Sandbox 52
From Proteopedia
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The <scene name='Sandbox_52/Adenylate_kinase_chain_a/1'>secondary structure</scene> in chain A of adenylate kinase shows multiple alpha helicies and beta sheets. These <scene name='Sandbox_52/Helicies_and_beta_sheets/1'>alpha helicies and beta sheets</scene> can be shown in different colors, with the alpha helicies shown in cyan and the beta sheets shown in red. | The <scene name='Sandbox_52/Adenylate_kinase_chain_a/1'>secondary structure</scene> in chain A of adenylate kinase shows multiple alpha helicies and beta sheets. These <scene name='Sandbox_52/Helicies_and_beta_sheets/1'>alpha helicies and beta sheets</scene> can be shown in different colors, with the alpha helicies shown in cyan and the beta sheets shown in red. | ||
==Hydrogen Bonding== | ==Hydrogen Bonding== | ||
| - | The <scene name='Sandbox_52/Hydrogen_bonds_shown/1'>hydrogen bonds</scene> within the structure of the protein can also be displayed in green. These can be | + | The <scene name='Sandbox_52/Hydrogen_bonds_shown/1'>hydrogen bonds</scene> within the structure of the protein can also be displayed in green. These can be seen within the alpha helicies, helping maintain the structure of the helix, and are also between beta sheets. Most of the beta sheets are running parallel, as indicated by the crooked hydrogen bonds. They are crooked due to the position of the carbonyl oxygens and amide hydrogens in the structure. This formation is less stable than the straight, parallel hydrogen bonding of the antiparallel sheets. |
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==Hydrophobic and Hydrophilic Interactions== | ==Hydrophobic and Hydrophilic Interactions== | ||
The <scene name='Sandbox_52/Hydrophobic_residues/2'>hydrophobic residues</scene> on the structure can be seen in yellow sticks. Generally, these residues are clustered in the center of the protein due to the hydrophobic effect created by the surrounding water molecules. The <scene name='Sandbox_52/Hydrophilic_residues/2'>hydrophilic residues</scene> are shown in purple here, and they are generally on the outside of the protein, shielding the hydrophobic residues. There are also <scene name='Sandbox_52/Water_placement/1'>water molecules</scene> around and inside the protein. Water helps stabilize the protein through the hydrophobic effect and also interacts/surrounds the binding site in the center of the protein. | The <scene name='Sandbox_52/Hydrophobic_residues/2'>hydrophobic residues</scene> on the structure can be seen in yellow sticks. Generally, these residues are clustered in the center of the protein due to the hydrophobic effect created by the surrounding water molecules. The <scene name='Sandbox_52/Hydrophilic_residues/2'>hydrophilic residues</scene> are shown in purple here, and they are generally on the outside of the protein, shielding the hydrophobic residues. There are also <scene name='Sandbox_52/Water_placement/1'>water molecules</scene> around and inside the protein. Water helps stabilize the protein through the hydrophobic effect and also interacts/surrounds the binding site in the center of the protein. | ||
==Ligand Binding== | ==Ligand Binding== | ||
The <scene name='Sandbox_52/Ligand_binding/1'>ligand</scene> is able to bind to the protein through the polar, charged parts of the active site that are shown in red and blue (red being anionic and blue being cationic). The <scene name='Sandbox_52/Catalytic_residues/1'>catalytic residues</scene> are also shown in green. These residues specifically react with the substrate. | The <scene name='Sandbox_52/Ligand_binding/1'>ligand</scene> is able to bind to the protein through the polar, charged parts of the active site that are shown in red and blue (red being anionic and blue being cationic). The <scene name='Sandbox_52/Catalytic_residues/1'>catalytic residues</scene> are also shown in green. These residues specifically react with the substrate. | ||
Revision as of 21:30, 18 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 |
Introduction
The in chain A of adenylate kinase shows multiple alpha helicies and beta sheets. These can be shown in different colors, with the alpha helicies shown in cyan and the beta sheets shown in red.
Hydrogen Bonding
The within the structure of the protein can also be displayed in green. These can be seen within the alpha helicies, helping maintain the structure of the helix, and are also between beta sheets. Most of the beta sheets are running parallel, as indicated by the crooked hydrogen bonds. They are crooked due to the position of the carbonyl oxygens and amide hydrogens in the structure. This formation is less stable than the straight, parallel hydrogen bonding of the antiparallel sheets.
Hydrophobic and Hydrophilic Interactions
The on the structure can be seen in yellow sticks. Generally, these residues are clustered in the center of the protein due to the hydrophobic effect created by the surrounding water molecules. The are shown in purple here, and they are generally on the outside of the protein, shielding the hydrophobic residues. There are also around and inside the protein. Water helps stabilize the protein through the hydrophobic effect and also interacts/surrounds the binding site in the center of the protein.
Ligand Binding
The is able to bind to the protein through the polar, charged parts of the active site that are shown in red and blue (red being anionic and blue being cationic). The are also shown in green. These residues specifically react with the substrate.
