Sandbox Reserved 1569
From Proteopedia
(Difference between revisions)
| Line 11: | Line 11: | ||
== Structural highlights and structure-function relationships == | == Structural highlights and structure-function relationships == | ||
There are many key structures one can highlight for Bap1, such as its two different sized connected domains, 8-bladed β-propeller region, active site location outside of the central cavity, and carbohydrate binding site. | There are many key structures one can highlight for Bap1, such as its two different sized connected domains, 8-bladed β-propeller region, active site location outside of the central cavity, and carbohydrate binding site. | ||
| + | |||
When looking at the (secondary structure) of Bap1, the two different sized domains are easily seen. The larger domain of the protein is the 8-bladed β-propeller region. The smaller domain of the protein is a β-prism that is connected to the propeller region via a loop in between blade 6. When zooming in on what connects them, it is just two small strands. This makes the protein very flexible. | When looking at the (secondary structure) of Bap1, the two different sized domains are easily seen. The larger domain of the protein is the 8-bladed β-propeller region. The smaller domain of the protein is a β-prism that is connected to the propeller region via a loop in between blade 6. When zooming in on what connects them, it is just two small strands. This makes the protein very flexible. | ||
| - | When looking at a space-fill view of Bap1 and colored based on hydrophobicity, one can easily identify the binding pocket that carbohydrates bind to in the β-prism. Bap1 is known for its sugar binding properties. | ||
| - | It is important to note that this protein did not have a catalytic triad mentioned in the paper. Instead, highlighting the <scene name='82/823093/Key_amino_acids/1'>key amino acids</scene> that are important to the function of Bap1 should be mentioned. These amino acids are Gly 344, Ala 345, Val 346, Lys 501, Asp 348, and His 500. The actual ligand was not mentioned in the paper either, but citrate was bound near the sites and can be used for important functionality of the protein. Gly 344, Ala 345, Val 346, Lys 501 all interact with citrate via hydrogen bonding. Asp 348 and His 500 interact with citrate via van der Waals interactions. | + | When looking at a space-fill view of Bap1 and colored based on <scene name='82/823093/Hydrophobicity/2'>hydrophobicity</scene>, one can easily identify the binding pocket that carbohydrates bind to in the β-prism. Bap1 is known for its sugar binding properties. The hydrophobic molecules are colored in dark gray. The charged molecules are colored in white. The neutral molecules are colored in dark green. Anionic polysaccharides, sugars that are negative, want their amino acid to be negative to bind to. Lysine, which makes up a large portion of the binding pocket is critical to identify when talking about the function of this protein. It is colored in orange. |
| + | |||
| + | It is important to note that this protein did not have a catalytic triad mentioned in the paper. Instead, highlighting the <scene name='82/823093/Key_amino_acids/1'>key amino acids</scene> that are important to the function of Bap1 should be mentioned. These amino acids are Gly 344, Ala 345, Val 346, Lys 501, Asp 348, and His 500. The actual ligand was not mentioned in the paper either, but citrate was bound near the sites and can be used for important functionality of the protein. Gly 344, Ala 345, Val 346, Lys 501 all interact with citrate via hydrogen bonding. Asp 348 and His 500 interact with citrate via van der Waals interactions. The protein is colored in a light tan and the amino acids are highlighted in CPK to be able to visualize the hydrogen bonding areas. | ||
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. | This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. | ||
Revision as of 02:54, 1 December 2019
| This Sandbox is Reserved from Aug 26 through Dec 12, 2019 for use in the course CHEM 351 Biochemistry taught by Bonnie_Hall at the Grand View University, Des Moines, USA. This reservation includes Sandbox Reserved 1556 through Sandbox Reserved 1575. |
To get started:
More help: Help:Editing |
Bap1
| |||||||||||
References
- ↑ 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
<https://www.cdc.gov/cholera/general/index.html/> <https://learn-us-east-1-prod-fleet01-xythos.s3.us-east-1.amazonaws.com/5b158bd279e57/1084854?response-content-disposition=inline%3B%20filename%2A%3DUTF-8%27%27J.%2520Biol.%2520Chem.-2019-Kaus-14499-511%2520Bap1%2520and%2520Biofilms.pdf&response-content-type=application%2Fpdf&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Date=20191129T222123Z&X-Amz-SignedHeaders=host&X-Amz-Expires=21599&X-Amz-Credential=AKIAIBGJ7RCS23L3LEJQ%2F20191129%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Signature=ed78695b2e7f71eacab1d648cabfd0bdc32d25d4c7e7baa05f136386ac3844b6/> [1]
