Epitope Prediction Based on Carbon Content 25

Epitope Prediction Based on Carbon Content

S. Princeinal Suganthi 1, S. Shiney Valentina 1, S. Arul Mugilan1 and E. Rajasekaran1*
1
Department of Bioinformatics, School of Biotechnology and Health Sciences, Karunya University,
Coimbatore 641114, Tamil Nadu, India.
* Corresponding Authors: ersekaran@gmail.edu.

ABSTRACT
Epitope are portion of protein antigen that helps virus-antibody interactions for entry of foreign body into B-cell. Epitope
prediction based on carbon content is reported here. The study is carried out on glycoprotein of rapies virus. The carbon
based analysis program (CARBANA) predicts the epitope region clearly. The predicted results are in agreement with
reported sites. The study suggests that the epitope are hydrophobic in nature. The carbon based analysis can be an alternative
method for predicting epitope and will aid in redesign of epitope regions.
Keywords: Glycoprotein; antigenic determinant; epitope prediction; carbon content; hydrophobicity;

1. INTRODUCTION CARBANA is available online. This paper investigates

Many epitope prediction tools, servers, methods and
databases are being added every now and then on the
Internet. BcePred, for example, is a server based tool,
uses physico chemical properties for prediction of
epitope in antigenic sequences [Saha and Raghava 2004].
This program has several physico chemical properties
for prediction. For example it uses semi-empirical
method used by Kolaskar et al. [Kolaskar and
Tongaonkar 1990] for prediction of antigenic determi-
nants on protein antigen. It is mentioned that when the
hydrophobic residues cystein, leucine and valine occur
on the surface of a protein then there is likely to be an
antigenic site. Other investigations have demonstrated
that antigenic determinants are surface features of
proteins and found exposed to solvent (Hopp and
Woods, 1981). It is reported that polar and charged amino
acid are common features of antigenic determinants. The
question is what drives an antigenic site? Hydrophobic
or hydrophilic! If hydrophobic interaction is the
dominant force then the statement by Kolaskar et al. is
true. But most often discussed that the antigenic sites
are hydrophilic in nature and contain charged and polar
residues. If this so then the ions and water molecules
can neutralize these charges and polarity. To address
these issues this work has been taken up here.
2. METHODOLOGY
The principle behind the hydrophobicity interaction is
the carbon distribution along the sequence. This is
because carbon is the one and only element contributes
towards the hydrophobicity. It is reported that protein
prefers to have 31.45% of carbon in its structure and sequ-
ence for its stability (Rajasekeran et al, 2009). Taking this
as scale, a carbon analysis tool (CARBANA) has been
developed [Rajasekaran and Vijayasarathy 2011].
the carbon distribution along the glycoprotein of rabies
virus [Benmansour et al. 1991] and compared with reported
sites and also with results of other prediction program.
The protein sequence is downloaded from SWISS
PROT. The carbon distribution along the sequence is
measured by a simple averaging. A window length 500
atoms and step size of 17 atoms are taken as default
values. The output of CARBANA is plotted as carbon
distribution plot as shown in the figure.
For comparison, the epitope were predicted using
BCPREDS (B-cell epitope prediction server). The method
used in this program was fixed length epitope prediction
by AAP program. The server based program predicts
linear B-cell epitopes using amino acid pair antigenicity
scale [Chen et al. 2007]. The input parameters of epitope
length of 22 amino acids and classifier specificity of 75%
were chosen. Only the non overlapping epitope were opted
to report. The predicted results are shown and discussed.
3. RESULTS AND DISCUSSION
The CARBANA computed carbon distribution along the
glycoprotein of rabies virus [Benmansour et al. 1991] is
plotted in Figure 1. The percentage of carbon (Y-axis) is
plotted against amino acid position (X-axis). The line at
31.45% of carbon shows the threshold value, above which
the carbon contents are high. The first length of 40 amino
acids shows rich in carbon content. Similarly the
stretches, 60-150, 170-208, 259-277, 327-350 and 415-475
are rich in carbon. These sites are considered to be
epitope. It is reported that amino acids 34-42 and
198-200 are involved in antigenic site II of glycoprotein
[Prehaud 1988, Mansfield et al 2004].
Both these small stretches are in hydropbhobic
regions as per carbon distribution plot (Figure 1).

International Journal of Bioinformatics • July-December 2011 • Volume 4 • Issue 2

26 S. Princeinal Suganthi, S. Shiney Valentina, S. Arul Mugilan & E. Rajasekaran

Similarly amino acids from 330 to 338 are involved to be It is also reported that the amino acids 333, 340,
in the antigenic site III of glycoprotein of rapies virus. 342-343 and 357 are involved in antigenic sites which
This site again involved in hydrophobic region in the are again in carbon rich region. One can conclude that a
carbon distribution plot. Both these sites in carbon stretch of amino acids involved in epitope rather one or
distribution plot reveal that hydrophobic interaction is two amino acid. Further modification or mutations can
the dominant force that involved in antigen-antibody be suggested based on the carbon distribution plot. Many
interactions. times the mutations that alter the interactions are due to
changes in the domain structure.
The epitope predicted using AAP of BCPREDS
(B-cell epitope prediction server) is given in Table 1. The
program was instructed to predict epitope of length
22 amino acid as shown in the output. The start of each
epitope, the sequence and score values are listed in the
table. In another output the complete glycoprotein
sequence with predicted epitope are given. This program
predicts that a length of 22 amino acid starting from 83,
114, 160, 210, 274, 324, 419 and 488 are epitope. Majority
Figure 1: Plot of Carbon Percentage vs Amino Acid in of these sites are in hydrophobic regions and in agreement
Glycoprotein. The Points Above the Threshold Line (31.45%) with carbon distribution plot except at 210 and 488.
are Considered as Epitope Regions.
Table 1
BCPREDS Output: Epitope Predicted using AAP.
Position Epitope Score
419 ADPSTVFKEGDEAEDFVEVHLP 1
488 SKQRSFGGTGGNVSVTSQSGKV 1
274 DQLVNLHDFRSNEIEHLVVEDL 1
324 RKLVPGFGKAYTIFNKTLMEAD 1
160 DLDPYDKSLHSRVFPGGKCSGI 1
114 RAAYNWKMAGDPRYEESLQNPY 1
210 IFTNSRGKRASNGNKTCGFVDE 1
83 VVTEAETYTNFVGYVTTTFKRK 0.616
Another output of BCPREDS (the E labeled amino acids involved to have epitope site).
1 11 21 31 41 51 60
| | | | | | |
MVPQVLLFVLLLGFSLCFGKFPIYTIPDKLGPWSPIDIHHLRCPNNLVVEDEGCTNLSGF 60
...........................................................................................................................................................
SYMELKVGYISAIKVNGFTCTGVVTEAETYTNFVGYVTTTFKRKHFRPTPDACRAAYNWK 120
.........................................................EEEEEEEEEEEEEEEEEEEEEE............................EEEEEEE
MAGDPRYEESLQNPYPDYHWLRTVRTTKESLIIISPSVTDLDPYDKSLHSRVFPGGKCSG 180
EEEEEEEEEEEEEEE....................................................................EEEEEEEEEEEEEEEEEEEEE
ITVSSTYCSTNHDYTIWMPEDPRPGTPCDIFTNSRGKRASNGNKTCGFVDERGLYKSLKG 240
E..........................................................................................EEEEEEEEEEEEEEEEEEEEEE.........
ACRLKLCGVLGLRLMDGTWVAMQTSDETKWCSPDQLVNLHDFRSNEIEHLVVEDLVKKRE 300
................................................................................................EEEEEEEEEEEEEEEEEEEEEE.....
ECLDTLESIMTTKSVSFRRLSHLRKLVPGFGKAYTIFNKTLMEADVHYKSVRTWNEIIPS 360
.........................................................EEEEEEEEEEEEEEEEEEEEEE............................................
KGCLKVGGRCHPHVNGVFFNGIILGPDDRVLIPEMQSSLLRQHMELLESSVIPLMHPLAD 420
.....................................................................................................................................................EE
PSTVFKEGDEAEDFVEVHLPDVYKKISGVDLGLPNWGKYVLMTAGAMIGLVLIFSLMTWC 480
EEEEEEEEEEEEEEEEEEEE..........................................................................................................
RRANRPESKQRSFGGTGGNVSVTSQSGKVIPSWESYKSGGEIRL 524
.........................EEEEEEEEEEEEEEEEEEEEEE...................................

International Journal of Bioinformatics • July-December 2011 • Volume 4 • Issue 2

 Epitope Prediction Based on Carbon Content
Overall the carbon distribution plot obtained from
CARBANA program is quite good in predicting epitope.
This might help in vaccine design.
4. CONCLUSION
Epitope prediction based on carbon content is reported
here. This carbon distribution based method is an
accurate method for epitope prediction. This new
method and tool developed is hoped to help redesign
epitope regions in antigen. These studies also conclude
that the epitopes are hydrophobic in nature.
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