User:Nikhil Malvankar/Cytochrome nanowires: Difference between revisions
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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). | ||
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=== | |||
In the [[6ef8]] structure for OmcS, the sidechains of Arg333, Arg344, and Arg375 are buried, and none have anions within 5 Å (not shown). The cationic sidechains of Arg333 and Arg344 touch each other (3.0 Å; not shown). These characteristics are confirmed in [[6nef]]. The presence of these cations deep within OmcS is reasonable, since proteins of this size have, on average, several buried charges<ref name="pace">PMID: 19164280</ref><ref name="kajander">PMID: 11080642</ref>. | |||
Revision as of 03:23, 14 February 2020
Interactive 3D Complement in Proteopedia
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Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers[1].
Fengbin Wang,
Yanqui Gu,
J. Patrick O'Brien,
Sophia M. Yi,
Sibel Ebru Yalcin,
Vishok Srikanth,
Cong Shen,
Dennis Vu,
Nicole L. Ing,
Allon I. Hochbaum,
Edward H. Egelman,
and
Nikhil S. Malvankar.
Cell 177:361-9,
April 4, 2019. doi:10.1016/j.cell.2019.03.029
Structure TourStructure Tour
BackgroundThe 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)[1]. Surprisingly, these nanowires are assembled from outer membrane cytochrome OmcS. These findings were confirmed a short time later (6nef)[2]. Nanowire StructureA 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 (). 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 .
The amino terminus forms a bulge that fits into the slightly concave carboxy-terminal face of the contacting subunit. OmcS StructureThe OmcS monomer has . Alpha Helices, 310 Helices, Beta Strands , Loops . 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. HemesEach OmcS monomer : C O N Fe. The hemes are arranged in parallel-displaced pairs. Each pair is orthogonal to the next pair. The , which likely contributes to the stability of the filament. More importantly, this produces a . This continuous chain of hemes is believed to be the basis of the electrical conductivity. Cysteine AnchorsEach heme is , which form thioether bonds with the heme vinyl groups (opposite the heme carboxyls): C O N S Fe. 12 CxxCH motifs in the OmcS sequence anchor the 6 hemes within each OmcS chain. Histidine to IronEach heme , 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 BridgesUsing 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. 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 CationsIn the 6ef8 structure for OmcS, the sidechains of Arg333, Arg344, and Arg375 are buried, and none have anions within 5 Å (not shown). The cationic sidechains of Arg333 and Arg344 touch each other (3.0 Å; not shown). These characteristics are confirmed in 6nef. The presence of these cations deep within OmcS is reasonable, since proteins of this size have, on average, several buried charges[3][4].
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See AlsoSee Also
- Malvankar: A list of all interactive 3D complements for publications from the Malvankar group.
Notes & ReferencesNotes & References
- ↑ 1.0 1.1 Wang F, Gu Y, O'Brien JP, Yi SM, Yalcin SE, Srikanth V, Shen C, Vu D, Ing NL, Hochbaum AI, Egelman EH, Malvankar NS. Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers. Cell. 2019 Apr 4;177(2):361-369.e10. doi: 10.1016/j.cell.2019.03.029. PMID:30951668 doi:http://dx.doi.org/10.1016/j.cell.2019.03.029
- ↑ Filman DJ, Marino SF, Ward JE, Yang L, Mester Z, Bullitt E, Lovley DR, Strauss M. Cryo-EM reveals the structural basis of long-range electron transport in a cytochrome-based bacterial nanowire. Commun Biol. 2019 Jun 19;2(1):219. doi: 10.1038/s42003-019-0448-9. PMID:31925024 doi:http://dx.doi.org/10.1038/s42003-019-0448-9
- ↑ Pace CN, Grimsley GR, Scholtz JM. Protein ionizable groups: pK values and their contribution to protein stability and solubility. J Biol Chem. 2009 May 15;284(20):13285-9. doi: 10.1074/jbc.R800080200. Epub 2009 , Jan 21. PMID:19164280 doi:http://dx.doi.org/10.1074/jbc.R800080200
- ↑ Kajander T, Kahn PC, Passila SH, Cohen DC, Lehtio L, Adolfsen W, Warwicker J, Schell U, Goldman A. Buried charged surface in proteins. Structure. 2000 Nov 15;8(11):1203-14. PMID:11080642