Conformational Epitope
Prediction Server
Developed@Bioinformatics Centre, University of Pune, INDIA
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What
are epitopes?
The identification of the regions of
interaction between an antigen
(Ag) and an antibody (Ab) is one of the most interesting problems in
molecular immunology. Antigen-antibody (Ag-Ab) complexes are
non-obligatory heterocomplexes that are made and broken according to
the environment or the external factors and involve proteins (antigen
and antibody) that must also exist independently. The
most remarkable feature of antigen-antibody interactions is the high
affinity and strict specificity of antibodies for their antigens. It is
known that antibodies recognize the unique conformations and spatial
locations on the surface of antigens. Therefore,
epitopes
are defined as the portions of the antigen molecules, which are
responsible for specificity of the antigens in Ag-Ab reactions and that
interact with the antigen binding site of antibody (paratope) to which
they are complementary.
Types of Epitopes
Both humoral and cellular arms of immune system
recognise and react
with only specific regions of the pathogen, called epitopes. It has
been known that B and T cells recognize different epitopes on the same
antigenic molecule. Thus, there are two types of
epitopes, B cell epitope and Th cell epitope. The B cell epitopes
are accessible, hydrophilic regions and majority of them are capable of
neutralisation. Antibodies produced by B cells recognise the
intact antigen in its native conformation. The epitopes
recognized by T cells are products of processed or partially degraded
proteins that are bound to MHC molecules and are usually amphipathic
(i.e., alternating hydrophobic and hydrophilic) regions.
The B cell
epitopes can
be contiguous / Sequential (when Ab binds to a contiguous stretch of amino acid residues
that are linked by peptide bond) or non-contiguous / Conformational (when Ab binds to non-contiguous residues, brought together
by folding of polypeptide chain). The specificity of sequential
epitopes (SE) is determined by the sequence of subunits (e.g. amino
acids). On the other hand, specificity of conformational epitopes (CE)
depends on the spatial folding or conformation of the contributing
individual sequential epitopes.
Existing Approaches to predict B-cell
epitopes
Sequential
epitopes
- Hopp
& Woods (1981)
- Kyte
& Doolittle (1982)
- Welling
et al. (1985)
- Parker
et al. (1986)
- Kolaskar
& Tongaonkar (1990)
- PEOPLE
(Alix, 2000)
Conformational
epitopes
- The only
existing
algorithm for the prediction of conformational epitopes is CE (Kolaskar & Urmila Kulkarni, 1999)
CE Algorithm
- The
percent accessible surface area (%ASA) of each amino acid residue
is calculated using an implementation of Voronoi procedure (1908) by
McConky etal (2002) which is consistent with Lee
& Richards (1971).
- Residues
having %ASA >= 25% are termed as accessible residues.
- A
contiguous stretch of more than three accessible residues is termed as
an antigenic
determinant.
- Every
antigenic determinant is extended to N- and C-terminals, only if,
accessible amino acid(s) were present after an inaccessible amino acid
residue.
- Single
residues which have %ASA>=25% and does not satisfy above criterion
are also taken into
consideration.
- The
antigenic determinants are then listed with details like the chain ID,
length of determinant, start and end position and the amino acid
sequence.
- The
inaccessible
amino acid residues that are part of antigenic determinants are shown
in lower
case.
- The
distance between every atom of residues from the ith determinant and
every atom of residues
from the jth determinants is calculated.
- If the
distance between any pair of atoms of at
least two residues from sequentially distinct determinants was found to
be <= predetermined
cutoff distance, then jth determinant was termed to be part of a
conformational epitope that
consists of ith and jth determinants.
- Single
residues which are not part of AD and satisfy
distance and %ASA criteria are also included as a part of CE.
- Such
distance calculations
were carried out for every sequential determinant (j =1, n and j != i)
with ith determinant as
a reference.
- The
reference sequential determinant was then varied from i = 1 to n. The
list of
conformational epitopes is computed.
- The
cutoff distance 6A is found to be optimum.
Accuracy
of Algorithm
CE predicts the Conformational
Epitopes with an accuracy of 75%, when
tested using 21 X-ray diffracted co-crystal structure complexes of
antigen and antibodies that are available in PDB database (unpublished).
Software
details
Scripting language: CGI Perl
Accessibility calculation: Voronoi procedure implemented by McConkey et
al (2002).
Server : Apache on Linux 9.2
System
requirements
IE4+ and Netscape 4 and above.
How
to Calculate CE
Click on upload button to start
calculation. Once the message "Processing Completed" appears, results
can be accessible for both sequential epitopes and conformational
epitopes using hyperlinks .
CE
Home Page
http://bioinfo.net.in/cep.htm
Input
files
User has to upload 3D coordinate
file in PDB format
Sample
input file
Output
file
CE lists both, Conformational
and Sequential epitopes. Results
are saved as html file.
Sample output file
Publications
-
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.
-
Kulkarni-Kale, U.
(2003). prediction of 3D structure & function of protein. Ph.D.
Thesis. University of Pune.
-
A. S. Kolaskar &
Urmila Kulkarni-Kale. CE: An algorithm to predict the conformational
epitopes (in preparation).
Algorithm
development
Urmila Kulkarni- Kale & A. S.
Kolaskar
Server
implementation
Shriram Bhosle
Evaluation
Sunita Manjari
Contact
Details
Prof. A. S.
Kolaskar
Dr.Urmila Kulkarni-Kale
Former Vice-Chancellor,
Information Scientist
University of
Pune
Bioinformatics Centre
Pune 411
007
University of Pune, Pune 411 007
Phone:
+91 20
2569 0195/2569 2039
Fax:
+91 20 2569 0087
e-mail:
urmila@bioinfo.net.in
kolaskar@bioinfo.net.in