Sandbox 35: Difference between revisions

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==Adenylate Kinase==

Adenylate kinase, also known as "ADK", is an enzyme which speeds up the reaction that includes the interconversion of adenine nucleotides. The protein's flexibility allows it to bind to certain substrates known as ligands.

Adenylate kinase, also known as "ADK", is an enzyme which speeds up the reaction that includes the interconversion of adenine nucleotides. The protein's flexibility allows it to bind to certain substrates known as ligands. Adenylate kinase is known for influencing cellular energy homeostasis.

==Structure==

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==Water and Solvent==

Water is very important when it comes to protein folding and structure. It determines the conformation of exposed side chains, stabilizes the ends of secondary structures, and occupy positions at active sites where they influence substrate binding and sometimes catalysis. Adenylate kinase in <scene name='Sandbox_35/Secondary_with_water_molecules/1'>solvent</scene> is mostly surrounded by water molecules around the exterior area of the protein; However, it also can utilizes the water molecules to increase efficent substrate binding. The water molecules (light blue) surround the outside of the protein, interacting with the polar hydrophilic residues. However, some water molecules are seen in contact with the ligand (light green center) where the molecules are influencing catalysis.

==Adenylate Kinase and The Ligand==

The ligand(dark pink) in the center of the protein has specific residues surrounding it that are also known as the <scene name='Sandbox_35/Secondary_with_ligand_in_cente/1'>ligand contacts</scene>. These residues have polar-charged side chains, which stabilize the ligand. The ligand in Adenylate kinase is a molecule which is able to bind to the protein's specific active site.

==Catalytic Residues==

The <scene name='Sandbox_35/Secondary_catalytic_residues/1'>catalytic residues</scene> (black) are found in the center of the protein, lining the active site where the ligand binds. These residues, also known as "active site residues", help with recognition of the ligand. The ligand binds with the protein in various ways: hydrogen bonds, hydrophobic interactions, temporary covalent interactions, or a mixture of the mentioned methods. The catalytic residues assist the reaction by acting as proton donors or acceptors. In the big picture, all of this helps the enzyme protein lower the activation energy of the ligand to speed up the reaction efficiently.

Sandbox 35: Difference between revisions

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@@ Line 4: / Line 4: @@
 <Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Insert optional scene name here' />
 ==Adenylate Kinase==
-Adenylate kinase, also known as "ADK", is an enzyme which speeds up the reaction that includes the interconversion of adenine nucleotides. The protein's flexibility allows it to bind to certain substrates known as ligands.
+Adenylate kinase, also known as "ADK", is an enzyme which speeds up the reaction that includes the interconversion of adenine nucleotides. The protein's flexibility allows it to bind to certain substrates known as ligands. Adenylate kinase is known for influencing cellular energy homeostasis.
 ==Structure==
@@ Line 13: / Line 13: @@
 ==Water and Solvent==
 Water is very important when it comes to protein folding and structure. It determines the conformation of exposed side chains, stabilizes the ends of secondary structures, and occupy positions at active sites where they influence substrate binding and sometimes catalysis. Adenylate kinase in <scene name='Sandbox_35/Secondary_with_water_molecules/1'>solvent</scene> is mostly surrounded by water molecules around the exterior area of the protein; However, it also can utilizes the water molecules to increase efficent substrate binding. The water molecules (light blue) surround the outside of the protein, interacting with the polar hydrophilic residues. However, some water molecules are seen in contact with the ligand (light green center) where the molecules are influencing catalysis.
+==Adenylate Kinase and The Ligand==
+The ligand(dark pink) in the center of the protein has specific residues surrounding it that are also known as the <scene name='Sandbox_35/Secondary_with_ligand_in_cente/1'>ligand contacts</scene>. These residues have polar-charged side chains, which stabilize the ligand. The ligand in Adenylate kinase is a molecule which is able to bind to the protein's specific active site.
+==Catalytic Residues==
+The <scene name='Sandbox_35/Secondary_catalytic_residues/1'>catalytic residues</scene> (black) are found in the center of the protein, lining the active site where the ligand binds. These residues, also known as "active site residues", help with recognition of the ligand. The ligand binds with the protein in various ways: hydrogen bonds, hydrophobic interactions, temporary covalent interactions, or a mixture of the mentioned methods. The catalytic residues assist the reaction by acting as proton donors or acceptors. In the big picture, all of this helps the enzyme protein lower the activation energy of the ligand to speed up the reaction efficiently.