Sandbox 33: Difference between revisions

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the helices are shown in hot pink and the beta sheets are shown in a purple, other features??  
the helices are shown in hot pink and the beta sheets are shown in a purple, other features??  


Adenylate Kinase is made up of 214 amino acids, and the backbone of the protein can be seen on the right in light blue surrounding the non-hydrolysable substrate analogue (red). The secondary_structure of the protein contains 12 alpha helices (yellow) and 7 beta sheets (green). This secondary structure is held together by hydrogen_bonds, which are anti-parallel between the beta sheets. This hydrogen bond network also assists in the flexibility of the enzyme.
[edit] Hydrophobic and Hydrophilic Residues


The hydrophobic_residues of ADK, seen in gray, is buried in the interior of the protein. While the hydrophilic_residues, all the charged and polar side chains (purple), are on the surface of the protein and exposed. The location of the residues depend on the solvent and the environment that the protein is found in. All the hydrophobic residues aggregate together, and bury themselves in the interior of the protein to minimize their contact with their environment. The hydrophilic residues, on the other hand, is exposed on the surface because the enzyme is in an hydrophilic environment. Although, most of the hydrophilic residues would be exposed, it is possible for some of the to be buried in the interior, but they would interact with each other be stabilized there. There are also hydrophilic residues in the active site of the enzyme, where the ligand binds, to help it enter so that the reaction can take place.




Revision as of 02:51, 19 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.

Adenylate Kinase

Drag the structure with the mouse to rotate

Adenylate Kinase

adenylate kinase Adenylate kinase (also known as 1AKE) is a phosphotransferase enzyme that catalyzes the interconversion of adenine nucleotides. Adenylate Kinase thus plays an important role in cellular metabolism. The images of Adenylate Kinase in this sandbox are from Yersinia Pestis, or yeast.


Secondary Structure

Adenylate Kinase the helices are shown in hot pink and the beta sheets are shown in a purple, other features??

Adenylate Kinase consists of 214 amino acids which form 12 alpha helices and 7 beta sheets. The secondary structure is held together by hydrogen bonds.


the helices are shown in hot pink and the beta sheets are shown in a purple, other features??



hbond In the text around your green link, make sure you talk about the hydrogen bonds. Seeing the hydrogen bonds on the beta sheets should also help you to decide if they are parallel or anti-parallel, and you should comment on that as well.

hydrophobic residues describe representation

hydrophilic residues describe representation polar and charged residues

Solvent

waters write something about where the waters are, and arent

waters of hydration ligand highlighted brown

Enzyme Activity

ligand contacts

When you add the green link to the top part of the page, make sure you say something about what kinds of side-chains interact with the non-hydrolysable substrate, and if that makes sense.


catalytic residues catalytic residues, check w/ dr tims to see if i have selected the rite ones

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