Sandbox 47: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Updated to the stuff I forgot to post last night. |
|||
| Line 11: | Line 11: | ||
The <scene name='Sandbox_47/Ad_k_hydrophobic/3'>Hydrophobic Residues</scene> of the protein's structure are primarily buried in the structure due to the hydrophobic effect. On the other hand, many of the <scene name='Sandbox_47/Adenylate_kinase_hydrophillic/1'>polar residues</scene> are either on the exterior surface, where they can be accessed by the solvent, or in close interaction with each other. Some polar residues also center around the entrance to the active site, to aid the desolvation of the ligand. A combined view of both the <scene name='Sandbox_47/Ad_k_hydrophillic_and_phobic/1'>Hydrophillic and Hydrophobic Residues</scene> allows one to see the general patterns of arrangement relative to each other. | The <scene name='Sandbox_47/Ad_k_hydrophobic/3'>Hydrophobic Residues</scene> of the protein's structure are primarily buried in the structure due to the hydrophobic effect. On the other hand, many of the <scene name='Sandbox_47/Adenylate_kinase_hydrophillic/1'>polar residues</scene> are either on the exterior surface, where they can be accessed by the solvent, or in close interaction with each other. Some polar residues also center around the entrance to the active site, to aid the desolvation of the ligand. A combined view of both the <scene name='Sandbox_47/Ad_k_hydrophillic_and_phobic/1'>Hydrophillic and Hydrophobic Residues</scene> allows one to see the general patterns of arrangement relative to each other. | ||
The hydrophillic residues often find themselves in interactions with the <scene name='Sandbox_47/Adenylate_kinase_water/1'>water</scene> | The hydrophillic residues often find themselves in interactions with the <scene name='Sandbox_47/Adenylate_kinase_water/1'>water</scene> that is solvating the enzyme. Water surrounds the outer surface of the protein, which is to be expected, but it is also possible to see that water molecules have interactions in some of the deeper parts of the protein as well, especially near the active site. | ||
that is solvating the enzyme. Water surrounds the outer surface of the protein, which is to be expected, but it is also possible to see that water molecules have interactions in some of the deeper parts of the protein as well, especially near the active site. | |||
Of course, the areas of the protein that interact with the substrates are the most interesting parts, so the <scene name='Sandbox_47/Ad_k_ligand_interaction/1'>ligand stabilizing residues</scene> are important to note. The residues of the active site are the most critical parts of the protein, because they actually do the chemical reactions of the enzyme. The <scene name='Sandbox_47/Ad_k_active_site/1'>active site</scene> residues are shown here. | Of course, the areas of the protein that interact with the substrates are the most interesting parts, so the <scene name='Sandbox_47/Ad_k_ligand_interaction/1'>ligand stabilizing residues</scene> are important to note. The residues of the active site are the most critical parts of the protein, because they actually do the chemical reactions of the enzyme. The <scene name='Sandbox_47/Ad_k_active_site/1'>active site</scene> residues are shown here. | ||
