Sandbox 46

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<applet load='1QLQ' size='300' frame='true' align='right' caption='Trypsin' />
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<!-- PLEASE DO NOT DELETE THIS TEMPLATE -->
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{{Template:Oberholser_Sandbox_Reservation}}
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<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
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<Structure load='1AKE A' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Sandbox_46/1ake_main/2' />
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=Adenylate Kinase=
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<scene name='Sandbox_46/1ake_main/2'>Adenylate kinase</scene> is a enzyme that catalyzes the conversion of 2 units of ADP into a unit of ATP and a unit of AMP. It is because of this catalytic role that adenylate kinase is an important part of homeostasis. Consisting of only 211 amino acids, adenylate kinase is not that large of an enzyme, despite its vital role in metabolism.
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=Structure=
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=Trypsin=
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The <scene name='Sandbox_46/1ake_secondary/1'>secondary structure</scene> of adenylate kinase shows alpha helices (blue) and beta sheets (teal) surrounding the non-hydrolysable substrate analogue. The enzyme is comprised of 9 helices and 9 sheets constituting the secondary structure. As with any enzyme, the <scene name='Sandbox_46/1ake_hydrogen/1'>hydrogen bonds</scene> (May not load) between the residues of the peptide chains supply the final folded protein with structural stability which helps hold it in its folded configuration.
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Trypsin, a member of the serine protease family, is produced in the pancreas and found in the digestive tracks of vertebrates. To avoid pancreatic self-degradation, trypsin is synthesized as trypsinogen, a zymogen. Cleavage by enteropeptidase allows tryspin to enter its active form. As a serine protease, trypsin contains a serine residue in its active site.
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This secondary structure is oriented as such so that the <scene name='Sandbox_46/1ake_phobicphilic/2'>hydrophobic and hydrophilic residues</scene> are buried or exposed depending on their individual properties. The hydrophobic, represented in grey, are buried as to avoid as much contact with water as possible. Similarly, the hydrophilic, or polar, residues are colored purple and exposed as much to water as possible. This is further illustrated by the <scene name='Sandbox_46/1ake_water/1'>water solvation</scene> model, displaying water molecules as pink orbs and the enzyme as a translucent white. These hydrophobic interactions, burying of non polar residues and exposure of polar ones, is another main driving force conserving the tertiary structure of the enzyme.
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==Structure==
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The model of adenylate kinases shows displays the non-hydrolysable substrate as the ligand. The <scene name='Sandbox_46/1ake_ligandinteract/1'>residues interacting with the ligand</scene> are polar as the substrate is also highly negatively charged. The ligand can be seen in the active site of the enzyme, and shown in standard atomic coloring scheme. The <scene name='Sandbox_46/1ake_catalytic/1'>catalytic residues</scene> are the residues that directly interact with the ligand, and can be seen in yellow.
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The trypsin structure displayed is a mutant form isolated from a bovine pancreas. It contains 58 amino acid residues as well as an altered binding loop. To follow the primary structure (amino acid sequence) of Trypsin, click <scene name='Sandbox_46/Secondary_structure_tryp/2'>here.</scene> Begin at the N-terminus (blue) and move toward the C-terminus (red).
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The <scene name='Sandbox_46/Tryp_secondary_color/2'>secondary structure</scene> of Trypsin consists of two alpha helices (light green) and two beta sheets (peach).
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Hydrophobic interactions - mainly the hydrophobic collapse - significantly contribute to both secondary and tertiary structure. This <scene name='Sandbox_46/Polar_vs_nonpolar_wire/1'>structure</scene> shows that the majority of the residues are non-polar/hydrophobic (maroon). These residues tend to congregate on the interior of the structure while polar/hydrophilic residues (blue) remain on the exterior. This orientation allows polar molecules to maximize interaction with water and other polar molecules while non-polar molecules minimize such interactions. Adding water molecules to the model, the <scene name='Sandbox_46/Polar_vs_nonpolar/1'>polar/non-polar</scene> interactions can be seen.
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===Stability===
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<scene name='Sandbox_46/Disulfide_bonds/3'>Disulfide</scene>
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<scene name='Sandbox_46/Disulfide_bonds_123/1'>DS bonds labeled</scene>
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<scene name='Sandbox_46/Hbonds_backbone/1'>H bonds backbone</scene>
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<scene name='Sandbox_46/H_bonds_r_groups/1'>H bonds r groups</scene>
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The yellow and red molecules represent SO4 (2-) moieties which are not part of the traditional trypsin structure; they were added during crystallization to freeze Trypsin in a specific conformation. '''Fix THIS. they bind at active site'''
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==Function==
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The reaction catalysed by Enteropeptidase:
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trypsinogen → trypsin + hexapeptide
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Val--(Asp)4--Lys--Ile--Val~ (trypsinogen) → Val--(Asp)4--Lys (hexapeptide) + Ile--Val~ (trypsin)
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Enteropeptidase cleaves after Lysine if the Lys is preceded by four Asp and not followed by a Pro.
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'''Source''' ^ "Enterokinase, light chain (P8070), Proteases, NEB". http://www.neb.com/nebecomm/products/productP8070.asp.
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Retrieved 2007-10-04.
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<scene name='Sandbox_46/Ac1/1'>Active Site 1</scene>
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<scene name='Sandbox_46/Ac2/1'>Active Site 2</scene>
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<scene name='Sandbox_46/Ac3/1'>Active Site 3</scene>
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<scene name='Sandbox_46/Ac4/1'>Active Site 4</scene>
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<scene name='Sandbox_46/Ac_all/1'>All active sites</scene> '''Shared active site'''
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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

Adenylate Kinase

is a enzyme that catalyzes the conversion of 2 units of ADP into a unit of ATP and a unit of AMP. It is because of this catalytic role that adenylate kinase is an important part of homeostasis. Consisting of only 211 amino acids, adenylate kinase is not that large of an enzyme, despite its vital role in metabolism.

Structure

The of adenylate kinase shows alpha helices (blue) and beta sheets (teal) surrounding the non-hydrolysable substrate analogue. The enzyme is comprised of 9 helices and 9 sheets constituting the secondary structure. As with any enzyme, the (May not load) between the residues of the peptide chains supply the final folded protein with structural stability which helps hold it in its folded configuration.

This secondary structure is oriented as such so that the are buried or exposed depending on their individual properties. The hydrophobic, represented in grey, are buried as to avoid as much contact with water as possible. Similarly, the hydrophilic, or polar, residues are colored purple and exposed as much to water as possible. This is further illustrated by the model, displaying water molecules as pink orbs and the enzyme as a translucent white. These hydrophobic interactions, burying of non polar residues and exposure of polar ones, is another main driving force conserving the tertiary structure of the enzyme.

The model of adenylate kinases shows displays the non-hydrolysable substrate as the ligand. The are polar as the substrate is also highly negatively charged. The ligand can be seen in the active site of the enzyme, and shown in standard atomic coloring scheme. The are the residues that directly interact with the ligand, and can be seen in yellow.

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_46"
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