Sandbox 47
From Proteopedia
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The <scene name='Sandbox_47/Ad_k_hydrophobic/3'>Hydrophobic Residues</scene> (gray) 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> (orange) 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> (gray) 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> (orange) 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> |
| - | (purple) 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. | + | (purple) 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. | ||
Revision as of 22:53, 20 October 2012
| Please do NOT make changes to this Sandbox. Sandboxes 30-60 are reserved for use by Biochemistry 410 & 412 at Messiah College taught by Dr. Hannah Tims during Fall 2012 and Spring 2013. |
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Introduction
Adenylate kinase has homologs in many species and is an enzyme that converts one ATP and one AMP into two ADP molecules. For simplicity this page will focus on the form found in the bacterium Yersinia pestis. It usually functions with two identical subunits, and chain B, but for simplicity it is easier to focus on one chain.
Structural Elements
Adenylate kinase has multiple units of , including alpha helices (blue) and beta sheets (red). The protein structure is held together with (green, not working). Looking at the hydrogen bonds demonstrates that the sheets are parallel in conformation, because the hydrogen bonds form trapezoids.
The (gray) of the protein's structure are primarily buried in the structure due to the hydrophobic effect. On the other hand, many of the (orange) 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 allows one to see the general patterns of arrangement relative to each other.
The hydrophillic residues often find themselves in interactions with the (purple) 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 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 residues are shown here.
Sources
http://www.proteopedia.org/wiki/index.php/Adenylate_kinase
Green Hydrogen Bonds demonstrate that the beta sheets are parallel.
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