Protein-Protein Interaction (PPI); Case Study BRCA2 — [Bioinformatics Eps.3]

Proteins in cells don’t usually float around by themselves. Instead, they work with other proteins to make more effective systems inside the cell. If proteins aren’t attached to anything, this likely happens when a signal is sent to a membrane-bound protein that catches the signal. The protein will then attach itself to other parts of proteins. So, interactions among proteins are an essential part of biology.

BRCA2 is a gene that all people have that stops cancer from growing. The BRCA2 protein is what comes out of this gene. Italicizing BRCA2 is for the gene, while just writing BRCA2 is for the protein. This protein may cause Type 2 Breast Cancer to happen. BRCA2 and RAD51 work together to fix DNA damage. Mutations in proteins in the DNA damage response pathway, such as BRCA1, BRCA2, and RAD51, have been linked to different types of cancer, including breast cancer.

Figure 1 Molecular structure of BRCA2 (Source: Uniprot)

1. Database of Interacting Protein (DIP)

DIP is a database that stores information about how proteins interact that has been found through experiments. This database is meant to give scientists a complete and integrated way to search for and get information about how proteins interact with each other and with other proteins in biological processes.

a) Go to the DPI link

link: https://dip.doe-mbi.ucla.edu/dip/Main.cgi

Figure 2 Home view of the DIP website

b) Select the Search menu

Figure 3 Select the Search Menu

The Search menu will appear as follows:

Figure 4 Search menu view

In this section, you can choose from the following:

• Node: Use identifiers or annotations to search the database for protein names that match.
• BLAST: searches the database for sequences that match a specific sequence.
• Motif: Look for information based on motif domains
• Article: Look for research articles about how the results of experiments interact.
• IMEx: Use the rules for curation set by IMEx to look for interaction data that backs up the described experiments.
• pathBLAST: Search the protein-protein interaction network of the target organism to find all protein interaction pathways that match the query pathway.

c) Select the Node Submenu

We will look for information about how BRCA2 proteins interact by directly entering the name of the protein. We’ll go to the Node menu to do that.

Figure 5 “Node” Submenu View

In the “Node Annotation” section, type “BRCA2” and then choose “Homo sapiens” as the organism. Click Query DIP to look for interactions between proteins. The node results will show up as a table of lists. Choose the BRCA2 protein, and then choose the “graph” section on the right side of the table. There will be a graph of how BRCA2 proteins interact with each other, which has been studied before.

Figure 6 BRCA2 Protein Description on DIPs

The DIP database has graphical structures for protein interaction topologies confirmed by research and publications. This means that the data found in this database is good data that can be used for analysis.

Figure 7 BRCA2 Protein Interaction Graph

Go back to the last search result for a node. Choose the BRCA2 protein result and the round dot logo in the Links column. There will be a page with a more detailed list of how proteins work together.

Figure 8 BRCA2 protein interaction details page in the DIP

On the page about the interaction, there is a table with a more detailed description. Each data point in the table shows the exchange that took place between the protein in the “Interactor(s)” column and the interaction that is well described in the “Interaction” column. Each data set has reference data from PIR, SWISSPROT, and GENBANK, and there is a column called “Protein Name” that gives a description of the protein name.

Figure 9 Example of BRCA2 Interaction with BRCA1

In the right column, there is a column called “Type.” The value of this column is a code that shows the results of the interaction. Figure 10 shows a fuller explanation of what is going on

Figure 10 DIP Evidance Code

2. BioGRID

BioGRID, “General Repository for Interaction Datasets,” is a database of over 2,392,652 interactions between genes and proteins. It is made and kept up to date by the lab of Mike Tyers at the Université de Montréal. Figure 12 shows how the BioGRID database is built. It brings together a lot of big data from other databases. This database lets us see how the observed proteins interact with each other.

Figure 11 BioGRID Data Model

a) Go to BioGRID link

link : https://thebiogrid.org/index.php

Figure 12 BioGRID Page View

b) Enter the keyword BRCA2 in the search field

Figure 13 A partial view of BRCA2 search results on BioGRID

The search results will be in the form of a table. This table will show the Interactor, organism origin, alias, description, and research pieces of evidence in the search results table.

Figure 14 BRCA2 interaction results in the BioGRID database

c) Click “view” in the evidence section

There is a type of research evidence that can be looked at for each piece of data. In the “Evidence” section, click “View” to see more information about the published and curated research used to figure out how the protein interacts.

Figure 15 View button in the Evidence column

The details of the view will show what experiments were done and what types of papers were written about them.

Figure 16 Research details related to RAD51 and BRCA2 interaction on BioGRID

d) Click Network to view the interaction graph

BioGRID shows a graphical representation of each interaction in the form of a topology, and it has a filter that lets you choose which results to show.

Figure 17 Graphical display on BRCA2 protein interaction in BioGRID