Extremophile

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (09:37, 2 February 2016) (edit) (undo)
 
(39 intermediate revisions not shown.)
Line 1: Line 1:
-
<StructureSection load='1mbn' size='350' side='right' caption='myoglobin - how the chain cradles the heme (PDB entry [[1mbn]])' scene='55/557585/Align_test/4'>
 
== Extraordinary Proteins ==
== Extraordinary Proteins ==
-
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 tuning protein 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 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 tuning protein structures to an extreme environment is of paramount value to an evolving organism. In this article, we present the biophysical modifications present in extreme protein structures.
-
== Positively charged myoglobin allows whales to hold their breaths during long dives ==
+
== Positively charged myoglobin allows whales to hold their breath during long dives ==
-
Whales and elephants are both large animals that take life slow - walking slow, singing slow.. But whales swim underwater while holding their breaths for long periods of time, and elephants can not: ''Why can whales hold their breaths for long, and elephants can not?'' One clue to this discrepancy is the difference in concentrations of <scene name='55/557585/Align_test/5'>myoglobin</scene> in whale and elephant muscle tissue: ''More myoglobin means more oxygen storage capacity'', and whales have over ''15 times'' the concentration of myoglobin as elephants do (''70 mg/g'' wet mass compared to the elephants ''4.6''). But this leads to a biophysical question.
+
Elephants can hold their breath for 2 minutes, but whales can hold their breath for 60 minutes - and they do, migrating underwater around the world. To get a clue as to why whales can hold their breath for so long, several researchers gathered tissue samples from hundreds of aquatic and terrestrial mammalian species (mainly from museum collections)<ref name="whaleMyo"> DOI:10.1126/science.1234192</ref>. They measured the concentration of [[myoglobin]], the protein that stores oxygen in muscle tissue, which is used for muscle activity, and also sequenced each specie's myoglobin gene, and used this sequence - as well as the protein's mobility on a native gel (which depends soley on the 3D structure and charge - with myoglobin from different species all having the same overall 3D structure), when possible - to calculate the net charge of each myoglobin protein.
-
A very high concentration of myoglobin should lead to aggregation, which would prevent myoglobin from functioning, so ''how do whales' myoglobin deal with this extreme demand, and why can't elephants' myoglobin accumulate to high concentrations as well?'' In a recent article in the journal Science<ref name="whaleMyo"> DOI:10.1126/science.1234192</ref>, the laboratories of Professors Berenbrink, Campbell, and Cossins demonstrate that ''natural variation in net positive charge explains aquatic and terrestrial animals' different diving abilities''. Following this pattern, whale myoglobin has a net charge ''two formal charges higher'' than in elephants: ''+4 compared to +2'' in the elephant. Apparently a protein's solubility is a function of its net charge<ref>PMID: 14741208 </ref>, where ''a protein with a higher net charge is much more soluble''.
+
Amazingly, they found that aquatic mammals, across the mammalian phylogeny, independently had acquired the ability to hold their breath, by increasing the concentration of myoglobin, via increasing the net charge of myoglobin. Typically, purified terrestrial mammal's myoglobin has a solubility of 20 mg/g in an aqueous solution at neutral pH ([[http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Product_Information_Sheet/2/m0630pis.pdf Sigma Aldrich]]) which turns out to be the maximum level of myoglobin found in most terrestrial mammal's tissue. But whales and other aquatic mammals far exceed this solubility limit, e.g., whales have 70 mg/g. The way that they overcome the solubility constraint may be traced back to a modest increase in the net charge of myoglobin - from around +2 in terrestrial animals to around +4 in aquatic animals.
-
It comes down to <scene name='55/557585/Align_test/18'>eight divergent amino acids (elephant's amino acids in yellow halos)</scene>. Without these amino acids, myoglobin in both whale and elephants has a charge of ''+1''. Calculate along the chain, in the N to C-terminal direction how just several amino acid switches bring the positive net charge of whale myoglobin up to ''+4'' and elephants to ''+2'': <scene name='52/523344/Elephantwhale/19'>residue position 8</scene>, <scene name='52/523344/Elephantwhale/21'>12</scene>, <scene name='52/523344/Elephantwhale/22'>27</scene>, <scene name='52/523344/Elephantwhale/23'>34</scene>, <scene name='52/523344/Elephantwhale/24'>87</scene>, <scene name='52/523344/Elephantwhale/26'>116</scene>, <scene name='52/523344/Elephantwhale/27'>132</scene>, <scene name='52/523344/Elephantwhale/28'>140</scene>.
+
However, a 3-fold increase in concentration of myoglobin ought to result in a similar fold increase in max time of breath holding, and the researchers show that body mass also makes a critical contribution to an animal's ability to hold its breath, with the overall equation for the contribution of body mass and myoglobin net charge as follows:
-
*<span style="color:red">'''Asp and Glu'''</span> have a charge of ''-1'', <span style="color:blue">'''Arg and Lys'''</span> have a charge of ''+1'', <span style="color:lightblue">'''His'''</span> in the positions shown here - ''12'' and ''116'' (Table S2<ref name="whaleMyo" />) - have a charge of about ''+0.5''.
+
-
<!--
+
log (maximum time underwater) = 0.223*log(body mass) + 0.972*log(myoglobin net charge) + 0.891
-
The <scene name='55/557585/Align_test/5'>classic myoglobin structure (default scene)</scene> was solved by John Kendrew in the mid-1900s,and continues to be a classic in protein structure research. Myoglobin is a relatively small protein at 153 (sometimes 154) amino acids. The polypeptide <scene name='55/557585/Align_test/4'>chain simply folds over the heme ligand</scene>, cradling it between halves of the protein chain. But myoglobin research has revealed that proteins are dynamic: myoglobin the protein "breaths" in molecular imitation of our lungs movement, as it changes conformations to take up oxygen and release it. This is one example among many, of the contributions myoglobin has made to the structural biology field of research.
+
-
Over half a century after the myoglobin structure was solved, in a fascinating article<ref>DOI:10.1126/science.1234192</ref>, a team of researchers illuminate how a 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 greater net positive charge than terrestrial animals. They 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 muscle cells, 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. The higher net charge prevent myoglobin from aggregating at high concentrations.
+
As Asian elephant's weight is ~3K Kg, and a sperm whale's weight is ~50K Kg, it is clear that the modest increase in net charge contributes about the same as the enormous difference in body mass to the maximum time underwater.
-
Here we see the whale and elephant myoglobin proteins aligned, with the <scene name='55/557585/Align_test/18'>elephant's amino acids in yellow halos</scene>. Without these divergent amino acids, the whole protein has a net charge. Following along the protein chain from end to end, and 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, we see that whales overall have a net charge of +3.5, while elephants have only +1.
+
<StructureSection load='1mbn' size='350' side='right' caption='myoglobin (PDB entry [[1mbn]])' scene='55/557585/Align_test/5'>
-
 
+
==Molecular Tour==
-
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 unfavorably 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.
+
The ability of increasing net charge to enable higher solubility is a known phenomenon<ref>doi: 10.1073/pnas.0402797101</ref>, and this study is consistent with previous reports<ref>PMID: 14741208 </ref>. The aquatic animals have increased their net charge in a variety of ways - different combinations of amino acids switches. We present one such manifestation of this overall trend, by comparing the elephant and whale myoglobin structures.
-
 
+
-
[http://www.chem.utoronto.ca/coursenotes/GTM/JM/Mbstart.htm excellent myoglobin tutorial to complement proteopedia articles]
+
It comes down to <scene name='55/557585/Align_test/18'>eight divergent amino acids (elephant's amino acids in yellow halos, and whale's amino acids without yellow halos, next to each other)</scene> that affect that charge - out of a total of 27 divergent amino acids. Without these eight differently charged amino acids, myoglobin in both whale and elephants has a charge of ''+1''. With them, whale myoglobin has a net charge of ''+4'' and elephants of ''+2''. Importantly, all eight of these divergent amino acids are <scene name='52/523344/Elephantwhale/34'>surface residues</scene>. It is interesting to note that in this comparison (between whale and elephant) that there is no difference in net charge in the region in the vicinity of the heme group. This may reflect the key role of the heme group and residues near it, which can not be easily changed without a drastic affect on function.
-
 
+
-
-->
+
Calculate along the chain, how just several amino acid switches bring the positive net charge of whale myoglobin up to ''+4'' and elephants to ''+2'': (summing up the total charge of the protein) <scene name='52/523344/Elephantwhale/19'>residue position 8</scene> (<span style="color:red">'''glu'''</span> in elephents versus gln in whales), <scene name='52/523344/Elephantwhale/21'>12</scene> (<span style="color:blue">'''lys'''</span> vs. <span style="color:lightblue">'''his'''</span>), <scene name='52/523344/Elephantwhale/22'>27</scene> (thr vs. <span style="color:red">'''asp'''</span>), <scene name='52/523344/Elephantwhale/23'>34</scene> (thr vs. <span style="color:blue">'''lys'''</span> ), <scene name='52/523344/Elephantwhale/24'>87</scene> (gln vs. <span style="color:blue">'''lys'''</span> ), <scene name='52/523344/Elephantwhale/26'>116</scene> (gln vs. <span style="color:lightblue">'''his'''</span>), <scene name='52/523344/Elephantwhale/27'>132</scene> (<span style="color:blue">'''lys'''</span> vs. asn), <scene name='52/523344/Elephantwhale/28'>140</scene> (asn vs. <span style="color:blue">'''lys'''</span> ).
 +
'''note about this scene''': <span style="color:red">'''Asp and Glu'''</span> have a charge of ''-1'', <span style="color:blue">'''Arg and Lys'''</span> have a charge of ''+1'', <span style="color:lightblue">'''His'''</span> in the positions shown here - ''12'' and ''116'' (Table S2<ref name="whaleMyo" />) - have a charge of about ''+0.5''.
</StructureSection>
</StructureSection>
{{Reflist}}
{{Reflist}}

Current revision

Extraordinary Proteins

Life 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 tuning protein structures to an extreme environment is of paramount value to an evolving organism. In this article, we present the biophysical modifications present in extreme protein structures.

Positively charged myoglobin allows whales to hold their breath during long dives

Elephants can hold their breath for 2 minutes, but whales can hold their breath for 60 minutes - and they do, migrating underwater around the world. To get a clue as to why whales can hold their breath for so long, several researchers gathered tissue samples from hundreds of aquatic and terrestrial mammalian species (mainly from museum collections)[1]. They measured the concentration of myoglobin, the protein that stores oxygen in muscle tissue, which is used for muscle activity, and also sequenced each specie's myoglobin gene, and used this sequence - as well as the protein's mobility on a native gel (which depends soley on the 3D structure and charge - with myoglobin from different species all having the same overall 3D structure), when possible - to calculate the net charge of each myoglobin protein.

Amazingly, they found that aquatic mammals, across the mammalian phylogeny, independently had acquired the ability to hold their breath, by increasing the concentration of myoglobin, via increasing the net charge of myoglobin. Typically, purified terrestrial mammal's myoglobin has a solubility of 20 mg/g in an aqueous solution at neutral pH ([Sigma Aldrich]) which turns out to be the maximum level of myoglobin found in most terrestrial mammal's tissue. But whales and other aquatic mammals far exceed this solubility limit, e.g., whales have 70 mg/g. The way that they overcome the solubility constraint may be traced back to a modest increase in the net charge of myoglobin - from around +2 in terrestrial animals to around +4 in aquatic animals.

However, a 3-fold increase in concentration of myoglobin ought to result in a similar fold increase in max time of breath holding, and the researchers show that body mass also makes a critical contribution to an animal's ability to hold its breath, with the overall equation for the contribution of body mass and myoglobin net charge as follows:

log (maximum time underwater) = 0.223*log(body mass) + 0.972*log(myoglobin net charge) + 0.891

As Asian elephant's weight is ~3K Kg, and a sperm whale's weight is ~50K Kg, it is clear that the modest increase in net charge contributes about the same as the enormous difference in body mass to the maximum time underwater.

myoglobin (PDB entry 1mbn)

Drag the structure with the mouse to rotate
  1. ↑ 1.0 1.1 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
  2. ↑ Brocchieri L. Environmental signatures in proteome properties. Proc Natl Acad Sci U S A. 2004 Jun 1;101(22):8257-8. Epub 2004 May 24. PMID:15159533 doi:http://dx.doi.org/10.1073/pnas.0402797101
  3. ↑ Goh CS, Lan N, Douglas SM, Wu B, Echols N, Smith A, Milburn D, Montelione GT, Zhao H, Gerstein M. Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis. J Mol Biol. 2004 Feb 6;336(1):115-30. PMID:14741208 doi:http://dx.doi.org/10.1016/S0022283603014748
Retrieved from "http://52.214.119.220/wiki/index.php/Extremophile"
Personal tools