_This web page was produced as an assignment for Genetics 677, an undergraduate course at UW-Madison.
Subcellular Localization
Like the human body, a cell contains "organs," or subcellular compartments. Again, like human organs, cellular compartments have distinct functions. Examples of subcellular compartments include: mitochondria, endoplasmic reticulum, golgi apparatus, endosomes, ect. Certain proteins are localized to these compartments ,whether that be inside, in the membrane, or just outside. Knowing the localization of a protein can help identify and understand its function. ORGANELLE DB and SherLoc2 are databases that predict sub-cellular protein localization.
Analysis
The localization for HLA-C was determined using two databases, ORGANELLE DB and SherLoc2. ORGANELLE DB localized HLA-C to the plasma membrane. This is consistent with the function of HLA-C, which is to present antigens to T-Cells at the cell surface. SherLoc2 localized HLA-C to numerous subcellular compartments involved in the secretory pathway, most strongly to the Golgi apparatus. It is unclear, functionally, why the Golgi has a more significant localization score than the endoplasmic reticulum, or the lysosome.
ORGANELLE DB
http://biopleasure.wordpress.com/2011/02/17/the-structure-of-plasma-membrane/
ORGANELLE DB, a database for organelles and protein complexes, localized the HLA-C gene to the plasma membrane. This is consistent with the function of HLA-C, that is, to present antigens to T-cells at the cellular membrane.
SherLoc2
http://en.wikipedia.org/wiki/File:MHC_Class_I_processing.svg
HLA-C is part of the MHC class 1 molecule, whose processing pathway is well understood. MHC class 1 molecules are made in the Endoplasmic Reticulum (ER) and are transported to the Golgi, then to the vesicles (lysosomes), and, finally, to the cell membrane. The image to the left visually shows the processing pathway of the MHC molecule.
SherLoc2 is a database that localizes proteins to specific subcellular compartments. It localized HLA-C to many different cellular organelles, organelles which are consistent with the MHC class 1 transport pathway (see scores below). The most significant localization was in the Golgi.
Golgi Apparatus: 0.85
Extracellular: 0.05
Lysosomal: 0.04
Endoplasmic Reticulum: 0.03
Cytoplasmic: 0.02
SherLoc2 is a database that localizes proteins to specific subcellular compartments. It localized HLA-C to many different cellular organelles, organelles which are consistent with the MHC class 1 transport pathway (see scores below). The most significant localization was in the Golgi.
Golgi Apparatus: 0.85
Extracellular: 0.05
Lysosomal: 0.04
Endoplasmic Reticulum: 0.03
Cytoplasmic: 0.02
References
_Site created by Valeri Lapacek
Genetics 677 Assignment, Spring 2012
University of Wisconsin-Madison
Last Updated: 5/23/2012
Genetics 677 Assignment, Spring 2012
University of Wisconsin-Madison
Last Updated: 5/23/2012