JMS/sandbox9

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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'>
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== Extraordinary Proteins ==
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'''Extraordinary Proteins'''
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<br/>
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By adapting their proteins, organisms have managed to colonize extraordinary environments. "Extreme" proteins demonstrate many intriguing biophysical features neccessary for living in harsh environments.
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Life - DNA, Proteins, physiology, behavior, and all - has managed to weather extreme environments - almost every hole we've poked a stick into contains thriving living communities. Proteins are a necessity for living, and therefore guarding - or more accurately put, "tuning" - their structures to an extreme environment is of paramount value to an evolving organism seeking an extraordinary niche. In this article we'll present the biophysical strategies apparent from some extreme protein structures.
 
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== Salty conditions can be overcome with extra negative surface charge density ==
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----
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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 (see an interesting ''Scientific American'' article about life in the Dead Sea [http://blogs.scientificamerican.com/artful-amoeba/2011/10/09/fountains-of-life-found-at-the-bottom-of-the-dead-sea/]). The problem for its proteins is staying soluble in both solvents. In 2005, Professors Sussman and Zamir from the Weizmann Institute reported the first crystal structure for such a protein - a <scene name='JMS/sandbox9/Carbonic_anhydrase/1'>halotolerant carbonic anhydrase</scene>([[1y7w]]) - and suggest that the protein's relative increase of negative surface charge density turns the protein into a anion-like molecule capable of dissolving in high salt. However, unlike the <scene name='Extremophile/1hlp_secondary/2'>halophilic malate/lactate dehydrogenase</scene> from ''Haloarcula marismortui'' which Profs. Sussman and Maverach (Tel Aviv University) crystallized earlier, the negative surface charge is not so high that the protein becomes insoluble in lower salt concentrations. The three-way comparison between the salt-adapting properties of a mesophilic, halotolerant, and halophilic enzyme illuminates a biophysical strategy for tuning protein structures to extreme salt conditions.
 
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In the list below, the increasing negative charge density on the surface is apparent. Notice also that while the halotolerant enzyme only switches positive amino acids to neutral, the halophilic enzyme also switches neutral amino acids to become negative.
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'''Well-tuned surface charges enable solubility in a broad range of salt conditions'''
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<br/>
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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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* <scene name='JMS/sandbox9/1raz/1'>''mesophilic'' carbonic anhydrase with "normal" amount of positively- and negatively-charged regions</scene> [[1raz]]
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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''.
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* <scene name='JMS/sandbox9/1y7w/1'>''halotolerant'' carbonic anhydrase with less positively-charged regions but normal amount of positively-charged regions</scene> [[1y7w]]
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* <scene name='JMS/sandbox9/Mesophile_dehydrogenase/2'>''mesophilic'' malate/lactate dehydrogenase with "normal" amount of positively- and negatively-charged regions</scene>[[1ldm]]
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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.
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* <scene name='JMS/sandbox9/1hlp/1'>''halophilic'' malate/lactate dehydrogenase with less positively-charged regions and more positively-charged regions</scene> [[1hlp]]
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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.
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{|
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|<applet load='1raz.pdb' name='A' size='300' frame='true' align='right' caption='Mesophilic carbonic anhydrase' align='left' scene='JMS/sandbox9/1raz/5'/>
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|<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'/>
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|}
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In a nutshell, the problem of salty condition includes the problem of how to remain soluble; the general solution is to become anion-like through increasing the negative charge surface density; and the molecular implementation is through decreasing the relative amount of positively charged amino acids and/or increasing the relative amount of negatively charged amino acids.
 
{{Clear}}
{{Clear}}
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== High temperatures encourage using proline to lower entropy loss and between-chain ion-network bonding to increase enthalpy gain ==
 
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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℃, and makes a <scene name='JMS/sandbox5/Tbadh/1'>thermophilic alcohol dehydrogenase</scene> ([[1ykf]]) that maintains its structure in over 83℃. Professors Yigal Burstein (Weizmann Institute) and Felix Frolow (Tel Aviv University) identified two contributing factors to this enzymes thermal prowess. Firstly, he found the thermophilic enzyme had a unique <scene name='JMS/sandbox5/Ion_network/4'>four amino acid binding-network</scene> that encompassed two monomers of the tetrameric enzyme, repeating between each monomer and its two partner monomers. This network apparently makes the oligomer more stable. Secondly, the thermophilic enzyme was <scene name='JMS/sandbox5/Proline/2'>enriched for proline</scene>. Because proline's side chain has minimal degree of freedom, proline's, unlike other amino acids, are minimally restricted by folding. There is therefore a smaller loss of entropy upon folding into the native structure.
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{|
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|<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'/>
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|<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'/>
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|}
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{{Clear}}
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<!--
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'''High temperatures encourage using proline to lower entropy loss'''
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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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Professors Yigal Burstein (Weizmann Institute) and Felix Frolow (Tel Aviv University) studied a<scene name='JMS/sandbox5/Tbadh/1'>thermophilic alcohol dehydrogenase</scene> ([[1ykf]]) from ''T. brockii'' that maintains its structure in over 83℃.
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They identified that the hyperthermophilic enzyme was <scene name='JMS/sandbox5/Proline/2'>enriched for proline</scene> in position 275, as was the thermophilic enzyme in position 100. Because proline's side chain has minimal degree of freedom, proline's, unlike other amino acids, are minimally restricted by folding. There is therefore a smaller loss of entropy upon folding into the native structure.
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<scene name='JMS/sandbox9/Tbadh/1'>TextToBeDisplayed</scene>
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<scene name='JMS/sandbox9/Ehadh1/1'>TextToBeDisplayed</scene>
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<scene name='JMS/sandbox9/Cbadh/1'>TextToBeDisplayed</scene>
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//-->
</StructureSection>
</StructureSection>

Current revision

halophilic enzyme (PDB entry 1hlp)

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Proteopedia Page Contributors and Editors (what is this?)

Joseph M. Steinberger

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