What are protein domains?
Protein domains are units within a protein with a distinct function or structure whose particular interaction defines the overall role of the protein. Domains can be found in proteins with different functions, however, often contribute to a similar function. Proteins can be composed of a number of recognized protein domains. These domains can have various functions including binding particular molecules or catalyzing reactions (What are protein domains 2016).
What domains are found in SHANK3?
Using programing websites Pfam, SMART, InterPRo, and PROSITE to search SHANK3 protein domains, I found a variety of representations of the SHANK3 gene. I used these sites to ensure that the results were consistent across programs. This has allowed me to be confident understand the protein domains of SHANK3 in multiple species.
Results from Pfam
Results from SMART
The diagrams created by Pfam and SMART vary only be the presence or absence of FERM. This is likely a protein domain that SMART does not recognize.
What is the importance of each protein domain?
FERM_f0
FERM_f0 forms a stable globular structure involved in integrin-activation. At this point, there is no recognized binding partner.
Ank-2
The ankyrin repeat is a 33-residue motif that occurs in proteins with two alpha helices. These domains mediate protein to protein interactions. This repeat is one of the most common motifs in proteins.
SH3
The SRC Homology 3 Domain (SH3) is a small protein domain consisting of approximately 60 amino acid residues. They interact with adaptor proteins and/or protein kinases typically far from the active site. The main function of these domains is in signaling pathways which regulate the cytoskeleton, the Ras protein and the Src kinase to name a few. It has also been connected to protein to protein interactions in signal transduction pathways and cytoplasmic signaling.
PDZ
The PDZ domain is made up of approximately 80 to 90 amino acids residues. It is involved in anchoring receptor proteins in the membrane to cytoskeletal components. They play a role in signal transduction pathways with the cells (Pfam 2015).
SAM-1
The Sterile alpha motif (SAM) is made up of approximately 70 amino acid residues. It is commonly associated with RNA binding.
Is protein domain conserved between species?
Protein conservation refers to the retention of domain architecture across gene homologs. Assessing the level of domain architecture conservation across species allows us to compare the similarities and differences between protein function of the same gene in various species. This may help us account for differences in species. In the case of SHANK3, protein domain conservation may help us account for the neurological gene ontology differences among species. Shown below is a diagram depicting many important model organisms and their protein domains.
Discussion
Comparison of SHANK3 protein domain conservation across species reveals some notable findings. The observation that most stands out is that the Ank protein, and with the exception of Arabidopsis, Ank-2, is present in all of the shown model organisms. This highlights the fact that SHANK3 plays a role in protein to protein interaction which is further discussed in the website section, gene ontology. It has been previously shown that nervous system development varies between species. Because SHANK3 is known to play a role in this development, there may be a correlation between the conserved protein domains in different species and their respective intelligence levels. This may be a possible approach for further research and investigation.
References:
Pfam. (2015). Retrieved February 25, 2018, from http://pfam.xfam.org/search/sequence
What are protein domains? (2016, July 20). Retrieved February 24, 2018, from https://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/protein-classification/what-are-protein-domains
Header:
https://scitechdaily.com/proteins-engineered-with-predictable-structures/
Pfam. (2015). Retrieved February 25, 2018, from http://pfam.xfam.org/search/sequence
What are protein domains? (2016, July 20). Retrieved February 24, 2018, from https://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/protein-classification/what-are-protein-domains
Header:
https://scitechdaily.com/proteins-engineered-with-predictable-structures/
This web page was produced as an assignment for Genetics 564, an undergraduate capstone course at UW-Madison.