Sandbox 42: Difference between revisions
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The protein's <scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> are shown here in stick/wire form, colored gray, while the <scene name='Sandbox_42/Wes_-_polar-charged_residues/1'>polar and charged residues</scene> are colored brown. It is interesting to see the arrangement of these residues in the protein. The hydrophobic residues lie mostly on the interior of the molecule, with most of the polar and charged residues being on the outside. There also seems to be a pocket in the structure where the outer surface dips in, and polar/charged residues are found lining the outside of this pocket as well. This indicates where the ligand enters the active site from being solvated. | The protein's <scene name='Sandbox_42/Wes_-_hydrophobic_residues/1'>hydrophobic residues</scene> are shown here in stick/wire form, colored gray, while the <scene name='Sandbox_42/Wes_-_polar-charged_residues/1'>polar and charged residues</scene> are colored brown. It is interesting to see the arrangement of these residues in the protein. The hydrophobic residues lie mostly on the interior of the molecule, with most of the polar and charged residues being on the outside. There also seems to be a pocket in the structure where the outer surface dips in, and polar/charged residues are found lining the outside of this pocket as well. This indicates where the ligand enters the active site from being solvated. | ||
In biological systems the primary solvent is water, so it is helpful to see how water interacts with the protein. <scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> molecules are added here to the general secondary structure and colored yellow. It is interesting to see where they are, and where they aren't, within the protein. For starters, water surrounds the outer surface. This is because the protein would be in solution in vivo, so it will almost always be solvated. This can be seen in <scene name='Sandbox_42/Wes_-_water-ball_and_stick/2'>another view</scene> with the protein shown again in stick and wire representation. What is interesting about these models is that | In biological systems the primary solvent is water, so it is helpful to see how water interacts with the protein. <scene name='Sandbox_42/Wes_-_water-secondary_update/2'>Water</scene> molecules are added here to the general secondary structure and colored yellow. It is interesting to see where they are, and where they aren't, within the protein. For starters, water surrounds the outer surface. This is because the protein would be in solution in vivo, so it will almost always be solvated. This can be seen in <scene name='Sandbox_42/Wes_-_water-ball_and_stick/2'>another view</scene> with the protein shown again in stick and wire representation. What is interesting about these models is that water permeates the molecule at least part way. However, as has just been shown, the path to the active site contains a large number of polar and charged amino acid residues, so this is really not surprising. The solvated ligand enters through the channel where water is still present before it becomes unsolvated, at which point it can bind to the protein. | ||
<scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent. | The <scene name='Sandbox_42/Wes_-_ligand/1'>ligand</scene> and interacting side chains are shown here in stick/wire representation, with the rest of the protein semi-transparent. This view shows how | ||
<scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> in purple | <scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> in purple | ||
