Sandbox 43
From Proteopedia
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| - | + | <Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate kinase' scene='Scene 1' /> | |
| - | + | ==Introduction== | |
| + | <scene name='Sandbox_43/Samaniego_scene/1'>Adenylate kinase</scene> is an enzyme that catalyzes the reversible reaction in which a molecule of ATP and a molecule of AMP are converted into two molecules of ADP through the following reaction scheme: | ||
| - | + | ATP + AMP ⇔ 2 ADP | |
| - | + | ||
| - | + | Adenylate kinase is integral in maintaining cellular energy homeostasis by providing ADP, which is later utilized in oxidative phosphorylation in metabolic pathways for energy production. This enzyme also possesses a unique flexibility to bind to ligands, pictured as the space filling region. | |
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| + | ==Structural Elements== | ||
| + | The <scene name='Sandbox_43/Samaniego_scene_bg/2'>secondary structural elements</scene> of adenylate kinase show alpha helices (black) and beta sheets (blue) surrounding the non-hydrolysable substrate analogue (orange). <scene name='Sandbox_43/Samaniego_scene_hbonds/1'>Hydrogen bonds</scene> should be visible in green but may not load. These hydrogen bonds connect amino acids of alpha helices and beta sheets, which comprise the backbone of the protein. The anti-parallel configuration of the hydrogen bonds on beta sheets provides stability for the protein. | ||
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| + | The <scene name='Sandbox_43/Samaniego_scene_stickswires/1'>hydrophobic residues</scene> of adenylate kinase are depicted in the black and blue ball and stick representation. These are buried on the interior of the enzyme to avoid contact with the solvent, demonstrating the hydrophobic effect. The protein is surround by <scene name='Sandbox_43/Samaniego_scene_hydrophobic/1'>hydrophilic residues</scene> depicted in the yellow portions. These hydrophilic portions can include polar and charged amino acids, which have a high affinity for the intermolecular solvent interactions in terms of hydrogen bonding and solubility. | ||
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| + | ==Solvent Accessibility== | ||
| + | When dissolved in <scene name='Sandbox_43/Samaniego_scene_water2/1'>water</scene> (light blue), the hydrophilic residues of adenylate kinase interact with this polar solvent to fold the protein into its most stable conformation through hydrogen bonding. It can be seen that water interacts with the ligand (green) at its center, where catalysis occurs. However, water mostly surrounds the hydrophilic exterior of the molecule, where the majority of hydrogen bonding occurs. | ||
| + | |||
| + | ==Ligand Interactions== | ||
| + | Portions of adenylate kinase which interact with the ligand are shown here in purple. These are called the <scene name='Sandbox_43/Samaniego_scene_ligand2/1'>ligand contacts</scene> and have polar-charged side chains, which help to stabilize the ligand as it binds to the protein's active site. The catalytic resides (unable to be pictured) are able to directly interact/bind to the ligand. | ||
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| + | ==Sources== | ||
| + | Library CHEM410 page: http://libguides.messiah.edu/content.php?pid=279182&sid=2407875 | ||
| + | Wikipedia: http://en.wikipedia.org/wiki/Adenylate_kinase | ||
| + | European Bioinformatics Institute: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR000850 | ||
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 |
Introduction
is an enzyme that catalyzes the reversible reaction in which a molecule of ATP and a molecule of AMP are converted into two molecules of ADP through the following reaction scheme:
ATP + AMP ⇔ 2 ADP
Adenylate kinase is integral in maintaining cellular energy homeostasis by providing ADP, which is later utilized in oxidative phosphorylation in metabolic pathways for energy production. This enzyme also possesses a unique flexibility to bind to ligands, pictured as the space filling region.
Structural Elements
The of adenylate kinase show alpha helices (black) and beta sheets (blue) surrounding the non-hydrolysable substrate analogue (orange). should be visible in green but may not load. These hydrogen bonds connect amino acids of alpha helices and beta sheets, which comprise the backbone of the protein. The anti-parallel configuration of the hydrogen bonds on beta sheets provides stability for the protein.
The of adenylate kinase are depicted in the black and blue ball and stick representation. These are buried on the interior of the enzyme to avoid contact with the solvent, demonstrating the hydrophobic effect. The protein is surround by depicted in the yellow portions. These hydrophilic portions can include polar and charged amino acids, which have a high affinity for the intermolecular solvent interactions in terms of hydrogen bonding and solubility.
Solvent Accessibility
When dissolved in (light blue), the hydrophilic residues of adenylate kinase interact with this polar solvent to fold the protein into its most stable conformation through hydrogen bonding. It can be seen that water interacts with the ligand (green) at its center, where catalysis occurs. However, water mostly surrounds the hydrophilic exterior of the molecule, where the majority of hydrogen bonding occurs.
Ligand Interactions
Portions of adenylate kinase which interact with the ligand are shown here in purple. These are called the and have polar-charged side chains, which help to stabilize the ligand as it binds to the protein's active site. The catalytic resides (unable to be pictured) are able to directly interact/bind to the ligand.
Sources
Library CHEM410 page: http://libguides.messiah.edu/content.php?pid=279182&sid=2407875 Wikipedia: http://en.wikipedia.org/wiki/Adenylate_kinase European Bioinformatics Institute: http://www.ebi.ac.uk/interpro/IEntry?ac=IPR000850
