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''' | |
+ | <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. | ||
- | Organisms have managed to colonize extraordinary environments, but without proteins, living doesn't happen. "Extreme" proteins demonstrate many intriguing biophysical features neccessary for living in harsh environments. | ||
- | + | ---- | |
+ | |||
+ | '''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. | ||
- | In 2005, | + | In 2005, scientists from the Weizmann Institute reported the first crystal structure of a halotolerant enzyme, from ''D. salina'', a <scene name='JMS/sandbox9/Carbonic_anhydrase/1'>carbonic anhydrase</scene> ([[1y7w]]). In 1995, they solved (together with scientists from Tel Aviv University) the first structure of a halophilic enzyme, a <scene name='Extremophile/1hlp_secondary/2'>malate/lactate dehydrogenase</scene> ([[1hlp]]) from ''Haloarcula marismortui''. |
- | They conclude that a general solution for remaining soluble in salty conditions | + | 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 is | + | 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. |
- | === A comparative representation of the three forms of DNA === | ||
- | ''Sources''<ref>http://203.129.231.23/indira/nacc/</ref> | ||
{| | {| | ||
- | |<applet load='1raz.pdb' name='A' size='300' frame='true' align='right' caption=' | + | |<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=' | + | |<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'/> |
- | + | ||
- | + | ||
|} | |} | ||
{{Clear}} | {{Clear}} | ||
- | <center> | ||
- | '''Synchronize the three applets showing A-, B- and Z-DNA 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> | ||
- | </center> | ||
- | { | + | {| |
+ | |<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='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}} | ||
- | + | ||
+ | <!-- | ||
+ | '''High temperatures encourage using proline to lower entropy loss''' | ||
Some bacteria and even animals can survive great temperatures. Eggs fry - meaning their proteins denature, at 65℃. But ''Thermoanearobacter brockii'', discovered in Yellowstone Park, continues to grow in 80℃. | Some bacteria and even animals can survive great temperatures. Eggs fry - meaning their proteins denature, at 65℃. But ''Thermoanearobacter brockii'', discovered in Yellowstone Park, continues to grow in 80℃. | ||
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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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