Introduction of New Computer Softwares for Classification and Prediction Purposes of Bioactive Peptides: Case Study in Antioxidative Tripeptides

Figures & data

Table 1 Relative antioxidative activity values of antioxidative tripeptides

Number	Peptide	Relative antioxidative activity*	Number	Peptide	Relative antioxidative activity*	Number	Peptide	Relative antioxidative activity*
1	FHH	1.8	18	DHH	1	35	HEH	1.5
2	LHH	2	19	RHH	0	36	HDH	1.5
3	IHH	2	20	HFH	2	37	HRH	0
4	YHH	1.8	21	HLH	1	38	HHF	3.6
5	WHH	1.8	22	HIH	1	39	HHL	0
6	VHH	2	23	HYH	2	40	HHI	0
7	MHH	2	24	HWH	2	41	HHY	3.6
8	CHH	1	25	HVH	1	42	HHW	3.6
9	AHH	2	26	HMH	0.8	43	HHV	0
10	GHH	1	27	HCH	1	44	HHM	0
11	THH	1.3	28	HAH	1	45	HHC	0
12	SHH	1.3	29	HGH	0.8	46	HHA	0
13	KHH	0	30	HTH	0.7	47	HHG	0.3
14	QHH	1	31	HSH	0.7	48	HHT	0
15	NHH	1	32	HKH	0	49	HHS	0
16	HHH	0	33	HQH	0.8	50	HHK	0
17	EHH	1	34	HNH	0.8	51	HHQ	0.3
52	HHN	0.3	69	QYY	5	86	YKY	10
53	HHE	0.2	70	NYY	5	87	YQY	3
54	HHD	0.2	71	HYY	2	88	YNY	3
55	HHR	0	72	EYY	3.2	89	YHY	10
56	FYY	2	73	DYY	3.2	90	YEY	3
57	LYY	3	74	RYY	2	91	YDY	3
58	IYY	3	75	YFY	2	92	YRY	10
59	YYY	2	76	YLY	3.7	93	YYF	4
60	WYY	2	77	YIY	3.7	94	YYL	3
61	VYY	3	78	YWY	2	95	YYI	3
62	MYY	2	79	YVY	3.7	96	YYW	4
63	CYY	0	80	YMY	1.8	97	YYV	3
64	AYY	3	81	YCY	2.8	98	YYM	2
65	GYY	5	82	YAY	3.7	99	YYC	0.3
66	TYY	3	83	YGY	3	100	YYA	3
67	SYY	3	84	YTY	3	101	YYG	2.7
68	KYY	2	85	YSY	3	102	YYT	4
103	YYS	4	120	LHT	5.5	137	PHG	5
104	YYK	5	121	LHS	4	138	PHT	6
105	YYQ	2.7	122	LHK	4	139	PHS	4
106	YYN	2.7	123	LHQ	4	140	PHK	3.5
107	YYH	5	124	LHN	5	141	PHQ	3.5
108	YYE	4	125	LHH	5	142	PHN	6
109	YYD	4	126	LHE	6	143	PHE	6
110	YYR	5	127	LHD	3.7	144	PHD	4.5
111	LHF	3.5	128	LHR	5	145	PHR	4.5
112	LHL	6	129	PHF	4	146	PHH	5.8
113	LHI	6.5	130	PHL	5	147	RHF	3
114	LHY	4	131	PHI	5	148	RHL	3.5
115	LHW	7	132	PHY	4	149	RHI	5
116	LHV	3.5	133	PHW	6	150	RHY	3
117	LHM	5	134	PHV	3	151	RHH	3
118	LHA	4	135	PHM	4	152	RHV	3
119	LHG	6.7	136	PHA	6	153	RHM	3
154	RHA	5	171	LWM	1.5	188	PWV	1
155	RHG	5.5	172	LWA	1.25	189	PWM	0.75
156	RHT	6	173	LWG	1.25	190	PWA	1.5
157	RHS	3	174	LWT	2	191	PWG	2.75
158	RHK	2.5	175	LWS	2	192	PWT	2.5
159	RHQ	3	176	LWK	2	193	PWS	1
160	RHN	5.5	177	LWQ	2.5	194	PWK	0.5
161	RHH	3	178	LWN	1.25	195	PWQ	1.25
162	RHE	5	179	LWH	3.25	196	PHN	2.1
163	RHD	3	180	LWE	1.75	197	PWH	1.25
164	RHR	4	181	LWD	1.75	198	PWE	1
165	LWF	1.5	182	LWR	3	199	PWD	1
166	LWL	0.5	183	PWF	1	200	PWR	2.5
167	LWI	1	184	PWL	1	201	RWF	1
168	LWY	2.25	185	PWI	1.5	202	RWL	3
169	LWW	3.5	186	PWY	1	203	RWI	1.25
170	LWV	1.5	187	PWW	3	204	RWY	0.75
205	RWW	2.5	210	RWT	3.75	215	RWH	1
206	RWV	0.5	211	RWS	0.75	216	RWE	1
207	RWM	0.75	212	RWK	0.5	217	RWD	1
208	RWA	1.25	213	RWQ	0.5	218	RWR	2.5
209	RWG	1.75	214	RWN	2.5
*The relative antioxidative activity was tabulated from the data of Saito et al.[18]

Table 2 Cumulative eigenvalues of antioxidative tripeptides when hydrophobicity was used as the property characteristic

Principal component	Eigenvalue	Variance	Cumulation (%)
1	3.8682	19.3408	19.3408
2	3.1629	15.8145	35.1553
3	2.2616	11.3082	46.4634
4	2.2316	11.3082	57.7716
5	1.7819	8.9094	66.6809
6	1.0917	5.4585	72.1395
7	1.0849	5.4246	77.5641
8	1.0849	5.4246	82.9888
9	1.0849	5.4246	88.4134
10	1.0527	5.2634	93.6768
11	0.9496	4.7478	98.4246
12	0.2197	1.0987	99.5234
13	0.0258	0.1290	99.6524
14	0.0194	0.0972	99.7496
15	0.0154	0.0770	99.8266
16	0.0148	0.0739	99.9005
17	0.0148	0.0739	99.9744
18	0.0037	0.0185	99.9929
19	0.0014	0.0071	100.0000
20	0.0000	0.0000	100.0000

Figure 1 SPCS scattergram of antioxidative tripeptides. The tripeptides in x position varied from Asp (D), Glu (E), His (H), Lys (K), Arg (R), Ala (A), Ile (I), Leu (L), Val (V), Phe (F), Trp (W),Tyr (Y),Gly (G), Asp (N), Gln (Q), Met (M), Ser (S) and Thr (T). Hydrophobicity was chosen as the property characteristic. Two histidine-containing peptide were used as the references. The digits attached to datapoints in the blanket are means of relative antioxidative activity values from Saito et al.[18]

Table 3 Major protein fractions in fourteen protein sources

Protein source	Major protein fractions	Primary Accession number/Protein name
1. Fish	Actin	O42161/Actin, cytoplasmic 1
	Myosin heavy chain	Q2HXU3/Myosin heavy chain
	Myosin light chain	Q06B21/ Myosin light chain
	Tropomyosin	Q91472/Fast myotomal muscle tropomyosin
2. Milk	Alpha S1casein	P02662/Alpha-S1-casein
	Alpha-S2 casein	P02663/ Alpha-S2 casein
	Alpha-lactalbumin	P00711/ Alpha-lactalbumin
	Beta casein	P02662/ Beta casein
	Beta-lactoglobulin	P02754/Beta-lactoglobulin
	Lactoferrin	Q6LC78/ Lactoferrin
3. Soy	Conglycinin alpha chain	P13916/Beta-conglycinin, alpha chain
	Conglycinin beta chain	P25974/Beta-conglycinin, beta chain
	7S globulin	P13917/Basic 7s globulin
	2S albumin	P19594/2S albumin
	Glycinin	P02858/Glycinin G4
4. Cotton	Legumin A	P09802/Legumin A
	Legumin B	P09800/Legumin B
5. Canola	11S globulin	P33525/Cruciferin CRU1
6. Barley	Globulin	Q84NG7/Globulin
	B-hordein	Q40026/ B-hordein
	C-hordein	Q41210/C-hordein
	D-hordein	Q84LE9/D-hordein
7. Buckwheat	13S globulin	O23878/13S globulin seed storage protein
8. Rice	Globulin	P29835/19 kDa globulin
	Glutenin	Q9ZWJ8/Glutelin
	Prolamin	Q9ZWJ7/Prolamin PPROL 17D
9. Rye	Glutenin subunit X	Q93WF0/HMW glutenin subunit X
	Glutenin subunit Y	Q93WM1/HMW glutenin subunit Y
10. Sunflower	Albumin	P15416/2S Albumin storage protein
	11S globulin	P19084/11S Globulin seed storage protein
11. Oat	11S globulin	Q38780/11S globulin
	12S globulin	P12615/12S seed storage globulin1
12. Pea	Convicillin	P13915/Convicillin
	Legumin A	P02857/Lecumin A
	Legumin J	P05692/ Legumin J
	Vicillin	P13918/ Vicillin
13. Wheat	Alpha/beta gliadin	P02863/ Alpha-beta gliadin
	Gamma gliadin	P08453/Gamma-gliadin
	High molecular weight glutenin	Q41516/ High molecular weight glutenin
	Low molecular weight glutenin	Q5MFH2/ Low molecular weight glutenin
14. Egg	Apovitellenin	P02659/ Apovitellenin 1
	Lipovitellin and Phosphovitin	P02845/Vitellogenin 2
	Ovalbumin	P01012/ Ovalbumin
	Ovomucoid	P01005/ Ovomucoid
	Ovotransferrin	P02789/ Ovotransferrin

Table 4 Number of homology similarity sequence presenting in protein chain

Source of protein	Number of residue	YHY (10) ^a	LHW (6.8) ^a	LHG (6.8) ^a	Average relative antioxidative activity
1. Fish protein (Salmon)
- Actin	375	12	12	30	1.08
- Myosin heavy chain	228	2	16	19	1.13
- Myosin Light chain ^b	186	9	8	16	1.36
- Tropomyosin	284	7	9	24	1.04
2. Milk protein
- Alpha S1 Casein	214	6	10	14	1.04
- Alpha-S2 casein	222	7	8	17	1.08
- Alpha lactalbumin	142	7	10	13	1.59
- Beta casein	214	8	10	21	1.36
- Beta lactoglobulin ^b	178	11	12	16	1.69
- Lactoferrin	117	2	4	13	1.16
3. Soy protein
- Conglycinin alpha chain	605	23	27	52	1.27
- Conglycinin beta chain	439	24	22	40	1.51
- 7S Globulin ^b	427	28	29	41	1.77
- 2S Albumin	158	7	7	13	1.30
- Glycinin	562	27	29	53	1.47
4. Cotton protein
- Legumin A	509	21	21	38	1.20
- Legumin B ^b	516	19	21	45	1.24
5. Canola protein
- 11S globulin ^b	509	22	25	54	1.49
6. Barley protein
- Globulin	224	4	4	14	0.73
- B-hordein	290	14	14	46	1.89
- C-hordein ^b	310	15	15	69	2.33
- D-hordein	757	37	27	63	1.30
7. Buckwheat protein
- 13S Globulin ^b	565	28	24	43	1.30
8. Rice protein
- Globulin	186	6	7	10	0.94
- Glutelin	510	20	25	57	1.49
- Prolamin ^b	156	12	13	19	2.16
9. Rye protein
- Glutenin subunit X ^b	754	11	10	43	0.62
- Glutenin subunit Y	713	7	8	43	0.58
10. Sunflower protein
- Albumin	295	2	2	12	0.39
- 11S Globulin ^b	493	15	19	52	1.36
11. Oat protein
- 11S globulin ^b	527	23	22	58	1.45
- 12S globulin	518	23	20	53	1.34
12. Pea protein
- Convicillin	571	24	25	51	1.34
- Legumin A	517	19	27	54	1.59
- Legumin J	503	23	26	47	1.50
- Vicillin ^b	459	24	23	42	1.46
13. Wheat protein
- Alpha/Beta Gliadin	286	14	16	36	1.73
- Gamma gliadin ^b	327	15	16	50	1.83
- HMW glutenin	405	6	6	29	0.74
- LMW glutenin	388	11	11	55	1.44
14. Egg protein
- Apovitellenin ^b	106	4	10	13	1.85
- Lipovitellin and Phosphovitin	1,850	42	42	67	0.63
- Ovalbumin	386	20	15	30	1.31
- Ovomucoid	210	12	8	13	1.25
- Ovotransferrin	705	28	29	68	1.33
^aThe relative activity was tabulated from the data of Saito et al.[18] ^bProtein fraction in bold showed the highest average relative antioxidative activity in each protein source.

Figure 2 BIOPEP print-out of digested C hordein after a trypsin-pepsin combined action.

Saito , K. , Jin , D.H. , Ogawa , T. , Muramoto , K. , Hatakeyama , E. , Yasuhara , T. and Nokihara , K. 2003 . Antioxidative properties of tripeptide libraries prepared by the combinatorial chemistry . J. Agric. Food Chem. , 51 : 3668 – 3674 .

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