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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.
Biological relevance and broader implications
Candida glabrata is a fungus that is able to infect a human host through the bloodstream. Unfortunately, this is a life-threatening infection for humans. By trying to understand the structure of the epithelial adhesion on the outer surface of the fungus. There could be a possibility of stopping the adhesion from attaching to the host cell and stop host cell recognition altogether. This approach could help in lowering the high amount of cases that are life-threatening as there are upwards of 29% of cases of Candida glabrata infections.
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 are able to 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. There are also some more conservative structures within the beta-sheets that 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.
