This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison
Protein Domain
Protein domains are parts of a protein which can form functional units within the protein. They are stable by themselves and therefore can exist without being integrated in the protein. These independent domains are useful to us, because they allow us to predict how a protein might function in different environments. They also help us predict and identify how various proteins might interact with other proteins according to their domains.
There are several online databases which allow people to search specific proteins of interest and they will determine any known protein domains within that protein. I used both Pfam and SMART (simple modular architecture research tool) to search for protein domains in the hypoctrein receptor 1 protein. Both of these websites returned the same results:
There are several online databases which allow people to search specific proteins of interest and they will determine any known protein domains within that protein. I used both Pfam and SMART (simple modular architecture research tool) to search for protein domains in the hypoctrein receptor 1 protein. Both of these websites returned the same results:
Figure 1: This figure depicts the only known protein domain for the hypocretin receptor 1 protein. The domain is a 7-transmembrane G-protein coupled receptor. This domain starts at position 57 and ends at position 373. The pink blocks on either side of the domain are segments of low compositional complexity. Photo courtesy of SMART.
Analysis
The database websites returned only one protein domain for the hypocretin receptor 1 protein. I was not surprised by this though, because this particular protein is only 425 amino acids long, and protein domains can be up to 500 amino acids long. The protein domain is a 7-transmembrane G-protein coupled receptor. This makes sense because as we learned from the general protein information page: the hypocretin receptor 1 is a G-protein coupled receptor. Because the hypocretin receptor 1 is a transmembrane protein, and it's domain functions both in the extracellular matrix and inside the cell in the cytoplasm. The information from the domain websites helps us by identifying the hypocretin receptor 1 as a G-coupled protein receptor, which can help us if we know anything about the characteristics or interactions of this family of proteins, which we do know something about from the general protein data page.
References:
Eric Suchy, Email: [email protected], last updated: May 15, 2010
