Sandbox 48: Difference between revisions

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== 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.

<scene name='Sandbox_48/Full_adenylate_kinase/1'>Adenylate kinase</scene> (or ADK) is an enzyme known to catalyze the reversible interconversion of adenosine triphosphate (ATP) and adenosine monophosphate (AMP) to two molecules of adenosine diphosphate (ADP).

Reaction Scheme: ATP + AMP ⇔ 2 ADP

This enzyme is important 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 <scene name='Sandbox_48/Adenylate_kinase__chain_a/1'>chain A in adenylate kinase</scene>.

The structure of <scene name='Sandbox_48/Adenylate_kinase__chain_a/1'>chain A in adenylate kinase</scene> demonstrates the types of secondary structure that make up the enzyme.

The <scene name='Sandbox_48/Secondary__structure__greenblu/1'>secondary structures</scene> 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 <scene name='Sandbox_48/2_structure_hbondson/1'>hydrogen bonds</scene> (black) within the~~ secondary structure ~~demonstrates how~~ the ~~alpha-helices and beta-sheets are hydrogen bonded~~.

The <scene name='Sandbox_48/Secondary__structure__greenblu/4'>secondary structures</scene> of chain A of adenylate kinase includes alpha-

<scene name='Sandbox_48/Secondary__structure__helix/1'>helices</scene> (green), and <scene name='Sandbox_48/Secondary__structure__betashee/1'>beta sheets</scene> (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 <scene name='Sandbox_48/2_structure_hbondson/1'>hydrogen bonds</scene> (black) within the secondary structure demonstrates how the alpha-helices and beta-sheets are hydrogen bonded.

== Hydrophobic and Hydrophilic Residues ==

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== 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.

~~To assess~~ the ~~solvent accessibility~~ of ~~adenylate kinase,~~ <scene name='Sandbox_48/Chain_a__w__waterligand/1'>~~water molecules~~</scene> (purple) ~~are shown on the molecule~~. ~~These are the spaces in the protein that are capable of being accessed by~~ solvent~~. Solvent accumulates~~ near the center of the molecule, and is ~~found~~ 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 ==

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@@ Line 7: / Line 7: @@
 == 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.
+<scene name='Sandbox_48/Full_adenylate_kinase/1'>Adenylate kinase</scene> (or ADK) is an enzyme known to catalyze the reversible interconversion of adenosine triphosphate (ATP) and adenosine monophosphate (AMP) to two molecules of adenosine diphosphate (ADP).
+Reaction Scheme: ATP + AMP ⇔ 2 ADP
+This enzyme is important 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 <scene name='Sandbox_48/Adenylate_kinase__chain_a/1'>chain A in adenylate kinase</scene>.
+The structure of <scene name='Sandbox_48/Adenylate_kinase__chain_a/1'>chain A in adenylate kinase</scene> demonstrates the types of secondary structure that make up the enzyme.
-The <scene name='Sandbox_48/Secondary__structure__greenblu/1'>secondary structures</scene> 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 <scene name='Sandbox_48/2_structure_hbondson/1'>hydrogen bonds</scene> (black) within the secondary structure demonstrates how the alpha-helices and beta-sheets are hydrogen bonded.
+The <scene name='Sandbox_48/Secondary__structure__greenblu/4'>secondary structures</scene> of chain A of adenylate kinase includes alpha-
+<scene name='Sandbox_48/Secondary__structure__helix/1'>helices</scene> (green), and <scene name='Sandbox_48/Secondary__structure__betashee/1'>beta sheets</scene> (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 <scene name='Sandbox_48/2_structure_hbondson/1'>hydrogen bonds</scene> (black) within the secondary structure demonstrates how the alpha-helices and beta-sheets are hydrogen bonded.
 == Hydrophobic and Hydrophilic Residues ==
@@ Line 22: / Line 28: @@
 == 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.
-To assess the solvent accessibility of adenylate kinase, <scene name='Sandbox_48/Chain_a__w__waterligand/1'>water molecules</scene> (purple) are shown on the molecule. These are the spaces in the protein that are capable of being accessed by solvent. Solvent accumulates near the center of the molecule, and is found 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 ==