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> | ||
</td></tr></table> | |||
==Structure Tour== | ==Structure Tour== | ||
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===Background=== | ===Background=== | ||
The electrically conductive nanowires that extend from cells of ''Geobacter sulfurreducens'' have long been thought to be pili assembled from PilA protein. However, the evidence was indirect. Here, the structure of filaments of wild type ''Geobacter sulfurreducens'', confirmed to be electrically conductive, was determined by [[cryo-electron microscopy]] ([[6ef8]])<ref name="m3">PMID:30951668</ref>. Surprisingly, these nanowires are assembled from outer membrane cytochrome OmcS. These findings were confirmed a short time later ([[6nef]])<ref name="strauss">PMID:31925024</ref>. | The electrically conductive nanowires that extend from cells of ''Geobacter sulfurreducens'' have long been thought to be pili assembled from PilA protein. However, the evidence was indirect. Here, the structure of filaments of wild type ''Geobacter sulfurreducens'', confirmed to be electrically conductive, was determined by [[cryo-electron microscopy]] ([[6ef8]])<ref name="m3">PMID:30951668</ref>. Surprisingly, these nanowires are assembled from outer membrane cytochrome OmcS. These findings were confirmed a short time later ([[6nef]])<ref name="strauss">PMID:31925024</ref> by a group expressing alternative interpretations<ref>PMID:31608018</ref>. | ||
===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 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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<center>''References for the assertions below are cited in the journal publication<ref name="m3" />. | <center>''References for the assertions below are cited in the journal publication<ref name="m3" />. | ||
</center> | </center> | ||
Seamless micrometer-long polymerization of hundreds of cytochromes is without precedent, to the knowledge of the authors. The filaments whose structure was determined here were obtained from electrode-grown cells. However, fumarate-grown cells produced filaments with similar sinusoidal morphology. The purified OmcS filaments have morphology and power spectra similar to cell-attached filaments previously thought to be type IV pili. Direct current electrical conductivity of | Seamless micrometer-long polymerization of hundreds of cytochromes is without precedent, to the knowledge of the authors. The filaments whose structure was determined here were obtained from electrode-grown cells. However, fumarate-grown cells produced filaments with similar sinusoidal morphology. The purified OmcS filaments have morphology and power spectra similar to cell-attached filaments previously thought to be type IV pili. Direct current electrical conductivity of individual wild type ~4 nm OmcS filaments was confirmed, and was comparable to previously reported filament conductivity values. | ||
Cells with the ''omcS'' gene deleted (''ΔomcS'') produced thinner (~1.7 nm) filaments that were smooth (not sinusoidal) and had electrical conductivity >100-fold lower than the OmcS filaments. ''ΔomcS'' cells can produce electrically conductive biofilms, but that conductivity might well depend on filaments of OmcZ, whose expression is known to increase in ''ΔomcS'' cells. | Cells with the ''omcS'' gene deleted (''ΔomcS'') produced thinner (~1.7 nm) filaments that were smooth (not sinusoidal) and had electrical conductivity >100-fold lower than the OmcS filaments. ''ΔomcS'' cells can produce electrically conductive biofilms, but that conductivity might well depend on filaments of OmcZ, whose expression is known to increase in ''ΔomcS'' cells. | ||
Previous studies showed that PilA is required for export of OmcS. However, PilA was not found in the | Previous studies showed that PilA is required for export of OmcS. However, PilA was not found in the structure of the OmcS nanowires studied here. Thus, PilA appears to be required for production of OmcS nanowires, but not to be a structural component of those nanowires. | ||
</StructureSection> | </StructureSection> | ||
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<hr><br> | <hr> | ||
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==See Also== | ==See Also== | ||