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.
IntroductionIntroduction
Adenylate kinase is an enzyme that catalyzes the following reaction: ATP+ AMP <-> ADP + ADP. This is a very useful reaction in the body, since it allows the body to maintain homeostasis of ATP, an energy source in the body, in the cells. Its unique structure allows it to bind the substrates or other non-hydrolysable ligands. The in chain A of adenylate kinase shows multiple .
Hydrogen BondingHydrogen Bonding
The within the structure of the protein can also be displayed in green. These can be seen within the alpha helicies, helping maintain the structure of the helix, and are also between beta sheets. These hydrogen bonds keep the protein in its native form and help prevent it from denaturing, although the hydrophobic effect plays the biggest role in protein structure. Most of the beta sheets are running parallel, as indicated by the crooked hydrogen bonds. They are crooked due to the position of the carbonyl oxygens and amide hydrogens in the structure. This formation is less stable than the straight, parallel hydrogen bonding of the antiparallel sheets.
Hydrophobic and Hydrophilic InteractionsHydrophobic and Hydrophilic Interactions
The on the structure can be seen in yellow sticks, revealing the distinct structural features, such as side-chains of those residues. Most of these hydrophobic residues are clustered in the center of the protein due to the hydrophobic effect created by the surrounding water molecules. are shown in purple here, and they are generally on the outside of the protein, shielding the hydrophobic residues. There are also around and inside the protein. Water helps stabilize the protein through the hydrophobic effect and also interacts/surrounds the binding site in the center of the protein.
Ligand BindingLigand Binding
The is able to bind to the protein through the polar, charged parts of the active site that are shown in red and blue (red being anionic and blue being cationic). The are also shown in green. These residues specifically react with the substrate, although a non-hydrolysable ligand can interact and prevent these residues from reacting with the substrates.
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