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| | {{Template:Oberholser_Sandbox_Reservation}} | | {{Template:Oberholser_Sandbox_Reservation}} |
| | <!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | | <!-- PLEASE ADD YOUR CONTENT BELOW HERE --> |
| | + | <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''' ==
| + | 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. |
| - | 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. | + | 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' /> | + | The <scene name='Sandbox_37/Matt_hydrophobic_good/1'>Hydrophobic Interactions</scene> are shown here in red. |
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| - | = Secondary Structure = | + | 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. | + | 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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| - | ===Disulfide Bonds=== | + | 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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| - | Found throughout the structure of lysozyme are <scene name='Sandbox_37/Disulfide_and_cys/1'>disulfide bonds </scene> which are labelled yellow and cysteine residues which are labelled blue. Seen here are 8 cysteine residues along with 4 disulfide bonds. The bonds are an integral part of the strucutre and stability of lysozyme.<ref>Disulfide Bonds. (n.d.). Harvard University- Personal Home Pages. Retrieved October 31, 2010, from http://http://beck2.med.harvard.edu/protein_folding/protein_folding.htm</ref>.
| + | 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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| - | ===Hydrogen Bonds===
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| - | <scene name='Sandbox_37/H_bonds/1'>Hydrogen bond</scene> interactions are seen in light blue (the yellow represents the disulfide bonds). Hydrogen bonding occurs between proton donors and acceptors of specific residues. In this way, hydrogen bonds greatly impact the overall structure and stability of the lysozyme molecule as a whole. | + | |
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| - | = Distribution of Polar and NonPolar residues =
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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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| - | = Ligand =
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| - | In biochemistry, a ligand is considered any substance which is able to bind to a biomolecule, in this case an enzyme, and form a complex which serves a biological purpose, in this case the hydrolysis of a glycosidic bond.
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| - | The ligand of lysozyme is thus N-acetylmuramic acid and N-acetylglucosamine which bind to the active site of lysozyme very specifically. Lysozyme is only capable of binding polysaccharide chains six sugars in length. The enzyme binds to the fourth sugar and distorts it into a a half chair conformation which results in the glycosidic bond becoming quite weak.
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| - | In the binding site of lysozyme are the residues glutamic acid 35 and aspartate 52.
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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 , 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.
