Sandbox 43: Difference between revisions

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==Structural Elements==

The <scene name='Sandbox_43/Samaniego_scene_bg/2'>secondary structural elements</scene> of adenylate ~~cyclase~~ 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> ~~of are~~ visible in green. These ~~hydrogren~~ 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 <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.

The <scene name='Sandbox_43/Samaniego_scene_stickswires/1'>hydrophobic residues</scene> of adenylate ~~cyclase~~ 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.

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.

==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.

Sandbox 43: Difference between revisions

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@@ Line 11: / Line 11: @@
 ==Structural Elements==
-The <scene name='Sandbox_43/Samaniego_scene_bg/2'>secondary structural elements</scene> of adenylate cyclase 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> of are visible in green. These hydrogren 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 <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.
-The <scene name='Sandbox_43/Samaniego_scene_stickswires/1'>hydrophobic residues</scene> of adenylate cyclase 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.
+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.
 ==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.