User:Nikhil Malvankar/Cytochrome nanowires: Difference between revisions
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[[Interactive_3D_Complement_in_Proteopedia|Interactive 3D Complement in Proteopedia]]<br> | [[Interactive_3D_Complement_in_Proteopedia|Interactive 3D Complement in Proteopedia]]<br> | ||
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<span style="font-size:160%"><b>Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers<ref name="m3" />.</b></span>< | <span style="font-size:160%"><b>Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers<ref name="m3" />.</b></span> | ||
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<span style="font-size:120%"> | <span style="font-size:120%"> | ||
Fengbin '''Wang''', | Fengbin '''Wang''', | ||
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April 4, 2019. [http://doi.org/10.1016/j.cell.2019.03.029 doi:10.1016/j.cell.2019.03.029] | April 4, 2019. [http://doi.org/10.1016/j.cell.2019.03.029 doi:10.1016/j.cell.2019.03.029] | ||
</span> | </span> | ||
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==Structure Tour== | ==Structure Tour== | ||
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===Nanowire Structure=== | ===Nanowire Structure=== | ||
<center>{{Template:Green links zoom}}</center> | |||
A nanowire model composed of 7 OmcS protein chains, each shown a different color, was constructed from the 3.2-3.7 Å cryo-EM density (<scene name='83/835223/Filament/1'>restore initial scene</scene>). The filament is ~4 nm in diamater, and has a characteristic undulating or sinusoidal form with a wavelength (pitch) of ~20 nm. The OmcS monomers have 407 amino acids each. The <scene name='83/835223/Filament/4'>carboxy terminus of each monomer contacts the amino terminus of the next</scene>. | A nanowire model composed of 7 OmcS protein chains, each shown a different color, was constructed from the 3.2-3.7 Å cryo-EM density (<scene name='83/835223/Filament/1'>restore initial scene</scene>). The filament is ~4 nm in diamater, and has a characteristic undulating or sinusoidal form with a wavelength (pitch) of ~20 nm. The OmcS monomers have 407 amino acids each. The <scene name='83/835223/Filament/4'>carboxy terminus of each monomer contacts the amino terminus of the next</scene>. | ||
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===Salt Bridges=== | ===Salt Bridges=== | ||
Using a 4.0 Å cutoff, [[6ef8]] has 7 salt bridges between amino acid sidechains (not shown). One of these, Arg176 to Asp432, is between protein chains, further strengthening the interfaces between monomers in the filament. | Using a 4.0 Å cutoff, [[6ef8]] has 7 salt bridges between amino acid sidechains (not shown). One of these, <scene name='83/835223/Inter-chain_salt_bridge/2'>Arg176 to Asp432 (2.6 Å)</scene> (<font color="#6070cf">'''Chain A'''</font>, <font color="#40af58">'''Chain B'''</font>, | ||
{{Template:ColorKey_Element_O}}, | |||
{{Template:ColorKey_Element_N}}), | |||
is between protein chains, further strengthening the interfaces between monomers in the filament. (These opposing charges are 4.9 Å apart in [[6nef]].) | |||
The amino-terminal NH<sup>3</sup>+ on Phe 1 forms a salt bridge with one carboxy of heme 2 (HEC503; 3.65 Å; not shown). | The amino-terminal NH<sup>3</sup>+ on Phe 1 forms a salt bridge with one carboxy of heme 2 (HEC503; 3.65 Å; not shown). | ||
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===Buried Cations=== | ===Buried Cations=== | ||
The <scene name='83/835223/Buried_cations/1'>sidechain nitrogens of Arg333, Arg344, and Arg375 are buried</scene>. None have anions within 5 Å (not shown). The | The <scene name='83/835223/Buried_cations/1'>sidechain nitrogens of Arg333, Arg344, and Arg375 are buried</scene>. None have anions within 5 Å (not shown). The sidechain nitrogens of Arg333 and Arg344 touch each other (3.0 Å). These characteristics are confirmed in [[6nef]]. The presence of these cations deep within OmcS is plausible, since proteins of this size have, on average, several buried charges<ref name="pace">PMID: 19164280</ref><ref name="kajander">PMID: 11080642</ref>. Moreover, on average from many proteins, more than half of all arginine guanidiniums are buried<ref name="pace" />. Burying charge seems to be an important factor in how evolution regulates protein stability<ref name="pace" /><ref name="kajander" />. | ||
The buried contact between two usually-cationic sidechains of Arg333 and Arg344 is also plausible because, when buried, the positive charge of the guanidinium group can be greatly diminished due to dehydration and nearby positive charges<ref name="pace" />. Although hydrated guanidinium retains more than half of its charge when the pH is below ~12 (its intrinsic pKa<ref name="pace" />), dehydration due to burial decreases the pKa. Furthermore, the samples for cryo-electron microscopy were prepared at pH 10.5<ref name="m3" /> (despite the pH being incorrectly stated as 7.0 in REMARK 245 of the PDB file). | The buried contact between two usually-cationic sidechains of Arg333 and Arg344 is also plausible because, when buried, the positive charge of the guanidinium group can be greatly diminished due to dehydration and nearby positive charges<ref name="pace" />. Although hydrated guanidinium retains more than half of its charge when the pH is below ~12 (its intrinsic pKa<ref name="pace" />), dehydration due to burial decreases the pKa. Furthermore, the samples for cryo-electron microscopy were prepared at pH 10.5<ref name="m3" /> (despite the pH being incorrectly stated as 7.0 in REMARK 245 of the PDB file). | ||
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<hr><br> | <hr> | ||
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==See Also== | ==See Also== | ||