Sandbox 33
From Proteopedia
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In aqueous, physiological environments the <scene name='Sandbox_33/Stickwire_hydrophobic/1'>hydrophobic residues</scene> of adenylate kinase, seen in grey, are buried in the interior of the protein. The hydrophobic residues cluster together in the interior of the protein in order to avoid the exterior aqueous environment. | In aqueous, physiological environments the <scene name='Sandbox_33/Stickwire_hydrophobic/1'>hydrophobic residues</scene> of adenylate kinase, seen in grey, are buried in the interior of the protein. The hydrophobic residues cluster together in the interior of the protein in order to avoid the exterior aqueous environment. | ||
| - | The <scene name='Sandbox_33/Stickwire_charged/1'>hydrophilic</scene> polar and charged residues, seen in yellow, are found on the exterior of adenylate kinase. It might be easier to visualize in <scene name='Sandbox_33/Hydrophilic_better/1'>this</scene> depiction of adenylate kinase, where the hydrophilic residues are depicted in red. Hydrophilic residues are on the exterior of the protein because they can interact with the aqueous exterior environment. Hydrophilic residues can exist on the interior of a protein by interacting solely with one another and avoiding interaction with hydrophobic residues. Hydrophilic residues also exist in the interior active site to stabilize hydrophilic portions of the substrate during catalysis. | + | The <scene name='Sandbox_33/Stickwire_charged/1'>hydrophilic</scene> polar and charged residues, seen in yellow while the hydrophobic residues are grey, are found on the exterior of adenylate kinase. It might be easier to visualize in <scene name='Sandbox_33/Hydrophilic_better/1'>this</scene> depiction of adenylate kinase, where the hydrophilic residues are depicted in red. Hydrophilic residues are on the exterior of the protein because they can interact with the aqueous exterior environment. Hydrophilic residues can exist on the interior of a protein by interacting solely with one another and avoiding interaction with hydrophobic residues. Hydrophilic residues also exist in the interior active site to stabilize hydrophilic portions of the substrate during catalysis. |
==Water== | ==Water== | ||
Revision as of 00:59, 20 October 2012
| Please do NOT make changes to this Sandbox. Sandboxes 30-60 are reserved for use by Biochemistry 410 & 412 at Messiah College taught by Dr. Hannah Tims during Fall 2012 and Spring 2013. |
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Contents |
Adenylate Kinase
(also known as 1AKE) is an enzyme that performs a reaction that quickly converts ATP to ADP. Adenylate Kinase thus plays an important role in cellular metabolism. The images of Adenylate Kinase in this sandbox are from Yersinia Pestis, which is commonly called yeast.
Secondary Structure
The of adenylate kinase consists of 214 amino acids which form 12 alpha helices and 7 beta sheets. The helices in this image are displayed in pink and the anti-parallel beta sheets are shown in purple. The secondary structure is held together by , which is depicted by black lines.
Hydrophobic and Hydrophilic Residues
In aqueous, physiological environments the of adenylate kinase, seen in grey, are buried in the interior of the protein. The hydrophobic residues cluster together in the interior of the protein in order to avoid the exterior aqueous environment.
The polar and charged residues, seen in yellow while the hydrophobic residues are grey, are found on the exterior of adenylate kinase. It might be easier to visualize in depiction of adenylate kinase, where the hydrophilic residues are depicted in red. Hydrophilic residues are on the exterior of the protein because they can interact with the aqueous exterior environment. Hydrophilic residues can exist on the interior of a protein by interacting solely with one another and avoiding interaction with hydrophobic residues. Hydrophilic residues also exist in the interior active site to stabilize hydrophilic portions of the substrate during catalysis.
Water
write something about where the waters are, and arent
The which is depicted in blue. The water surrounds the exterior of the protein and interacts with the hydrophilic proteins. There are also water molecules in the active site. Again, the water is the cause of the aqueous environment YOU REALLY WANT TO SAY THAT? which causes adenylate kinase to fold in the conformation that it does. There are some water molecules in the open spaces between the backbone. The hydrophilic residues only interact with the water. the ligand is highlighted brown in respect to the hydration shell.
Enzyme Activity
DONT FORGET: When you add the green link to the top part of the page, make sure you say something about what kinds of side-chains interact with the non-hydrolysable substrate, and if that makes sense.
The active site is where the substrate binds to the enzyme to be catalyzed. The ligand binds to the (depicted in color) of the protein. There are mostly hydrophilic residue in the active site because water enter the active site. As previously mentioned, there are some hydrophobic interactions in the active site, which interacts with the hydrophobic portions of the substrate (or more likely, the transition state) to stabilize it during catalysis. There are SIX CHECK TO SEE IF RIGHT ONES which are highlighted in blue while all the ligand contacts are depicted in pink, which help perform the catalysis by forming hydrogen bonds with the substrate to hold it in place for the reaction. The catalytic residues are all charged residues, including lysinE, aspartic acid, and arginine. These residues also allow for electrostatic interactions but can be effected by water in the active site.
