Supramolecular Assemblies of C-Type Cytochromes Based on 3D Domain Swapping
Authors: Hirota Shun 
Published: February 2020

We have previously shown that horse cytochrome (cyt) c forms polymers from monomers by 3D domain swapping (herein domain swapping) its C-terminal α-helix successively (runaway domain swapping) [1]. The C-terminal α-helix of dimeric horse cyt c was displaced from its original position in the monomer, and the Met80–heme coordination was perturbed significantly in the dimer, causing higher cyanide ion binding affinity and peroxidase activity compared to those in the monomer.

Cyt c formed domain-swapped oligomers by the interaction between the N- and C-terminal α-helices at the early stage of folding from its unfolded state [2], and the interaction important for domain swapping was detected in the monomer molten globule state [3]. However, cyt c domain swapping occurred regardless of Met80 mutation to Ala, and the domain-swapped dimer stability was less affected by the Met80–heme coordination [4]. High-order domain-swapped oligomers of HT cyt c
552 were produced during E. coli culture, whereas the domain-swapped protein amount decreased when the protein stability was decreased by mutation, indicating that exceedingly stable proteins may have disadvantages forming domain-swapped oligomers in cells [5].

Cyt cb
562 also domain swapped and formed a dimer, where the two helices in the N-terminal region of one protomer interacted with the other two helices in the C-terminal region of the other protomer. In the crystal, three domain-swapped cyt cb
562 dimers formed a unique cage structure with a Zn-SO4 cluster inside the cavity [6]. We have previously shown that myoglobin (Mb) forms a domain-swapped dimer with two extended α-helices, and constructed an artificial heterodimeric protein with two different heme active sites (a bis-histidine-coordinated heme and a H2O/histidine-coordinated heme) by domain swapping two Mb surface mutants with opposite charges [7]. In this study, to obtain a c-type cyt heterodimer, we constructed two c-type cyt-based chimeric proteins and domain swapped them. The two chimeric proteins formed a domain-swapped dimer with two His/Met coordinate hemes. By mutating the heme coordination structure of one of the two chimeric proteins, a domain-swapped c-type cyt heterodimer with His/Met and His/H2O coordinate hemes was formed [8].

Protein amyloids receive much attention due to their correlation with serious diseases and to their promising mechanical and optical properties as future materials. A single spherical assembly of amyloid fibrils has been shown to generate by laser trapping domain-swapped dimeric cyt c [2]. Amyloid formation dynamics and amyloid-based micro-structure fabrication were demonstrated based on direct observation of a single spherical assembly, which foresees a new approach in amyloid studies.

References

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[4] S. Hirota, et al., J. Biol. Inorg. Chem., 22, 705 (2017).

[5] Y. Hayashi, et al., Sci. Rep., 6, 19334 (2016).

[6] T. Miyamoto, et al., Chem. Sci., 6, 7336 (2015).

[7] Y.-W. Lin, et al., Angew. Chem. Int. Ed., 54, 511 (2015).

[8] M. Zhang, et al., ChemBioChem, 18, 1712 (2017).

[9] K. Yuyama, et al., Angew. Chem. Int. Ed., 56, 6739 (2017).