Unlocking the Secrets of Proteins: Protein Information Query Tools and User Guides

In the vast field of biomedical research, proteins play a crucial role. They are not only the main components of cells but also involved in almost all biochemical processes. Understanding the structure, function, and interactions of proteins is essential for deciphering disease mechanisms, discovering drug targets, and applying biotechnology. This article will introduce a series of protein information query tools and provide detailed user guides to help you easily unlock the in-depth information of proteins.

There are various protein information query tools available on the market, each with its own advantages and serving different research needs. The following are several widely used databases:

1.       UniProt: Query basic information such as protein localization, modification, and molecular weight, query protein sequences, and find proteins with high homology;

2.       The Human Protein Atlas: Query protein localization and basic information, as well as the expression of proteins in human cells, normal tissues, and cancerous tissues;

3.       The Human Immune System: Provides the first map of the dialogue between all immune cells in the human body.

UniProt Database

UniProt (full name: UniProt Protein Resource), a commonly used database in proteomics, was established in 1986. It is jointly founded by three major protein databases: Swiss-Protein, TrEMBL, and PIR-PSD. With rich information and extensive resources, it is currently recognized as the preferred free protein database.

So how to use such a powerful tool to query our protein information?

1. Enter https://www.uniprot.org/ in the browser to open the UniProt page. Enter the protein name or ID in the top search bar, select the database and advanced filters as needed, and click "Search" to enter the search results page.

2. Taking mouse-derived CD8 protein as an example, after entering the detailed protein information page, you can first see the [Function] section, which summarizes the basic functions of CD8 protein and the main biological processes it participates in.

3. Next is the [Names & Taxonomy] section, which introduces the naming of CD8 protein, source species, NCBI taxonomic ID, phylogenetic tree, detailed species information, proteomic information, etc.

    (BLAST Align, Peptide search, ID mapping, SPARQL; UniProtKB; Search, Advanced | List, History; Entry, Variant viewer 2, Feature viewer, Genomic coordinates, Publications, External links; Function, Names & Taxonomy, Subcellular Location, Phenotypes & Variants, PTM/Processing, Expression, Interaction, Structure, Family & Domains, Sequence, Similar Proteins, GO annotations; Function description: Integral membrane glycoprotein that plays an essential role in the immune response and serves multiple functions in responses against both external and internal offenses. In T-cells, functions primarily as a coreceptor for MHC class I molecule-peptide complex. The antigens presented by class I peptides are derived from cytosolic proteins while class II derived from extracellular proteins. Interacts simultaneously with the T-cell receptor (TCR) and the MHC class I proteins presented by antigen presenting cells (APCs). In turn, recruits the src kinase LCK to the vicinity of the TCR-CD3 complex. LCK then initiates different intracellular signaling pathways by phosphorylating various substrates ultimately leading to lymphokine production, motility, adhesion and activation of cytotoxic T-lymphocytes (CTLs). This mechanism enables CTLs to recognize and eliminate infected cells and tumor cells. In K-cells, the presence of CD8A homodimers at the cell surface provides a survival mechanism allowing conjugation and lysis of multiple target cells. CD8A homodimer molecules also promote the survival and differentiation of activated lymphocytes into memory CD8 T-cells. By Similarity; Access the complete set of GO annotations on QuickGo)

4. The following sections are closely related to our protein experiments, including [Subcellular Location], [PTM/Processing] (Post-Translational Modification/Processing), [Expression], [Interaction] (Protein-Protein Interaction), etc.

In these sections, we can find the expression of proteins or genes in cells/tissues, the localization of proteins in subcellular structures, the post-translational modifications of proteins, and the proteins that interact with CD8.

For example, CD8 is mainly expressed in the thymus and 17 other cell types or tissues, and its subcellular localization is the cell membrane. Therefore, we should know the correct location of CD8 positive signals when performing IHC or IF experiments.

    (UniProtKB; Search, BLAST Align, Peptide search, ID mapping, SPARQL; Advanced | List; Function, Entry, Variant viewer2, Publications, External links, History, Feature viewer, Genomic coordinates, Names & Taxonomy, Subcellular Location, Phenotypes & Variants, PTM/Processing, Expression, Interaction, Structure, Family & Domains, Sequence, Similar Proteins; Features: Showing features for signal, chain, disulfide bond, glycosylation, lipidation; Download; POSITION/S, DESCRIPTION, ID; 1-26: Signal, PRO 0000014641; 27-236: Chain, T-cell surface glycoprotein CD8 alpha chain; 47-119: Disulfide bond, PROSITE-ProRule Annotation; 63: Glycosylation, N-linked (GlcNAc..) asparagine, 1 Publication; 144: Glycosylation, O-linked (GalNAc..) threonine, partial, 1 Publication; 148: Glycosylation, O-linked (GalNAc...) threonine, 1 Publication; 152: Glycosylation, O-linked (GalNAc...) threonine, 1 Publication; 158: Glycosylation, O-linked (GalNAc...) threonine, 1 Publication; 160: Glycosylation, O-linked (GalNAc...) threonine, 1 Publication)

5. In WB experiments, we often find that the actual detected molecular weight of some proteins differs from the expected molecular weight. At this time, we can use the [Sequence] (Protein Sequence and Post-Translational Modification) section for comparison. With this information, we can easily predict the correct WB band position.

For example, for CD8 protein, Mass (Da) shows that its molecular weight is about 26 kDa. However, in practice, the WB positive band of PD1 may appear at a position greater than 30 kDa (as shown in the figure below). The reason for this difference may be post-translational modifications such as glycosylation.

The Human Protein Atlas Database

Attention researchers conducting Immunohistochemistry (IHC)! The following database to be introduced, The Human Protein Atlas, contains tissue and cell distribution information of nearly 30,000 human proteins and provides free queries.

The Knut & Alice Wallenberg Foundation in Sweden uses immunohistochemical technology to examine the distribution and expression of each protein in 48 types of normal human tissues, 20 types of tumor tissues, 47 cell lines, and 12 types of blood cells. The results are represented by at least 576 immunohistochemical staining images, which have been reviewed and indexed by professionals to ensure that the staining results are sufficiently representative.

We take Epidermal Growth Factor Receptor (EGFR) as an example to query its expression:

1. Enter https://www.proteinatlas.org/ in the browser to enter the query page, and enter the name of the target protein "EGFR" in the search bar. After entering the detailed protein page, you can find brief introductions of important information such as Tissue specificity, Single cell type specificity, Predicted location, Extracellular location, Protein function, and Biological process in the front-end.

2. Click the "Tissue" menu bar at the top to enter the detailed information page of protein tissue specificity. Here you can find the expression of proteins in different tissues. For example, EGFR is found to have high RNA and protein expression levels in the placenta.

Click the immunohistochemical images on the right to view the immunohistochemical verification results of various cells. This image can be referred to as a positive control image for immunohistochemistry.

3. Click the "SUBCELL" menu bar at the top to query the expression level of proteins in various cells, as well as the localization in human cell lines and mouse cell lines. When viewing cell localization fluorescence images, you can select to display or overlay fluorescence effects individually by clicking the content to be displayed, such as antibodies, cell nuclei, microtubules, etc.

4. Click "Pathology" in the top menu bar to enter the cancer-related research of proteins. Here you can view the expression of proteins in different tumor samples. The data in this column integrates another powerful database of Atlas, The Cancer Genome Atlas (TCGA), and you can query immunohistochemical maps of various tumor samples.

With such a powerful The Human Protein Atlas database, we can easily query the information of target proteins in immunohistochemistry or tumor immunity experiments, helping us accelerate the experiments!

The Human Immune System

The immune system is composed of specialized cells, some of which travel through the body individually to scan for signs of damage or disease. Once these cells detect a threat, they need to communicate this information to other cells to generate an effective immune response. One method of this intercellular signaling is through the binding of proteins on the cell surface to matching "receptor" proteins on other cells. In the past, scientists and clinicians only had an incomplete map of receptor connections between all different types of immune cells in the body. If we are to develop therapies that enhance the immune system to fight diseases, namely immunotherapy, a deep understanding of the interactions between immune cells and how this communication integrates into the entire human body is crucial.

Through the following figure, we can see the impact of different diseases on the entire immune system and study new therapies that bind to different proteins on the surface of immune cells. Cell surface proteins serve as the basis for new drugs more often than any other protein type because they are accessible to drugs and exert powerful effects on the signals received by cells.

Core Products of ANT BIO PTE. LTD. for Protein Research

Brand Mission

ANT BIO PTE. LTD. is dedicated to advancing life science research by providing high-quality, reliable reagents and comprehensive solutions. We recognize the critical role of protein information query tools and supporting research reagents in protein research, and the urgent need for standardized, specialized experimental tools. Through our specialized sub-brands (Absin, Starter, UA), we have developed a targeted product portfolio for protein research, covering core antibodies for protein detection, protein extraction and quantification kits, WB experimental reagents, and protein markers.

Our team adheres to stringent quality control standards throughout the product development and production process, ensuring the high specificity, sensitivity, and reproducibility of each product. We are committed to providing professional technical support and customer-centric services, helping researchers overcome experimental challenges such as inaccurate protein localization verification, unstable protein extraction, and low detection signal sensitivity, and accelerating the pace of scientific research breakthroughs in protein research. ANT BIO PTE. LTD. strives to be a trusted partner for scientists worldwide, contributing to the advancement of protein mechanism research and the development of innovative biological technologies.

Disclaimer

This article is AI-compiled and interpreted based on the original work related to protein information query tool research. All intellectual property (e.g., experimental protocols, data, images) of the original publication shall belong to the relevant research team. For any infringement, please contact us promptly and we will take immediate action.

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At ANTBIO, we are committed to advancing life science research through high-quality, reliable reagents and comprehensive solutions. Our specialized sub-brands (Absin, Starter, UA) cover a full spectrum of research needs, from protein detection antibodies and extraction kits to WB experimental reagents and protein markers. With a focus on innovation, quality, and customer-centricity, we strive to be your trusted partner in unlocking the secrets of proteins and driving biological technology progress. Explore our product portfolio today and elevate your research to new heights.