Sandbox Reserved 1633

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Revision as of 21:53, 8 November 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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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 == The apparent function of the protein is its ability to prevent decarboxylation at the C5’ position of the 4-keto-hexose-uronic acid intermediate.

My protein has a very .

== Biological relevance and broader implications == It also belongs to the SDR family. The enzymes work to prevent an overabundance of 4-keto-hexose-uronic acid, which lessens the release of reactive intermediates or decarboxylation. Because of the intense amount of research and findings, this organism is very relevant now.

== Important amino acids == important amino acids include arginine, serine, aspartic acid, and tyrosine. The catalytic triad is Ser/Thr-Tyr-Lys.

== Structural highlights == The protein has an A chain and a B chain. The protein contains a secondary structure of alpha helices, beta sheets, and beta turns. As with many proteins, the alpha helices are abundant than beta-sheets. However, beta sheets are rather plentiful in this protein. Just based on visual aids, I would say that the protein is made up of 30% beta-sheets, 60% alpha-helices, and 10% other structures. I was able to identify seven beta turns in the protein as well. Chain A contains what appears to be ten alpha-helices, three beta-sheets, and three beta turns. Chain B contains what appears to be ten alpha-helices, four beta-sheets, and four beta turns. From what I could gather from the image, the catalytic triad amino acids appear to be close to both the alpha-helices and the beta-sheets.

== Other important features == I know that I am still learning about this protein and I will likely discover things that I identify as correct, and some incorrect, but I am excited to research and learn more.

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

== References == ^[3]

↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
↑ 32661196

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Sandbox Reserved 1633

From Proteopedia

Revision as of 21:53, 8 November 2020

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@@ Line 14: / Line 14: @@
 == Important amino acids == important amino acids include arginine, serine, aspartic acid, and tyrosine. The catalytic triad is Ser/Thr-Tyr-Lys.
-== Structural highlights == The protein has an A chain and a B chain. The protein contains a secondary structure of alpha helices, beta sheets, and beta turns. As with many proteins, the alpha helices are abundant than beta-sheets. However, beta sheets are rather plentiful in this protein. Just based on visual aids, I would say that the protein is made up of 30% beta-sheets, 60% alpha-helices, and 10% other structures. I was able to identify seven beta turns in the protein as well. Chain A contains what appears to be ten alpha-helices, three beta-sheets, and three beta turns. Chain B contains what appears to be ten alpha-helices, four beta-sheets, and four beta turns.
+== Structural highlights == The protein has an A chain and a B chain. The protein contains a secondary structure of alpha helices, beta sheets, and beta turns. As with many proteins, the alpha helices are abundant than beta-sheets. However, beta sheets are rather plentiful in this protein. Just based on visual aids, I would say that the protein is made up of 30% beta-sheets, 60% alpha-helices, and 10% other structures. I was able to identify seven beta turns in the protein as well. Chain A contains what appears to be ten alpha-helices, three beta-sheets, and three beta turns. Chain B contains what appears to be ten alpha-helices, four beta-sheets, and four beta turns. From what I could gather from the image, the catalytic triad amino acids appear to be close to both the alpha-helices and the beta-sheets.
 == Other important features == I know that I am still learning about this protein and I will likely discover things that I identify as correct, and some incorrect, but I am excited to research and learn more.