class II molecules in APCs such as DCs and macrophages.
 B lymphocytes constitutively express class II molecules and can increase
expression in response to antigen recognition and cytokines produced by helper
T cells, thus enhancing antigen presentation to helper cells .
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14. Expression of MHC Molecules
 The rate of transcription is the major determinant of the level of MHC
molecule synthesis and expression on the cell surface.
 Cytokines enhance MHC expression by stimulating the transcription of class I
and class II genes in a wide variety of cell types. These effects are mediated by
the binding of cytokine-activated transcription factors to DNA sequences in the
promoter regions of MHC genes.
 Several transcription factors may be assembled and bind a protein called the
class II transcription activator (CIITA), which is a member of the NOD-like
receptor family, and the entire complex binds to the class II promoter and
promotes efficient transcription of the gene.
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15. General Properties of MHC Molecules
Each MHC molecule consists of an extracellular peptide-
binding cleft, followed by an immunoglobulin (Ig)–like
domain and transmembrane and cytoplasmic domains.
Class I molecules are composed of one polypeptide
chain encoded in the MHC and a second, non-
MHC–encoded chain, whereas class II molecules
are made up of two MHC-encoded polypeptide
chains.
Despite this difference, the overall three-
dimensional structures of class I and class II
molecules are similar.
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16. General Properties of MHC Molecules
The polymorphic amino acid residues of
MHC molecules are located in and
adjacent to the peptide-binding cleft.
 This cleft is formed by the folding of the
amino termini of the MHC-encoded proteins
and is composed of paired α helices forming
the two walls of the cleft, resting on a floor
made up of an eight-stranded β-pleated
sheet.
 This portion of the MHC molecule binds
peptides for display to T cells, and the
antigen receptors of T cells interact with the
displayed peptide and also with the α helices
of the MHC molecules.
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17. General Properties of MHC Molecules
 The nonpolymorphic Ig-like domains of class II and class I MHC
molecules contain binding sites for the T cell molecules CD4 and
CD8, respectively.
 CD4 and CD8 are expressed on distinct subpopulations of mature T
lymphocytes and participate, together with antigen receptors, in the
recognition of antigen.
 CD4 binds selectively to class II MHC molecules, and CD8 binds to class
I molecules.
 This is why CD4+ helper T cells recognize class II MHC molecules
displaying peptides, whereas CD8+ T cells recognize class I MHC
molecules with bound peptides..
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18. Class I MHC Molecules
• Class I MHC molecules consist
of two noncovalently linked
polypeptide chains, an MHC-
encoded α chain (or heavy
chain) and a non-MHC–
encoded subunit called β2-
macroglobulin.
• The amino-terminal α1 and α2
segments of the α chain interact
to form a platform of an eight-
stranded, antiparallel β-pleated
sheet supporting two parallel
strands of α helix.
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19. Class I MHC Molecules
• This forms the peptide-binding cleft of class I molecules.
Its size is large enough to bind peptides of 8 to 11 amino
acids in a flexible, extended conformation.
• The α3 segment of the α chain folds into an Ig domain
whose amino acid sequence is conserved among all
class I MHC molecules.
• This segment contains most of the binding site for CD8,
but β2-microglobulin and a small part of the
nonpolymorphic C-terminal portion of the α2 domain
also contribute.
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20. Class I MHC Molecules
• The fully assembled class I molecule is a trimeric
complex consisting of an α chain, β2-microglobulin, and
a bound peptide, and stable expression of class I
molecules on cell surfaces requires the presence of all
three components of the complex.
• Most individuals are heterozygous for MHC genes and
therefore express six different class I molecules on
every cell, containing α chains encoded by the two
inherited alleles of HLA-A, B, and C genes.
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21. Class II MHC Molecules
• Class II MHC molecules are
composed of two noncovalently
associated polypeptide chains, a
32- to 34-kD α chain, and a 29- to
32-kD β chain.
• Unlike class I molecules, the genes
encoding both chains of class II
molecules are polymorphic and
located in the MHC locus.
• The amino-terminal α1 and β1
segments of the class II chains
interact to form the peptide-binding
cleft, which is structurally similar to
the cleft of class I molecules.
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22. Class II MHC Molecules
• The ends of the peptide-binding cleft of class II
MHC molecules are open, so peptides of 30
residues or more can bind.
• The α2 and β2 segments of class II MHC
molecules, like class I α3 and β2-microglobulin,
are folded into Ig domains and are
nonpolymorphic—that is, they do not vary among
alleles of a particular class II gene.
• Both the α2 and β2 domains of class II molecules
contribute to a concavity that accommodates a
protrusion of the CD4 protein, thus allowing
binding to occur.
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23. Class II MHC Molecules
• The fully assembled class II MHC molecule is a trimer
consisting of one α chain, one β chain, and a bound
antigenic peptide, and stable expression of class II
molecules on cell surfaces requires the presence of all
three components of the complex.
• Humans inherit, from each parent, one DPA and one
DPB gene encoding, respectively, the α and β chains of
an HLA-DP molecule; one functional DQA and one DQB
gene; one DRA and one or two functional DRB genes.
• Thus, each heterozygous individual expresses six to
eight pairs of class II MHC α and β chain molecules, one
set each of DP and DQ, and one or two of DR.
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24. Features of Class I and Class II MHC Molecules
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25. Features of Class I and Class II MHC Molecules
Cont…..
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26. Binding of Peptides To MHC
 Characteristics of Peptide-MHC Molecule Interactions
• MHC molecules show a broad specificity for peptide binding, in
contrast to the fine specificity of antigen recognition by the antigen
receptors of lymphocytes.
• In other words, a single MHC allele (e.g., HLA-A2) can present any
one of many different peptides to T cells, but a single T cell will
recognize only one of these many possible HLA-A2/peptide
complexes.
• There are several important features of the interactions of MHC
molecules and antigenic peptides.
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27. Binding of Peptides To MHC
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28. 6/18/2023 Vickie 28

29. Binding of Peptides To MHC
Each class I or class II MHC molecule has a
single peptide-binding cleft that binds one
peptide at a time, but each MHC molecule can
bind many different peptides.
It is not surprising that a single MHC molecule
can bind multiple peptides, because each
individual contains only a few different MHC
molecules and these must be able to present
peptides from the enormous number of protein
antigens that one is likely to encounter.
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30. Binding of Peptides To MHC
The peptides that bind to MHC molecules share
structural features that promote this interaction.
 One of these features is the size of the peptide—class I
molecules can accommodate peptides that are 8 to 11
residues long, and class II molecules bind peptides that
may be 10 to 30 residues long or longer, the optimal
length being 12 to 16 residues.
 In addition, peptides that bind to a particular MHC
molecule contain amino acid residues that allow
complementary interactions between the peptide and
that MHC molecule.
 The residues of a peptide that bind to MHC molecules
are distinct from those that are recognized by T cells.
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31. Binding of Peptides To MHC
MHC molecules acquire their peptide cargo during
their biosynthesis and assembly inside cells.
Therefore, MHC molecules display peptides
derived from microbial antigens that are inside host
cells, and this is why MHC-restricted T cells are
able to recognize microbes that infect or are
ingested into cells.
Importantly, class I MHC molecules acquire
peptides from cytosolic proteins that are digested
into peptides by a cytosolic enzyme complex, and
class II molecules acquire peptides from
extracellular proteins that are ingested into and
digested in endocytic vesicles.
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32. Binding of Peptides To MHC
The association of peptides and MHC molecules is a
saturable interaction with a very slow off-rate.
 In a cell, several chaperones and enzymes facilitate the
binding of peptides to MHC molecules.
 Once formed, most peptide-MHC complexes are stable,
and kinetic dissociation constants are indicative of long
half-lives that range from hours to many days.
 This extraordinarily slow off-rate of peptide dissociation
from MHC molecules ensures that after an MHC
molecule has acquired a peptide, it will display the
peptide long enough to maximize the chance that a
particular T cell will find the peptide it can recognize and
initiate a response.
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33. Binding of Peptides To MHC
 Very small numbers of peptide-MHC complexes are capable of
activating specific T lymphocytes.
 Because APCs continuously present peptides derived from all the
proteins they encounter, only a very small fraction of cell surface
peptide–MHC complexes will contain the same peptide.
 It has been estimated that as few as 100 complexes of a particular
peptide with a class II MHC molecule on the surface of an APC can
initiate a specific T cell response.
 This represents less than 0.1% of the total number of class II
molecules likely to be present on the surface of the APC.
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34. Binding of Peptides To MHC
The MHC molecules of an individual can bind and
display foreign peptides (e.g., those derived from
microbial proteins) as well as peptides derived from the
proteins of that individual (self antigens)
 In fact, most of the peptides being displayed normally by
APCs are derived from self proteins.
 Self peptide–MHC complexes do not induce
autoimmunity because T cells specific for such
complexes are killed or inactivated.
 In fact, T cells with receptors for self antigens must
recognize self peptides displayed by self MHC
molecules in order to be eliminated or made
unresponsive. These processes ensure that T cells are
normally tolerant to self antigens.
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35. The Phenomenon Of MHC Restriction
The formal proof that the MHC is involved in
antigen recognition by T cells came from the
experimental demonstration of MHC restriction by
Rolf Zinkernagel and Peter Doherty.
Thus, T cells must be specific not only for the
antigen but also for MHC molecules, and T cell
antigen recognition is restricted by the MHC
molecules a T cell sees.
Subsequent studies established that the
recognition of antigens by CD8+ CTLs is restricted
by class I MHC molecules, and the responses of
CD4+ helper T lymphocytes to antigens are
restricted by class II MHC molecules.
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36. The Phenomenon Of MHC Restriction
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37. T-cell Receptors
• Protein complex found on the surface of T Lymphocytes
that is responsible for recognizing fragments of antigens
as peptides bound to major histocompatibility complex
molecules.
• The practical function of these receptors is to enable a
T‐cell to probe the surfaces of cells looking for nonself
peptides.
 If a T‐cell finds a peptide–MHC combination that is a good
match for its TCR it will become activated, undergo clonal
expansion, and differentiate to a mature effector T‐cell capable
of joining the fight against the infectious agent generating these
nonself peptides.
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38. T-cell Receptors
Structure:
 The antigen receptor is a heterodimer consisting of two
transmembrane polypeptide chains, designated TCR α and
β, covalently linked to each other by a disulfide bridge
between extracellular cysteine residues.
 Each TCR α and β chain consists of one Ig-like N-terminal
variable (V) domain, one Ig-like constant (C) domain, a
hydrophobic transmembrane region, and a short cytoplasmic
region.
 Thus, the extracellular portion of the TCR αβ heterodimer is
structurally similar to the antigen-binding fragment (Fab) of
an Ig molecule, which is made up of the V and C regions of a
light chain and the V region and the first C region of a heavy
chain.
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39. T-cell Receptors
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Structure of the T-cell Receptor:

40. T-cell Epitopes
• T-cell epitopes are peptides derived from antigens and
recognized by the TCR when bound to MHC molecules
displayed on the cell surface of APCs.
• CD4 T-cells express the CD4 coreceptor, which binds to
MHC II, and recognize peptides presented by MHC II
molecules.
• CD8 T-cells express the CD8 coreceptor, which binds to
MHC I, and recognize peptides presented by MHC I
molecules.
• T cell epitopes presented by MHC class I molecules are
typically peptides between 8 and 11 amino acids in
length whereas MHC class II molecules present 13-17
a.acids.
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41. Function of T cell receptor
What Does the αβ T Cell Receptor (TCR)
Recognize?
• Only fragments of proteins (peptides)
associated with MHC molecules on
surface of cells
• Helper T cells (Th) recognize peptide
associated with MHC class II molecules
• Cytotoxic T cells (Tc) recognize peptide
associated with MHC class I molecules
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42. T-cell Epitopes
T-cell
epitope
recognit
ion
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43. T-cell Markers
• Is a group of cell surface protein marker on the
white blood cells used to classify immune cell
types and establish international nomenclature
standards.
• The markers are found on many blood cells and
are most often used to refer Lymphocytes,
• The system of assigning markers is intended for
classification of many monoclonal antibodies
generated by different laboratories around the
world against epitopes on the surface
molecules of leukocytes.
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44. T-cell Markers
Designation/Nomenclature
These cell surface markers are designated by
prefix CD followed by a number. The number
reflect the order in which the cell surface
marker was discovered.
At present it ranges from CD1 to CD371. It is
useful in identifying many different types of
Leukocytes.
It tells about cell lineage, species to which cell
belong, stage of maturation or activation of the
cell.
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45. B-cell Epitopes
• Antigen-antibody interaction is a key event in
humoral immune response to invading pathogen.
• A specific antibody (Ab) recognizes antigen (Ag)
at discrete regions known as antigenic
determinants or B-cell epitopes.
• B-cell epitopes can be defined as a surface
accessible clusters of amino acids, which are
recognized by secreted antibodies or B-cell
receptors and are able to elicit cellular or humoral
immune response
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46. B-cell Epitopes
• B-cell epitopes are
solvent-exposed
portions of the
antigen that bind to
secreted and cell-
bound Igs.
• B-cell receptors
encompass cell-
bound Igs, consisting
of two heavy chains
and two light chains.
• The different chains
and regions are
annotated.
B-cell epitope
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47. B-cell Epitopes
• Based on the spatial structure B-cell epitopes
can be categorized as;
– a continuous (linear or sequential) and
– discontinuous (nonlinear or conformational)
epitopes;
• in the latter case amino acid residues are in
close contact due to the three-dimensional
conformation.
• Antibodies are developed to bind the epitope
with high affinity by using complementary
determining regions (CDRs).
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48. Function of B Cell
What Does The B Cell Immunoglobulin
(Ig) Receptor Recognize?
• Proteins (conformational determinants,
denatured or proteolyzed determinants)
• Nucleic acids
• Polysaccharides
• Some lipids
• Small chemicals (haptens)
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49. Toll-like Receptors
• Toll-like receptors (TLRs) are an evolutionarily
conserved family of pattern recognition receptors
expressed on many cell types that recognize products of
a wide variety of microbes, as well as molecules
expressed or released by stressed and dying cells.
• Named on the basis of their similarity to the Toll receptor
in the fruit fly, Drosophila.
• There are 10 expressed TLR genes in humans and each
is devoted to recognizing a distinct set of molecular
patterns that are not found in healthy vertebrate cells.
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50. Toll-like Receptors
Structure
 All TLRs have the same basic structural features, with
multiple N‐terminal leucine‐rich repeats (LRRs)
arranged in a horseshoe‐ or crescent‐shaped solenoid
structure that acts as the PAMP‐binding domain.
 All mammalian TLR proteins have a TIR (for Toll-IL-l
receptor) domain in their cytoplasmic tail, which
interacts with other TIR-type domains, usually in other
signalling molecules.
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51. Toll-like Receptors
Structure
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52. Toll-like Receptors
Location
 TLRs are found on the cell surface and on intracellular
membranes and are thus able to recognize microbes in
different cellular locations.
 TLRs 1, 2, 4, 5, and 6 are expressed on the plasma
membrane, where they recognize various PAMPs in the
extracellular environment.
 In contrast, TLRs 3, 7, 8, and 9 are mainly expressed
inside cells on endoplasmic reticulum and endosomal
membranes, where they detect several different
microbial nucleic acids.
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53. Toll-like Receptors
Location
The cellular locations of the mammalian Toll-like receptors
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54. Toll-like Receptors
Ligands
 Mammalian TLRs are involved in responses to a wide
variety of molecules that are expressed by microbes
but not by healthy mammalian cells.
 The ligands that the different TLRs recognize are
structurally diverse and include products of all classes
of microorganisms.
– Examples of bacterial products that bind to TLRs are the
bacterial cell wall constituents (LPS and lipoteichoic acid),
flagellin, a protein subunit component of the flagella of motile
bacteria.
– Examples of nucleic acids that are TLR ligands are double-
stranded RNAs, single-stranded RNAs, and unmethylated
CpG dinucleotides
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55. 6/18/2023 Vickie 55

56. Toll-like Receptors
• Upon binding of a PAMP, TLRs transduce signals into
the cell via their TIR domains, which recruit adaptor
proteins within the cytoplasm that possess similar TIR
motifs.
• These adaptors propagate the signal downstream,
culminating in activation of NFκB and interferon
regulatory family (IRF) transcription factors (AP-1, IRF3,
and IRF7).
• NF-κB and AP-1 stimulate the expression of genes
encoding many of the molecules required for
inflammatory responses, including inflammatory
cytokines (TNF and IL-1), chemokines (CCL2 and
CXCL8), and endothelial adhesion molecules ( E-
selectin).
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57. Toll-like Receptors
• IRF3 and IRF7 promote production of type I interferons
(IFN-α and IFN-β), which are important for antiviral
innate immune responses.
• Different combinations of adaptors and signaling
intermediates are used by different TLRs, accounting for
the common and unique downstream effects of the
TLRs.
• For example, cell surface TLRs that engage the adaptor
MyD88 lead to NF-κB activation, and TLR signaling that
uses the adaptor called TRIF (TIR domain– containing
adaptor inducing IFN-β) leads to IRF3 activation.
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58. Toll-like Receptors
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59. REFERENCES
1. Delves, P., Martin, S., Burton, D. and Roitt, I., 2017. Roitt's essential
immunology. 13th ed. Oxford: WILEY Blackwell, pp.23-24.
2. Potocnakova, L., Bhide, M., & Pulzova, L. B. (2016). An Introduction to B-
Cell Epitope Mapping and In Silico Epitope Prediction. Journal of
immunology research, 2016, 6760830.
https://doi.org/10.1155/2016/6760830
3. Abbas, A., Lichtman, A. and Pillai, S., 2018. Cellular and molecular
immunology. 9th ed. Philadelphia: ELSEVIER.
4. Kenneth, M., Weaver, C. and Janeway, C., 2017. Janeway's
immunobiology. 9th ed. New York: Garland Science.
5. Handbook of Systemic Autoimmune Diseases, 2017
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60. •THANK
YOU
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