Sandbox 37

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<Structure load='1AKE' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Matt's Beautiful Protein' />
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The <scene name='Sandbox_37/Matt_adenylate_kinase_37/1'>Adenylate Kinase</scene> protein is shown here with alpha helices (cyan) and beta sheets (green) surrounding the non-hydrolysable substrate analogue (orange).
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== '''LYSOZYME''' ==
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The <scene name='Sandbox_37/Matt_helix_beta_colored/1'>Secondary Structure</scene> of the protein is shown here with alpha helices (green) and beta sheets (blue) highlighted appropriately.
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Lysozyme, pictured to the right, is an enzyme found commonly in saliva, tears, mucus, and even egg whites. This particular enzyme breaks down bonds of bacterial cell walls. Specifically, lysozyme serves to catalyze the hydrolysis of the Beta (1->4) glycosidic linkage which occurs between N-acetylmuramic acid and N-acetylglucosamine (NAG) of peptidoglycan. Lysozyme is also capable of hydrolyzing polyNAG which constitutes chitin, a major component of fungi cell walls as well as the exoskeletons of insects and crustaceans.
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The Lysozyme in egg white, specifically hen egg whites (HEW), is the most widely studied and hence the most widely understood species of the enzyme. The picture to the right reveals a HEW lysozyme's cartoon structure with the secondary structure in grey and the yellow being salt bridges throughout the molecule.
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The <scene name='Sandbox_37/Matt_hydrogen_bonds_good/1'>Hydrogen Bonds</scene> of chain A of the protein are highlighted in orange here.
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<applet load='3IJU' size='300' frame='true' align='right' caption='Insert caption here' />
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The <scene name='Sandbox_37/Matt_hydrophobic_good/1'>Hydrophobic Interactions</scene> are shown here in red.
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= Secondary Structure =
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The <scene name='Sandbox_37/Matt_hydrophilic_good/1'>Hydrophilic Interactions</scene> are shown here in black.
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The secondary structure of lysozyme consists of 5 beta pleated sheets along with 5 alpha helices. These structures are displayed as <scene name='Sandbox_37/1/1'>cartoon rockets</scene> (click link to view in Jmol) where the alpha helices are labelled pink and the beta pleated sheets are yellow. The two shortest cartoon rockets which should be yellow beta pleated sheets are labelled pink by the program when told to label different secondary structures differently. This is due to the fact that two of the beta pleated sheets are slightly abnormally shaped and thus can be confused for alpha helices.
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The <scene name='Sandbox_37/Matt_solvent/1'>Solvent</scene> , which is water, is shown here in red. Water's primary location is on the outer parts of the protein, or the hydrophilic regions.
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= Distribution of Polar and NonPolar residues =
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The side chains that interact with the <scene name='Sandbox_37/Matt_ligand/1'>ligand</scene> are shown here in crimson. The interactions occur with the hydrophobic side chains. The rest of the protein is faded blue.
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A distribution of polar vs nonpolar residues can be viewed <scene name='Sandbox_37/Polarblue_nonpolarred/1'>here</scene>. The residues on this backbone stucture of lysozyme are labelled blue if they are polar and red if they are nonpolar. By viewing this structure one is capable of seeing the overall dispersion of polar vs. nonpolar residues. Polar residues, which are hydrophillic, are generally found on the outside of a molecule so that they can interact with surrounding water molecules. This is much more apparent when viewing <scene name='Sandbox_37/Polarblue_nonpolarred2/1'>this</scene> structural format (blue again represents polar while red represents nonpolar residues. Lysozyme is slightly unique in its polar vs nonpolar residues in that, as is apparent in the structure just mentioned, there are still a large number of nonpolar residues towards the outside surface of the molecule. This is due to the fact that lysozyme is a relatively "open" molecule meaning that it is not tightly bound and thus does not hide all of its nonpolar residues with an outward polar residue shell.
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The <scene name='Sandbox_37/Matt_catalytic_residues/1'>catalytic residues</scene> of this protein are shown here in lime green.
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= Ligand =
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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.

Adenylate Kinase

Drag the structure with the mouse to rotate

The protein is shown here with alpha helices (cyan) and beta sheets (green) surrounding the non-hydrolysable substrate analogue (orange).

The of the protein is shown here with alpha helices (green) and beta sheets (blue) highlighted appropriately.

The of chain A of the protein are highlighted in orange here.

The are shown here in red.

The are shown here in black.

The , which is water, is shown here in red. Water's primary location is on the outer parts of the protein, or the hydrophilic regions.

The side chains that interact with the are shown here in crimson. The interactions occur with the hydrophobic side chains. The rest of the protein is faded blue.

The of this protein are shown here in lime green.

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