Nowadays it is an era of great explosion of information, the vast flow of information is like an ocean which has surrounded everyone tightly. It has been very important for people especially the researchers to search the useful information with existing tools. In the work of immunology, medicine, pharmaceutical research, we often use the Protein Database. There is a lot of database about protein structure, proteomic, today we will introduce the uniprot database which is most frequently used with lowest redundancy. Hope it can help you.
As in the following, we will give an example with IL-6 that we have studies a lot, and share with you how to organically combine database and product information.
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Open the web https://www.uniprot.org/, enter the key word IL-6, click the Search button on the top-right, and then find the species you need, it will appear the detailed information of the protein.
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Open the web https://www.uniprot.org/, enter the key word IL-6, click the Search button on the top-right, and then find the species you need, it will appear the detailed information of the protein.
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In the section of “Names & Taxonomy”, it has shown you the information of the name, origin, species, NCBI and Enzembl gene database links, if necessary, you can clink NCBI and Enzembl gene database links for more information.
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Then it is the important information for experiments: the protein parenchyma cells expression profile and protein subcellular localization.
When we do IHC and IF experiments, we often meet an important but knotty problem: is the positive signal specific? UniProt can support you to offer some information. In the section of “Expression”, it has explained the how the gene (mRNA Level/protein level) expressed in cells or tissues. In the section of “Subcellular location”, it has shown the localization of mature proteins in cells and topology information.
In conclusion, we can find that IL-6 is ubiquitous in the body, it exists more in fat and lymphatic tissues. Its subcellular localization is endoplasmic reticulum, membrane and secretory expression. So the IHC positive signal mainly exists in cell space, the layer outside the cell wall and the nucleus of the cell.
The following pictures are the human tonsil (see picture on the left) IHC experiment data (The FineTest antibody cat NO. is FNab04282), and the cervical cancer tissue (see picture on the right) IHC experiment data (The FineTest antibody cat NO. is FNab04283). You can see the IL-6 expression clearly.
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After the subcellular localization, let’s see the topological structure of the protein. In the section of “Topology” from “Subcellular location”, it has shown the location for IL-6 extracellular region, transmembrane domain and intracellular region, and also presented its corresponding amino acid sequence. They are important clues to choose protein products.
The FineTest IL-6 is the recombinant protein product. The product will indicate its sequence range, for example, for the product in the following picture (FineTest cat NO. P0051), the protein sequence is 29-212aa, if you check it with the UniProt sequence and structure information, you can see that this recombinant protein sequence covers all the extracellular region of IL-6. Then, you can choose a suitable protein product according to your experiments.
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In the section of “PTM/Processing”, the UniProt database has shown the information for molecule process technique, amino acid motif, posttranslational modification (such as shearing, glycosylation, lipoacylation, disulfide bond positions) in the protein synthesis process. What will the information works for the practical experiment?
In the section of “Sequences”, it has indicated the IL-6 protein basic molecular weight with different pri-miRNA. For example, for the pri-miRNA with the longest sequence, the Mass (Da) information shows that the protein basic molecular weight is about 24KD (see picture on the left).
While sometimes in tissues, the WB positive band of some proteins has appeared big errors due to the modification. This is one of the reasons why the actual detection of molecular weight is different from predicted molecular weight for some antibodies. The protein posttranslational modification plays an important assistant role in the determination of WB results. With this information, it is no worry to find the target band in WB experiments.
In a word, we can know about the protein basic function, its name, origin, subcellular localization, structural domain, sequence, posttranslational modification and so on from the UniProt database. It is said that "Jade can be polished by stones from other hills", so the information searched from UniProt database can help to promote the research work a lot.