Sandbox 35: Difference between revisions
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==Water and 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> 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. | 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. | |||
