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Sandbox 32

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<Structure load='1ake' size='500' frame='true' align='right' caption='Adenylate Kinase' scene='Insert optional scene name here' /><!-- PLEASE DO NOT DELETE THIS TEMPLATE -->
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=Trypsin=
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Trypsin is a medium size globular protein that functions as a pancreatic serine protease. Trypsin was first discovered in 1876 by Kuhne, who investigated the proteolytic activity of the enzyme.
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== '''Adenylate Kinase''' (PDB ID #: 1ake)==
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==Structure==
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The <scene name='Sandbox_32/N-c_rainbow/2'>pathway</scene> of the protein can be followed from N-terminus of the protein (blue) to the C-terminus of the protein (red).
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The <scene name='Sandbox_32/Chain_a/2'>A Chain</scene> by itself may be in a slightly different conformation than when it is <scene name='Sandbox_32/Both_chains/1'>attached</scene> to the B chain (as found in nature).
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Trypsin has many important structural aspects. The <applet scene='Sandbox_32/Secondary_structure/1' size='225' frame='true' align='true' align='right' caption='Trypsin protein with structural aspects shown.'/>secondary structures are shown this figure <scene name='Sandbox_32/Secondary_structure/1'>(Secondary Structure)</scene>. The main backbone of the trypsin protein is shown in yellow <scene name='Sandbox_32/Secondary_structure_main_chain/1'>(main backbone)</scene>. Trypsin has two alpha helices shown in blue <scene name='Sandbox_32/Secondary_structure_alpha/1'>(alpha helices)</scene> and two beta sheets shown in green <scene name='Sandbox_32/Secondary_structure_beta/1'>(beta Sheets)</scene>. The beta sheets in the Trypsin protein are antiparallel to each other and connected by a Beta-hairpin turn.
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==Polar vs. Nonpolar Residues==
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Adenylate Kinase contains both types of secondary structure, <scene name='Sandbox_32/Helices_sheets/2'>alpha helices and beta sheets</scene>. In this scene, alpha helices are in light blue and beta sheets are in yellow.
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This image shows the <scene name='Sandbox_32/Polar_versus_nonpolar/2'>polarity</scene> of the residues in the protein. The polar areas of the protein are shown in pink, while the non-polar areas of the molecule are shown in light blue. The polarity of the individual amino acid residues can be seen better in the <scene name='Sandbox_32/Polar_vs_non_stick/1'>stick model</scene>. The polar amino acid residues are again shown in pink, while the non-polar amino acid residues are shown in blue. By rotating the two representations of the polar versus non-polar areas of the protein to an aerial view, it can be seen that the polar (hydrophilic) areas are located toward the outside of the protein, while the non-polar (hydrophobic) areas are located toward the inside of the protein.
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The <scene name='Sandbox_32/H_bonds_2/1'>hydrogen bonding</scene> highlighted in this scene shows us that the secondary structure (helices and sheets) is held together by hydrogen bonds. The beta sheets appear to be parallel, as the H-bonds are not all aligned in one direction.
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<scene name='Sandbox_32/Hydrophobic_stickandwireframe/1'>Hydrophobic side chains</scene>, highlighted here in pink, tend to point towards the inside of the molecule where they do not have to interact with the polar water molecules.
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The <scene name='Sandbox_32/Hydrophilic/1'>hydrophilic side chains</scene>, highlighted here in blue along with the transparent pink hydrophobic residues, tend to be pointed towards the outside of the protein, where it will interact with the cytosol.
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<scene name='Sandbox_32/Water_ligand/3'>Water molecules</scene> (shown in blue) surround and solvate the protein. The ligand is highlighted in green. The waters seem to congregated on one side than the other, possibly to make room for chain B to bind.
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Sidechain and ligand <scene name='Sandbox_32/Sidechain_ligand_interaction/2'>interactions</scene> are shown in this scene. The ligand is in orange, and the interacting side chains are in dark blue and red. Of these contacting residues, only some actually catalyze the reaction on the substrate. These <scene name='Sandbox_32/Active_site_2/1'>active site</scene> residues are highlighted in red. These are the residues which interact chemically with the substrate to turn it into product. The non-active site residues are important in substrate (or ligand) binding.

Current revision

Adenylate Kinase

Drag the structure with the mouse to rotate
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 (PDB ID #: 1ake)

The by itself may be in a slightly different conformation than when it is to the B chain (as found in nature).

Adenylate Kinase contains both types of secondary structure, . In this scene, alpha helices are in light blue and beta sheets are in yellow.

The highlighted in this scene shows us that the secondary structure (helices and sheets) is held together by hydrogen bonds. The beta sheets appear to be parallel, as the H-bonds are not all aligned in one direction.

, highlighted here in pink, tend to point towards the inside of the molecule where they do not have to interact with the polar water molecules.

The , highlighted here in blue along with the transparent pink hydrophobic residues, tend to be pointed towards the outside of the protein, where it will interact with the cytosol.

(shown in blue) surround and solvate the protein. The ligand is highlighted in green. The waters seem to congregated on one side than the other, possibly to make room for chain B to bind.

Sidechain and ligand are shown in this scene. The ligand is in orange, and the interacting side chains are in dark blue and red. Of these contacting residues, only some actually catalyze the reaction on the substrate. These residues are highlighted in red. These are the residues which interact chemically with the substrate to turn it into product. The non-active site residues are important in substrate (or ligand) binding.

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