Sandbox SouthUniversity1: Difference between revisions

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'''Turn off''' (toggle) '''spinning''' of the protein by clicking on the button below the structure. The quality of the molecule rendering can also be increased by clicking the '''"toggle quality"''' button, although this may decrease the smoothness when the molecule is rotating.
'''Turn off''' (toggle) '''spinning''' of the protein by clicking on the button below the structure. The quality of the molecule rendering can also be increased by clicking the '''"toggle quality"''' button, although this may decrease the smoothness when the molecule is rotating.


Now '''rotate''' the molecule by clicking and dragging in the window with your cursor. '''Resize''' the molecule by holding down the shift key and dragging up and down. Rotate and resize the molecule until you can clearly see that there are 2 molecules shown in a "space-filling" representation in the middle of the protein (they are more or less perpendicular to each other). These are a heme molecule, which is absolutely vital for the enzyme's function, and a second molecule (alpha-naphthoflavone) which represents a compound that is about to be metabolized.
Now '''rotate''' the molecule by clicking and dragging in the window with your cursor or using the scroll wheel on your mouse. '''Resize''' the molecule by holding down the shift key and dragging up and down. Rotate and resize the molecule until you can clearly see that there are 2 molecules shown in a "space-filling" representation in the middle of the protein (they are more or less perpendicular to each other, and almost touching). These are a heme molecule, which is absolutely vital for the enzyme's function, and a second molecule (alpha-naphthoflavone) which represents a compound that is about to be metabolized.


First, lets look at the heme. Click the following link to hide the rest of the protein and <scene name='Sandbox_SouthUniversity1/Heme_only/1'>highlight the heme ring system.</scene> Carbon atoms are shown in grey, Nitrogen atoms are blue, Oxygen is red, and the central iron atom is orange. The iron atom is a vital center for oxidation of substrates (drugs or other xenobiotics). It is shown <scene name='Sandbox_SouthUniversity1/Heme_sticks_fe_ball/1'>here,</scene> with the protein strands displayed partially transparent to highlight the heme ring system and iron atom.
First, lets look at the heme. Click the following link to hide the rest of the protein and <scene name='Sandbox_SouthUniversity1/Heme_only/1'>highlight the heme ring system.</scene> Carbon atoms are shown in grey, Nitrogen atoms are blue, Oxygen is red, and the central iron atom is orange. The iron atom is a vital center for oxidation of substrates (drugs or other xenobiotics). It is shown <scene name='Sandbox_SouthUniversity1/Heme_sticks_fe_ball/1'>here,</scene> with the protein strands displayed partially transparent to highlight the heme ring system and iron atom.


Now look at the substrate molecule being oxidized and view its orientation relative to the heme group by clicking <scene name='Sandbox_SouthUniversity1/Heme_and_flavone/3'>this link</scene> Resize and rotate the molecules until you can see how the two molecules are oriented in relationship to each other.  
Now look at the substrate molecule being oxidized and view its orientation relative to the heme group by clicking <scene name='Sandbox_SouthUniversity1/Heme_and_flavone/3'>this link</scene> Resize and rotate the molecules until you can see how the two molecules are oriented in relationship to each other. The flavone is metabolized (oxidized) by introduction of a hydroxy group onto the phenyl ring that is attached to the tricyclic ring system. Note particularly the distance and orientation of the heme iron and the phenyl group.
 
 
Purely based on the distance between the pheny ring of the flavone substrate and the heme iron, oxidation might be expected to take place at the 4 (para) position. However, other factors also help determine the regioselectivity of the metabolism (selectivity for oxidation at the different possible positions). One of these factors is the relative reactivity of the various positions on the substrate.
 
 
The '''substrate''' (flavone) shown here is different from many other substrates of this CYP. Besides being a substrate of CYP1A2, it is also an '''inhibitor'''. It inhibits the metabolism of other CYP1A2 substrates because it binds very tightly to this enzyme. Thus, while the CYP is bound, it is unavailable to metabolize other substrates (e.g. drugs). Therefor, if a drug were coadministered with this compound, it might not be broken down to the extent expected, and could build up to toxic levels.
 
The reason that this flavone is bound so tightly to the enzyme is that it's shape and electronic charge are complementary to the binding pocket. This is examined <scene name='Sandbox_SouthUniversity1/2hi4_blue_transparent_ribbons/1'>next.</scene>
 
First examine the shape of the VDW area <scene name='Sandbox_SouthUniversity1/2hi4_bl_transp_rib_flav_vdw/1'>around the flavone.</scene> The reddish areas show places where there are particularly close contacts with the binding pocket. These contacts can be caused by ionic, hydrophobic, or hydrogen bonding. Now we will examine what exactly is responsible for the tight binding.
 
Lets remove the rest of the protein, so we can better see these interactions.
 
First examine the shape of the <scene name='Sandbox_SouthUniversity1/2hi4_bl_transp_ribbon_flav_spc/1'>flavone </scene>bound to the protein.
Next, the Van derWaals surface of the cavity is  <scene name='Sandbox_SouthUniversity1/displayed./1'>TextToBeDisplayed</scene>
 
Different members of the CYP450 enzymes preferentially metabolize different xenobiotics. What features of a drug do you think might cause it to be metabolized by one CYP versus another?


The flavone is metabolized (oxidized) by introduction of a hydroxy group onto the phenyl ring that is attached to the tricyclic ring system.
</StructureSection>
</StructureSection>


<quiz display=simple>
{On what position(s) of the phenyl ring next to the heme might you expect this oxidation to take place?
|type="()"}
+ The para position.
|| This is a valid assumption, based solely on the orientation of the substrate relative to the heme.
- One of the meta positions.
|| This is a possibility, based solely on the orientation of the substrate relative to the heme. However, in this case other factors come into play, such as relative reactivity of the ortho, meta, and para positions.
- One of the ortho positions.
|| You would not expect this to be likely, based on the distance from the active iron center to either of the ortho positions.
</quiz>




<Draft Quiz>
<quiz display=simple>
<quiz display=simple>
{Where on the phenyl ring do you expect the oxidation to take place?
{Question
|type="[]"}
|type="()"}
- At the two (ortho) position.
+ The correct answer.
- At the three (meta) position.
|| Feedback for correct answer.
+ At the 4 (para) position.
- Distractor.
|| Feedback for distractor.
- Distractor.
|| Feedback for distractor.
- Distractor.
|| Feedback for distractor.
</quiz>
</quiz>


Purely based on the distance between the pheny ring of the flavone substrate and the heme iron, oxidation would be expected to take place at the 4 (para) position. However, other factors also help determine the regioselectivity of the metabolism (selectivity for oxidation at the different possible positions). One of these factors is the relative reactivity of the various positions on the substrate.


Different members of the CYP450 enzymes preferentially metabolize different xenobiotics. What features of a drug do you think might cause it to be metabolized by one CYP versus another?
Draft: <illustration of residues in active site>  
Draft: <illustration of residues in active site>  
Draft animation <scene name='Sandbox_SouthUniversity1/Act_residues_shown/1'>Highlighting residues around ligand</scene>
Draft animation <scene name='Sandbox_SouthUniversity1/Act_residues_shown/1'>Highlighting residues around ligand</scene>
Line 56: Line 83:
<scene name='Sandbox_SouthUniversity1/Act_residues_shown/1'>Highlighting residues around ligand</scene>
<scene name='Sandbox_SouthUniversity1/Act_residues_shown/1'>Highlighting residues around ligand</scene>


<quiz display=simple>
{Question
|type="()"}
+ The correct answer.
|| Feedback for correct answer.
- Distractor.
|| Feedback for distractor.
- Distractor.
|| Feedback for distractor.
- Distractor.
|| Feedback for distractor.
</quiz>




<Draft Quiz>
<quiz display=simple>
{Where on the phenyl ring do you expect the oxidation to take place?
|type="[]"}
- At the two (ortho) position.
- At the three (meta) position.
+ At the 4 (para) position.
</quiz>




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Arthur Cox
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