Sandbox 50: Difference between revisions

The <scene name='Sandbox_50/Ak_hydrophobic_residues/1'>hydrophobic_residues</scene> of ADK, seen in gray, is buried in the interior of the protein. While the <scene name='Sandbox_50/Ak_hydrophiblic_residues2/1'>hydrophilic_residues</scene>, all the charged and polar side chains (purple), are on the surface of the protein and exposed. The location of the residues depend on the solvent and the environment that the protein is found in. All the hydrophobic residues aggregate together, and bury themselves in the interior of the protein to minimize their contact with their environment. The hydrophilic residues, on the other hand, is exposed on the surface because the enzyme is in an hydrophilic environment. Although, most of the hydrophilic residues would be exposed, it is possible for some of the to be buried in the interior, but they would interact with each other be stabilized there. There are also hydrophilic  residues in the active site of the enzyme, where the ligand binds, to help it enter so that the reaction can take place.  

The active site, like mentioned above, is where the ligand/substrate binds to the enzyme to be catalyzed. In ADK, the <scene name='Sandbox_50/Ak_ligand_contact1/1'>ligand_contacts</scene> (gray, blue, pink), is in the interior of the protein. The pink is where the ligand binds directly. There are six <scene name='Sandbox_50/Ak_catalytic_residues1/1'>catalytic_residues</scene>, which are specifically involved in the catalyzes of the substrates forming hydrogen bonds with the ligands, and they are highlighted black on the image. The catalytic residues are all charged residues and include Lysine, Aspartic acid, and Arginine. The other residues also interact with the ligand, but only with weak electrostatic and hydrophobic interactions because they are further away.  

The <scene name='Sandbox_50/Ak_water6/1'>solvent</scene>, which is water (blue), can be co-crystallized with the enzyme. The water can be found all around the protein but there is also some water molecules in the active site, around the ligand. This further indicates why the hydrophilic residues are found on the surface, and the nonpolar residues are buried away. The water creates a hydrophilic environment, and the hydrophobic residues aggregate together in the interior, which is the hydrophobic effect and drives the water out. So for the most part, there are not water molecules in between the secondary structure, but there are some water molecules in the open spaces between the backbone.The hydrophilic residues in the active site cause water to be present there, and also make it easier for the ligand to enter and facilitates in the reaction.

Voet, D., Voet, J., and Pratt, C. W. ''Fundamentals of Biochemistry: Life at the Molecular Level''3rd Edition. (2008)