Download Prediction of B cell epitopes

Prediction of B cell epitopes
Pernille Haste Andersen
Immunological Bioinformatics
CBS, DTU
[email protected]
B cells and antibodies

Antibodies are produced by B lymphocytes
(B cells)

Antibodies circulate in the blood


They are referred to as “the first line of
defense” against infection
Antibodies play a central role in immunity
by attaching to pathogens and recruiting
effector systems that kill the invader
What is a B cell epitope?
B cell epitopes

Accessible and
recognizable structural
feature of a pathogen
molecule (antigen)

Antibodies are developed
to bind the epitope with
high affinity by using the
complementarity
determining regions
(CDRs)
Antibody Fab
fragment
B cell epitope
Motivations for prediction of B cell epitopes
 Prediction of B cell epitopes can potentially
guide experimental epitope mapping
 Predictions of antigenicity in proteins can be
used for selecting subunits in rational vaccine
design
 Predictions of B cell epitopes may also be
valuable for interpretation of results from
experiments based on antibody affinity binding
such as ELISA, RIA and western blotting
Computational Rational Vaccine
Design
>PATHOGEN PROTEIN
KVFGRCELAAAMKRHGLDNYR
GYSLGNWVCAAKFESNF
Rational Vaccine
Design
B cell epitopes, linear or
discontinuous?
 Classified into linear (~10%) and discontinuous
epitopes (~90%)
 Databases: AntiJen, IEDB, BciPep, Los Alamos
HIV database, Protein Data Bank
 Large amount of data available for linear epitopes
 Few data available for discontinuous epitopes
 In general, B cell epitope prediction methods have
relatively low performances
Discontinuous B cell epitopes
An example: The epitope of
the outer surface protein A
from Borrelia Burgdorferi
(1OSP)
SLDEKNSVSVDLPGEMKVLV
SKEKNKDGKYDLIATVDKLEL
KGTSDKNNGSGVLEGVKADK
CKVKLTISDDLGQTTLEVFKE
DGKTLVSKKVTSKDKSSTEE
KFNEKGEVSEKIITRADGTRLE
YTGIKSDGSGKAKEVLKG
•
..\Discotope\1OSP_epitope\1OSP_epitope.psw
A data set of 3D discontinuous
epitopes
 A data set of 75 discontinuous epitopes was
compiled from structures of antibodies/protein
antigen complexes in the PDB
 The data set has been used for developing a method
for predictions of discontinuous B cell epitopes
 Since about 30 of the PDB entries represented
Lysozyme, I have used homology grouping (25
groups of non-homologous antigens) and 5 fold
cross-validation for training of the method
 Performance was measured using ROC curves on a
per antigen basis, and by weighted averaging of AUC
values
Epitope log-odds ratios
Table 1. The Parker hydrophilicity
scale and epitope log-odds ratiosa
 Frequencies of amino acids in epitopes
Amino acid
Parker
Log-odds
Ratios
D
2.460
0.691
compared to frequencies of non-epitopes
E
1.860
0.346
N
1.640
1.242
S
1.500
-0.145
Q
1.370
1.082
G
1.280
0.189
K
1.260
1.136
T
1.150
-0.233
R
0.870
1.180
P
0.300
1.164
H
0.300
1.098
C
0.110
-3.519
A
0.030
-1.522
Y
-0.780
0.030
V
-1.270
-1.474
M
-1.410
0.273
I
-2.450
-0.713
F
-2.780
-1.147
L
-2.870
-1.836
W
-3.000
-0.064
Several discrepancies compared to the
Parker hydrophilicity scale which is often
used for epitope prediction
Both methods are used for predictions
using a sequential average of scores
Predictive performance of B cell epitopes:
Parker
0.614 AUC
Epitope log–odds
0.634 AUC
a
Amino acids are listed with descending
hydrophilicity using the values of the Parker
scale.
3D information: Contact numbers
Surface exposure and
structural protrusion can
be measured by residue
contact numbers
The predictive performance:
Parker
Epitope log–odds
Contact numbers
0.614 AUC
0.634 AUC
0.647 AUC
DiscoTope : Prediction of Discontinuous
epiTopes using 3D structures
A combination of:
– Sequentially averaged epitope logodds values of residues in spatial
proximity
– Contact numbers
.LIST..FVDEKRPGSDIVED……ALILKDENKTTVI.
-0.145
+0.691+0.346+1.136+1.180+1.164
+0.346
Contact number :
K 10
+1.136
Sum of log-odds
values
DiscoTope prediction
value
DiscoTope : Prediction of Discontinuous
epiTopes
 Improved prediction of residues in discontinuous B
cell epitopes in the data set
 The predictive performance on B cell epitopes:
Parker
0.614 AUC
Epitope log–odds
0.634 AUC
Contact numbers
0.647 AUC
DiscoTope
0.711 AUC
Evaluation example AMA1
• Apical membrane antigen 1 from
Plasmodium falciparum (not used
for training/testing)
• Two epitopes were identified using
phage-display, point-mutation
(black side chains) and sequence
variance analysis (side chains of
polyvalent residues in yellow)
• Most residues identified as epitopes
were successfully predicted by
DiscoTope (green backbone)
..\Discotope\1Z40_epitope\1Z40_movie.mov
DiscoTope is available as web server:
http://www.cbs.dtu.dk/services/DiscoTope/
Future improvements
 Add epitope predictions for protein-protein
complexes
 Visualization of epitopes integrated in web server
 Testing a score for sequence variability fx based on
entropy of positions in the antigens
 Combination with glycosylation site predictions
 Combination with predictions of trans-membrane
regions
 Assembling predicted residues into whole epitopes
Presentation of the web server
Presentation of the web server
output
Acknowledgements
DiscoTope
Ole Lund
 Ideas, supervision and support
Morten Nielsen
 Ideas, development of method and web server
Nicholas Gauthier
 Improving the method, improving the web server