Computational biology has been like a blessing to the fast-paced world with numerous data generated now and then. The field not only increases the speed of process and research but also greatly merges the interdisciplinary. This saves time and resources for better and precise work in future. In this study, we focused on the prediction of the epitopes and the cross-reactive species with similar amino acid sequences potent to cause an allergic reaction. The epitope recognition is of utmost importance for the precise study of antigen-antibody interaction. this not only serves as the base but also helps in the development of personalised medicine hence, preventing the reaction. The servers used in the study work on the pre-existing epitopes derived from experimental evidence increasing the accuracy. the present study comprises predicted epitopes of AMP23_MACIN, AMP1_MACIN, AMP21_MACIN, MATK_MACIN and 11S1_MACIN using the servers ABCpred, Bepipred, CBTope, DiscoTope2.0, Bcepred and Ellipro. The conformational epitopes and the prone sites for the highest Ag-Ab binding require the 3-d model. The unavailability of structures was resolved using the modelling server. The modelled and edited structure of the AMP1_MACIN is validated using the Rampage web servers. The residues are found to be in favourable regions making it an efficient model for use and refer to the Fig. 1.
Table I
Allergen
|
No. of epitopes
|
Start position
|
Predicted epitope residues
|
No. of residues
|
AMP23_MACIN
|
5
|
10
|
EEEEEYNRQRDPQQ
|
14
|
|
|
33
|
QRRETEPR
|
8
|
|
|
61
|
QKRYEEQQREDEEKYE
|
16
|
|
|
269
|
STPGQYKEFFPAGGQN
|
16
|
|
|
539
|
RQHQQQSPRSTKQQQP
|
16
|
AMP1_MACIN
|
4
|
14
|
MMLIAMASEMVMNGSAF
|
17
|
|
|
31
|
VWSGPGCNNRAERY
|
14
|
|
|
51
|
AIHQKGGYDFSYTGQT
|
15
|
|
|
84
|
GSSARACNPFGWKSIF
|
15
|
AMP21_MACIN
|
6
|
63
|
FEEDIDWSKYDNQEDP
|
15
|
|
|
89
|
CRQQES
|
6
|
|
|
111
|
EEEEEYNRQRDPQQY
|
15
|
|
|
134
|
QRRETEPRHM
|
10
|
|
|
161
|
QKRYEEQQREDEEKYE
|
16
|
|
|
226
|
GGDHHNPQRGGSGRYEEGEEEQSD
|
24
|
MATK_MACIN
|
3
|
54
|
MEKLQEYLEIDRSWQQ
|
16
|
|
|
319
|
PGRIDINQLSNYSFDL
|
15
|
|
|
342
|
MASRGTPLMMNKWKY
|
|
|
|
466
|
CKNISHYHSGSSKKS
|
15
|
11S1_MACIN
|
3
|
30
|
LNNQANQLDQK
|
11
|
|
|
45
|
LLPQGHA
|
7
|
|
|
155
|
VAHWCLNDGKHYLDNPR
|
17
|
TABLE II: LIST OF CONFORMATIONAL IGE BINDING EPITOPES PREDICTED BY ONLINE WEB - SERVERS
Allergen
|
No. of epitopes
|
Start position
|
Predicted epitope residues
|
No. of residues
|
AMP23_MACIN
|
5
|
10
|
MRRCVSQCDKRFEEDIDWSKYDNQEDPQ
|
27
|
|
|
145
|
RDPQQREY
|
8
|
|
|
204
|
EKQSDN
|
6
|
|
|
320
|
IAKFL
|
5
|
|
|
336
|
FFPAGGQNPEPY
|
12
|
AMP1_MACIN
|
3
|
26
|
GSAFTVWSGPGCNNAERY
|
18
|
|
|
63
|
TGQTAALY
|
8
|
|
|
84
|
GSSARAC
|
7
|
AMP21_MACIN
|
4
|
51
|
MRRCVSQCDKRFEEDIDWSKYDNQEDPQ
|
27
|
|
|
187
|
DPQQRE
|
6
|
|
|
377
|
FFPAGGQNPEPY
|
12
|
|
|
448
|
ESSRGPYN
|
8
|
MATK_MACIN
|
4
|
97
|
MISEG
|
5
|
|
|
274
|
KDPFTHY
|
7
|
|
|
295
|
PLMMNKWKY
|
9
|
|
|
321
|
IDINQL
|
6
|
11S1_MACIN
|
1
|
93
|
DGKHYLDNPR
|
10
|
TABLE III: CONSENSUS OF LINEAR AND CONFORMATIONAL IGE BINDING EPITOPES OF MACADAMIA ALLERGENS
Allergen
|
No. of epitopes
|
Start position
|
Predicted epitope residues
|
No. of residues
|
AMP23_MACIN
|
2
|
320
|
IAKFL
|
5
|
|
|
336
|
FFPAGGQNP
|
9
|
AMP1_MACIN
|
2
|
38
|
NNAERY
|
6
|
|
|
63
|
TGQTAALY
|
8
|
|
|
84
|
GSSARAC
|
7
|
AMP21_MACIN
|
2
|
63
|
FEEDIDWSKYDNQEDP
|
15
|
|
|
187
|
DPQQRE
|
6
|
MATK_MACIN
|
3
|
97
|
MISEG
|
5
|
|
|
295
|
PLMMNKWKY
|
9
|
|
|
321
|
IDINQL
|
6
|
11S1_MACIN
|
1
|
93
|
DGKHYLDNPR
|
10
|
The predicted linear and conformational epitopes are listed below. The use of computational tools gives the in-silico results which are asked to be proved using in vivo and in vitro experiments. These in silico results aid as the first hand-processed data. The linear and the conformational epitopes were assessed by consensus for the most potent epitopes listed in Table III.
TABLE IV:CROSS-REACTIVE SPECIES
Allergen
|
Crossreactive species
|
AMP23_MACIN
|
English walnut (Juglans regia), Pecan(Carya illinoinesis),Rice (Oryza sativa japonica)
|
AMP1_MACIN
|
Western white pine(Pinus monticola)
|
AMP21_MACIN
|
Common hazel(Corylus avellana), Pistachio(Pistacia vera), cacao(Theobroma cacao)
|
MATK_MACIN
|
Oriental plane tree(Plantus occidentalis), tea orchid(Chloranthus spicatus), Japanese boxwood(Buxus microphylla), Japanese witch hazel( Hamamelis japonica)
|
11S1_MACIN
|
English walnut (Juglans regia), Rice (Oryza sativa japonica), Oats(Avena sativa)
|
The physio-chemical properties of the predicted continuous/linear epitopes |
Table V
Protein
|
%Hydrophilicity
|
%Flexibility
|
%Accessbility
|
%Surface area exposed
|
%Polarity
|
%Antigenic propensity
|
AMP23_MACIN
|
27.2
|
16.48
|
49.76
|
22.56
|
38.72
|
7.68
|
AMP1_MACIN
|
5.88235294117647
|
1.96078431372549
|
6.86274509803922
|
1.96078431372549
|
5.88235294117647
|
8.82352941176471
|
AMP21_MACIN
|
27.1771771771772
|
15.1651651651652
|
49.3993993993994
|
21.021021021021
|
36.3363363363363
|
9.45945945945946
|
MATK_MACIN
|
2.55402750491159
|
5.10805500982318
|
22.3968565815324
|
4.91159135559921
|
17.8781925343811
|
21.2180746561886
|
11S1_MACIN
|
1.96078431372549
|
0
|
17.6470588235294
|
0.980392156862745
|
6.86274509803922
|
15.6862745098039
|
The physicochemical properties also give an interesting insight into the binding of the Ab molecules. The hydrophilicity is proportional to the power of IgE binding.
The hydrophilicity is recorded highest in ‘AMP23_MACIN’ possesses the maximum
percentage of hydrophilic residues with 27.2%, followed by‘AMP21_MACIN’ with 27.17%, ‘AMP1_MACIN’ with 5.88%, ‘MATK_MACIN’ with 2.55% and ‘11S1_MACIN’ with 1.96%(Fig. 2).
On comparing percentage polarity in the epitopic regions, the value observed for ‘AMP23_MACIN’ was found to be the highest (38.72%), followed by ‘AMP21_MACIN’(36.33%), ‘MATK_MACIN’(17.87%), ‘11S1_MACIN’(6.86%) and ‘AMP1_MACIN’(5.88%) (Fig. 2).
Percentage of Surface Exposed Residues was also estimated for all five macadamia allergens. The highest percentage was observed for ‘AMP23_MACIN’ being 22.56% followed by ‘AMP21_MACIN’(21.06%), ‘MATK_MACIN’(4.91%), ‘AMP1_MACIN’(1.96%) and ‘11S1_MACIN’(0.98%). The results have been summarised in Fig. 2.