C1orf41 Introduction
Bioinformatics is an important tool in acquiring new information on uncharacterized proteins usually based on their sequence and sometimes their structure. Databases and programs such as Protein Data Bank (PDB), Interpro, BLAST, ClustalX and DALI contributes to the growing knowledge about proteins and their functions. This project aims at predicting the function of an unknown protein based on its sequence and structure by utilizing the various bioinformatics tools available.
Our protein of interest is known as chromosome 1 open reading frame 41 (c1orf41) which is an intracellular monomeric protein with 153 amino and was isolated from human term placentas. This protein was encoded by gene on chromosome 1 locus 1p32.1-p33. Besides c1orf41, this protein is also known as Pp25, Hspc034, Hsp16.2 and HspB11 (Bellyei et al., 2007; Bohn & Winkler, 1991). Studies have shown that this protein is highly expressed in certain cancer cells (Bellyei et al., 2007). From PDB, it was stated that this protein is a mutant due to deletion of aspartic acid at position 109. Initial information gathered from the PDB indicated that this protein could be a small heat shock protein (sHsp).
Heat shock protein (Hsp) is known to respond to many physiological and environmental stresses such as thermal and chemical stresses by acting as a chaperone protein and preventing protein aggregation (Bellyei et al., 2006; Concannon & Samali, 2003). Hsps in general will bind to damaged misfolded polypeptides and mediate their refolding, thus protecting cells from harmful effects and promoting cell recovery (Concannon & Samali, 2003). Hsp is categorized as small if it has a mass between 12 to 43 kDa. Therefore, this includes c1orf41 which has a mass of 16.2 kDa. sHsp usually interact with other monomers, forming oligomeric structures with the mass between 100 to 800 kDa. sHsps have a conserved sequence involving abut 90 residues which is known as the alpha crystallin domain. This domain is mainly fomrmed by beta-pleated sheets (Mac Rae, 2000). Currently, there are ten known sHsp in human but only two (Hsp27 and alpha B crystallin) are well characterized (Arrigo, 2005).
The structure of c1orf41 showed that this protein belongs to discoidin domain. Proteins that have this domain generally have cell adhesion property by binding to cell surface carbohydrates (Baumgartner et al., 1998). Discoidin is also known to bind to galactose to promote cell aggregation. Interactions between discoidin domain receptors and collagen regulates cell proliferation by inducing their tyrosine kinase activity (Dyka et al., 2008).
Based on the information gathered from sequence and structural analysis, we hope to infer a possible function for c1orf41.
