Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, Mexico.
Oracle MDC, Guadalajara, Mexico.
BMC Bioinformatics. 2018 Jun 25;19(1):238. doi: 10.1186/s12859-018-2237-8.
The influenza A virus (IAV) is a constant threat for humans worldwide. The understanding of motif-domain protein participation is essential to combat the pathogen.
In this study, a data mining approach was employed to extract influenza-human Protein-Protein interactions (PPI) from VirusMentha,Virus MINT, IntAct, and Pfam databases, to mine motif-domain interactions (MDIs) stored as Regular Expressions (RegExp) in 3DID database. A total of 107 RegExp related to human MDIs were searched on 51,242 protein fragments from H1N1, H1N2, H2N2, H3N2 and H5N1 strains obtained from Virus Variation database. A total 46 MDIs were frequently mapped on the IAV proteins and shared between the different strains. IAV kept host-like MDIs that were associated with the virus survival, which could be related to essential biological process such as microtubule-based processes, regulation of cell cycle check point, regulation of replication and transcription of DNA, etc. in human cells. The amino acid motifs were searched for matches in the immune epitope database and it was found that some motifs are part of experimentally determined epitopes on IAV, implying that such interactions exist.
The directed data-mining method employed could be used to identify functional motifs in other viruses for envisioning new therapies.
甲型流感病毒（IAV）是全球人类的持续威胁。了解基序结构域蛋白的参与对于对抗病原体至关重要。
本研究采用数据挖掘方法从 VirusMentha、Virus MINT、IntAct 和 Pfam 数据库中提取流感-人类蛋白-蛋白相互作用（PPI），并在 3DID 数据库中以正则表达式（RegExp）的形式挖掘基序结构域相互作用（MDIs）。在从 Virus Variation 数据库获得的 H1N1、H1N2、H2N2、H3N2 和 H5N1 株的 51242 个蛋白质片段上搜索了与人类 MDIs 相关的 107 个 RegExp。总共在 IAV 蛋白上频繁映射了 46 个 MDIs，并在不同株之间共享。IAV 保留了与宿主相似的 MDIs，这些 MDIs与病毒的存活有关，可能与人类细胞中重要的生物过程有关，如微管为基础的过程、细胞周期检查点的调节、DNA 的复制和转录的调节等。在免疫表位数据库中搜索了氨基酸基序的匹配，发现一些基序是 IAV 上实验确定的表位的一部分，这表明存在这种相互作用。
所采用的有针对性的数据挖掘方法可用于识别其他病毒中的功能基序，从而设想新的治疗方法。
