Sandbox Reserved 1632
From Proteopedia
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== Important amino acids == | == 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 all-red ball stick structures around the ligand are the amino acid residues interacting with the ligand. These residues are <scene name='86/861614/Protein_view_2/8'>Arg258, Asp257, Asp196, and Asp197.</scene> 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.[[Image: Inked4CP0 view of hydrogen bond interactions on ligand LI.jpg | thumb]] | + | 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 all-red ball stick structures around the ligand are the amino acid residues interacting with the ligand. These residues are <scene name='86/861614/Protein_view_2/8'>Arg258, Asp257, Asp196, and Asp197.</scene> 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.[[Image: Inked4CP0 view of hydrogen bond interactions on ligand LI.jpg | thumb]] Because the protein is forming hydrogen bonds with the carbohydrate this could be more of a spontaneous reaction. The bonds being formed are releasing energy and the body can use the energy released from those bonds formed. |
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== Other important features == | == 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 <scene name='86/861614/Cbls_and_outer_loops/5'>regular Epa9</scene> bound with lactose and then at <scene name='86/861614/Epa_9_mixed/3'>a mixed version of Epa9</scene>. 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. It has a role in the binding specificity of the Epa. Exchanging of the CBL2s does not entirely change the binding specificity of the protein but makes a novel binding pattern. Comparing these two there is not much difference to the eye, but that 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 is from the key residues are 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. | 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 <scene name='86/861614/Cbls_and_outer_loops/5'>regular Epa9</scene> bound with lactose and then at <scene name='86/861614/Epa_9_mixed/3'>a mixed version of Epa9</scene>. 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. It has a role in the binding specificity of the Epa. Exchanging of the CBL2s does not entirely change the binding specificity of the protein but makes a novel binding pattern. Comparing these two there is not much difference to the eye, but that 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 is from the key residues are 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. | ||
| - | 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. | + | 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. |
</StructureSection> | </StructureSection> | ||
Revision as of 02:28, 7 December 2020
| 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
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