Proteomics
This page was produced as an assignment for Genetics 564 an undergraduate capstone course at UW-Madison.
What is proteomics?
Proteomics is broadly described as the analysis of proteins. Protein analysis adds an extra dimension to the study of a gene. Sequenced based analysis, coupled with the analysis of proteins, help provide a more comprehensive and accurate picture of a gene's role rather than just bioinformatics alone.
Proteins often undergo post-translational modifications, which ultimately affect protein function. One of the most common forms of post-translational modifications is protein phosphorylation [1]. Protein phosphorylation is advantageous as a post-translation modification because of its versatility and reversibility. Phosphorylation helps contribute to chemical diversity, changes the activation state of the protein being phosphorylated, and often plays an important role in signaling pathways [2]. In eukaryotes, the amino acids most commonly phosphorylated are serine, threonine, and tyrosine.
Proteins often undergo post-translational modifications, which ultimately affect protein function. One of the most common forms of post-translational modifications is protein phosphorylation [1]. Protein phosphorylation is advantageous as a post-translation modification because of its versatility and reversibility. Phosphorylation helps contribute to chemical diversity, changes the activation state of the protein being phosphorylated, and often plays an important role in signaling pathways [2]. In eukaryotes, the amino acids most commonly phosphorylated are serine, threonine, and tyrosine.
ERCC6 phosphorylation sites in homologs
All predicted phosphorylation site data is from the NetPhos 3.1 Server [3]. Below are the predicted phosphorylation site data for humans, mice, rats, and zebrafish. All of the vertical colored lines above the horizontal pink line indicate amino acids where phosphorylation is possible and predicted. The vertical red, green, and blue lines correspond to potentially phosphorylated serine, threonine, and tyrosine, respectively.
Conclusions
ERCC6 has many possible phosphorylation sites in humans, mice, rats, and zebrafish, suggesting that ERCC6 is readily phosphorylated in many different organisms. Furthermore, there are regions where the potential phosphorylation pattern seem to overlap between the four organisms. There is less clustering of phosphorylated sites between amino acids 500-1,000, which is interesting because both major protein domains fall within this range for each of the four organisms. This suggests that these regions require less phosphorylation for proper function.
References
[1] Graves, P.R., & Haystead, T.A.J. (2002). Molecular Biologist's Guide to Proteomics. Microbiology and Molecular Biology Reviews, 66(1), 39-63. http://doi.org/10.1128/MMBR.66.1.39-63.20002
[2] Hunter, T. (2012). Why nature chose phosphate to modify proteins. Philosophical Transactions of the Royal Society B: Biological Sciences, 367(1602), 2513–2516. http://doi.org/10.1098/rstb.2012.0013
[3] Blom, N., Gammeltoft, S., & Brunak, S. (1999). Sequence- and structure-based prediction of eukaryotic protein phosphorylation sites. Journal of Molecular Biology, 294(5): 1351-1362.
Images and Videos
Cover image: http://www.tuscany-diet.net/proteins/definition-composition-structure/
Human silhouette: http://www.freevectors.net/human+silhouette
Mouse silhouette: http://www.stickthisgraphics.com/Mouse-Silhouette-2-Decal-Sticker-WILD175.htm
Zebrafish silhouette: https://www.colourbox.com/vector/vector-silhouette-of-fish-on-white-background-vector-1651696
Rat silhouette: http://www.publicdomainpictures.net/view-image.php?image=40297&picture=silhouette-rat
This website was created for Genetics 564 by Zachary Beethem, an undergraduate genetics major at UW-Madison.
He can be reached via email: [email protected]
Date of last website update: April 2017
[1] Graves, P.R., & Haystead, T.A.J. (2002). Molecular Biologist's Guide to Proteomics. Microbiology and Molecular Biology Reviews, 66(1), 39-63. http://doi.org/10.1128/MMBR.66.1.39-63.20002
[2] Hunter, T. (2012). Why nature chose phosphate to modify proteins. Philosophical Transactions of the Royal Society B: Biological Sciences, 367(1602), 2513–2516. http://doi.org/10.1098/rstb.2012.0013
[3] Blom, N., Gammeltoft, S., & Brunak, S. (1999). Sequence- and structure-based prediction of eukaryotic protein phosphorylation sites. Journal of Molecular Biology, 294(5): 1351-1362.
Images and Videos
Cover image: http://www.tuscany-diet.net/proteins/definition-composition-structure/
Human silhouette: http://www.freevectors.net/human+silhouette
Mouse silhouette: http://www.stickthisgraphics.com/Mouse-Silhouette-2-Decal-Sticker-WILD175.htm
Zebrafish silhouette: https://www.colourbox.com/vector/vector-silhouette-of-fish-on-white-background-vector-1651696
Rat silhouette: http://www.publicdomainpictures.net/view-image.php?image=40297&picture=silhouette-rat
This website was created for Genetics 564 by Zachary Beethem, an undergraduate genetics major at UW-Madison.
He can be reached via email: [email protected]
Date of last website update: April 2017