Extremophile

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*''note about illustration'': <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''.
*''note about illustration'': <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''.
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Considering that the proteins in the Protein Data Bank have net charges that tend to fall between -10 and +10<ref>doi: 10.1073/pnas.0402797101</ref> , it may seem surprising that an increase of just +2 results in such a huge increase in solubility. Consider though that many life processes, protein folding is a great example, exist in a near equilibrium state, where a relatively tiny change enthalpy or entropy (free energy together) can push the system to the other direction. In the case of solubility, where often the first dimer is neccessary to nucleate the subsequent aggregation, a small bias away from forming dimers may be sufficient to prevent nucleation of aggragation, and hence increase the molecule's solubility.
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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.
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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.
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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.
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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 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.
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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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Revision as of 12:06, 17 December 2013

myoglobin - how the chain cradles the heme (PDB entry 1mbn)

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  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. ↑ 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
  3. ↑ 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
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