Models for ferredoxins: electronic structures of iron-sulfur clusters with one, two, and four iron atoms

Noodleman, Louis; Norman, Joe G.; Osborne, Jason W.; Aizman, Arie; Case, David A.

doi:10.1021/ja00298a004

Cited by 285 publications

(197 citation statements)

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“…for model systems where R = CH3. These are based on electrostatic potential charge fits to quantum mechanical calculations using density functional methods for iron-sulfur clusters (Noodleman & Baerends, 1984;Noodleman et al, 1985;Noodleman & Case, 1992).…”

Section: Electrostatics Calculationsmentioning

confidence: 99%

Structural prototypes for an extended family of flavoprotein reductases: Comparison of phthalate dioxygenase reductase with ferredoxin reductase and ferredoxin

et al. 1993

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The structure of phthalate dioxygenase reductase (PDR), a monomeric iron-sulfur flavoprotein that delivers electrons from NADH to phthalate dioxygenase, is compared to ferredoxin-NADP+ reductase (FNR) and ferredoxin, the proteins that reduce NADP+ in the final reaction of photosystem I. The folding patterns of the domains that bind flavin, NAD(P), and [2Fe-2S] are very similar in the two systems. Alignment of the X-ray structures of PDR and FNR substantiates the assignment of features that characterize a family of flavoprotein reductases whose members include cytochrome P-450 reductase, sulfite and nitrate reductases, and nitric oxide synthase. Hallmarks of this subfamily of flavoproteins, here termed the FNR family, are an antiparallel 0-barrel that binds the flavin prosthetic group, and a characteristic variant of the classic pyridine nucleotide-binding fold. Despite the similarities between FNR and PDR, attempts to model the structure of a dissociable FNR:ferredoxin complex by analogy with PDR reveal features that are at odds with chemical crosslinking studies (Zanetti, G., Morelli, D., Ronchi, S . , Negri, A., Aliverti, A., & Curti, B., 1988, Biochemistry 27, 3753-3759).Differences in the binding sites for flavin and pyridine nucleotides determine the nucleotide specificities of FNR and PDR. The specificity of FNR for NADP' arises primarily from substitutions in FNR that favor interactions with the 2' phosphate of NADP'. Variations in the conformation and sequences of the loop adjoining the flavin phosphate affect the selectivity for FAD versus FMN.The midpoint potentials for reduction of the flavin and [2Fe-2S] groups in PDR are higher than their counterparts in FNR and spinach ferredoxin, by about 120 mV and 260 mV, respectively. Comparisons of the structure of PDR with spinach FNR and with ferredoxin from Anabaena 7120, along with calculations of electrostatic potentials, suggest that local interactions, including hydrogen bonds, are the dominant contributors to these differences in potential.

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Section: Electrostatics Calculationsmentioning

confidence: 99%

Structural prototypes for an extended family of flavoprotein reductases: Comparison of phthalate dioxygenase reductase with ferredoxin reductase and ferredoxin

et al. 1993

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“…[29][30][31][32][33][34][35][36] Moreover, the spin density-which serves as an additional fundamental quantity in the spin-DFT formalism commonly employed for open-shell systems-is qualitatively incorrect in some cases. [15,[37][38][39] To make things even worse, the treatment of low-spin states usually requires the use of a broken-symmetry description, [40][41][42][43] which provides an unphysical spin density by construction (see, e.g., Refs. [24,44] for a discussion).…”

Section: Introductionmentioning

confidence: 99%

Spin in density‐functional theory

Jacob¹,

Reiher²

2012

Int J of Quantum Chemistry

221

224

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The accurate description of open-shell molecules, in particular of transition metal complexes and clusters, is still an important challenge for quantum chemistry. Although density-functional theory (DFT) is widely applied in this area, the sometimes severe limitations of its currently available approximate realizations often preclude its application as a predictive theory. Here, we review the foundations of DFT applied to open-shell systems, both within the nonrelativistic and the relativistic framework. In particular, we provide an in-depth discussion of the exact theory, with a focus on the role of the spin density and possibilities for targeting specific spin states. It turns out that different options exist for setting up Kohn-Sham DFT schemes for open-shell systems, which imply different definitions of the exchangecorrelation energy functional and lead to different exact conditions on this functional. Finally, we suggest possible directions for future developments.

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“…The dimer of dimers arrangement of manganese ions required to account for the EPR signals from the S2 state could arise from a Mn404 "cubane"-like structure that is elongated along one of the three axes of the cube. Indeed, the combination of large antiferromagnetic and ferromagnetic exchange couplings is characteristic of cubane-like structures such as Fe4S4 (7,8) and Cu404 (9). A Jahn-Teller distortion of a Mn404 complex could easily give the dimer of dimers arrangement of manganese ions seen by EPR in the S2 state.…”

mentioning

confidence: 99%

Mechanism for photosynthetic O2 evolution.

Brudvig

Crabtree²

1986

Proc. Natl. Acad. Sci. U.S.A.

166

102

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We present a mechanism for photosynthetic 02 evolution based on a structural conversion of a Mn406 "adamantane"-like complex to a Mn404 "cubane"-like complex. EPR spectral data obtained from the S2 state of the 02-evolving complex are characteristic of a Mn404 cubane-like structure. Based on this structure for the manganese complex in the S2 state as well as a consideration of the other evidence available on the natural system and the coordination chemistry of manganese, structures are proposed for the five intermediate oxidation states of the manganese complex. A molecular mechanism for the formation of an 0-0 bond and the displacement of 02 from the S4 state is easily accommodated by the proposed model. The model is discussed in terms of recent EPR, x-ray, and UV spectral data obtained from the manganese site in the photosynthetic 02-evolving complex. A consideration of the evidence available on the natural system as well as of the coordination chemistry of manganese leads us to propose the model shown in Fig. 1. We have focused on the structural aspects of manganese in our proposal. For a complete account of the involvement of polypeptides and ions in photosynthetic 02 evolution, see the recent paper by Kambara and Govindjee (2). In our scheme, a tetrameric manganese site is sequentially oxidized by photosystem II. Each manganese ion in the tetrameric complex is proposed to be also coordinated to the protein via three N or 0 ligands to complete an octahedral coordination, although the protein-derived manganese ligands are not shown in Fig. 1 (13). In addition, the finding that the Mn x-ray absorption K-edge shifts to higher energy from S1 to S2 indicates that manganese is oxidized during the S1 to S2 transition (3). These two results point to 4586The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. §1734 solely to indicate this fact. 02

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Models for ferredoxins: electronic structures of iron-sulfur clusters with one, two, and four iron atoms

Cited by 285 publications

References 4 publications

Structural prototypes for an extended family of flavoprotein reductases: Comparison of phthalate dioxygenase reductase with ferredoxin reductase and ferredoxin

Structural prototypes for an extended family of flavoprotein reductases: Comparison of phthalate dioxygenase reductase with ferredoxin reductase and ferredoxin

Spin in density‐functional theory

Mechanism for photosynthetic O2 evolution.

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