Sandbox Reserved 1632

This Sandbox is Reserved from 09/18/2020 through 03/20/2021 for use in CHEM 351 Biochemistry taught by Bonnie Hall at Grand View University, Des Moines, IA. This reservation includes Sandbox Reserved 1628 through Sandbox Reserved 1642.

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Epithelial Adhesions in Candida Glabrata

spinqualitylabelsall models Basic structure of Epa9 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Function of your Protein This is an epithelial adhesion protein (Epa), specifically Epa9, it binds to a host cell (human epithelial cell) to provide a host cell recognition to invade the host. In this case, this epithelial adhesion belongs to the fungus Candida glabrata. This fungus has more than just one Epa to create host cell recognition, it has over 20 Epa's. These proteins can adhere Candida glabrata to a human epithelial cell by specifically binding to different carbohydrates on the outside of the cell. This interaction between the Epas and the carbohydrates is what creates the adhesion for host cell recognition. 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 conserved 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. How this protein binds can be tricky, it can better bind one carbohydrate or a multitude of them. The unconserved hot spots in the binding pocket help to achieve this property. In general, the pathway through this fungi infects the body is relevant to study for its ability to adapt in different situations. Understanding this protein's function is beneficial to understanding how to possibly slow binding or even stop the binding altogether by making it thermodynamically challenging for the organism. In this page we will highlight Epa9 specifically and how it can bind compared to other mutants created from the paper. 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 binding pocket. Though there are some important amino acid residues to highlight as they interact with the ligand (lactose). The ligand itself, lactose, is a small carbohydrate consisting of two sugars. In the diagram of the protein, we can observe the cpk colored, ball stick structures around the ligand are the amino acid residues interacting with the ligand. These residues are Arg258, Asp257, Asp196, and Asp197. They are all interacting via hydrogen bonds as depicted with this image off to the right. In the image, the hydrogen bonds involved are circled and we can see that there are only six hydrogen bonds that are binding the lactose to Epa9, which could account for a low binding affinity towards smaller carbohydrates. As it is noted that Epa9 is better at binding larger carbohydrates because of its elongated loop 1. Because the protein is forming hydrogen bonds with the carbohydrate this is a factor that is thermodynamically favorable. The bonds being formed are releasing energy and the body can use the energy released. This is an issue for binding, which could be something that could be looked into further when considering swapping different domains within the Epa. Making it thermodynamically favorable for one carbohydrate, but not for others. Trying to make the Epa unfavorable seems to be an issue with candida glabrata though as it is able to adapt in such a way that the unconserved loops 1, 2, and even CBL2 go under conformational changes to become favorable for another carbohydrate. This was seen a lot in the glycan arrays within the paper below. When changing the CBL2 it didn't follow patterns of the donor or recipient as much as made its own binding specificity. The Epa was able to adapt to the environment of interacting with different carbohydrates present. The amount of hydrogen bond formed can either make it more favorable or less favorable. Structural highlights Some things to note are that the main structure of the protein consists of 27% beta-sheets and only 7% alpha-helices. Observing this model we can see all the secondary structures and that 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 parts of the inner calcium-binding loops. The beta-sheets in this protein run anti-parallel and the structural shape is similar to that of a short cylinder. The structure of the stacked beta-sheets controls the shape to form binding sites. Domain A contains the binding site for carbohydrates, while the C-terminal domain contains a glycosylphosphatidylinositol (GPI) to bind the protein to the cell wall surface. The binding site in domain A has loop structures that help shape the pocket for binding the ligand. This includes two outer loops and two calcium-binding loops. The outer two loops are highly variable as compared to the highly conserved inner CBL1. The loop is conservative as it is crucial for achieving good host cell binding. The other calcium-binding loop, CBL2, is variable and tied to the protein's ligand-binding specificity. The outer pocket is made of two other loops and these are more variable, but still contain some key residues that are correlated with high binding affinity. To get a better look at the shape of the pocket there is a space fill view. We can observe that the shape of the binding pocket is dipped in and we can see where the outer two loops help shape that pocket as well as the inner CBL1 and CBL2. This allows for the space to interact with the carbohydrates on the host cell surface. Especially in Epa9 that is being represented, we can look at the elongated loop 1 in the dark navy that looks as though it cups around the pocket to interact and bind with the ligand. Because lactose is small loop 1 must curl in to help Epa9 bind to lactose. This is harder for Epa9 to do as it was found the elongated loop better for binding larger carbohydrates. Other important features Looking further into the structure studied we are going to compare two versions of the Epa's from the paper cited below. First looking at regular Epa9 bound with lactose and then at a mixed version of Epa9. The only difference is that its CBL2 loop is from Epa1. The reason for comparing these two is to show that when the CBL2 is changed that little interaction changes in the angles in the binding occur and that it can change the binding specificity of the protein to different carbohydrates. Remembering that this loop is a part of forming the inner binding pocket. Exchanging of the CBL2s does not change the binding specificity of the protein to the donor's binding specificity, but makes a novel binding specificity pattern. Comparing these two there is not much difference to the eye, but there is one residue in CBL2 in the mixed Epa9 vs. regular Epa9. Residue 258 in the mixed Epa9 is not an asparagine, but a glutamic acid. The angle and distance that carbon 6OH in the glucose ring could be changed partially by this, as interactions don't change but the distance in which the interaction happens will change. In the mixed Epa9, this distance change is actually why the binding pattern changes. It is to accommodate the change and find a better binding carbohydrate. Coming back to the concept of the binding interaction to be thermodynamically favorable can depend on the number of hydrogen bonds. The number of hydrogen bonds made with the beta lactose with the mixed Epa9 is 9 hydrogen bonds. It isn't shown bound with lactose as it isn't able to bind it the same as the regular Epa9 with 6 hydrogen bonds. Understanding that when more hydrogen bonds are formed the reaction of binding the ligand becomes more favorable. The Epa9 with the Epa1 CBL2 found a more favorable carbohydrate to bind as it was more thermodynamically favorable. It was found that with switching the CBL2 the Epa's were able to form novel binding specificity patterns. This shows that there is a conformational change that is different from that of what is expected and the interactions with the mixed loops have to be different to find a carbohydrate that can bind with high favorability. This concept of the candida glabrata being able to adapt to bind different carbohydrates makes it interesting for the fungus to infect its host. In part because the human body to remain in a steady-state (homeostasis). When candida glabrata is in an overgrowth state it begins to try and go somewhere else, which is when it enters the bloodstream through the interaction of carbohydrates and the adhesion protein. The human immune response will receive a signal response that something is not right. The body will respond to keep it in a steady state. But in the case of candida glabrata, the body's response to this infection is overwhelmed. This throws the body out of steady-state until we assist the immune response with intravenous antifungal medication.