Bioinformatic analysis of the structure and function of Mycobacterium tuberculosis epitope-tandem protein W541

doi:10.19982/j.issn.1000-6621.20220309

Abstract

Abstract:

Objective: To predict and analyze the structure and function of Mycobacterium tuberculosis (MTB) epitope-tandem protein W541 by bioinformatics method. Methods: W541 protein constructed in our laboratory was encoded by a novel multi-antigen epitope-tandem DNA vaccine composed of the epitopes of MTB proliferative antigens Ag85A, Ag85B, latent-related antigens Rv3407 and Rv1733c. Its amino acid sequence of physicochemical properties, hydrophilic (hydrophobic), transmembrane helix, secondary and tertiary structures, subcellular localization, signal peptide, glycosylation and phosphorylation sites, B cell, helper T (Th) and cytotoxic T lymphocyte (CTL) epitopes, the protein interaction network, the homology between W541 protein and human protein was analyzed using bioinformatics softwares ProtParam, Protscale, TMHMM, SOPMA, SWISS-MODEL, PSORT, SignalP, NetNGlyc, NetPhos, SYFPEITHI, RANKPEP, IEDB, NetMHC, STRING, and EXPASY, respectively. Results: W541 protein was composed of 704 amino acids, with the molecular formula of C₃₃₂₉H₅₀₃₅N₉₂₃O₉₉₃S₂₄, the instability index of 45.37, which was hydrophilic unstable protein. The proportions of α-helix, β-fold, β-corner and irregular crimp in its secondary structure were 26.99%, 19.03%, 11.51% and 42.47%, respectively. It had no transmembrane helix region or signal peptides, which was an intracellular membrane protein. W541 protein had 6 glycosylation sites, and 62 phosphorylation sites, including 15 threonine, 35 serine and 12 tyrosine phosphorylation sites, respectively. W541 protein had multiple potential T cell and B cell epitopes. W541 protein interacted with 10 proteins. The amino acid sequence of W541 protein had less than 3.27% homology with the human protein. Conclusion: MTB epitope-tandem protein W541 has multiple potential T-cell and B-cell epitopes. Among them, T-cell epitopes were dominant, which may have better immunogenicity, play an important regulatory role and lay a foundation for further animal experimental evaluation.

Key words: Immunity, Mycobacterium tuberculosis, Antigens, Models,structural

CLC Number:

R52
S852.4+3

Li Pengchuan, Liang Yan, Zhang Linxi, Wu Xueqiong. Bioinformatic analysis of the structure and function of Mycobacterium tuberculosis epitope-tandem protein W541[J]. Chinese Journal of Antituberculosis, 2022, 44(12): 1345-1357. doi: 10.19982/j.issn.1000-6621.20220309

Figures/Tables 14

表型	氨基酸起始位置	SYFPEITHI 氨基酸序列	得分	氨基酸起始位置	RANKPEP 氨基酸序列	得分
HLA-DRB1*0101	7	PVEYLQVPSPSMGRD	30	10	VLQVPSPSM	12.654
	80	SDWYQPACGKAGCQT	19	83	YQPACGKAG	12.113
	122	VVGLSMAASSALTLA	23	127	MAASSALTL	12.117
	147	GAMSGLLDPSQAMGP	23	145	YAGAMSGLL	14.746
	235	TSNIKFQDAYNAGGG	32	238	IKFQDAYNA	13.311
	304	RRLMIGTAAAVVLPG	24	304	RRLMIGTAA	14.952
	309	GTAAAVVLPGLVGLA	20	308	IGTAAAVVL	10.309
	316	LPGLVGLAGGAATAG	33	319	LVGLAGGAA	11.564
	337	LPVEYLQVPSPSMGR	21	341	YLQVPSPSM	12.654
	471	PQQFIYAGSLSALLD	25	476	YAGSLSALL	14.436
	572	QDAYNAAGGHNAVFN	28	571	FQDAYNAAG	12.192
	603	NAMKGDLQGPGPGLR	26	602	LNAMKGDLQ	15.046
	672	GPGPGIPFAAAAGTA	19	677	IPFAAAAGT	10.870
	674	GPGIPFAAAAGTAVQ	19	679	FAAAAGTAV	17.684
HLA-DRB1*0301	15	SPSMGRDIKVQFQSG	35	18	MGRDIKVQF	31.908
	271	LNAMKPDLQRALGAT	38	274	MKPDLQRAL	18.663
	346	SPSMGRDIKVQFQSG	35	349	MGRDIKVQF	31.908
HLA-DRB1*0401	142	QFVYAGAMSGLLDPS	28	143	FVYAGAMSG	16.991
	146	AGAMSGLLDPSQAMG	20	145	YAGAMSGLL	13.217
	188	WQRNDPLLNVGKLIA	18	186	PAWQRNDPL	12.403
	263	SWEYWGAQLNAMKPD	22	266	YWGAQLNAM	15.783
	264	WEYWGAQLNAMKPDL	22	267	WGAQLNAMK	12.536
	305	RLMIGTAAAVVLPGL	20	310	TAAAVVLPG	17.060
	390	EWYYQSGLSIVMPVG	22	391	WYYQSGLSI	14.604
	471	PQQFIYAGSLSALLD	28	474	FIYAGSLSA	15.043
	473	QFIYAGSLSALLDPS	22	476	YAGSLSALL	12.033
	496	GLAMGDAGGYKAADM	20	504	GYKAADMWG	12.665
	572	QDAYNAAGGHNAVFN	22	575	YNAAGGHNA	12.402
	594	SWEYWGAQLNAMKGD	22	597	YWGAQLNAM	15.783
	595	WEYWGAQLNAMKGDL	22	598	WGAQLNAMK	12.536
	690	SRSHVYAHQAQTRHP	18	695	YAHQAQTRH	17.406
HLA-DRB1*0701	57	AFEWYDQSGLSVVMP	18	60	WYDQSGLSV	13.132
				79	YSDWYQPAC	15.868
				83	YQPACGKAG	21.877
	94	TYKWETFLTSELPGW	26	94	TYKWETFLT	12.996
	407	SSFYSDWYSPACGKA	18	410	YSDWYSPAC	23.048
				414	YSPACGKAG	20.301
	425	TYKWETFLTSELPQW	26	425	TYKWETFLT	12.996
	572	QDAYNAAGGHNAVFN	20	571	FQDAYNAAG	14.758
	646	QNLLDVTAEPARGRK	22	643	RRPQNLLDV	13.518
表型	氨基酸起始位置	SYFPEITHI 氨基酸序列	得分	氨基酸起始位置	RANKPEP 氨基酸序列	得分
HLA-DRB1*0801				205	TRVWVYCGN	11.687
				264	WEYWGAQLN	15.670
		无法预测		436	LPQWLSANR	16.537
				536	TRLWVYCGN	11.212
				595	WEYWGAQLN	15.670
				692	SHVYAHQAQ	13.431
HLA-DRB1*1101	119	GSAVVGLSMAASSAL	18	95	YKWETFLTS	15.631
	105	LPGWLQANRHVKPTG	19	107	GWLQANRHV	14.071
	106	PGWLQANRHVKPTGS	21	108	WLQANRHVK	10.986
	160	GPTLIGLAMGDAGGY	18	165	GLAMGDAGG	11.757
	191	NDPLLNVGKLIANNT	27	173	GYKASDMWG	16.074
	207	VWVYCGNGKPSDLGG	18	201	IANNTRVWV	14.316
	272	NAMKPDLQRALGATP	21	260	GTHSWEYWG	12.318
	313	AVVLPGLVGLAGGAA	20	299	GGSGGRRLM	15.719
	436	LPQWLSANRAVKPTG	19	426	YKWETFLTS	15.631
	491	GPSLIGLAMGDAGGY	18	496	GLAMGDAGG	11.757
				504	GYKAADMWG	12.782
	522	NDPTQQIPKLVANNT	21	531	LVANNTRLW	12.181
				532	VANNTRLWV	17.764
	618	QHASRYLARVEAGGP	20	591	GTHSWEYWG	12.813
HLA-DRB1*1501	140	PQQFVYAGAMSGLLD	22	138	YHPQQFVY	10.212
	226	AKFLEGFVRTSNIKF	24	226	AKFLEGFVR	12.196
	250	HNGVFDFPDSGTHSW	24	253	VFDFPDSGT	11.383
	319	LVGLAGGAATAGAFS	18	320	VGLAGGAAT	10.085
	463	AMILAAYHPQQFIYA	24	463	AMILAAYHP	11.442
	470	HPQQFIYAGSLSALL	18	469	YHPQQFIYA	12.231
	557	AEFLENFVRSSNLKF	24	557	AEFLENFVR	14.516
	581	HNAVFNFPPNGTHSW	28	584	VFNFPPNGT	20.508

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表型的分类	SYFPEITHI 表位个数 (分数范围)	RANKPEP 表位个数 (分数范围)
HLA-DRB1*0101	173(18~33)	14(10.309~17.684)
HLA-DRB1*0301	43(18~38)	3(18.663~31.908)
HLA-DRB1*0401	98(18~28)	14(12.033~17.406)
HLA-DRB1*0701	64(18~32)	9(12.996~23.048)
HLA-DRB1*0801	无法预测	6(11.212~16.537)
HLA-DRB1*1101	26(18~27)	14(10.986~17.764)
HLA-DRB1*1501	109(18~28)	8(10.085~20.508)

表型分类	SYFPEITHI (得分≥18)	NetMHC (个)		IEDB (得分>0.5)
表型分类	SYFPEITHI (得分≥18)	强结合肽的数目	弱结合肽的数目	IEDB (得分>0.5)
HLA-A2	57	3	12	10
HLA-A3	35	0	6	2
HLA-B7	18	9	16	8

表型分类	氨基酸起始位	氨基酸序列	RANKPEP	SYFPEITHI (得分≥18)	NetMHC	IEDB (得分>0.5)
HLA-A2	10	YLQVPSPSM	/	20	1.40≤WB	0.685026
	136	AIYHPQQFV	/	22	2.00≤WB	0.669353
	158	AMGPTLIGL	68	27	0.70≤WB	0.748173
	199	KLIANNTRV	86	23	0.40≤SB	0.761698
	314	VVLPGLVGL	/	28	1.30≤WB	0.723346
	341	YLQVPSPSM	/	20	1.40≤WB	0.685026
	474	FIYAGSLSA	/	19	0.17≤SB	0.592681
	482	ALLDPSQGM	/	21	1.70≤WB	0.763105
	489	GMGPSLIGL	/	26	0.80≤WB	0.675624
	662	TLSDVLNEM	83	22	0.60≤WB	0.799273
HLA-A3	167	AMGDAGGYK	9.914	18	0.60≤WB	0.506313
	498	AMGDAGGYK	9.914	18	0.60≤WB	0.506313
HLA-B7	3	RPGLPVEYL	/	26	0.40≤SB	0.850273
	70	MPVGGQSSF	18.044	18	0.12≤SB	0.910081
	160	GPTLIGLAM	/	20	0.08≤SB	0.811608
	334	RPGLPVEYL	/	26	0.40≤SB	0.850273
	401	MPVGGQSSF	18.044	18	0.12≤SB	0.910081
	491	GPSLIGLAM	/	22	0.06≤SB	0.893546
	631	GPGPGSGVL	/	23	0.15≤SB	0.893886
	640	IPARRPQNL	18.587	22	0.25≤SB	0.966787