Xinjiang Agricultural Sciences ›› 2024, Vol. 61 ›› Issue (11): 2844-2852.DOI: 10.6048/j.issn.1001-4330.2024.11.026
• Facility Agriculture·Animal Husbandry Veterinarian • Previous Articles Next Articles
LU Guili(), MIAO Shukui(
), WEI Jie, WEI Yurong, MI Xiaoyun, Hailiqiemu Maimaitiyiming
Received:
2024-04-11
Online:
2024-11-20
Published:
2025-01-08
Correspondence author:
MIAO Shukui
Supported by:
陆桂丽(), 苗书魁(
), 魏婕, 魏玉荣, 米晓云, 海力且木·买买提依明
通讯作者:
苗书魁
作者简介:
陆桂丽(1977-),女,江苏人,研究员,博士,研究方向为动物传染病防控,(E-mail)66498744@qq.com
基金资助:
CLC Number:
LU Guili, MIAO Shukui, WEI Jie, WEI Yurong, MI Xiaoyun, Hailiqiemu Maimaitiyiming. Structure and function analysis of spike protein of bovine coronavirus[J]. Xinjiang Agricultural Sciences, 2024, 61(11): 2844-2852.
陆桂丽, 苗书魁, 魏婕, 魏玉荣, 米晓云, 海力且木·买买提依明. 牛冠状病毒纤突蛋白的结构与功能分析[J]. 新疆农业科学, 2024, 61(11): 2844-2852.
引物 Primer | 序列(5'-3') Sequence (5'-3') | 产物长度 Product length (bp) |
---|---|---|
BCoV S1F | TACCTATTTGTGTGTATG | 923 |
BCoV S1R | ATTCTAAAGTCATAGCAC | |
BCoV S2F | GGTGTTGTTTCCTGTTTA | 919 |
BCoV S2R | AAGACCCATCCAATTTAC | |
BCoV S3F | ATTTACCTGCTGCTAATGT | 911 |
BCoV S3R | GACAACACAACCAAGATAG | |
BCoV S4F | CTACGGTTTTAGAGATTAC | 876 |
BCoV S4R | AACACCTTGATACCATTAT | |
BCoV S5F | TGTATTAGGTTGTTTAGGA | 908 |
BCoV S5R | CAGTGAACATCCAAGTATT | |
BCoV S6F | TTTTGTGGTAATGGTAATC | 904 |
BCoV S6R | GAACAGTAATAGGCATAAT |
Tab.1 Primers of S gene of bovine coronavirus
引物 Primer | 序列(5'-3') Sequence (5'-3') | 产物长度 Product length (bp) |
---|---|---|
BCoV S1F | TACCTATTTGTGTGTATG | 923 |
BCoV S1R | ATTCTAAAGTCATAGCAC | |
BCoV S2F | GGTGTTGTTTCCTGTTTA | 919 |
BCoV S2R | AAGACCCATCCAATTTAC | |
BCoV S3F | ATTTACCTGCTGCTAATGT | 911 |
BCoV S3R | GACAACACAACCAAGATAG | |
BCoV S4F | CTACGGTTTTAGAGATTAC | 876 |
BCoV S4R | AACACCTTGATACCATTAT | |
BCoV S5F | TGTATTAGGTTGTTTAGGA | 908 |
BCoV S5R | CAGTGAACATCCAAGTATT | |
BCoV S6F | TTTTGTGGTAATGGTAATC | 904 |
BCoV S6R | GAACAGTAATAGGCATAAT |
分析项目 Items analyzed | 工具 Tools | 网址/软件 Website/Software |
---|---|---|
理化性质分析 Analysis of physico chemical properties | Expasy-ProtScale | https://web.expasy.org/protparam |
跨膜结构 Transmembrane structure | TMHMM Server v2.0 | https://services.healthtech.dtu.dk/service.php?DeepTMHMM |
测亲/疏水性 Test for kin ship/hydrophobicity | ExPAsy | https://web.expasy.org/protscale |
信号肽Signal peptide | SignalP | https://services.healthtech.dtu.dk/service.php?SignalP-5.0 |
亚细胞定位Subcellular localization | PSORT Ⅱ | https://psort.hgc.jp/form2.html |
糖基化位点Glycosy lation site | NetNGlyc-1.0 | https://services.healthtech.dtu.dk/service.php?NetNGlyc |
磷酸化位点Phosphorylation site | NetPhos-3.1 | http://www.cbs.dtu.dk/services/NetPhos |
结构域Domain | SMART | http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORM |
受体结合结构域 Receptor binding domain | NPS@SOPMA | https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html |
B细胞抗原表位B cell antigenic | ABCpred | https://webs.iiitd.edu.in/raghava/abcpred/index.html |
T细胞抗原表位T cell antigenic | SYFPEITHI | http://www.syfpeithi.de/bin/mhcserver.dll/epitopeprediction.htm |
二级结构Seconclary structure | PRABI | https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html |
三级结构Tertiary structure | SWISS-MODEL | https://swissmodel.expasy.org/interactive |
遗传进化分析Genetic evolution analysis | Mega | Mega 5.0 |
Tab.2 Prediction website and software
分析项目 Items analyzed | 工具 Tools | 网址/软件 Website/Software |
---|---|---|
理化性质分析 Analysis of physico chemical properties | Expasy-ProtScale | https://web.expasy.org/protparam |
跨膜结构 Transmembrane structure | TMHMM Server v2.0 | https://services.healthtech.dtu.dk/service.php?DeepTMHMM |
测亲/疏水性 Test for kin ship/hydrophobicity | ExPAsy | https://web.expasy.org/protscale |
信号肽Signal peptide | SignalP | https://services.healthtech.dtu.dk/service.php?SignalP-5.0 |
亚细胞定位Subcellular localization | PSORT Ⅱ | https://psort.hgc.jp/form2.html |
糖基化位点Glycosy lation site | NetNGlyc-1.0 | https://services.healthtech.dtu.dk/service.php?NetNGlyc |
磷酸化位点Phosphorylation site | NetPhos-3.1 | http://www.cbs.dtu.dk/services/NetPhos |
结构域Domain | SMART | http://smart.embl-heidelberg.de/smart/set_mode.cgi?NORM |
受体结合结构域 Receptor binding domain | NPS@SOPMA | https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html |
B细胞抗原表位B cell antigenic | ABCpred | https://webs.iiitd.edu.in/raghava/abcpred/index.html |
T细胞抗原表位T cell antigenic | SYFPEITHI | http://www.syfpeithi.de/bin/mhcserver.dll/epitopeprediction.htm |
二级结构Seconclary structure | PRABI | https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html |
三级结构Tertiary structure | SWISS-MODEL | https://swissmodel.expasy.org/interactive |
遗传进化分析Genetic evolution analysis | Mega | Mega 5.0 |
Fig.1 Amplification results of S gene of BCoV Note:M: GeneRuler 1kb Plus DNA Ladder;1~6:Amplified products of BCoV-S1(923 bp), BCoV-S2(919 bp), BCoV-S3(911 bp), BCoV-S4(876 bp), BCoV-S5(908 bp) and BCoV-S6(904 bp), respectively
排序 Rank | 抗原表位序列 Sequence | 氨基酸 起始位置 Start position | 评分 Score |
---|---|---|---|
1 | TGSGYYYPEPITGNNV | 1 200 | 0.97 |
2 | HTGIGTCPAGTNYLTC | 509 | 0.96 |
3 | LYEIQIPSEFTIGNME | 797 | 0.92 |
3 | RRSITTGYRFTNFEPF | 767 | 0.92 |
3 | YPTSGSTYRNMALKGT | 68 | 0.92 |
3 | PVTCNSAMTLEYWVTP | 249 | 0.92 |
4 | CDNINATLTEVNELLD | 848 | 0.91 |
4 | FHFYQEGGTFYAYFTD | 210 | 0.91 |
5 | ANSSEPALLFRNIKCN | 695 | 0.9 |
5 | NGLGTYYVLDRVYLNT | 45 | 0.9 |
5 | PSISTDTVDVTNGLGT | 34 | 0.9 |
5 | KTLSIAPSTGVYELNG | 297 | 0.9 |
5 | SHYYVMPVTCNSAMTL | 243 | 0.9 |
5 | CCTGCGTSCFKKCGGC | 1 330 | 0.9 |
5 | TCAVNYTKAPDVMLNI | 1 220 | 0.9 |
Tab.3 Prediction of B cell epitopes of S protein
排序 Rank | 抗原表位序列 Sequence | 氨基酸 起始位置 Start position | 评分 Score |
---|---|---|---|
1 | TGSGYYYPEPITGNNV | 1 200 | 0.97 |
2 | HTGIGTCPAGTNYLTC | 509 | 0.96 |
3 | LYEIQIPSEFTIGNME | 797 | 0.92 |
3 | RRSITTGYRFTNFEPF | 767 | 0.92 |
3 | YPTSGSTYRNMALKGT | 68 | 0.92 |
3 | PVTCNSAMTLEYWVTP | 249 | 0.92 |
4 | CDNINATLTEVNELLD | 848 | 0.91 |
4 | FHFYQEGGTFYAYFTD | 210 | 0.91 |
5 | ANSSEPALLFRNIKCN | 695 | 0.9 |
5 | NGLGTYYVLDRVYLNT | 45 | 0.9 |
5 | PSISTDTVDVTNGLGT | 34 | 0.9 |
5 | KTLSIAPSTGVYELNG | 297 | 0.9 |
5 | SHYYVMPVTCNSAMTL | 243 | 0.9 |
5 | CCTGCGTSCFKKCGGC | 1 330 | 0.9 |
5 | TCAVNYTKAPDVMLNI | 1 220 | 0.9 |
排序 Rank | 抗原表位序列 Sequence | 氨基酸起始位置 Start position | 评分 Score |
---|---|---|---|
1 | 1 052 | ALNNLLQQL | 28 |
2 | 1 070 | SLQEILSRL | 28 |
3 | 1 090 | LINGRLTAL | 28 |
4 | 1 311 | WLLIGFAGV | 27 |
5 | 972 | TLAATSASL | 26 |
6 | 4 | ILLISLPTT | 25 |
7 | 95 | FLSDFTNGI | 25 |
8 | 850 | NINATLTEV | 25 |
9 | 853 | ATLTEVNEL | 25 |
10 | 1 279 | RLQEAIKVL | 25 |
11 | 1 320 | AMLVLLFFI | 25 |
Tab.4 Prediction of T cell epitopes of S protein
排序 Rank | 抗原表位序列 Sequence | 氨基酸起始位置 Start position | 评分 Score |
---|---|---|---|
1 | 1 052 | ALNNLLQQL | 28 |
2 | 1 070 | SLQEILSRL | 28 |
3 | 1 090 | LINGRLTAL | 28 |
4 | 1 311 | WLLIGFAGV | 27 |
5 | 972 | TLAATSASL | 26 |
6 | 4 | ILLISLPTT | 25 |
7 | 95 | FLSDFTNGI | 25 |
8 | 850 | NINATLTEV | 25 |
9 | 853 | ATLTEVNEL | 25 |
10 | 1 279 | RLQEAIKVL | 25 |
11 | 1 320 | AMLVLLFFI | 25 |
Fig.10 Ramachandran plots of protein encoded by BCoV S gene Note: Dark green: the optimum area; Green: the allowed area; Light green: the maximum allowable area; White: area not allowed
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