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Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551: structural insights into domain swapping of cytochrome c family proteins.

Nagao S, Ueda M, Osuka H, Komori H, Kamikubo H, Kataoka M, Higuchi Y, Hirota S - PLoS ONE (2015)

Bottom Line: The secondary structures of the M61A mutant of PA cyt c551 were perturbed slightly and its oligomer formation ability decreased compared to that of the wild-type protein, showing that the stability of the protein secondary structures is important for domain swapping.The hinge loop of domain swapping for cyt c family proteins corresponded to the unstable region specified by hydrogen exchange NMR measurements for the monomer, although the swapping region differed among proteins.These results show that the unstable loop region has a tendency to become a hinge loop in domain-swapped proteins.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.

ABSTRACT
Cytochrome c (cyt c) family proteins, such as horse cyt c, Pseudomonas aeruginosa cytochrome c551 (PA cyt c551), and Hydrogenobacter thermophilus cytochrome c552 (HT cyt c552), have been used as model proteins to study the relationship between the protein structure and folding process. We have shown in the past that horse cyt c forms oligomers by domain swapping its C-terminal helix, perturbing the Met-heme coordination significantly compared to the monomer. HT cyt c552 forms dimers by domain swapping the region containing the N-terminal α-helix and heme, where the heme axial His and Met ligands belong to different protomers. Herein, we show that PA cyt c551 also forms domain-swapped dimers by swapping the region containing the N-terminal α-helix and heme. The secondary structures of the M61A mutant of PA cyt c551 were perturbed slightly and its oligomer formation ability decreased compared to that of the wild-type protein, showing that the stability of the protein secondary structures is important for domain swapping. The hinge loop of domain swapping for cyt c family proteins corresponded to the unstable region specified by hydrogen exchange NMR measurements for the monomer, although the swapping region differed among proteins. These results show that the unstable loop region has a tendency to become a hinge loop in domain-swapped proteins.

No MeSH data available.


Structures of horse cyt c and PA cyt c551.Horse cyt c (upper left) and PA cyt c551 (upper right). The hemes and axial ligands are shown as stick models. The heme, the sulfur atoms of the heme axial Met ligand and heme-linked Cys, and the nitrogen atoms of the heme axial His ligand are shown in gray, yellow, and blue, respectively. The secondary structure diagrams of horse cyt c and PA cyt c551 are depicted at the bottom of the figure. The helices are depicted as arrows in the secondary structure diagrams. The helices and loops are labeled as H1–H4 and L1–L3, respectively.
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pone.0123653.g001: Structures of horse cyt c and PA cyt c551.Horse cyt c (upper left) and PA cyt c551 (upper right). The hemes and axial ligands are shown as stick models. The heme, the sulfur atoms of the heme axial Met ligand and heme-linked Cys, and the nitrogen atoms of the heme axial His ligand are shown in gray, yellow, and blue, respectively. The secondary structure diagrams of horse cyt c and PA cyt c551 are depicted at the bottom of the figure. The helices are depicted as arrows in the secondary structure diagrams. The helices and loops are labeled as H1–H4 and L1–L3, respectively.

Mentions: Cytochrome c (cyt c) is an electron transfer protein existing in the inner membrane space of mitochondria. Cyt c also plays a key role in apoptosis, where it is released to the cytosol when permeabilization of the mitochondrial outer membrane occurs [10,11]. Cyt c contains three long α-helices (helices 1, 3, and 4) and a short α-helix (helix 2). A hexacoordinated heme is attached covalently to two Cys residues through their sulfur atoms in cyt c (Fig 1 and Table 1). His and Met residues are coordinated to the heme iron of cyt c in its native state [12,13,14]. We have shown that horse cyt c forms polymers from monomers by domain swapping its C-terminal α-helix successively [15]. The C-terminal α-helix of dimeric horse cyt c was displaced from its original position in the monomer, and the Met–heme coordination was perturbed significantly in the dimer, causing higher cyanide ion binding affinity and peroxidase activity compared to those in the monomer [15,16,17]. Hydrogenobacter thermophilus cytochrome c552 (HT cyt c552) is a member of the cyt c protein family. We have shown that HT cyt c552 forms oligomers by domain swapping its N-terminal region containing the heme [18]. Psudomonas aeruginosa cytochrome c551 (PA cyt c551) is also a member of the cyt c protein family, and is considered to transfer electrons in the bacterial periplasm. Similar to other cyt c proteins, PA cyt c551 contains four α-helices (helices 1–4), and His16 and Met61 are coordinated to its heme iron (Fig 1 and Table 1) [19].


Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551: structural insights into domain swapping of cytochrome c family proteins.

Nagao S, Ueda M, Osuka H, Komori H, Kamikubo H, Kataoka M, Higuchi Y, Hirota S - PLoS ONE (2015)

Structures of horse cyt c and PA cyt c551.Horse cyt c (upper left) and PA cyt c551 (upper right). The hemes and axial ligands are shown as stick models. The heme, the sulfur atoms of the heme axial Met ligand and heme-linked Cys, and the nitrogen atoms of the heme axial His ligand are shown in gray, yellow, and blue, respectively. The secondary structure diagrams of horse cyt c and PA cyt c551 are depicted at the bottom of the figure. The helices are depicted as arrows in the secondary structure diagrams. The helices and loops are labeled as H1–H4 and L1–L3, respectively.
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4390240&req=5

pone.0123653.g001: Structures of horse cyt c and PA cyt c551.Horse cyt c (upper left) and PA cyt c551 (upper right). The hemes and axial ligands are shown as stick models. The heme, the sulfur atoms of the heme axial Met ligand and heme-linked Cys, and the nitrogen atoms of the heme axial His ligand are shown in gray, yellow, and blue, respectively. The secondary structure diagrams of horse cyt c and PA cyt c551 are depicted at the bottom of the figure. The helices are depicted as arrows in the secondary structure diagrams. The helices and loops are labeled as H1–H4 and L1–L3, respectively.
Mentions: Cytochrome c (cyt c) is an electron transfer protein existing in the inner membrane space of mitochondria. Cyt c also plays a key role in apoptosis, where it is released to the cytosol when permeabilization of the mitochondrial outer membrane occurs [10,11]. Cyt c contains three long α-helices (helices 1, 3, and 4) and a short α-helix (helix 2). A hexacoordinated heme is attached covalently to two Cys residues through their sulfur atoms in cyt c (Fig 1 and Table 1). His and Met residues are coordinated to the heme iron of cyt c in its native state [12,13,14]. We have shown that horse cyt c forms polymers from monomers by domain swapping its C-terminal α-helix successively [15]. The C-terminal α-helix of dimeric horse cyt c was displaced from its original position in the monomer, and the Met–heme coordination was perturbed significantly in the dimer, causing higher cyanide ion binding affinity and peroxidase activity compared to those in the monomer [15,16,17]. Hydrogenobacter thermophilus cytochrome c552 (HT cyt c552) is a member of the cyt c protein family. We have shown that HT cyt c552 forms oligomers by domain swapping its N-terminal region containing the heme [18]. Psudomonas aeruginosa cytochrome c551 (PA cyt c551) is also a member of the cyt c protein family, and is considered to transfer electrons in the bacterial periplasm. Similar to other cyt c proteins, PA cyt c551 contains four α-helices (helices 1–4), and His16 and Met61 are coordinated to its heme iron (Fig 1 and Table 1) [19].

Bottom Line: The secondary structures of the M61A mutant of PA cyt c551 were perturbed slightly and its oligomer formation ability decreased compared to that of the wild-type protein, showing that the stability of the protein secondary structures is important for domain swapping.The hinge loop of domain swapping for cyt c family proteins corresponded to the unstable region specified by hydrogen exchange NMR measurements for the monomer, although the swapping region differed among proteins.These results show that the unstable loop region has a tendency to become a hinge loop in domain-swapped proteins.

View Article: PubMed Central - PubMed

Affiliation: Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.

ABSTRACT
Cytochrome c (cyt c) family proteins, such as horse cyt c, Pseudomonas aeruginosa cytochrome c551 (PA cyt c551), and Hydrogenobacter thermophilus cytochrome c552 (HT cyt c552), have been used as model proteins to study the relationship between the protein structure and folding process. We have shown in the past that horse cyt c forms oligomers by domain swapping its C-terminal helix, perturbing the Met-heme coordination significantly compared to the monomer. HT cyt c552 forms dimers by domain swapping the region containing the N-terminal α-helix and heme, where the heme axial His and Met ligands belong to different protomers. Herein, we show that PA cyt c551 also forms domain-swapped dimers by swapping the region containing the N-terminal α-helix and heme. The secondary structures of the M61A mutant of PA cyt c551 were perturbed slightly and its oligomer formation ability decreased compared to that of the wild-type protein, showing that the stability of the protein secondary structures is important for domain swapping. The hinge loop of domain swapping for cyt c family proteins corresponded to the unstable region specified by hydrogen exchange NMR measurements for the monomer, although the swapping region differed among proteins. These results show that the unstable loop region has a tendency to become a hinge loop in domain-swapped proteins.

No MeSH data available.