User:Nikhil Malvankar/Cytochrome nanowires: Difference between revisions

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[[Interactive_3D_Complement_in_Proteopedia|Interactive 3D Complement in Proteopedia]]

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Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers<ref name="m3" />.

Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers<ref name="m3" />.

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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]

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==Structure Tour==

===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>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===

<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>.

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</center>

The structure assigned by the authors is '''77% loops'''; Jmol objectively assigns '''82%''' loops. The authors assigned 10% alpha helices, 7% 310 helices, and 6% beta strands.

The OmcS structure determined by Filman ''et al.'' was very similar, with '''80%''' loops assigned by the authors (86% by Jmol), having only 3% beta strand but otherwise very similar. We compared OmcS with three other c-type multi-heme cytochrome crystal structures: [[1ofw]], [[3ucp]], and [[3ov0]] had 45%, 49%, and 60% loops respectively.

The OmcS structure determined by Filman ''et al.'' <ref name="strauss" />was very similar, with '''80%''' loops assigned by the authors (86% by Jmol), having only 3% beta strand but otherwise very similar. We compared OmcS with three other c-type multi-heme cytochrome crystal structures: [[1ofw]], [[3ucp]], and [[3ov0]] had 45%, 49%, and 60% loops respectively.

===Hemes===

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====Cysteine Anchors====

Each heme is covalently anchored to two cysteines, which form thioether bonds with the heme vinyl groups (opposite the heme carboxyls).

Each heme is <scene name='83/835223/Heme_cysteine/4'>covalently anchored to two cysteines</scene>, which form thioether bonds with the heme vinyl groups (opposite the heme carboxyls):

{{Template:ColorKey_Element_Fe}}.

12 '''CxxCH''' motifs in the [https://www.uniprot.org/uniprot/Q74A86#sequences OmcS sequence] anchor the 6 hemes within each OmcS chain.

====Histidine to Iron====

Each heme <scene name='83/835223/Histidine-iron/1'>iron atom is coordinated by two histidine sidechain nitrogens</scene>, in addition to the four heme nitrogens. The iron of heme 5 (the next to last heme at the carboxy end of the chain) is bound to His 332 from its own chain ('''Chain A'''), and '''His 16''' in the N-terminal "bulge" of the '''next protein chain''' ('''Chain B''') in the filament. This inter-chain histidine-iron bond is undoubtedly important in strengthening the monomer-monomer interfaces in the filament. The histidines bound to hemes 1, 2, 3, 4, and 6 are all in the same protein chain that contains those hemes.

===Salt Bridges===

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> ('''Chain A''', '''Chain B''',

{{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 NH3+ on Phe 1 forms a salt bridge with one carboxy of heme 2 (HEC503; 3.65 Å; not shown).

Each heme has close to zero net charge, since the two carboxyls are compenated by Fe++. About half of the heme carboxyls are on the surface, exposed to water (not shown). Several of the heme carboxyls form salt bridges with sidechains of arginine or lysine (not shown).

===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).

===Other Findings & Conclusions===

<center>''References for the assertions below are cited in the journal publication<ref name="m3" />.

</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 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.

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>

<hr>

<hr>

~~==Download==~~

~~===Animations for Powerpoint===~~

~~Click images to see them full size, or to download them.~~

*

==See Also==

@@ Line 1: / Line 1: @@
 [[Interactive_3D_Complement_in_Proteopedia|Interactive 3D Complement in Proteopedia]]<br>
+<table width="95%" border="0"><tr><td>
 {| align="left"
 |-
@@ Line 8: / Line 9: @@
 </imagemap>
 |}
-<!-- cannot get a blank line here so using a blank white image; for more about linked images like the one above see Molecular Workbench -->
+</td></tr><tr><td>
-[[Image:Blank-white-30x460px.png]]<br>
-<span style="font-size:160%"><b>Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers<ref name="m3" />.</b></span><br><br>
+<span style="font-size:160%"><b>Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers<ref name="m3" />.</b></span>
+</td></tr><tr><td>
 <span style="font-size:120%">
 Fengbin '''Wang''',
@@ Line 28: / Line 31: @@
 April 4, 2019. [http://doi.org/10.1016/j.cell.2019.03.029 doi:10.1016/j.cell.2019.03.029]
 </span>
+</td></tr></table>
 ==Structure Tour==
-<StructureSection size='[250,500]' side='right' caption='' scene='83/835223/Filament/1'>
+<StructureSection size='[250,500]' side='right' caption="Geobacter sulfurreducens outer membrane cytochrome S (OmcS) [[6ef8]]." scene='83/835223/Filament/1'>
 ===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>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===
+<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>.
@@ Line 50: / Line 55: @@
 </center>
 The structure assigned by the authors is '''77% loops'''; Jmol objectively assigns '''82%''' loops. The authors assigned 10% alpha helices, 7% 3<sub>10</sub> helices, and 6% beta strands.
-The OmcS structure determined by Filman ''et al.'' was very similar, with '''80%''' loops assigned by the authors (86% by Jmol), having only 3% beta strand but otherwise very similar. We compared OmcS with three other c-type multi-heme cytochrome crystal structures: [[1ofw]], [[3ucp]], and [[3ov0]] had 45%, 49%, and 60% loops respectively.
+The OmcS structure determined by Filman ''et al.'' <ref name="strauss" />was very similar, with '''80%''' loops assigned by the authors (86% by Jmol), having only 3% beta strand but otherwise very similar. We compared OmcS with three other c-type multi-heme cytochrome crystal structures: [[1ofw]], [[3ucp]], and [[3ov0]] had 45%, 49%, and 60% loops respectively.
 ===Hemes===
@@ Line 63: / Line 68: @@
 ====Cysteine Anchors====
-Each heme is covalently anchored to two cysteines, which form thioether bonds with the heme vinyl groups (opposite the heme carboxyls).
+Each heme is <scene name='83/835223/Heme_cysteine/4'>covalently anchored to two cysteines</scene>, which form thioether bonds with the heme vinyl groups (opposite the heme carboxyls):
+{{Template:ColorKey_Element_C}}
+{{Template:ColorKey_Element_O}}
+{{Template:ColorKey_Element_N}}
+{{Template:ColorKey_Element_S}}
+{{Template:ColorKey_Element_Fe}}.
+'''CxxCH''' motifs in the [https://www.uniprot.org/uniprot/Q74A86#sequences OmcS sequence] anchor the 6 hemes within each OmcS chain.
+====Histidine to Iron====
+Each heme <scene name='83/835223/Histidine-iron/1'>iron atom is coordinated by two histidine sidechain nitrogens</scene>, in addition to the four heme nitrogens. The iron of heme 5 (the next to last heme at the carboxy end of the chain) is bound to His 332 from its own chain (<font color="#6070cf">'''Chain A'''</font>), and '''His 16''' in the N-terminal "bulge" of the '''next protein chain''' (<font color="#40af58">'''Chain B'''</font>) in the filament. This inter-chain histidine-iron bond is undoubtedly important in strengthening the monomer-monomer interfaces in the filament. The histidines bound to hemes 1, 2, 3, 4, and 6 are all in the same protein chain that contains those hemes.
+===Salt Bridges===
+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).
+Each heme has close to zero net charge, since the two carboxyls are compenated by Fe<sup>++</sup>. About half of the heme carboxyls are on the surface, exposed to water (not shown). Several of the heme carboxyls form salt bridges with sidechains of arginine or lysine (not shown).
+===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).
+===Other Findings & Conclusions===
+<center>''References for the assertions below are cited in the journal publication<ref name="m3" />.
+</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 individual wild type ~4 nm OmcS filaments was confirmed, and was comparable to previously reported filament conductivity values.
+Cells with the ''omcS'' gene deleted (''&Delta;omcS'') produced thinner (~1.7 nm) filaments that were smooth (not sinusoidal) and had electrical conductivity >100-fold lower than the OmcS filaments. ''&Delta;omcS'' cells can produce electrically conductive biofilms, but that conductivity might well depend on filaments of OmcZ, whose expression is known to increase in ''&Delta;omcS'' cells.
+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>
 <br>
-<hr><br>
+<hr>
+<br>
-==Download==
-===Animations for Powerpoint===
-Click images to see them full size, or to download them.
-*
 ==See Also==