C1orf41 Discussion
From the information collected based on sequence and structural database and literature searches, we found that there are two possibilities of what c1orf41 function could be. Firstly, it might be a heat shock protein and secondly it might have a function that is related to galactose binding or cell adhesion.
Heat Shock Protein
Based on Blast, it was shown that this protein has high similarity sequence with small heat shock proteins (sHsp) from various eukaryotes. Our protein was a mutant of sHsp family B member 11 where aspartic acid at position 109 has been deleted. The first ten residues were believed not to be part of the protein but most likely an N-terminal histidine tag used during purification of the protein. This was proven by the multiple sequence alignment as these residues does not align with other organisms. Therefore, there is a possibility that c1orf41 may be a sHsp.
sHsps are molecular chaperones that can be found in various organisms, however their sequences are poorly conserved. Studies have shown that the number of gene encoding sHsp increases in higher eukaryote. This may be due to the specific function and localization of sHsp (Haslbeck et al., 2005). Since it was shown to be highly expressed in cancer cell, the function of this protein may be related to cancer. The loss of Asp109 may cause cancer or cancer cells produce this mutated protein.
Many publication reported that sHsps have antiapoptotic activity which if over expressed will lead to tumor growth and resistance to chemo or radiotheraphy (Bellyei et al, 2006; Pozsgai et al, 2007). The stimulation of apoptosis was activated by one or more transduction pathway signal which then will activate a conserved family of aspartic-acid specific cysteine protease (caspase). Casapase is expressed within cells as inactive precursor enzyme which once it is activated by apoptosis initiation, it will resulting in biochemical and morphological changes of apoptosis (Concannon & Samali, 2003). As previously mentioned, our protein was a mutant of sHsp family where aspartic acid at position 109 has been deleted. As caspase play essential role in apoptosis, the deletion of this precursore enzyme resulted in the deletion of the function. According to Concannon & Samali (2003), when cells are induced by stress, Hsps will be accumulated, and at some point it will be more tolerant to cytotoxic stress. This phenomenon termed as ‘thermotollerance’. During the thermotollerance,due to its protective effect Hsps will inhibit apoptosis.
The Gene Ontology (GO) suggests that the cellular component of 1tvg is cell, cell part, intracellular and/or intracellular part that involves in cellular process and/or cell adhesion. Many of apoptotic key molecules (such as cytochrome c and pro-caspase 3) are located within mitochondria. It is suggested that many of cellular protein that function as anti-apoptotic are also located within mitochondria, thus they could prevent the release of pro-apoptotic proteins (Concannon & Samali, 2003). However, Kang et al. (2004) suggest that in normal conditions, sHsps located in cytoplasm, near golgi complex and will move to the nucleus when cell was induced by stress.
mention bout calcium binding
Galactose-binding protein
DALI result showed that c1orf41 has high structural similarities to sialidases, galactose oxidases and numerous other proteins. A search using Pfam indicated that this protein has a F5/8 type C domain which is a member of the discoidin domain family. The Pfam search also showed that proteins from the DALI result also have this domain. We concluded that the DALI result obtained was based on the presence of this domain in c1orf41 and the other proteins.
The discoidin protein is also known as the galactose binding domain -like. Members of this family such as bacterial sialidase and galactose oxidase has a galactose-binding characteristic. It is also known that pproteins with F5/8 type C domain are involved in cell adhesion. Therefore, we hypothesized that this protein may have a galactose-binding property and possibly cell adhesion function.
As described in the Results section, c1orf41 has a beta barrel structure where the beta strands are organized to form a barrel structure. As for the structure of the protein, we found that c1orf41 has a jelly-roll fold that is characteristic of a discoidin domain member. Description from Pfam indicated that this domain has two conserved alpha helices which are also present in c1orf41. These alpha helices are known to interact with cell membrane. However we found the residues on c1orf41 alpha helices to be mainly charged, therefore it is less likely to bind to the membrane. Also, many proteins with this domain have disuplhide bonds. This is not observed on our protein. In addition to that, members of the discodin family are generally extracellular or membrane proteins. Previous literature have reported that c1orf41 was found in the cytoplasm and the surface of the protein are mostly charged, therefore we do not think that it is a membrane protein.
F5/8 type C domain is involved in cell-cell interaction and cell recognition. Highly expressed, the protein can lead to breast carcinoma (ref). Apart from that, this domain is also involved in cell adhesion. However, due to the lack of the RGD motif that is present in cell adhesion proteins, we deduces that this protein is not involved in cell adhesion (Bianchet et al., 2002).
From previous literatures H-(2x)-W-(29x)-R-(2x)-S-(2x)-E are the residues important for galactose binding within this family, however these residues were absent in c1orf41 (Gaskell et al., 1995). Even though the structure showed similarity with galactose binding domain, the absence of galactose binding site indicates that this protein does not bind to galactose.
The proteins from the DALI result showed minimal sequence similarity with c1orf41.
