Homology Modeling - Cayetano Heredia University

Report
Role of Bioinformatics in designing
vaccines
Urmila Kulkarni-Kale
Information Scientist
Bioinformatics Centre
University of Pune, Pune 411 007 India
[email protected]
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
1
Biological Research
• Biology is study of life and is a
descriptive science.
• Macro
micro properties
• Research methods are
• In vivo
• In vitro
Diversity:
forms and functions
• In silico
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
2
What is Bioinformatics?
Bioinformatics is a “scientific
discipline that encompasses all
aspects of biological information
acquisition, processing, storage,
distribution, analysis and
interpretation”.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
3
B I O L O G Y
P H Y S I O M I C S
Bioinformatics
C E bridges
L L O Mmany
I C Sdisciplines
B I O T E C H
E V O L U T I O N
I N F O T E C H
Bioinformatics combines the tools of
O N T O L O G Y
P R O Mathematics,
T E O M I C S
Biology, Chemistry,
M O L E C U L A R M O D E L I N G
Statistics and Computer Science to
M A T H E M A T I C S
understand Life
M E&
T its
A Bprocesses.
O L O M I
C S
T R A N S C R I P T O M I C S
G E N O M I C S
S T A T I S T I C S
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
4
B I O
The “omics” Series
L O G Y
P H Y S I O M I C S
C E L L O M I C S
Omics is
B I O T E C H
Latin word for
Genomics
Transcriptomics
E V O L U T I O N
‘Give us
Gene identification
profiles
I N F Expression
O T&
E C H
money’!
Genomics
Proteomics
O N T Structural
O L O G of
Y mRNA
characterization
P RLarge
O T E scale
O M I structure
C S
functions & interactions
M O L E C U L A R M O Ddetermination
E L I N G
of proteins
Cellinomics
M A T H E M A T I C S
Pharmacogenomics
MetabolicMPathways
E T A B O L O M I C S
design
T R A N Sinteractions
CGenome-based
R I P T O M I C drug
S
Cell-cell
G E N O M I C S
S T A T I S T I C S
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
5
Nature of
Biological data
Post-Genomic era:
Genomes
Proteomes
Metabolomes
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
6
Approaches for vaccine development
 Recombinant DNA vaccines
 Peptide Vaccines
 Polytope Vaccines
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
7
Vaccine development
In Post-genomic era:
Reverse Vaccinology
Approach.
•
September 2K3
Rappuoli R. (2000). Reverse
vaccinology.
Curr
Opin
Microbiol. 3:445-450.
Bioinformatics Centre, University of
Pune, Pune.
8
Genome Sequence
Proteomics
Technologies
In silico
analysis
DNA
microarrays
High throughput
Cloning and expression
In vitro and in vivo assays for
Vaccine candidate identification
Global
genomic
approach
to Centre,
identify
new
vaccine candidates
September
2K3
Bioinformatics
University
of
9
Pune, Pune.
In Silico Analysis
Peptide
Multiepitope
vaccines
VACCINOME
Candidate Epitope DB
Epitope prediction
Disease related protein DB
September 2K3
Bioinformatics
Centre, University
of
Gene/Protein
Sequence
Database
Pune, Pune.
10
What Are Epitopes?
Antigenic determinants or Epitopes are the
portions of the antigen molecules which are
responsible for specificity of the antigens in
antigen-antibody (Ag-Ab) reactions and
that combine with the antigen binding site
of Ab, to which they are complementary.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
11
Epitopes …
B-cell epitopes
September 2K3
Th-cell epitopes
Bioinformatics Centre, University of
Pune, Pune.
12
Methods to identify epitopes
1. Immunochemical methods
•
•
•
ELISA : Enzyme linked immunosorbent assay
Immunoflurorescence
Radioimmunoassay
2. X-ray crystallography: Ag-Ab complex is
crystallized and the structure is scanned for contact
residues between Ag and Ab. The contact residues on
the Ag are considered as the epitope.
3. Prediction methods: Based on the X-ray crystal
data available for Ag-Ab complexes, the propensity
of an amino acid to lie in an epitope is calculated.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
13
Epitope prediction methods
B cell epitope prediction algorithms :
• Hopp and Woods –1981
• Welling et al –1985
• Parker & Hodges - 1986
• Kolaskar & Tongaonkar – 1990
• Kolaskar & Urmila Kulkarni - 1999
T cell epitope prediction algorithms :
•
•
•
•
Margalit, Spouge et al - 1987
Rothbard & Taylor – 1988
Stille et al –1987
Tepitope -1999
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
14
Resources
Programs available:
• ANTIGEN: Kolaskar & Tongaonkar’s method.
Available in EMBOSS program as antigenic.
• url:
http://bioweb.pasteur.fr/seqanal/interfaces/antigeni
c.html
• EPIPLOT: Compilation of T and B cell prediction
algorithms. Stand-alone program for PC.
Databases of interest:
• BIMAS
• SYFPEITHI
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
15
Prediction of epitopes
 Knowledge of antigenic structure
 Delineation of sequential and conformational
epitopes
 Knowledge of the 3-D structure of antigen
 A method to map conformational epitopes
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
16
Conformational epitope prediction method
Sequential epitope prediction methods
The accuracy of prediction: 50-75%.
Conformational epitope prediction method
Kolaskar & Kulkarni-Kale, 1999.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
17
Properties of Amino Acids: predictors
for Epitopes
Theoretical methods are based on
properties of amino acids and their
propensity scales.
The accuracy of prediction: 50-75%.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
18
An Algorithm to Identify
Conformational Epitopes
Calculate the percent accessible
surface area (ASA) of the amino acid
residues.
If ASA  30%, then residue was
termed as accessible residues.
A contiguous stretch of more than
three accessible residues was
termed as the antigenic determinant.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
19
…Cont.
A determinant is extended to N- and
C-terminals, only if, accessible amino
acid(s) are present after an
inaccessible amino acid residue.
A list of sequential antigenic
determinants was prepared
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
20
Methods
&
Materials
Prediction of antigenic determinants using 3-D structural information of Egp of JEV
SR.
NO.
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
Predicted determinant
Kolaskar & Kulkarni-Kale, 1999
13
-EGASGATWVD-22
64
-SVTDISTV-71
85
-ADSSY-90
101
-WGNGCGLFGK-110
118
-KFSCTSKAI-126
131
-QPE-133
150
-ENHGNY-155
158QVGAS-162
170
-TPNAPSITLK-179
214
-HREW-217
229
-SSTAWRMRE-237
249
-RQSVVALGSQEGGLHQALAGAIVVEYSS-276
279
-KLTSGHLKCRLKMDKLALKGTTYGM-303
307
-KFSFAKNPADTGHG-320
329
-SGSDGP-334
344
-SLNDMTP-350
Kolaskar &
Tongaonkar, 1990
Parker
et al (1986)
18-33
40-46
48-75
88-95
75-92
113-124
147-157
155-181
155-182
185-191
199-206
208-216
262-268; 273-290
273-290; 292-298
226-237
243-251
309-319
328-335
351-358
385
-GRGDKQINHHWHKA-399
-17-
367-375
379-387
-17-
 2K3
Amino acid residues having <
30% accessibilityCentre,
are underlined
and highlighted.
September
Bioinformatics
University
of
 Determiniants predicted by Kolaskar & Tongaonkar (1990) & Parker et al (1986) are listed.
Pune, Pune.
363-369
-7-
21
…Contd.
The distance between every atom of
th
residues from the i determinant and
every atom of residues from the
remaining
determinants
was
calculated. If the distance between
the residues from sequentially
o
distinct determinants was  5 A ,
then such determinants were
defined as a conformational epitope.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
22
We Have Chosen JE Virus,
Because
 JE virus is endemic in South-east Asia
including India.
 JE virus causes encephalitis in children
between 5-15 years of age with fatality rates
between 21-44%.
 Man is a "DEAD END" host.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
23
We Have Chosen JE Virus,
Because
• Killed virus vaccine purified from mouse brain
is used presently which requires storage at
specific temperatures and hence not cost
effective in tropical countries.
• Protective prophylactic immunity is induced
only after administration of 2-3 doses.
• Cost
of
vaccination,
transportation is high.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
storage
and
24
Why Synthetic Peptide Vaccines?
 Chemically well defined, selective and safe.
 Stable at ambient temperature.
 No cold chain requirement hence cost
effective in tropical countries.
 Simple and standardised production facility.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
25
Egp of JEV as an Antigen
 Is a major structural antigen.
 Responsible for viral haemagglutination.
 Elicits neutralising antibodies.
 ~ 500 amino acids long.
 Structure of extra-cellular domain (399) was
predicted using knowledge-based homology
modeling approach.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
26
MULTIPLE SEQUENCE ALIGNMENT OF FLAVIVIRUSES.
PREDICTED ANTIGENIC DETERMINANTS
USING KOLASKAR & TONGAONKAR, 1990 ARE MARKED.
PART 1/5
JE
FNCLGMGNRDFIEGASGATWVDLVLEGDSCLTIMANDKPTLDVRMINIEASQLAEVRSYC
MVE FNCLGMSSRDFIEGASGATWVDLVLEGDSCITIMAADKPTLDIRMMNIEATNLALVRNYC
WNE FNCLGMSNRDFLEGVSGATWVDLVLEGDSCVTIMSKDKPTIDVKMMNMEAANLADVRSYC
KUN FNCLGMSNRDFLEGVSGATWVDLVLEGDSCVTIMSKDKPTIDVKMMNMEAANLAEVRSYC
SLE FNCLGTSNRDFVEGASGATWIDLVLEGGSCVTVMAPEKPTLDFKVMKMEATELATVRKYC
DEN2 MRCIGMSNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYC
YF
AHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVC
TBE SRCTHLENRDFVTGTQGTTRVTLVLELGGCVTITAEGKPSMDVWLDAIYQENPAKTREYC
*
***. * * . .
**
*.* . **..* .
* * *
JE
MVE
WNE
KUN
SLE
DEN2
YF
TBE
YHASVTDISTVARCPTTGEAHNEKRADSSYVCKQGFTDRGWGNGCGLFGKGSIDTCAKFS
YAATVSDVSTVSNCPTTGESHNTKRADHNYLCKRGVTDRGWGNGCGLFGKGSIDTCAKFT
YLASVSDLSTRAACPTMGEAHNEKRADPAFVCKQGVVDRGWGNGCGLFGKGSIDTCAKFA
YLATVSELSTKAACPTMGEAHNDKRADPSFVCKQGVVDRGWGNGCGLFGKGSIDTCAKFA
YEATLDTLSTVARCPTTGEAHNTKRSDPTFVCKRDVVDRGWGNGCGLFGKGSIDTCAKFT
IEAKLTNTTTESRCPTQGEPSLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFR
YNAVLTHVKINDKCPSTGEAHLAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFT
LHAKLSDTKVAARCPTMGPATLAEEHQGGTVCKRDQSDRGWGNHCGLFGKGSIVACVKAA
* .
**. *
**.
****** ******* * .*
PART 2/5
JE
CTS--KAIGRTIQPENIKYEVGIFVHGTTTSENHGNYSAQVGASQAAKFTITPNAPSITL
MVE CSN--SAAGRLILPEDIKYEVGVFVHGSTDSTSHGNYSTQIGANQAVRFTISPNAPAITA
WNE CTT--KATGWIIQKENIKYEVAIFVHGPTTVESHG----KIGATQAGRFSITPSAPSYTL
KUN CST--KATGRTILKENIKYEVAIFVHGPTTVESHGNYFTQTGAAQAGRFSITPAAPSYTL
SLE CKN--KATGKTILRENIKYEVAIFVHGSTDSTSHGNYSEQIGKNQAARFTISPQAPSFTA
DEN2 CKK--NMEGKVVQPENLEYTIVITPHSGEEHAVGNDTG-----KHGKEIKITPQSSTTEA
YF
CAK--SMSLFEVDQTKIQYVIRAQLHVGAKQENWN--------TDIKTLKFDALSGSQEV
TBE CEAKKKATGHVYDANKIVYTVKVEPHTGDYVAANETHS----GRKTASFTIS--SEKTIL
. * .
.
*
*
September 2K3
JE
MVE
WNE
KUN
SLE
DEN2
YF
TBE
KLGDYGEVTLDCEPRSGLNTEAFYVMTVGS------KSFLVHREWFHDLALPWTSPSSTKMGDYGEVTVECEPRSGLNTEAYYVMTIGT------KHFLVHREWFNDLLLPWTSPASTKLGEYGEVTVDCEPRSGIDTSAYYVMSVGE------KSFLVHREWFMDLNLPWSSAGSTKLGEYGEVTVDCEPRSGIDTSAYYVMTVGT------KTFLVHREWFMDLNLPWSSAESNNMGEYGTVTIDCEARSGINTEDYYVFTVKE------KSWLVNRDWFHDLNLPWTSPATTELTGYGTVTMECSPRTGLDFNEMVLLQMEN------KAWLVHRQWFLDLPLPWLPGADTQ
EFIGYGKATLECQVQTAVDFGNSYIAEMET------ESWIVDRQWAQDLTLPWQSGSGGBioinformatics Centre, University of
TMGEYGDVSLLCRVASGVDLAQTVILELDKTVEHLPTAWQVHRDWFNDLALPWKHEGAQ** .. *
. .
. .
* * * ** ***
Pune, Pune.
27
PART 3/5
JE
--AWRNRELLMEFEEAHATKQSVVALGSQEGGLHQALAGAIVVEYSSS----VKLTSGHL
MVE --EWRNREILVEFEEPHATKQSVVALGSQEGALHQALAGAIPVEFSSST---LKLTSGHL
WNE --TWRNRETLMEFEEPHATKQSVVALGSQEGALHQALAGAIPVEFSSNT---VKLTSGHL
KUN --VWRNRETLMEFEEPHATKQSVIALGSQEGALHQALAGAIPVEFSSNT---VKLTSGHL
SLE --DWRNRETLVEFEEPHATKQTVVALGSQEGRPATALAGAIPATVSSST---LTLQSGHL
DEN2 GSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSG----NLLFTGHL
YF
--VWREMHHLVEFEPPHAATIRVLALGNQEGSLKTALTGAMRVTKDTNDNNLYKLHGGHV
TBE --NWNNAERLVEFGAPHAVKMDVYNLGDQTGVLLKALAGVPVAHIEGTK---YHLKSGHV
*
*. *
**
* ** * *
**.*
* **.
JE
MVE
WNE
KUN
SLE
DEN2
YF
TBE
KCRLKMDKLALKGTTYGMCTE-KFSFAKNPADTGHGTVVIELSYSGSDGPCKIPIVSVAS
KCRVKMEKLKLKGTTYGMCTE-KFTFSKNPADTGHGTVVLELQYTGSDGPCKIPISSVAS
KCRVKMEKLQLKGTTYGVCSK-AFKFARTPADTGHGTVVLELQYTGTDGPCKVPISSVAS
KCRVKMEKLQLKGTTYGVCSK-AFRFLGTPADTGHGTVVLELQYTGTDGPCKIPISSVAS
KCRAKLDKVKIKGTTYGMCDS-AFTFSKNPTDTGHGTVIVELQYTGSNGPCRVPISVTAN
KCRLRMDKLQLKGMSYSMCTG-KFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDSCRVKLSALTLKGTSYKICTD-KMFFVKNPTDTGHGTVVMQVKVS-KGAPCRIPVIVADD
TCEVGLEKLKMKGLTYTMCDKTKFTWKRAPTDSGHDTVVMEVTFS-GTKPCRIPVRAVAH
*
. . .** .* .*
... * *... .
**..*
PART 4/5
JE
LNDMTPVGRLVTVNPFVATSSANSKVLVEMEPPFGDSYIVVGRGDKQINHHWHKAGSTLG
MVE LNDMTPVGRMVTANPYVASSTANAKVLVEIEPPFGDSYIVVGRGDKQINHHWHKEGSSIG
WNE LNDLTPVGRLVTVNPFVSVATANSKVLIELEPPFGDSYIVVGRGEQQINHHWHKSGSSIG
KUN LNDLTPVGRLVTVNPFVSVSTANAKVLIELEPPFGDSYIVVGRGEQQINHHWHKSGSSIG
SLE LMDLTPVGRLVTVNPFISTGGANNKVMIEVEPPFGDSYIVVGRGTTQINYHWHKEGSSIG
DEN2 LEKRHVLGRLITVNPIVTE--KDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKKGSSIG
YF
LTAAINKGILVTVNPIASTN--DDEVLIEVNPPFGDSYIIVGRGDSRLTYQWHKEGSSIG
TBE GSPDVNVAMLITPNPTIEN---NGGGFIEMQLPPGDNIIYVG----ELSHQWFQKGSSIG
..* **
.*
* ** * .*
.
* . **..*
JE
MVE
WNE
KUN
SLE
DEN2
YF
TBE
September 2K3
KAFSTTLKGAQRLAALGDTAWDFGSIGGVFNSIGKAVHQVFGGAFRTLFGGMSWITQGLM
KAFSTTLKGAQRLAALGDTAWDFGSVGGVFNSIGKAVHQVFGGAFRTLFGGMSWISQGLL
KAFTTTLRGAQRLAALGDTAWDFGSVGGVFTSVGKAIHQVFGGAFRSLFGGMSWITQGLL
KAFTATLKGAQRLAALGDTAWDFGSVGGVFTSVGKAVHQVFGGAFRSLFGGMSWITQGLL
KALATTWKGAQRLAVLGDTAWDFGSIGGVFNSIGKAVHQVFGGAFRTLFGGMSWITQGLL
QMFETTMRGAKRMAILGDTAWDFGSLGGVFTSIGKALHQVFGAIYGAAFSGVSWTMKILI
KLFTQTMKGVERLAVMGDTAWDFSSAGGFFTSVGKGIHTVFGSAFQGLFGGLNWITKVIM
RVFQKTKKGIERLTVIGEHAWDFGSAGGFLSSIGKAVHTVLGGAFNSIFGGVGFLPKLLL
.
* .* *.. .*. **** * **
*.** .* * * .
* *.
. ..
PART 5/5
JE
GALLLWMGVNARDRSIALAFLATGGVLVFLATNVHA
MVE GALLLWMGVNARDKSIALAFLATGGVLLFLATNVHA
WNE GALLLWMGINARDRSIAMTFLAVGGVLLFLSVNVHA
KUN GALLLWMGINARDRSIALTFLAVGGVLLFLSVNVHA
SLE GALLLWMGLQARDRSISLTLLAVGGILIFLATSVQA
DEN2 GVIITWIGMNSRSTSLSVTLVLVGIVTLYLGVMVQA
YF
GAVLIWVGINTRNMTMSMSMILVGVIMMFLSLGVGA
Bioinformatics Centre, University
TBE GVALAWLGLNMRNPTMSMSFLLAGGLVLAMTLGVGA
* . *.*.. * ..... . * .Pune,
. . Pune.
* *
of
28
Multiple alignment of Predicted TH-cell epitope in the JE_Egp
with corresponding epitopes in Egps of other Flaviviruses
426
457
JE
DFGSIGGVFNSIGKAVHQVFGGAFRTLFGGMS
MVE DFGSVGGVFNSIGKAVHQVFGGAFRTLFGGMS
WNE DFGSVGGVFTSVGKAIHQVFGGAFRSLFGGMS
KUN DFGSVGGVFTSVGKAVHQVFGGAFRSLFGGMS
SLE DFGSIGGVFNSIGKAVHQVFGGAFRTLFGGMS
DEN2 DFGSLGGVFTSIGKALHQVFGAIYGAAFSGVS
YF
DFSSAGGFFTSVGKGIHTVFGSAFQGLFGGLN
TBE DFGSAGGFLSSIGKAVHTVLGGAFNSIFGGVG
COMM DF S GG
S GK H V G
F G
Multiple alignment of JE_Egp with Egps of other Flaviviruses in
the YSAQVGASQ region.
151
183
JE
SENHGNYSAQVGASQAAKFTITPNAPSITLKLG
MVE STSHGNYSTQIGANQAVRFTISPNAPAITAKMG
WNE VESHG----KIGATQAGRFSITPSAPSYTLKLG
KUN VESHGNYFTQTGAAQAGRFSITPAAPSYTLKLG
SLE STSHGNYSEQIGKNQAARFTISPQAPSFTANMG
DEN2 HAVGNDTG-----KHGKEIKITPQSSTTEAELT
YF
QENWN--------TDIKTLKFDALSGSQEVEFI
September 2K3
Bioinformatics Centre, University of
29
TBE VAANETHS----GRKTASFTIS--SEKTILTMG
Pune, Pune.
STEPS in Homology Modeling
• Template structure (PDB entry: 1SVB). (Rey
et al., 1995).
• Alignment of Egp of JEV and Egp of TBEV.
• Definition of SCRs and Loops.
• Assignment of Initial co-ordinates to
Backbone & Side-chains.
• Rotamer search for the favored side-chain
conformations.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
30
Model Refinement
PARAMETERS USED
• force field:
• Dielectric const:
• Optimisation:
AMBER all atom
Distance dependent
Steepest Descents &
Conjugate Gradients.
• rms derivative 0.1 kcal/mol/A for SD
• rms derivative 0.001 kcal/mol/A for CG
• Biosym from InsightII, MSI and modules
therein.m
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
31
ORDER OF REFINEMNT of MODEL
 Loops
 MD at 300K for 500ps and equilibration of
100ps.
 SCRs adjacent to the loop:
SCRn-1, loopn, SCRn+1
 Domains: I, II, III
 Full molecule
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
32
Model For Solvated Protein
 Egp of JEV molecule was soaked in the
water layer of 10A.
 4867 water molecules were added.
 The system size was increased to
20,648 atoms from 6047.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
33
Model Evaluation I:Energy Profile
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
34
Model Evaluation II:
Ramachandran Plot
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
35
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
36
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
37
Strain specific properties:
JEVN & JEVS
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
38
Peptide Modeling
Initial random conformation
Force field: Amber
Distance dependent dielectric constant 4rij
Geometry optimization: Steepest descents & Conjugate gradients
Molecular dynamics at 400 K for 1ns
Peptides are:
SENHGNYSAQVGASQ
NHGNYSAQVGASQ
YSAQVGASQ
YSAQVGASQAAKFT
NHGNYSAQVGASQAAKFT
SENHGNYSAQVGASQAAKFT
149
168
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
39
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
40
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
41
CONCLUSIONS
 3-D structure of Egp of JEV has been
predicted
 A method based on objective criteria and
knowledge of 3-D structure has been
developed to predict the conformational
epitopes.
 The method helps to identify the antigenic
determinants
that
are
part
of
conformational epitopes as well as the
sequential ones.
 The experimental results using synthetic
peptides as antigens in case of Egp of JEV
show a great promise.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
42
Publication/Patent
• A.S. Kolaskar and Urmila Kulkarni-Kale, 1999
- Prediction of three-dimensional structure
and mapping of conformational epitopes of
envelope
glycoprotein
of
japanese
encephalitis virus,Virology, 261, 31-42.
• Chimeric T helper - B cell peptide as a
vaccine for Flaviviruses
Gore, MM; Dewasthaly, SS; Kolaskar, AS;
Kulkarni-Kale, Urmila
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
43
Epitope prediction: References
• Hopp, Woods, 1981, Prediction of protein antigenic determinants
from amino acid sequences, PNAS U.S.A 78, 3824-3828
• Parker, Hodges et al, 1986, New hydrophilicity scale derived from
high performance liquid chromatography peptide retention data:
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September 2K3
Bioinformatics Centre, University of
Pune, Pune.
44
Acknowledgements
• Department of Biotechnology, Govt. of
India.
• Immunology Div., NIV.
September 2K3
Bioinformatics Centre, University of
Pune, Pune.
45

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