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 ~~which~~ 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.

==Structure==

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Adenylate kinase is composed of both hydrophobic and hydrophilic residues, and folds accordingly to obtain the optimum environments for the nature of both kinds of residues. The <scene name='Sandbox_35/Secondary_hydrophobs_only_gre/1'>hydrophobic residues</scene> shown in grey are buried within the folded protein, away from contact with the solvent. This action represents the hydrophobic effect taking place, which is mainly driven by entropy. Surrounding the outside of the protein are the <scene name='Sandbox_35/Secondary_hphobic_and_hphilic/1'>hydrophilic residues</scene> (dark green). These residues are polar and can be in caontact with the surrounding solvent in the protein's environment. These residues can either be charged or uncharged, can hydrogen bond with water, and are generally more soluble. They cover the hydrophobic amino acid residues to protect them from the solvent.

==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> ~~uses it's outside structures to protect~~ the ~~interior ligand~~, ~~but~~ also 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.

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.

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 which 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.
 ==Structure==
@@ Line 12: / Line 12: @@
 Adenylate kinase is composed of both hydrophobic and hydrophilic residues, and folds accordingly to obtain the optimum environments for the nature of both kinds of residues. The <scene name='Sandbox_35/Secondary_hydrophobs_only_gre/1'>hydrophobic residues</scene> shown in grey are buried within the folded protein, away from contact with the solvent. This action represents the hydrophobic effect taking place, which is mainly driven by entropy. Surrounding the outside of the protein are the <scene name='Sandbox_35/Secondary_hphobic_and_hphilic/1'>hydrophilic residues</scene> (dark green). These residues are polar and can be in caontact with the surrounding solvent in the protein's environment. These residues can either be charged or uncharged, can hydrogen bond with water, and are generally more soluble. They cover the hydrophobic amino acid residues to protect them from the solvent.
 ==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> uses it's outside structures to protect the interior ligand, but also 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.
+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.