Computer-aided vaccine designing approach against fish pathogens Edwardsiella tarda and Flavobacterium columnare using bioinformatics softwares

Figures & data

Table 1 Antigenic sites in the OMP of E. tarda

S No	Start position	End position	Peptide	Peptide length, amino acids
1	4	24	KKLLPLLIGLSLSGFSALSQA	21
2	27	34	LMQVYQQA	8
3	60	69	SPLLPQLGLG	10
4	91	98	ASLALTQT	8
5	107	112	QLSLTE	6
6	117	124	IQDVSYQS	8

Notes: Six antigenic sites were identified in the OMP of E. tarda. Proline (in bold) at the eighth position has a maximum residual score of 1.164 (threshold =1.000).

Abbreviations: OMP, outer membrane protein; E. tarda, Edwardsiella tarda; S, Serial Number.

Table 2 Antigenic sites in the OMP of F. columnare

S No	Start position	End position	Peptide	Peptide length, amino acids
1	4	17	IILFTVLGLSLHGG	14
2	32	49	NGLAYVDAIDTYLKVAQK	18
3	53	59	SKELFQR	7
4	61	86	GDSYYYNAKLVDAHKWY AELFALGET	26
5	88	105	EPEYYYRYAQTLKSVEDY	18
6	113	118	SKFYEL	6
7	147	153	IKPVSIN	7
8	165	172	GDKVLFAS	8
9	177	182	IGVFKA	6
10	192	197	TNLYAA	6
11	223	229	DSPVFTK	7
12	231	236	LKTVYF	6
13	253	261	IINLKIYRA	9
14	270	276	INIVELP	7
15	281	291	QYSVAHPALSP	11
16	294	299	KTLYFA	6
17	311	317	LFKVAIL	7
18	345	353	DKGVLYYAT	9
19	359	369	LGGLDIYAAQL	11
20	375	385	VSNLVNVGSPV	11
21	415	429	DDIYSFIEKSPLNLE	15
22	431	440	QHELAGVVTN	10
23	444	456	REVIPGATVTLYD	13
24	462	468	IGKVLAD	7
25	475	488	FKKVPAGKKYYVRA	14
26	518	525	KVRVIQEG	8
27	528	544	LAKIFEIKIIYFDLDKS	17
28	547	563	RADAAVELAKILEVMKQ	17
29	566	586	TMKVDVRSHTDCCRQTV AYNAK	21
30	594	603	ETVAWLVKNG	10
31	616	626	ESQLVNDCGCE	11

Notes: Number of antigenic sites identified in the OMP of F. columnare is 31. Phenylalanine (in bold) at the seventh position has a maximum residue score of 1.170 (threshold =1.000).

Abbreviations: OMP, outer membrane protein; F. columnare, Flavobacterium columnare; S, Serial Number.

Table 3 CTL epitopes predicted for E. tarda

Residue number	Peptide sequence	Predicted MHC binding affinity	Rescale binding affinity	C-terminal cleavage affinity	Transport affinity	Prediction score	MHC ligands
23	QAENLMQVY	0.5080	2.1567	0.9746	2.9000	2.4479	E
81	SSGLNSNNY	0.4391	1.8645	0.9507	2.7160	2.1429	E
114	QAGIQDVSY	0.1322	0.5613	0.9648	2.9280	0.8524	E
123	QSSEQTLML	0.2315	0.9829	0.9559	0.9520	1.1739	E

Notes: Prediction of CTL was carried out using MHC supertype A1. Prediction score should be >0.75000. Bold indicates amino acids Q and A are also predicted as antigenic sites.

Abbreviations: CTL, cytotoxic T-lymphocyte; E. tarda, Edwardsiella tarda; MHC, major histocompatibility complex.

Table 4 CTL epitopes predicted for F. columnare

Residue number	Peptide sequence	Predicted MHC binding affinity	Rescale binding affinity	C-terminal cleavage affinity	Transport affinity	Prediction score	MHC ligands
36	YVDAIDTYL	0.2217	0.9415	0.9655	1.0510	1.1388	E
85	ETVEPEYYY	0.1547	0.6566	0.9700	2.7470	0.9395	E
97	QTLKSVEDY	0.3957	1.6799	0.9271	3.0880	1.9734	E
107	KADEYMSKF	0.2138	0.9079	0.8821	2.6190	1.1711	E
120	SKDTRANIY	0.4282	1.8182	0.9309	2.8610	2.1009	E
151	SINGSSSDY	0.2323	0.9865	0.9569	3.0590	1.2830	E
155	SSSDYGTAF	0.2948	1.2519	0.9398	2.5940	1.5225	E
156	SSDYGTAFY	0.7716	3.2759	0.8263	2.8960	3.5447	E
212	FAKEINSKY	0.2298	0.9758	0.9764	3.0120	1.2729	E
227	FTKDLKTVY	0.4014	1.7043	0.9283	2.8530	1.9862	E
278	NSDQYSVAH	0.3665	1.5559	0.2328	−0.7390	1.5539	E
289	LSPDEKTLY	0.4668	1.9818	0.9711	3.1080	2.2828	E
298	FASNMPGTY	0.5098	2.1646	0.9467	2.8260	2.4479	E
342	FITDKGVLY	0.3314	1.4072	0.9735	2.7770	1.6921	E
343	ITDKGVLYY	0.8205	3.4838	0.9769	2.6450	3.7626	E
465	VLADEKGFY	0.3778	1.6040	0.8288	3.1240	1.8845	E
485	YVRAEKEDY	0.1300	0.5518	0.8316	3.0400	0.8286	E
574	HTDCRQTVA	0.2482	1.0539	0.6383	−0.7700	1.1112	E

Notes: Prediction of CTL was carried out using MHC supertype A1. Prediction score should be >0.75000. Amino acids in bold indicate that they are also predicted as antigenic sites.

Abbreviations: CTL, cytotoxic T-lymphocyte; F. columnare, Flavobacterium columnare.

Table 5 Peptide QAENLMQVY–MHC HLA-A0201 interaction

H-bond interaction
(Peptide–protein)	Distance (Å)
Asn O–Thr O	2.882885
Gln O–Thr N	2.982010
Tyr O–Thr O	2.843064
Tyr N–Asp O	2.999412
Tyr O–Tyr O	2.735772
Val O–Tyr O	2.863572
Val N–Trp O	2.822387
Glu O–Tyr O	2.986599
Asn O–Gln N	2.824341
Ala O–Glu O	2.893713
Ala O–Glu O	2.643045
Val N–Gln O	2.837853

Note: Interaction profile of peptide QAENLMQVY and MHC.

Abbreviations: MHC, major histocompatibility complex; HLA, human leukocyte antigen.

Table 6 Peptide SSGLNSNNY-MHC HLA-A0201 interaction

H-bond interaction
(Peptide–protein)	Distance (Å)
Ser N–Glu O	2.937921
Ser O–Tyr O	2.686530
Gly N–Tyr O	2.983901
Tyr N–Asp O	2.852504

Note: Interaction profile of peptide SSGLNSNNY with MHC.

Abbreviations: HLA, human leukocyte antigen; MHC, major histocompatibility complex.

Figure 1 Docking results for OMPs of E. tarda.

Notes: (A) QAENLMQVY–MHC. (B) SSGLNSNNY–MHC.
Abbreviations: MHC, major histocompatibility complex; OMPs, outer membrane proteins.

Table 7 Peptide ETVEPEYYY–MHC HLA-B2705 interaction

H-bond interaction
(Peptide–protein)	Distance (Å)
Tyr O–Asn N	2.927478
Tyr O–Tyr O	2.826191
Tyr O–Thr O	2.885364
Tyr O–Trp N	2.865319
Thr O–Asn O	2.886496
Thr N–Asn O	2.906432
Glu N–Tyr O	2.832275
Glu N–Tyr O	2.684366

Note: Interaction profile of peptide ETVEPEYYY with MHC.

Abbreviations: HLA, human leukocyte antigen; MHC, major histocompatibility complex.

Table 8 Peptide FAKEINSKY–MHC HLA-B2705 interaction

H-bond interaction
(Peptide–protein)	Distance (Å)
Lys N–Asn O	2.513240
Tyr O–Tyr O	2.906147
Tyr O–Thr O	2.438210
Lys O–Trp N	2.853989
Ser O–Trp O	2.681267
Ile O–Thr O	2.680878
Tyr N–Ser O	2.818796
Phe N–Tyr O	2.626686
Ile N–Asn O	2.903029
Ala N–Asn O	2.932375
Phe N–Tyr O	2.927618
Phe O–Tyr O	2.622406
Lys N–Asp O	2.616177
Lys O–Asn N	2.948305
Lys N–Tyr–O	2.943702

Note: Interaction profile of peptide FAKEINSKY and MHC.

Abbreviations: HLA, human leukocyte antigen; MHC, major histocompatibility complex.

Table 9 Peptide FASNMPGTY–MHC HLA-B2705 interaction

H-bond interaction
(Peptide–protein)	Distance (Å)
Thr O–Trp N	2.707887
Tyr O–Tyr O	2.843315
Tyr O–Asn N	2.811533
Met O–Thr O	2.795226
Met N–Asn O	2.901555
Ser O–Asn N	2.862460
Ala N–Asn O	2.836011
Phe O–Tyr O	2.824663
Phe N–Tyr O	2.688093
Phe N–Tyr O	2.756931
Thr O–Trp N	2.925384
Asn N–Asn O	2.925179

Note: Interaction profile of peptide FASNMPGTY with MHC.

Abbreviations: HLA, human leukocyte antigen; MHC, major histocompatibility complex.

Table 10 Peptide HTDCRQTVA–MHC HLA-B2705 interaction

H-bond interaction
(Peptide–protein)	Distance (Å)
His N–Arg N	2.929034
His N–Tyr O	2.743620
Thr N–Asn O	2.840459
Thr O–Asn O	2.935561
His O–Tyr O	2.795949
Asp N–Tyr O	2.738891
Arg N–Asp O	2.861077
Arg N–Asn O	2.701008
Val O–Trp N	2.835952
Thr O–Trp N	2.871054
Ala O–Tyr O	2.855676
Ala O–Asn N	2.738801
Ala O–Lys N	2.888888
His N–Tyr O	2.702608
Arg N–Ser O	2.702492
Arg O–Thr O	2.733620

Note: Interaction profile of peptide HTDCRQTVA and MHC.

Abbreviations: HLA, human leukocyte antigen; MHC, major histocompatibility complex.

Table 11 Peptide NSDQYSVAH–MHC HLA-B2705 interaction

H-bond interaction
(Peptide–protein)	Distance (Å)
His O–Tyr O	2.906147
His O–Thr O	2.438210
Ala O–Trp O	2.853989
His N–Ser O	2.818796
Tyr O–Thr O	2.680878
Tyr N–Asn N	2.903029
Asp O–Asn N	2.948305
Ser N–Asn O	2.932375
Asn N–Tyr O	2.626686
Asn N–Tyr O	2.927618
Asn O–Tyr O	2.622406
Asp N–Tyr O	2.943702

Note: Interaction profile of peptide NSDQYSVAH with MHC.

Abbreviations: HLA, human leukocyte antigen; MHC, major histocompatibility complex.

Figure 2 Docking results for OMPs of F. columnare.

Notes: (A) ETVEPEYYY–MHC. (B) FAKEINSKY–MHC. (C) FASNMPGTY–MHC. (D) HTDCROTVA–MHC. (E) NSDQYSVAH–MHC.
Abbreviations: MHC, major histocompatibility complex; OMPs, outer membrane proteins.