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B-Cell Epitopes
Chapter 10
Claus
Lundegaard
Antibodies
Antibodies. What are they?
• Virtually any substance can elicit an antibody
response.
• Clear extra cellular pathogens
• neutralizing antibodies
• Antibody repertoire
• >
11
10
in humans
• How is this possible?
• ~ 30.000 genes in the humans genome!
• Immunoglobulin gene rearrangement
Antibody Effect. Neutralizing Antibodies
Virus or Toxin
Neutralizing Antibodies
Inhibit cellular infection
Clear pathogen infection
Antibody - Antigen interaction
Antigen
Fab (fragment antigen binding)
Epitope
Paratope
Antibody
B-Cells. How are they made?
Stem Cell
Precurser Blymphocytes
Gene
rearrangements
B-lymphocytes each displaying a unique B-cell receptor
Gene Shuffling
Number of gene segments
The 12/23 rule of recombination
{
recombination signal sequence (RSS)
Only combined 12 RSS to 23 RSS
Mechanism of gene rearrangement
RAG proteins (recombinationactivating genes)
Addition of P and N nucleotides
Antibody variable regions, CDR’s
(Complementarity-determining regions)
CDR Regions
Variable regions
Alpha-carbon trace of the structure of the heavy chain and light chain variable regions
of a typical antibody. The framework regions of both chains are shown in grey whilst the
complementarity determining regions (CDRs) are coloured individually, i.e.
CDR = complementarity determining region
Heavy chain
CDR 1 = Light blue
CDR 2 = Cerise
CDR 3 = Yellow
Light Chain
CDR 1 = Red
CDR 2 = Green
CDR 3 = Blue
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.
http://212.219.234.139/html/anti_alpha.html
Identifying CDR regions
• The Kabat definition is based on sequence
variability and is the most commonly used
• The Chothia definition is based on the location
of the structural loop regions
• The AbM definition is a compromise between
the two used by Oxford Molecular's AbM
antibody modelling software
• The contact definition has been recently
introduced by us and is based on an analysis of
the available complex crystal structures.
Identification of CDR’s (II)
CDR-H1
Start Approx residue 26 (always 4 after a Cys) [Chothia / AbM defintion];
Kabat definition starts 5 residues later
Residues before always Cys-XXX-XXX-XXX
Residues after always a Trp. Typically Trp-Val, but also, Trp-Ile, Trp-Ala
Length 10 to 12 residues [AbM definition];
Chothia definition excludes the last 4 residues
CDR-H2
Start always 15 residues after the end of Kabat / AbM definition) of CDR-H1
Residues before typically Leu-Glu-Trp-Ile-Gly, but a number of variations
Residues after Lys/Arg-Leu/Ile/Val/Phe/Thr/Ala-Thr/Ser/Ile/Ala
Length Kabat definition 16 to 19 residues;
AbM (and recent Chothia) definition ends 7 residues earlier
CDR-H3
Start always 33 residues after end of CDR-H2 (always 2 after a Cys)
Residues before always Cys-XXX-XXX (typically Cys-Ala-Arg)
Residues after always Trp-Gly-XXX-Gly
Length 3 to 25(!) residues
Example
>BU02A02.1
GVQCEVHLLESGGGLVQPGGSLRLSCAASGFTF
YSYAMSWVRQAPGKGLEWVSANSGSGGSTY
YADSVRGRFTISRDNSKNTLYLQMNSLSAEDT
AVYFCAKAPGYYYYYGMDVWGQGTTVTVSSG
KNGHSRAFV
15 amino acids after end of CDR1
Somatic hypermutations
B-Cell Activation
(Proliferation depends on affinity)
No Affinity
Low Affinity
No Affinity
Somatic Hypermutations
High Affinity
Plasma cells
Memory B-cells
B-Cell Activation
T Helper Cell
TCR
B Cell
Class II MHC
Bound Peptide
Cartoon by Eric Reits
Controversial issues
• Is the 11/23 rule always obeyed?
• Can you have multiple D genes?
• Can D genes be inserted backwards?
• I.e can both D and the inverted D genes be
used?
• Does V, D and J palindrom segments exits?
What did we find?
• Issue of next talk