结核分枝杆菌Rv3248c生物信息学分析及同源建模
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摘要
运用生物信息学方法对结核分枝杆菌Rv3248c进行结构功能分析及同源建模。通过NCBI、BLAST、ProtParam和Interproscan等生物信息学方法对Rv3248c进行同源性、理化性质、保守序列、跨膜、信号肽二级结构和三级结构预测分析。结果显示Rv3248c的氨基酸序列与腺苷高半胱氨酸水解酶高度一致,该蛋白包含495个氨基酸,没有跨膜及信号肽结构,其二级结构α螺旋占43%,无规则卷曲占41.8%,β折叠占15.2%,利用同源建模法构建该蛋白的三级结构,并对该模型进行质量评估。研究结果有望对结核病的诊断和治疗提供参考。为进一步研究该蛋白质的结构与功能打下基础。
To analyze Mycobacterium tuberculosis Rv3248 c and its encoding protein. To predict its structure and function with bioinformatices methods. According to the amino acid sequences from NCBI of protein encoded by the Mycobacterium tuberculosis Rv3248 c from NCBI databases,use BLAST,ProtParam,Interproscan and other online bioinformatics tools to predict the protein's homology,biochemical properties,conserved sequence,transmembrane,signal peptide,secondary structure and tertiary structure. The amino acid sequences of the protein encoded by Rv3248 c is highly similar to adenosylhomocysteinase,the protein contains 495 amino acids and no,transmembrane and signal peptide structure,the percent of the alpha helix is 43%,coil is 41.8%,beta sheet is 15.2%,use homology modeling method to construct the tertiary structure of the protein performance good in quality evaluation. The result is to establish foundation for future research on the structures and function of Rv3248 c,and to make preparation for the diagnosis and treatment of tuberculosis.
To analyze Mycobacterium tuberculosis Rv3248 c and its encoding protein. To predict its structure and function with bioinformatices methods. According to the amino acid sequences from NCBI of protein encoded by the Mycobacterium tuberculosis Rv3248 c from NCBI databases,use BLAST,ProtParam,Interproscan and other online bioinformatics tools to predict the protein's homology,biochemical properties,conserved sequence,transmembrane,signal peptide,secondary structure and tertiary structure. The amino acid sequences of the protein encoded by Rv3248 c is highly similar to adenosylhomocysteinase,the protein contains 495 amino acids and no,transmembrane and signal peptide structure,the percent of the alpha helix is 43%,coil is 41.8%,beta sheet is 15.2%,use homology modeling method to construct the tertiary structure of the protein performance good in quality evaluation. The result is to establish foundation for future research on the structures and function of Rv3248 c,and to make preparation for the diagnosis and treatment of tuberculosis.
引文
[1] World Health Organization Global tuberculosis report 2018[R].Geneva:World Health Organization,2018.
[2] Reddy M C,Kuppan G,Shetty N D,et al.Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors.[J].Protein Sci,2008 ,17(12):2134-44.
[3] Jena L,Deshmukh S,Waghmare P,et al.Study of mechanism of interaction of truncated isoniazid-nicotinamide adenine dinucleotide adduct against multiple enzymes of Mycobacterium tuberculosis by a computational approach.[J]Int J Mycobacteriol.2015 ,4(4):276-83.
[4] Yari S,Hadizadeh Tasbiti A,Ghanei M,et al.Proteome-scale MDR-TB-antibody responses for identification of putative biomarkers for the diagnosis of drug-resistant Mycobacterium tuberculosis.[J]Int J Mycobacteriol.2016 ,5 Suppl 1:S134-S135.
[5] Dziadek B,Brzostek A,Grzybowski M,et al.Mycobacterium tuberculosis AtsG (Rv0296c),GlmU (Rv1018c) and SahH (Rv3248c) Proteins Function as the Human IL-8-Binding Effectors and Contribute to Pathogen Entry into Human Neutrophils.[J]PLoS One.2016,11(2):e0148030.
[6] 李岱容,穆柳青,张春燕,等.结核分枝杆菌ClpC2基因序列分析及功能预测[J].重庆医科大学学报,2014(01):57-61.
[7] 薛庆中.DNA和蛋白质序列数据分析工具[M].北京:科学出版社,2012:105-113.
[8] Arnold K,Bordoli L,Kopp J T.The SWISS-MODEL workspace:a web-based environment for protein structure homology modelling[J].Bioinformatics,2006,22(2):195-201(7).
[9] 张悦宁,陈慧敏,邬强.结核分枝杆菌rmlA基因的生物信息学分析[J].海南医学院学报,2012(02):145-148.
[10] 吴祖建.生物信息学分析实践[M].北京:科学出版社,2010:105-112.
[11] Ponnaluri V K C,Estève P O,Ruse C I,et al .S-adenosylhomocysteine Hydrolase Participates in DNA Methylation Inheritance.[J].J Mol Biol,2018 ,430(14):2051-2065.
[2] Reddy M C,Kuppan G,Shetty N D,et al.Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors.[J].Protein Sci,2008 ,17(12):2134-44.
[3] Jena L,Deshmukh S,Waghmare P,et al.Study of mechanism of interaction of truncated isoniazid-nicotinamide adenine dinucleotide adduct against multiple enzymes of Mycobacterium tuberculosis by a computational approach.[J]Int J Mycobacteriol.2015 ,4(4):276-83.
[4] Yari S,Hadizadeh Tasbiti A,Ghanei M,et al.Proteome-scale MDR-TB-antibody responses for identification of putative biomarkers for the diagnosis of drug-resistant Mycobacterium tuberculosis.[J]Int J Mycobacteriol.2016 ,5 Suppl 1:S134-S135.
[5] Dziadek B,Brzostek A,Grzybowski M,et al.Mycobacterium tuberculosis AtsG (Rv0296c),GlmU (Rv1018c) and SahH (Rv3248c) Proteins Function as the Human IL-8-Binding Effectors and Contribute to Pathogen Entry into Human Neutrophils.[J]PLoS One.2016,11(2):e0148030.
[6] 李岱容,穆柳青,张春燕,等.结核分枝杆菌ClpC2基因序列分析及功能预测[J].重庆医科大学学报,2014(01):57-61.
[7] 薛庆中.DNA和蛋白质序列数据分析工具[M].北京:科学出版社,2012:105-113.
[8] Arnold K,Bordoli L,Kopp J T.The SWISS-MODEL workspace:a web-based environment for protein structure homology modelling[J].Bioinformatics,2006,22(2):195-201(7).
[9] 张悦宁,陈慧敏,邬强.结核分枝杆菌rmlA基因的生物信息学分析[J].海南医学院学报,2012(02):145-148.
[10] 吴祖建.生物信息学分析实践[M].北京:科学出版社,2010:105-112.
[11] Ponnaluri V K C,Estève P O,Ruse C I,et al .S-adenosylhomocysteine Hydrolase Participates in DNA Methylation Inheritance.[J].J Mol Biol,2018 ,430(14):2051-2065.