Heme binding mechanism of structurally similar iron-regulated surface determinant near transporter domains of staphylococcus aureus exhibiting different affinities for heme

Yoshitaka Moriwaki, Tohru Terada, Jose M.M. Caaveiro, Yousuke Takaoka, Itaru Hamachi, Kouhei Tsumoto, Kentaro Shimizu

研究成果: ジャーナルへの寄稿記事

14 引用 (Scopus)

抄録

Near transporter (NEAT) domains of the iron-regulated surface determinant (Isd) proteins are essential for the import of nutritional heme from host animals to Gram-positive pathogens such as Staphylococcus aureus. The order of transfer of heme between NEAT domains occurs from IsdH to IsdA to IsdC, without any energy input despite the similarity of their three-dimensional structures. We measured the free energy of binding of heme and various metalloporphyrins to each NEAT domain and found that the affinity of heme and non-iron porphyrins for NEAT domains increased gradually in the same order as that for heme transfer. To gain insight into the atomistic mechanism for the differential affinities, we performed in silico molecular dynamics simulation and in vitro site-directed mutagenesis. The simulations revealed that the negatively charged residues that are abundant in the loop between strand β1b and the 310 helix of IsdH-NEAT3 destabilize the interaction with the propionate group of heme. The higher affinity of IsdC was in part attributed to the formation of a salt bridge between its unique residue, Glu88, and the conserved Arg100 upon binding to heme. In addition, we found that Phe130 of IsdC makes the β7-β8 hairpin less flexible in the ligand-free form, which serves to reduce the magnitude of the entropy loss on binding to heme. We confirmed that substitution of these key residues of IsdC decreased its affinity for heme. Furthermore, IsdC mutants, whose affinities for heme were lower than those of IsdA, transferred heme back to IsdA. Thus, NEAT domains have evolved the characteristic residues on the common structural scaffold such that they exhibit different affinities for heme, thus promoting the efficient transfer of heme.

元の言語英語
ページ(範囲)8866-8877
ページ数12
ジャーナルBiochemistry
52
発行部数49
DOI
出版物ステータス出版済み - 12 10 2013
外部発表Yes

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Heme
Staphylococcus aureus
Iron
Metalloporphyrins
Mutagenesis
Porphyrins
Propionates
Entropy
Pathogens
Molecular Dynamics Simulation
Site-Directed Mutagenesis
Scaffolds
Computer Simulation
Free energy
Molecular dynamics
Membrane Proteins
Animals
Substitution reactions
Salts
Ligands

All Science Journal Classification (ASJC) codes

  • Biochemistry

これを引用

Heme binding mechanism of structurally similar iron-regulated surface determinant near transporter domains of staphylococcus aureus exhibiting different affinities for heme. / Moriwaki, Yoshitaka; Terada, Tohru; Caaveiro, Jose M.M.; Takaoka, Yousuke; Hamachi, Itaru; Tsumoto, Kouhei; Shimizu, Kentaro.

:: Biochemistry, 巻 52, 番号 49, 10.12.2013, p. 8866-8877.

研究成果: ジャーナルへの寄稿記事

Moriwaki, Yoshitaka ; Terada, Tohru ; Caaveiro, Jose M.M. ; Takaoka, Yousuke ; Hamachi, Itaru ; Tsumoto, Kouhei ; Shimizu, Kentaro. / Heme binding mechanism of structurally similar iron-regulated surface determinant near transporter domains of staphylococcus aureus exhibiting different affinities for heme. :: Biochemistry. 2013 ; 巻 52, 番号 49. pp. 8866-8877.
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abstract = "Near transporter (NEAT) domains of the iron-regulated surface determinant (Isd) proteins are essential for the import of nutritional heme from host animals to Gram-positive pathogens such as Staphylococcus aureus. The order of transfer of heme between NEAT domains occurs from IsdH to IsdA to IsdC, without any energy input despite the similarity of their three-dimensional structures. We measured the free energy of binding of heme and various metalloporphyrins to each NEAT domain and found that the affinity of heme and non-iron porphyrins for NEAT domains increased gradually in the same order as that for heme transfer. To gain insight into the atomistic mechanism for the differential affinities, we performed in silico molecular dynamics simulation and in vitro site-directed mutagenesis. The simulations revealed that the negatively charged residues that are abundant in the loop between strand β1b and the 310 helix of IsdH-NEAT3 destabilize the interaction with the propionate group of heme. The higher affinity of IsdC was in part attributed to the formation of a salt bridge between its unique residue, Glu88, and the conserved Arg100 upon binding to heme. In addition, we found that Phe130 of IsdC makes the β7-β8 hairpin less flexible in the ligand-free form, which serves to reduce the magnitude of the entropy loss on binding to heme. We confirmed that substitution of these key residues of IsdC decreased its affinity for heme. Furthermore, IsdC mutants, whose affinities for heme were lower than those of IsdA, transferred heme back to IsdA. Thus, NEAT domains have evolved the characteristic residues on the common structural scaffold such that they exhibit different affinities for heme, thus promoting the efficient transfer of heme.",
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T1 - Heme binding mechanism of structurally similar iron-regulated surface determinant near transporter domains of staphylococcus aureus exhibiting different affinities for heme

AU - Moriwaki, Yoshitaka

AU - Terada, Tohru

AU - Caaveiro, Jose M.M.

AU - Takaoka, Yousuke

AU - Hamachi, Itaru

AU - Tsumoto, Kouhei

AU - Shimizu, Kentaro

PY - 2013/12/10

Y1 - 2013/12/10

N2 - Near transporter (NEAT) domains of the iron-regulated surface determinant (Isd) proteins are essential for the import of nutritional heme from host animals to Gram-positive pathogens such as Staphylococcus aureus. The order of transfer of heme between NEAT domains occurs from IsdH to IsdA to IsdC, without any energy input despite the similarity of their three-dimensional structures. We measured the free energy of binding of heme and various metalloporphyrins to each NEAT domain and found that the affinity of heme and non-iron porphyrins for NEAT domains increased gradually in the same order as that for heme transfer. To gain insight into the atomistic mechanism for the differential affinities, we performed in silico molecular dynamics simulation and in vitro site-directed mutagenesis. The simulations revealed that the negatively charged residues that are abundant in the loop between strand β1b and the 310 helix of IsdH-NEAT3 destabilize the interaction with the propionate group of heme. The higher affinity of IsdC was in part attributed to the formation of a salt bridge between its unique residue, Glu88, and the conserved Arg100 upon binding to heme. In addition, we found that Phe130 of IsdC makes the β7-β8 hairpin less flexible in the ligand-free form, which serves to reduce the magnitude of the entropy loss on binding to heme. We confirmed that substitution of these key residues of IsdC decreased its affinity for heme. Furthermore, IsdC mutants, whose affinities for heme were lower than those of IsdA, transferred heme back to IsdA. Thus, NEAT domains have evolved the characteristic residues on the common structural scaffold such that they exhibit different affinities for heme, thus promoting the efficient transfer of heme.

AB - Near transporter (NEAT) domains of the iron-regulated surface determinant (Isd) proteins are essential for the import of nutritional heme from host animals to Gram-positive pathogens such as Staphylococcus aureus. The order of transfer of heme between NEAT domains occurs from IsdH to IsdA to IsdC, without any energy input despite the similarity of their three-dimensional structures. We measured the free energy of binding of heme and various metalloporphyrins to each NEAT domain and found that the affinity of heme and non-iron porphyrins for NEAT domains increased gradually in the same order as that for heme transfer. To gain insight into the atomistic mechanism for the differential affinities, we performed in silico molecular dynamics simulation and in vitro site-directed mutagenesis. The simulations revealed that the negatively charged residues that are abundant in the loop between strand β1b and the 310 helix of IsdH-NEAT3 destabilize the interaction with the propionate group of heme. The higher affinity of IsdC was in part attributed to the formation of a salt bridge between its unique residue, Glu88, and the conserved Arg100 upon binding to heme. In addition, we found that Phe130 of IsdC makes the β7-β8 hairpin less flexible in the ligand-free form, which serves to reduce the magnitude of the entropy loss on binding to heme. We confirmed that substitution of these key residues of IsdC decreased its affinity for heme. Furthermore, IsdC mutants, whose affinities for heme were lower than those of IsdA, transferred heme back to IsdA. Thus, NEAT domains have evolved the characteristic residues on the common structural scaffold such that they exhibit different affinities for heme, thus promoting the efficient transfer of heme.

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