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You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.
Function of your Protein
it binds to a host cell (human epithelial cell) to provide a host cell recognition to invade the human cell. In this case, these epithelial adhesions belong to the fungus Candida glabrata. So, these proteins are adhering Candida glabrata to a human epithelial cell. The protein is specifically binding to different carbohydrates on the outside of the human epithelial cell to create an adhesion between the fungus and the host cell.
Biological relevance and broader implications
Candida glabrata is a fungus of high concern as it infects the host through the bloodstream. Unfortunately, this is a life-threatening infection for humans and upwards of 29% of all cases are life-threatening. As this does affect the human race is it of high relevance to study in health sciences. Understanding how this fungus can infect the bloodstream is needed to slow and possibly stop Candida glabrata from infecting other people. The approach in this paper is on the epithelial adhesions and altering their composition around the binding site. By altering conversed and un-conserved areas in its binding site we can better understand what hot spots are needed for good binding to the carbohydrates on the human epithelial cells.
Important amino acids
The type of protein that we are looking at is an adhesion protein, so it does not function as an enzyme. It does not have a catalytic triad within the active site. Though there are some important amino acid residues to highlight as they interact with the ligand (lactose). In the diagram of the protein, we can look to see the all-red ball stick structures by the ligand are the amino acid residues interacting with the ligand. . They are all interacting via hydrogen bonds.
Structural highlights
Some things to note are that the main structure of the protein consists of 27% beta-sheets and only 7% alpha-helices. The rest of the molecule contains a primary chain structure. It can also be noted that two beta-sheets contain at least one key residue that interacts with the ligand. These parts of the beta-sheets can help form a pocket to bind the ligand best suited for the structure. In this case, it is lactose. The rest of the protein has some loop structures that help shape this pocket for binding the ligand as well. There are some calcium-binding loops also involved in the binding pocket. These loops form the inner part of this pocket and are highly conservative. They are conservative as to keep a high-binding affinity. The outer pocket is made of three other loops these are more variable, but still contain some key residues that keep high binding affinity. Some more conservative structures within the beta-sheets don't allow for change as they are key portions for keeping a good binding affinity for the ligand.
Other important features
To look further into the structure studied we are going to compare two of the versions of the Epa's from the paper cited below. First looking at Epa9, this structure off to the right we can see the elongated loop 1. It was highlighted that this loop is important to the structure as it binds bigger sugars than an Epa1. It stays in an open state when bound to a bigger sugar, but as shown here it is in a more closed state as it is bound to a smaller sugar. Now looking at another structure for comparison, a mixed version of Epa9, but the only difference is that its CBL2 loop is from Epa1.
