This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
Sandbox 34
From Proteopedia
| (117 intermediate revisions not shown.) | |||
| Line 3: | Line 3: | ||
<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | <!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | ||
| + | ==Introduction to Adenylate Kinase== | ||
| + | <Structure load='1ake' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Awesomeness' /> | ||
| + | <scene name='Sandbox_34/Adenylate_kinase/1'>Adenylate Kinase</scene> is a very important protein in many biological processes, especially monitoring metabolism. | ||
| + | Adenylate Kinase is made up of <scene name='Sandbox_34/Adenylate_kinase_colors/1'>9 beta sheets (light blue) and 9 alpha helices (dark blue).</scene> These are very important for the conformation and function of the enzyme. The beta sheets are parallel in the protein which puts extra strain on the <scene name='Sandbox_34/Adenylate_kinase_hbonds_yell/1'>hydrogen bonds (yellow)</scene> within the protein. That is why there appear to be angled in stead of straight (which is found in anti-parallel beta sheets). These bonds are also very important in that they help to hold the helices and sheets together. These hydrogen bonds are formed from interactions among the proteins many hydrogen containing residues. Without them the protein would unravel and denature. | ||
| + | The <scene name='Sandbox_34/Adenylate_kinasehydrophobic_go/3'>hydrophobic interactions (deep pink)</scene> also play a huge role in holding this protein together. These interactions are formed by the hydrophobic or non-polar residues of the proteins. | ||
| + | However, the hydrophobic interactions are not the only thing holding it together or helping to keep its conformation. There are also many <scene name='Sandbox_34/Adenylate_kinase_andpolarside/1'>polar and charged side groups (green)</scene> that help maintain the hydrophobic interactions and help stabilize the protein by interacting with one another. The interaction between the polar groups and the hydrophobic groups can be seen by the pink transparent hydrophobic groups and the green polar groups. | ||
| + | ==Structual Properties of Adenylate Kinase== | ||
| + | Proteins can be crystallized which can be very helpful for understanding the relative shape and sometimes functions of the protein. When proteins are crystallized they often have water molecules embedded in them because of how tightly and deep the water molecules can become wedged within the protein. The <scene name='Sandbox_34/Adenylate_kinase_water/1'>water molecule interactions (magenta)</scene> with the protein can be seen surrounding and inside some parts of the protein. The <scene name='Sandbox_34/Adenylate_kinase_h2o_interact/1'>hydrophilic (blue) and hydrophobic (green)</scene> parts of the protein act differently with the water molecules. As seen in the previous link, the hydrophilic parts interact with the water molecules while the hydrophobic parts of adenylate kinase stay away from them. Another view <scene name='Sandbox_34/Adenylate_kinase_waterextra/2'>here</scene> shows it transparently to better see the interactions. | ||
| - | == | + | Ligands on proteins vary greatly. The <scene name='Sandbox_34/Adenylate_kinase_ligand/1'>ligand and residue interactions</scene> of adenylate kinase are based on the non-hydrolysable ligand of the protein. The residues interacting with the ligand are polar and charged because this ligand is also polar and charged, it is therefore stabilized by the residues. Also the <scene name='Sandbox_34/Adenylate_kinase_activeresidue/1'>active site residues(yellow)</scene> are also interacting with the ligand. |
| - | + | ==Conclusion== | |
| - | + | Adenylate Kinase is a very cool and important protein. Many of the internal interactions of the protein, whether hydrophobic or hydrophilic, are very important for understanding the function of this protein. These interactions also help us to understand why the conformation of the protein is the shape that it is. These are all very important for understanding the protein and how to use it in biological studies and treatments. | |
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
| - | + | ||
Current revision
| 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. |
Introduction to Adenylate Kinase
|
is a very important protein in many biological processes, especially monitoring metabolism. Adenylate Kinase is made up of These are very important for the conformation and function of the enzyme. The beta sheets are parallel in the protein which puts extra strain on the within the protein. That is why there appear to be angled in stead of straight (which is found in anti-parallel beta sheets). These bonds are also very important in that they help to hold the helices and sheets together. These hydrogen bonds are formed from interactions among the proteins many hydrogen containing residues. Without them the protein would unravel and denature. The also play a huge role in holding this protein together. These interactions are formed by the hydrophobic or non-polar residues of the proteins. However, the hydrophobic interactions are not the only thing holding it together or helping to keep its conformation. There are also many that help maintain the hydrophobic interactions and help stabilize the protein by interacting with one another. The interaction between the polar groups and the hydrophobic groups can be seen by the pink transparent hydrophobic groups and the green polar groups.
Structual Properties of Adenylate Kinase
Proteins can be crystallized which can be very helpful for understanding the relative shape and sometimes functions of the protein. When proteins are crystallized they often have water molecules embedded in them because of how tightly and deep the water molecules can become wedged within the protein. The with the protein can be seen surrounding and inside some parts of the protein. The parts of the protein act differently with the water molecules. As seen in the previous link, the hydrophilic parts interact with the water molecules while the hydrophobic parts of adenylate kinase stay away from them. Another view shows it transparently to better see the interactions.
Ligands on proteins vary greatly. The of adenylate kinase are based on the non-hydrolysable ligand of the protein. The residues interacting with the ligand are polar and charged because this ligand is also polar and charged, it is therefore stabilized by the residues. Also the are also interacting with the ligand.
Conclusion
Adenylate Kinase is a very cool and important protein. Many of the internal interactions of the protein, whether hydrophobic or hydrophilic, are very important for understanding the function of this protein. These interactions also help us to understand why the conformation of the protein is the shape that it is. These are all very important for understanding the protein and how to use it in biological studies and treatments.
