Comparison of low oxidoreduction potential cytochromec553 fromDesulfovibrio vulgaris with the class I cytochromec family

Blackledge, Martin; Guerlesquin, Françoise; Marion, Dominique

doi:10.1002/(sici)1097-0134(199602)24:2<178::aid-prot5>3.0.co;2-f

Cited by 24 publications

(7 citation statements)

References 64 publications

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“…Notably, the heme pocket architecture, the electrostatic surface distribution and the accessibility of the encounter surface at the system edge are conserved. The present data clearly demonstrate that the interacting site for cytochrome c 553 is that which was previously predicted from cytochrome c structure comparison [14]. In this low oxidoreduction potential cytochrome, the main structural variation observed when compared with other c ‐type cytochromes concerns the propionate 6 solvent accessibility.…”

Section: Discussionsupporting

confidence: 75%

“…Structural comparison [14] of cytochrome c 553 with other cytochromes c underlined that despite the lower sequence homology, the overall structure of cytochrome c 553 is similar to the rest of the cytochrome c family. Notably, the heme pocket architecture, the electrostatic surface distribution and the accessibility of the encounter surface at the system edge are conserved.…”

Section: Discussionmentioning

confidence: 97%

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Mapping the cytochrome c₅₅₃ interacting site using ¹H and ¹⁵N NMR

Morelli

Guerlesquin

1999

FEBS Letters

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Cytochrome c 553 is the electron transfer partner of formate dehydrogenase and of [Fe]-hydrogenase, two metalloenzymes essential in the metabolism of sulfate reducing bacteria. These two enzymes contain a`ferredoxin-like' domain which presents 30% identity with Desulfovibrio desulfuricans Norway ferredoxin I. This was chosen as a model for the`ferredoxin-like' domain involved in the electron transfer reaction with cytochrome c 553 . 1D NMR titration of complex formation gave us the stoichiometry (1:1) and the dissociation constant of the complex (K d V V3U U10 36 M). 2D heteronuclear NMR experiments were performed to analyze the 1 H and 15 N chemical shift variations that are induced by the protein-protein recognition. This is the first mapping of the interaction site on a c-type cytochrome, using heteronuclear NMR.z 1999 Federation of European Biochemical Societies.

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Section: Discussionsupporting

confidence: 75%

Section: Discussionmentioning

confidence: 97%

Mapping the cytochrome c₅₅₃ interacting site using ¹H and ¹⁵N NMR

Morelli

Guerlesquin

1999

FEBS Letters

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“…Heme propionates are traditionally thought to be electrostatic anchors and sites for proton‐coupled electron transfer . More recently, there has been a growing appreciation that heme propionates impact the macrocycle′s electronic structure.…”

Section: Effects Of Heme Propionates On Electronic Couplingmentioning

confidence: 99%

Going with the Electron Flow: Heme Electronic Structure and Electron Transfer in Cytochrome c

Bren

2016

Israel Journal of Chemistry

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Heme is an essential and functionally versatile cofactor. Our understanding of how the environment of a heme in a protein tunes its function has benefited from spectroscopic and functional investigations of heme proteins and their variants with altered heme environments. Two properties of current interest are the conformation of the heme and hydrogen bonding to heme propionates. By combining nuclear magnetic resonance experiments and density functional theory calculations, both of these characteristics have been shown to influence the distribution of the singly occupied molecular orbital on the heme of ferricytochrome c, which affects coupling to redox partners and electron‐transfer rates. In addition, heme conformation has been shown to tune reduction potential. These results reveal that subtle variations in heme conformation and in interactions with its propionates can have significant impacts on electron‐transfer activity.

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“…Based on a kinetic study [88], the electron donor of Fe-Hydrogenase was proposed to be the monohemic cytochrome c 553 (Figure 6B), a periplasmic, low potential cytochrome c analogue to the mitochondrial cytochrome c [89]. In this case, the NMR restrained docking approach was useful to filter docking solutions [40].…”

Section: Case Studiesmentioning

confidence: 99%

Predicting Protein-Protein Interactions Using BiGGER: Case Studies

et al. 2016

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Abstract:The importance of understanding interactomes makes preeminent the study of protein interactions and protein complexes. Traditionally, protein interactions have been elucidated by experimental methods or, with lower impact, by simulation with protein docking algorithms. This article describes features and applications of the BiGGER docking algorithm, which stands at the interface of these two approaches. BiGGER is a user-friendly docking algorithm that was specifically designed to incorporate experimental data at different stages of the simulation, to either guide the search for correct structures or help evaluate the results, in order to combine the reliability of hard data with the convenience of simulations. Herein, the applications of BiGGER are described by illustrative applications divided in three Case Studies: (Case Study A) in which no specific contact data is available; (Case Study B) when different experimental data (e.g., site-directed mutagenesis, properties of the complex, NMR chemical shift perturbation mapping, electron tunneling) on one of the partners is available; and (Case Study C) when experimental data are available for both interacting surfaces, which are used during the search and/or evaluation stage of the docking. This algorithm has been extensively used, evidencing its usefulness in a wide range of different biological research fields.

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Comparison of low oxidoreduction potential cytochromec553 fromDesulfovibrio vulgaris with the class I cytochromec family

Cited by 24 publications

References 64 publications

Mapping the cytochrome c₅₅₃ interacting site using ¹H and ¹⁵N NMR

Mapping the cytochrome c₅₅₃ interacting site using ¹H and ¹⁵N NMR

Going with the Electron Flow: Heme Electronic Structure and Electron Transfer in Cytochrome c

Predicting Protein-Protein Interactions Using BiGGER: Case Studies

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Comparison of low oxidoreduction potential cytochromec553 fromDesulfovibrio vulgaris with the class I cytochromec family

Cited by 24 publications

References 64 publications

Mapping the cytochrome c553 interacting site using 1H and 15N NMR

Mapping the cytochrome c553 interacting site using 1H and 15N NMR

Going with the Electron Flow: Heme Electronic Structure and Electron Transfer in Cytochrome c

Predicting Protein-Protein Interactions Using BiGGER: Case Studies

Contact Info

Product

Resources

About

Mapping the cytochrome c₅₅₃ interacting site using ¹H and ¹⁵N NMR

Mapping the cytochrome c₅₅₃ interacting site using ¹H and ¹⁵N NMR