Sandbox 42: Difference between revisions
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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. | 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. | ||
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 | 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 the ligand binds to the protein via interactions with protein side chains, as well as that it binds where we expect from the location of the internal polar and charged residues. <scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> are colored purple for this view. | ||
<scene name='Sandbox_42/Wes_-_active_site/1'>Active site residues</scene> | |||
