JMS/sandbox9
From Proteopedia
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<StructureSection load='1hlp' size='350' side='right' caption='halophilic enzyme (PDB entry [[1hlp]])' scene='Extremophile/1hlp_secondary/2'> | <StructureSection load='1hlp' size='350' side='right' caption='halophilic enzyme (PDB entry [[1hlp]])' scene='Extremophile/1hlp_secondary/2'> | ||
- | |||
'''Extraordinary Proteins''' | '''Extraordinary Proteins''' | ||
- | + | <br/> | |
+ | By adapting their proteins, organisms have managed to colonize extraordinary environments. "Extreme" proteins demonstrate many intriguing biophysical features neccessary for living in harsh environments. | ||
+ | |||
+ | |||
+ | ---- | ||
- | '''Well-tuned negative surface charge density enables solubility in a broad range of salt conditions''' | ||
+ | '''Well-tuned surface charges enable solubility in a broad range of salt conditions''' | ||
+ | <br/> | ||
The green alga ''Dunaliella salina'' lives in the Dead Sea of Israel where water currents can change its environment swiftly and dramatically from low to high salt concentrations. The problem for its proteins is staying soluble in both solvents. | The green alga ''Dunaliella salina'' lives in the Dead Sea of Israel where water currents can change its environment swiftly and dramatically from low to high salt concentrations. The problem for its proteins is staying soluble in both solvents. | ||
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They conclude that a general solution for remaining soluble in salty conditions is to become "anion-like" through increasing the negative charge surface density. Too little negative charge and the enzyme can only tolerate low salt conditions, too much negative charge and the enzyme can only stand high salt conditions, but the "right" amount of negative charge enables an enzyme to remain soluble in both low and high salt conditoins. | They conclude that a general solution for remaining soluble in salty conditions is to become "anion-like" through increasing the negative charge surface density. Too little negative charge and the enzyme can only tolerate low salt conditions, too much negative charge and the enzyme can only stand high salt conditions, but the "right" amount of negative charge enables an enzyme to remain soluble in both low and high salt conditoins. | ||
- | In the list below, notice how the negative surface charge density - the ratio of negative "redish" amino acids to positive "bluish" amino acids - is low for the mesophilic enzymes, high for the halophilic enzymes, and medium for the halotolerant enzyme. | + | In the list below, notice how the negative surface charge density - the ratio of negative "redish" amino acids to positive "bluish" amino acids - is low for the mesophilic enzymes, high for the halophilic enzymes, and medium for the halotolerant enzyme. These ratios are approximately ''1:1'' (negative to positive amino acids on the surface) for the mesophilic enzymes; ''3:1'' for the halophilic enzyme, and ''2:1'' for the halotolerant enzyme. |
{| | {| | ||
|<applet load='1raz.pdb' name='A' size='300' frame='true' align='right' caption='Mesophilic carbonic anhydrase' align='left' scene='JMS/sandbox9/1raz/5'/> | |<applet load='1raz.pdb' name='A' size='300' frame='true' align='right' caption='Mesophilic carbonic anhydrase' align='left' scene='JMS/sandbox9/1raz/5'/> | ||
|<applet load='1y7w.pdb' name='B' size='300' frame='true' align='right' caption='Halotolerant carbonic anhydrase. Notice this enzyme has fewer positive "blue" amino acids than its mesophilic counterpart' align='left' scene='JMS/sandbox9/1y7w/4'/> | |<applet load='1y7w.pdb' name='B' size='300' frame='true' align='right' caption='Halotolerant carbonic anhydrase. Notice this enzyme has fewer positive "blue" amino acids than its mesophilic counterpart' align='left' scene='JMS/sandbox9/1y7w/4'/> | ||
- | <!-- |<applet load='Z-DNA.pdb' name='Z' size='300' frame='true' align='right' caption='Z-DNA' align='left' scene='User:Adithya_Sagar/Sandbox_DNA/Z-dna/1'/> | ||
- | //--> | ||
|} | |} | ||
- | {{Clear}} | ||
- | |||
- | <!-- | ||
- | ''Synchronize the two figures by clicking the checkbox'' | ||
- | <jmol> | ||
- | <jmolCheckbox> | ||
- | <target>A</target> | ||
- | <scriptWhenChecked>set syncMouse ON;set syncScript OFF;sync jmolAppletB,jmolAppletZ; sync > "set syncMouse | ||
- | ON;set syncScript OFF"</scriptWhenChecked> | ||
- | <scriptWhenChecked> sync jmolAppletB,jmolAppletZ </scriptWhenChecked> | ||
- | <scriptWhenUnchecked> sync OFF</scriptWhenUnchecked> | ||
- | <text> Synchronize</text> | ||
- | </jmolCheckbox> | ||
- | </jmol> | ||
- | |||
- | //--> | ||
{{Clear}} | {{Clear}} | ||
{| | {| | ||
- | |<applet load='Ncbi.pdb' name=' | + | |<applet load='Ncbi.pdb' name='C' size='300' frame='true' align='right' caption='Mesophilic malate/lactate dehydrogenase' align='left' scene='JMS/sandbox9/1ldm_qua/3'/> |
- | |<applet load='4JCO.pdb' name=' | + | |<applet load='4JCO.pdb' name='D' size='300' frame='true' align='right' caption='Halophilic malate/lactate dehydrogenase. Notice this enzyme has both fewer positive "bluish" amino acids, as well as many more negative "redish" amino acids than its mesophilic counterpart' align='left' scene='JMS/sandbox9/1hlp_new/5'/> |
- | + | ||
- | //--> | ||
|} | |} | ||
{{Clear}} | {{Clear}} | ||
- | <!-- | ||
- | ''Synchronize the two figures by clicking the checkbox'' | ||
- | <jmol> | ||
- | <jmolCheckbox> | ||
- | <target>A</target> | ||
- | <scriptWhenChecked>set syncMouse ON;set syncScript OFF;sync jmolAppletB,jmolAppletZ; sync > "set syncMouse | ||
- | ON;set syncScript OFF"</scriptWhenChecked> | ||
- | <scriptWhenChecked> sync jmolAppletB,jmolAppletZ </scriptWhenChecked> | ||
- | <scriptWhenUnchecked> sync OFF</scriptWhenUnchecked> | ||
- | <text> Synchronize</text> | ||
- | </jmolCheckbox> | ||
- | </jmol> | ||
- | |||
- | {{Clear}} | ||
- | //--> | ||
<!-- | <!-- | ||
- | * <scene name='JMS/sandbox9/1raz/1'>''mesophilic'' carbonic anhydrase </scene> [[1raz]] | ||
- | * <scene name='JMS/sandbox9/1y7w/1'>''halotolerant'' carbonic anhydrase </scene> [[1y7w]] | ||
- | * <scene name='JMS/sandbox9/Mesophile_dehydrogenase/2'>''mesophilic'' malate/lactate dehydrogenase </scene>[[1ldm]] | ||
- | * <scene name='JMS/sandbox9/1hlp/1'>''halophilic'' malate/lactate dehydrogenase </scene> [[1hlp]] | ||
- | //--> | ||
- | {{Clear}} | ||
'''High temperatures encourage using proline to lower entropy loss''' | '''High temperatures encourage using proline to lower entropy loss''' | ||
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<scene name='JMS/sandbox9/Ehadh1/1'>TextToBeDisplayed</scene> | <scene name='JMS/sandbox9/Ehadh1/1'>TextToBeDisplayed</scene> | ||
<scene name='JMS/sandbox9/Cbadh/1'>TextToBeDisplayed</scene> | <scene name='JMS/sandbox9/Cbadh/1'>TextToBeDisplayed</scene> | ||
+ | //--> | ||
</StructureSection> | </StructureSection> |
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