Extremophile

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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.
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 condition can be overcome with extra negative surface charge density ==
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== 'Extreme Myoglobin' ==
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<StructureSection load='1mbn' size='350' side='right' caption='Structure of Myoglobin (PDB entry [[1mbn]])' scene='55/557585/Align_test/5'>
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The green alga ''Dunaliella salina'' lives in an environment where salt levels change swiftly and dramatically from low to high salt concentrations (see an interesting ''Scientific American'' article about life in the Dead Sea of Israel [http://blogs.scientificamerican.com/artful-amoeba/2011/10/09/fountains-of-life-found-at-the-bottom-of-the-dead-sea/]). The problem for its extra-cellular proteins is staying soluble in both solvents. Professors Sussman and Zamir from the Weizmann Institute report the first such protein crystal structure 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 halophilic enzyme 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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Myoglobin was the first solved protein structure and continues to be a classic in protein structure research, which has revealed much about protein dynamics, where myoglobin the protein breaths, if you will, as it changed conformations to take up oxygen and release it, in molecular imitation of our lungs movement. The <scene name='55/557585/Align_test/5'>classic myoglobin structure(default scene)</scene> was solved by John Kendrew in the mid-1900s. Myoglobin is a relatively small protein at 153(sometimes 154) amino acids, and immidiately one appreciates how the polypeptide <scene name='55/557585/Align_test/4'>chain folds over the heme ligand</scene>, cradling it between halves of the protein chain.
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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 (middle) switches positive amino acids to neutral, the halophilic enzyme (last), also switches neutral amino acids to become negative.
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Now, in a fascinating article<ref>DOI:10.1126/science.1234192</ref>, a team of researchers illuminate how behavior of animals across evolutionary time has been influenced by this <scene name='55/557585/Align_test/5'>classic protein</scene>. The researchers demonstrate that across the animal kingdom, aquatic animals have myoglobin protein with a great net positive charge than terrestrial animals. The calculate that for every increase in one positive net charge, the animal can accumulate a incredible additional ten times the amount of myoglobin in its cells (muscle cells, in fact), and for two more positive amino acids, the animal can actually accumulate 100 times more myoglobin. More myoglobin translates to more oxygen, which allows aquatic animals to hold their breath for long periods during dives underwater. While the exact mechanism is a fascinating area of ongoing research, it is apparent that myoglobin protein with a greater net positive charge remain soluble at much higher concentrations.
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* <scene name='JMS/sandbox7/1raz/2'>"Regular enzyme" with least negative charge</scene> [[1raz]]
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Here we see the whale and elephant myoglobin proteins aligned, with the elephant's amino acids in yellow halos. Without these divergent amino acids, the whole protein has a net charge. After summing the divergent amino acids in whales and elephant, where positive amino acids in blue have a charge value of +1, negative in red of -1, and histidine of +1/2, you'll see that whales overall have a net charge of +3.5, while elephants have only +1. Follow the protein from the beginning of the polypeptide chain until the end yourself, remembering that <scene name='55/557585/Align_test/18'>elephants are yellow and neutral</scene>.
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* <scene name='JMS/sandbox7/1y7w/3'>Halotolerant and more negative charge</scene> [[1y7w]]
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* <scene name='JMS/sandbox7/1hlp/4'>Halophilic with most negative charge</scene> [[1hlp]]
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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.
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Whether this effect is do to the overall charge of the protein, in repelling two strongly positive proteins; or, whether it is a more local effect, where two proteins cannot interact without unfavarobaly burying the positively charged amino acids; or whether the interactions between myoglobin and the other molecules in the cell, somehow affects its potential to bind to other myoglobins, again, awaits theoretical and experimental insight.
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{{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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[http://www.chem.utoronto.ca/coursenotes/GTM/JM/Mbstart.htm excellent myoglobin tutorial to complement proteopedia articles]
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Some bacteria and even animals can survive great temperatures. Studying <scene name='JMS/sandbox5/Tbadh/1'>a thermophilic enzyme</scene> ([[1ykf]]), Prof. Burstein noticed two special features that appear to explain this enzymes ability to maintain its structure in over 83℃ (!) For comparison, you could fry an egg at 65℃, which mean the protein in an egg denature at significantly less than 83℃. To demonstrate the special structural properties of the thermophilic enzyme underlies its thermophilic prowess, Prof Burstein selectively altered normal enzymes to have the two structural features, and indeed found that the normal enzymes had become thermophilic. The two properties relate to ∆H and to ∆S. 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, or ∆H more negative. 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. Therefore, ∆S is less negative.
 
</StructureSection>
</StructureSection>
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{{Reflist}}

Revision as of 19:38, 23 November 2013

halophilic enzyme (PDB entry 1hlp)

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  1. ↑ Mirceta S, Signore AV, Burns JM, Cossins AR, Campbell KL, Berenbrink M. Evolution of mammalian diving capacity traced by myoglobin net surface charge. Science. 2013 Jun 14;340(6138):1234192. doi: 10.1126/science.1234192. PMID:23766330 doi:http://dx.doi.org/10.1126/science.1234192
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