CHEM2052 Tutorial: Difference between revisions
No edit summary |
No edit summary |
||
| (6 intermediate revisions by 3 users not shown) | |||
| Line 16: | Line 16: | ||
This arrangement of amino acids is also called a '''charge relay system''' <ref>PMID: 7016210</ref>. | This arrangement of amino acids is also called a '''charge relay system''' <ref>PMID: 7016210</ref>. | ||
Now compare the active site residues of chymotrypsin to the <scene name='59/596400/Morph/ | Now compare the active site residues of chymotrypsin to the <scene name='59/596400/Morph/3'>trypsin catalytic triad and the elastase catalytic triad</scene> (<span style="color:lightblue;background-color:black;font-weight:bold;">trypsin is in light blue</span>, PDB code [[1aq7]] and <span style="color:pink;background-color:black;font-weight:bold;">elastase is in pink</span>, PDB code [[4est]]). <jmol><jmolButton><script>frame next</script><text>Click this button</text></jmolButton></jmol> to flip between structures. | ||
== '''Substrate Binding Pockets''' == | == '''Substrate Binding Pockets''' == | ||
The next links examine the binding pockets of each protein. The spacefilled residues have been color coded according to hydrophobicity (residues are indicated as: {{Template:ColorKey_Hydrophobic}} or {{Template:ColorKey_Polar}}, with <font color="FF0000">'''Aspartate'''</font> highlighted further ). | The next links examine the binding pockets of each protein. The spacefilled residues have been color coded according to hydrophobicity (residues are indicated as: {{Template:ColorKey_Hydrophobic}} or {{Template:ColorKey_Polar}}, with <font color="FF0000">'''Aspartate'''</font> highlighted further ). | ||
| Line 28: | Line 28: | ||
== '''Understanding the Mechanism''' == | == '''Understanding the Mechanism''' == | ||
==== '''Catalytic Mechanism''' ==== | ==== '''Catalytic Mechanism''' ==== | ||
The following animation describes the catalytic mechanism of chymotrypsin [http://www.sumanasinc.com/webcontent/animations/content/chymotrypsin.html]. <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/10'> | |||
This representation</scene> was designed to match the perspective given by those resources. To provide better orientation after this rotation, here are the <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/11'>binding pocket residues</scene> that were highlighted above. (Or you can <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/16'>label the catalytic triad and Gly193</scene>.) | This representation</scene> was designed to match the perspective given by those resources. To provide better orientation after this rotation, here are the <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/11'>binding pocket residues</scene> that were highlighted above. (Or you can <scene name='User:Amy_Kerzmann/Sandbox_5/New_chymotrypsin-triad/16'>label the catalytic triad and Gly193</scene>.) | ||