Sandbox 33
From Proteopedia
| (114 intermediate revisions not shown.) | |||
| Line 2: | Line 2: | ||
{{Template:Oberholser_Sandbox_Reservation}} | {{Template:Oberholser_Sandbox_Reservation}} | ||
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | <!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | ||
| + | <Structure load='1ake' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Insert optional scene name here' /> | ||
| + | ==Adenylate Kinase== | ||
| + | <scene name='Sandbox_33/1ake/1'>Adenylate kinase</scene> (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. | ||
| + | ==Secondary Structure== | ||
| + | The <scene name='Sandbox_33/Secondary_structure_colored/2'>secondary structure</scene> 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 <scene name='Sandbox_33/Hbond/1'>hydrogen bonding</scene>, which is depicted by black lines. | ||
| + | ==Hydrophobic and Hydrophilic Residues== | ||
| - | + | 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. Some hydrophobic residues are found on the exterior of adenylate kinase, but such residues decrease the stability of the protein. So often, hydrophobic residues on the exterior interact with other hydrophobic residues to avoid the stability loss. | |
| - | < | + | 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== | |
| - | = | + | The aqueous environment surrounding adenylate kinase causes it to fold in the conformation that it does. The <scene name='Sandbox_33/Waters/1'>water molecules</scene> that surround adenylate kinase in aqueous environments are depicted in blue. The water surrounds the exterior of the protein and interacts with the hydrophilic proteins only. There are also water molecules found in the active site. There are also some water molecules in the open spaces between the backbone. The waters are not found in the interior of the protein, between two residues. <scene name='Sandbox_33/Waters_with_ligand_highlighted/1'>Here</scene> the ligand is highlighted brown in respect to the hydration shell, for better visualization. |
| - | + | ||
| - | + | ||
| - | = | + | ==Enzyme Activity== |
| - | == | + | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| + | The active site is where the substrate binds to the enzyme to be catalyzed. The ligand binds to the <scene name='Sandbox_33/Ligand_contacts/1'>ligand contacts</scene> (depicted in color) of the protein. There are mostly hydrophilic residues in the active site because water enter the active site. There are also some hydrophobic residues 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 <scene name='Sandbox_33/Catalytic_residues/1'>catalytic residues</scene> (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. | ||
| - | = | + | ==Resources== |
| - | + | http://en.wikipedia.org/wiki/Adenylate_kinase | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
| 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. |
|
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.
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. Some hydrophobic residues are found on the exterior of adenylate kinase, but such residues decrease the stability of the protein. So often, hydrophobic residues on the exterior interact with other hydrophobic residues to avoid the stability loss.
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
The aqueous environment surrounding adenylate kinase causes it to fold in the conformation that it does. The that surround adenylate kinase in aqueous environments are depicted in blue. The water surrounds the exterior of the protein and interacts with the hydrophilic proteins only. There are also water molecules found in the active site. There are also some water molecules in the open spaces between the backbone. The waters are not found in the interior of the protein, between two residues. the ligand is highlighted brown in respect to the hydration shell, for better visualization.
Enzyme Activity
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 residues in the active site because water enter the active site. There are also some hydrophobic residues 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 (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.
