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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.


Topology diagrams of PA cyt c551 and horse cyt c.(A) Monomeric PA cyt c551, (B) dimeric PA cyt c551, (C) monomeric horse cyt c, and (D) dimeric horse cyt c. The helices and loops are labeled as H1–H4 and L1–L3, respectively. The helices are depicted as arrows. The hinge loops in the monomers are depicted in pink.
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pone.0123653.g005: Topology diagrams of PA cyt c551 and horse cyt c.(A) Monomeric PA cyt c551, (B) dimeric PA cyt c551, (C) monomeric horse cyt c, and (D) dimeric horse cyt c. The helices and loops are labeled as H1–H4 and L1–L3, respectively. The helices are depicted as arrows. The hinge loops in the monomers are depicted in pink.

Mentions: It has been suggested by molecular dynamics simulations that the native topology generally determines the domain-swapped structure [60]. Although the topology of the tertiary structure (Fig 5A and 5C) and folding features, such as the burst-phase collapse in the folding process, are similar between PA cyt c551 and horse cyt c, the swapping region was different between these proteins (Fig 5B and 5D); the hinge loops of PA cyt c551 and horse cyt c were Thr20–Met22 (at loop 1) and Thr78–Ala83 (at loop 3), respectively. According to hydrogen exchange NMR measurements, the thermodynamic property of foldons is different between PA cyt c551 and horse cyt c [20,21,24]. A foldon with low energy (small ΔGHX) loses its secondary structure at the early stage of unfolding, showing that the region corresponding to the low energy foldon has low structural stability. The region containing loop 1 and helix 2 of PA cyt c551 is low in stability [21], whereas that of loop 3 of horse cyt c is low [20,24]. Interestingly, the hinge loops of the domain-swapped structure in PA cyt c551 and horse cyt c correspond to the low stability regions of their monomers. Unfolding simulations have suggested that the hinge loop are ‘hot-spots’, around which proteins tend to locally unfold prior to complete unfolding [60]. These results show that the region with low stability in the monomer correlates to the hinge loop in domain swapping.


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)

Topology diagrams of PA cyt c551 and horse cyt c.(A) Monomeric PA cyt c551, (B) dimeric PA cyt c551, (C) monomeric horse cyt c, and (D) dimeric horse cyt c. The helices and loops are labeled as H1–H4 and L1–L3, respectively. The helices are depicted as arrows. The hinge loops in the monomers are depicted in pink.
© Copyright Policy
Related In: Results  -  Collection

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pone.0123653.g005: Topology diagrams of PA cyt c551 and horse cyt c.(A) Monomeric PA cyt c551, (B) dimeric PA cyt c551, (C) monomeric horse cyt c, and (D) dimeric horse cyt c. The helices and loops are labeled as H1–H4 and L1–L3, respectively. The helices are depicted as arrows. The hinge loops in the monomers are depicted in pink.
Mentions: It has been suggested by molecular dynamics simulations that the native topology generally determines the domain-swapped structure [60]. Although the topology of the tertiary structure (Fig 5A and 5C) and folding features, such as the burst-phase collapse in the folding process, are similar between PA cyt c551 and horse cyt c, the swapping region was different between these proteins (Fig 5B and 5D); the hinge loops of PA cyt c551 and horse cyt c were Thr20–Met22 (at loop 1) and Thr78–Ala83 (at loop 3), respectively. According to hydrogen exchange NMR measurements, the thermodynamic property of foldons is different between PA cyt c551 and horse cyt c [20,21,24]. A foldon with low energy (small ΔGHX) loses its secondary structure at the early stage of unfolding, showing that the region corresponding to the low energy foldon has low structural stability. The region containing loop 1 and helix 2 of PA cyt c551 is low in stability [21], whereas that of loop 3 of horse cyt c is low [20,24]. Interestingly, the hinge loops of the domain-swapped structure in PA cyt c551 and horse cyt c correspond to the low stability regions of their monomers. Unfolding simulations have suggested that the hinge loop are ‘hot-spots’, around which proteins tend to locally unfold prior to complete unfolding [60]. These results show that the region with low stability in the monomer correlates to the hinge loop in domain swapping.

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.