Sandbox Reserved 782
From Proteopedia
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<Structure load='3ie7' size='500' frame='true' align='right' caption='Phosphofructokinase from Listeria' scene='Scene 1' /> | <Structure load='3ie7' size='500' frame='true' align='right' caption='Phosphofructokinase from Listeria' scene='Scene 1' /> | ||
==Phosphofructokinase== | ==Phosphofructokinase== | ||
| - | This is the <scene name='56/563194/Phosphofructokinase_scene_1/1'> | + | This is the enzyme <scene name='56/563194/Phosphofructokinase_scene_1/1'>Phosphofructokinase</scene>. This particular phosphofructokinase comes from the microbe Listeria innocua. At the center you can see that the phosphofructokinase is bound to a molecule of ATP. In addition, the three green balls represent the three Mg atoms, and the small grey and red group off to the side is the glycerol. |
| - | The | + | The majority of the phosphofructokinase structure is made up of <scene name='56/563194/Alpha_helices_and_beta_sheets/1'>alpha helices and beta sheets</scene>. The alpha helices are in yellow and the beta sheets are in grey. |
<scene name='56/563194/Phosphofructokinase_hbonds/1'>Hydrogen bonding</scene> is a very important part of protein structure shape and stability. The hydrogen bonds of phosphofructokinase are designated by the orange dotted lines throughout the structure. Phosphofructokinase contains both anti-parallel and parallel sheets, which are identified by parallel hydrogen bonds and angled hydrogen bonds respectively. | <scene name='56/563194/Phosphofructokinase_hbonds/1'>Hydrogen bonding</scene> is a very important part of protein structure shape and stability. The hydrogen bonds of phosphofructokinase are designated by the orange dotted lines throughout the structure. Phosphofructokinase contains both anti-parallel and parallel sheets, which are identified by parallel hydrogen bonds and angled hydrogen bonds respectively. | ||
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As previously mentioned, the hydrophobic interactions are critical in determining the protein structure. Here, the <scene name='56/563194/Solvent/1'>interactions with water</scene> show that the water molecules predominantly gather around the outside of the protein, which is where most of the hydrophilic residues lie. | As previously mentioned, the hydrophobic interactions are critical in determining the protein structure. Here, the <scene name='56/563194/Solvent/1'>interactions with water</scene> show that the water molecules predominantly gather around the outside of the protein, which is where most of the hydrophilic residues lie. | ||
| - | <scene name='56/563194/ | + | The active site of a protein is the part that binds with substrates to catalyze a given reaction. Looking at phosphofructokinase you can see that the <scene name='56/563194/Alternate_interactions/1'>proteins involved with ligand interactions</scene> are mostly polar residues. This would be expected because... |
| - | + | Taking a further look into the active site, One can see that phosphofructokinase contains <scene name='56/563194/Interactions_with_catalyst/1'>catalytic residues</scene>, represented in pink, in the heart of the active site. This particular placement of catalytic residues is to be expected because it allows the catalytic residues to have direct contact with the ligand, thus enabling the reaction to proceed at a faster rate via a catalytic mechanism. | |
| - | + | ||
| - | Taking a further look into the active site, One can see that phosphofructokinase contains <scene name='56/563194/Interactions_with_catalyst/1'>catalytic residues</scene>, represented in pink, in the heart of the active site. This placement | + | |
Revision as of 23:35, 13 October 2013
| This Sandbox is Reserved from Oct 10, 2013, through May 20, 2014 for use in the course "CHEM 410 Biochemistry 1 and 2" taught by Hanna Tims at the Messiah College. This reservation includes Sandbox Reserved 780 through Sandbox Reserved 807. |
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Phosphofructokinase
This is the enzyme . This particular phosphofructokinase comes from the microbe Listeria innocua. At the center you can see that the phosphofructokinase is bound to a molecule of ATP. In addition, the three green balls represent the three Mg atoms, and the small grey and red group off to the side is the glycerol.
The majority of the phosphofructokinase structure is made up of . The alpha helices are in yellow and the beta sheets are in grey.
is a very important part of protein structure shape and stability. The hydrogen bonds of phosphofructokinase are designated by the orange dotted lines throughout the structure. Phosphofructokinase contains both anti-parallel and parallel sheets, which are identified by parallel hydrogen bonds and angled hydrogen bonds respectively.
One of the most important determining factors of protein structure lies in hydrophobic interactions between the with the surrounding environment. The hydrophobic residues are designated with light green while the hydrophobic residues are shown in blue. As would be expected the majority of the hydrophobic residues are located at the center of the protein where they are shielded from the hydrophobic environment.
As previously mentioned, the hydrophobic interactions are critical in determining the protein structure. Here, the show that the water molecules predominantly gather around the outside of the protein, which is where most of the hydrophilic residues lie.
The active site of a protein is the part that binds with substrates to catalyze a given reaction. Looking at phosphofructokinase you can see that the are mostly polar residues. This would be expected because...
Taking a further look into the active site, One can see that phosphofructokinase contains , represented in pink, in the heart of the active site. This particular placement of catalytic residues is to be expected because it allows the catalytic residues to have direct contact with the ligand, thus enabling the reaction to proceed at a faster rate via a catalytic mechanism.
