Sandbox 48
From Proteopedia
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== Solvent Accessibility == | == Solvent Accessibility == | ||
| - | + | In the presence of <scene name='Sandbox_48/Chain_a__w__waterligand/1'>solvent</scene>, the polar, hydrophilic residues of adenylate kinase interact with the molecules of solvent (purple). There is also solvent accessibility near the center of the molecule at the active site, and it is also accessible on the outward chains like the alpha helices. The ligand (green) is highlighted to show that the water molecules surround the ligand in the middle of the ligand, but not by the ends. | |
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== Ligand Interaction == | == Ligand Interaction == | ||
Revision as of 19:34, 19 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
Adenylate kinase (or ADK) is an enzyme known to catalyze the interconversion of adenosine triphosphate (ATP) and adenosine monophosphate (AMP) to two molecules of adenosine diphosphate (ADP), and vice versa. This enzyme is imporant for cellular energy homeostasis because the need for ADP. ADP is required for oxidative phosphorylation, an important step in multiple metabolic pathways.
Secondary Structure & Hydrogen Bonds
We will be examining the secondary structure of .
The of chain A of adenylate kinase includes alpha-helices (green), and beta-sheets (blue). There are 12 total helices in the enzyme, and 2 types of beta sheets, a parallel with 5 strands and an antiparallel with 2 strands. The location of the (black) within the secondary structure demonstrates how the alpha-helices and beta-sheets are hydrogen bonded.
Hydrophobic and Hydrophilic Residues
Within these structures the residues (purple) are located closest on the inside of the enzyme. The residues (green), which are those that are charged or polar, are on the outward face of the enzyme.
Solvent Accessibility
In the presence of , the polar, hydrophilic residues of adenylate kinase interact with the molecules of solvent (purple). There is also solvent accessibility near the center of the molecule at the active site, and it is also accessible on the outward chains like the alpha helices. The ligand (green) is highlighted to show that the water molecules surround the ligand in the middle of the ligand, but not by the ends.
Ligand Interaction
There are charged residues that , or make up the interaction site. The positively charged (blue) residues of the enzyme, which would include arginine (R123, R156, R167) and lysine (K13) interact with the negatively charged (red) residues of the ligand. There are also negatively charged portions of the active site, such as aspartic acid (D158, D159) that will interact with positively charged residues of the ligand.
The pictured is the inhibitory, non-hydrolyzable version of a substrate. It is similar in structure to ATP, but at the end of the triphosphate there is another adenosine. This will stop the reaction, and will allow our enzyme's structure to be analyzed in presence of a substrate.
