What is a protein interaction network?
A protein interaction network is a way to map the connections between interacting proteins. The diagrams allow us to make inferences about molecular function and biological processes of relevant proteins and the proteins that they interact with. Protein interactions allow for the formation of protein complexes and mediate post-translational protein modifications (Vazquez 2010). They can also contribute to cell-to-cell interactions and metabolic and developmental control as well as a wide variety of other processes (Rao 2014). Examining these interactions will allow us to gather much information about the SHANK3 protein.
How do you generate a protein interaction network?
In order to generate a protein interaction map using the database, STRING, we can simply search the name of the protein in question and the database will provide us with an network such as those seen below. We can use these maps to find proteins directly associated with our protein of interest as well as those participating in tangential interactions.
Discussion
Using SMART, I sorted SHANK3- interacting proteins of the zebrafish by proteins involved in signaling and learning and social behavior in order to determine which proteins to focus on when studying the effects of methylation of SHANK3 in autism patients. I found that DLGAP1, DLGAP2, DLGAP3, DLGAP4, GRB2, HOMER1, DLG4, NRX1, and NLGN3 and all involved in signaling in the nervous system of zebrafish. These are specific proteins that I will examine when SHANK3 is knocked out to determine SHANK3's role in regulation of other proteins. DLG4, NLGN3, and NRXN1, and NLGN4X are involved in learning and social behavior which are both impacted by ASD. Examining this interaction network as a whole shows promise for further understanding the mechanisms leading to and the phenotypic outcomes of autism.
References:
Rao, V. S., Srinivas, K., Sujini, G. N., & Kumar, G. N. S. (2014). Protein-Protein Interaction Detection: Methods and Analysis. International Journal of Proteomics, 2014, 147648. http://doi.org/10.1155/2014/147648
Vazquez A. Protein Interaction Networks. In: Alzate O, editor. Neuroproteomics. Boca Raton (FL): CRC Press/Taylor & Francis; 2010. Chapter 8.
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Rao, V. S., Srinivas, K., Sujini, G. N., & Kumar, G. N. S. (2014). Protein-Protein Interaction Detection: Methods and Analysis. International Journal of Proteomics, 2014, 147648. http://doi.org/10.1155/2014/147648
Vazquez A. Protein Interaction Networks. In: Alzate O, editor. Neuroproteomics. Boca Raton (FL): CRC Press/Taylor & Francis; 2010. Chapter 8.
Header:
http://chiefcustomerofficer.eu/tag/customer-interaction/
This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.