Sandbox Reserved 1670: Difference between revisions

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== Function of your protein ==

This protein can be found in the plant pathogenic microbe Pseudomonas syringae strain PtoDC3000. The p. syringae mutautes its host, which in this case is tomato. The p. syringae produces a toxin that cause the tomato to not be able to fight off, there for causing diseases in the tomato. The research focuses on aldehyde dehydrogenases specifically aldC. aldehyde dehydrogenases are known for its capability to detoxing aldehydes, this is important because aldehydes are very reactive, so for an example from the article they can be turned into carboxylic acids which are not as reactive, which I believe slows down the mutation. The substrate of the AldC PtoDC3000 shows that this enzyme functions as a long-chain aliphatic aldehyde dehydrogenase. This article states that they ran tests to find the best substrate for this enzyme, which they found multiple substrate such as aliphatic aldehydes of 5–9-carbon length, as well as hydrocinnamaldehyde and 4-pyridinecarboxyaldehyde but it shows that octanal has the highest activity. This protein structure is a homodimer meaning it is two identical chains (A and B) covalently bonded together.

This protein can be found in the plant pathogenic microbe Pseudomonas syringae strain PtoDC3000. The p. syringae mutautes its host, which in this case is tomato. The p. syringae produces a toxin that cause the tomato to not be able to fight off, there for causing diseases in the tomato. The research focuses on aldehyde dehydrogenases specifically aldC. aldehyde dehydrogenases are known for its capability to detoxing aldehydes, this is important because aldehydes are very reactive, so for an example from the article they can be turned into carboxylic acids which are not as reactive, which I believe slows down the mutation. The substrate of the AldC PtoDC3000 shows that this enzyme functions as a long-chain aliphatic aldehyde dehydrogenase. This article states that they ran tests to find the best substrate for this enzyme, which they found multiple substrate such as aliphatic aldehydes of 5–9-carbon length, as well as hydrocinnamaldehyde and 4-pyridinecarboxyaldehyde but it shows that octanal has the highest activity. This protein structure is a homodimer meaning it is two identical chains (A and B) covalently bonded together. the article states that there are still blurry areas to why the bacteria is able to grow on the plant in normal conditions rather than its preferred severe conditions. They continue their research to find these answers but there aren't any definitive answers now.

<scene name='87/873232/Rotating_homodimer_protein/3'>Spinning homodimer</scene>

== Biological relevance and broader implications ==

Learning about the mutant and its host is relevant because it can affect the food supply, which as humans we need. Studying this mutant will give us an understanding on what the mutation is and if it can be avoided. This research can lead the farming industry to a solution to the mutant. There are many chemicals that can be found being used with crops such as weed killers and fertilizers.

Learning about the mutant and its host is relevant because it can affect the food supply, which as humans we need. Studying this mutant will give us an understanding on what the mutation is and if it can be avoided. This research can lead the farming industry to a solution to the mutant. There are many chemicals that can be found being used with crops such as weed killers and fertilizers. The study of this helps humans be able to have a more abundant food supply that is disease and mutant free. This was also studied to get a better understanding of the p. syringae mutations and how to inhibit the tomatoes abilities to grow. The article states they didn't run any inhibitory trials but their research should be able to guide further research about this topic.

== Important amino acids==

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Secondary structure of this protein shows there is alpha helix and beta sheets at the C-terminus and only beta sheets in the N-terminus.<scene name='87/873232/Secondary_structure/1'>Cartoon Secondary Structure</scene> <scene name='87/873232/Protein_structure/2'>Ribbon Protein Structure</scene>

Each of the chains has 19 alpha helices, and 20 beta sheets.

Each of the chains has 19 alpha helices, and 20 beta sheets, for a total of 38 alpha helices and 40 beta sheets.

Tertiary structure of the protein, showing only chain B of the protein. <scene name='87/873232/Tertiary_structure_of_protein/2'>Tertiary structure</scene>

Spacefill view of protein shows clearly the protein is a homodimer, it looks like it is two chains back to back with the binding site facing outwards. The color are there to represent the charges on the protein, red for negatively charged amino acids and blue for positively charged.<scene name='87/873232/Space_fill_view/1'>Spacefill view</scene> This view also shows the quaternary structure of the protein which is the two chains together.

Sandbox Reserved 1670: Difference between revisions

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@@ Line 6: / Line 6: @@
 == Function of your protein ==
-This protein can be found in the plant pathogenic microbe Pseudomonas syringae strain PtoDC3000. The p. syringae mutautes its host, which in this case is tomato. The p. syringae produces a toxin that cause the tomato to not be able to fight off, there for causing diseases in the tomato. The research focuses on aldehyde dehydrogenases specifically aldC. aldehyde dehydrogenases are known for its capability to detoxing aldehydes, this is important because aldehydes are very reactive, so for an example from the article they can be turned into carboxylic acids which are not as reactive, which I believe slows down the mutation. The substrate of the AldC PtoDC3000 shows that this enzyme functions as a long-chain aliphatic aldehyde dehydrogenase. This article states that they ran tests to find the best substrate for this enzyme, which they found multiple substrate such as aliphatic aldehydes of 5–9-carbon length, as well as hydrocinnamaldehyde and 4-pyridinecarboxyaldehyde but it shows that octanal has the highest activity. This protein structure is a homodimer meaning it is two identical chains (A and B) covalently bonded together.
+This protein can be found in the plant pathogenic microbe Pseudomonas syringae strain PtoDC3000. The p. syringae mutautes its host, which in this case is tomato. The p. syringae produces a toxin that cause the tomato to not be able to fight off, there for causing diseases in the tomato. The research focuses on aldehyde dehydrogenases specifically aldC. aldehyde dehydrogenases are known for its capability to detoxing aldehydes, this is important because aldehydes are very reactive, so for an example from the article they can be turned into carboxylic acids which are not as reactive, which I believe slows down the mutation. The substrate of the AldC PtoDC3000 shows that this enzyme functions as a long-chain aliphatic aldehyde dehydrogenase. This article states that they ran tests to find the best substrate for this enzyme, which they found multiple substrate such as aliphatic aldehydes of 5–9-carbon length, as well as hydrocinnamaldehyde and 4-pyridinecarboxyaldehyde but it shows that octanal has the highest activity. This protein structure is a homodimer meaning it is two identical chains (A and B) covalently bonded together. the article states that there are still blurry areas to why the bacteria is able to grow on the plant in normal conditions rather than its preferred severe conditions. They continue their research to find these answers but there aren't any definitive answers now.
 <scene name='87/873232/Rotating_homodimer_protein/3'>Spinning homodimer</scene>
 == Biological relevance and broader implications ==
-Learning about the mutant and its host is relevant because it can affect the food supply, which as humans we need. Studying this mutant will give us an understanding on what the mutation is and if it can be avoided. This research can lead the farming industry to a solution to the mutant. There are many chemicals that can be found being used with crops such as weed killers and fertilizers.
+Learning about the mutant and its host is relevant because it can affect the food supply, which as humans we need. Studying this mutant will give us an understanding on what the mutation is and if it can be avoided. This research can lead the farming industry to a solution to the mutant. There are many chemicals that can be found being used with crops such as weed killers and fertilizers. The study of this helps humans be able to have a more abundant food supply that is disease and mutant free. This was also studied to get a better understanding of the p. syringae mutations and how to inhibit the tomatoes abilities to grow. The article states they didn't run any inhibitory trials but their research should be able to guide further research about this topic.
 == Important amino acids==
@@ Line 32: / Line 32: @@
 Secondary structure of this protein shows there is alpha helix and beta sheets at the C-terminus and only beta sheets in the N-terminus.<scene name='87/873232/Secondary_structure/1'>Cartoon Secondary Structure</scene> <scene name='87/873232/Protein_structure/2'>Ribbon Protein Structure</scene>
-Each of the chains has 19 alpha helices, and 20 beta sheets.
+Each of the chains has 19 alpha helices, and 20 beta sheets, for a total of 38 alpha helices and 40 beta sheets.
+Tertiary structure of the protein, showing only chain B of the protein. <scene name='87/873232/Tertiary_structure_of_protein/2'>Tertiary structure</scene>
+Spacefill view of protein shows clearly the protein is a homodimer, it looks like it is two chains back to back with the binding site facing outwards. The color are there to represent the charges on the protein, red for negatively charged amino acids and blue for positively charged.<scene name='87/873232/Space_fill_view/1'>Spacefill view</scene> This view also shows the quaternary structure of the protein which is the two chains together.