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JMS/sandboxBarkai

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<StructureSection load='1mbn' size='350' side='right' caption='myoglobin - how the chain cradles the heme (PDB entry [[1mbn]])' scene='55/557585/Align_test/5'>
<StructureSection load='1mbn' size='350' side='right' caption='myoglobin - how the chain cradles the heme (PDB entry [[1mbn]])' scene='55/557585/Align_test/5'>
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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''. 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>.
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It comes down to <scene name='55/557585/Align_test/18'>eight divergent amino acids (elephant's amino acids in yellow halos, whale next to it, without halos)</scene>. Without these amino acids, myoglobin in both whale and elephants has a charge of ''+1''. With them, whale myoglobin has net charge of ''+4'', which is significantly higher than elephants' ''+2''. Importantly, all eight of these divergent amino acids are <scene name='52/523344/Elephantwhale/34'>surface residues</scene>.
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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'': (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> ).
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These eight can be visualized: (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> ).
</StructureSection>
</StructureSection>

Revision as of 14:46, 25 December 2013

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

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Joseph M. Steinberger

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