Insights into properties and energetics of iron–sulfur proteins from simple clusters to nitrogenase

Noodleman, Louis; Lovell, Timothy; Liu, Tiqing; Himo, Fahmi; Torres, Rhonda A.

doi:10.1016/s1367-5931(02)00309-5

Cited by 130 publications

(127 citation statements)

References 73 publications

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“…As for the mixture of five d-orbitals occupied by ctelectrons, the mixing has no influence on the resulting Slater determinant. Note that in quantum chemical calculations, utilizing unrestricted self-consistent field theory (USCF) or unrestricted density functional theory (UDFT), 3d-orbitals for c~-and [3-electrons may be significantly different and split (by about 5 eV), because of the internal exchange polarization, which is typical for unrestricted methods [13,14]. In this case, the single determinant wave function for Fe 2 § is usually contaminated by the admixture of high-spin (S 2 > 2) components.…”

Section: Theoreticai Backgroundmentioning

confidence: 99%

Variations ofg-tensor principal values in reduced [2Fe−2S] cluster of iron-sulfur proteins

Shubin

Dikanov

2006

Appl. Magn. Reson.

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This article discusses the present status of the theoretical and experimental studies of the electronic structure of the reduced [2Fe-2S] cluster with a special emphasis on the g-tensor variations in the Rieske-type proteins. The necessity of this analysis is dictated by the fact that the changes in the electron paramagnetic resonance line shape of the redueed cluster are broadly exploited as the basis for different mechanistic conclusions in the stmcture-function studies of the bc~/b6f families.

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Section: Theoreticai Backgroundmentioning

confidence: 99%

Variations ofg-tensor principal values in reduced [2Fe−2S] cluster of iron-sulfur proteins

Shubin

Dikanov

2006

Appl. Magn. Reson.

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“…PB studies of redox proteins have progressed significantly since the early studies that considered the protein as a nonpolar sphere (see above). These studies (e.g., [108,111,[122][123][124]) started to reflect a gradual recognition of the importance of the protein permanent dipoles, although some confusion still exists (see discussion in Refs [108] and [114]). …”

Section: Redox and Electron Transport Processesmentioning

confidence: 99%

Electrostatics of Proteins: Principles, Models and Applications

Braun‐Sand¹,

Warshel²

2005

Protein Folding Handbook

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“…Computationally this implies severe limitations in terms of system size and coupling to molecular dynamics (MD). A well established compromise in terms of cost versus accuracy are spin-projection schemes (11, 12) that rely on an approximate purification of the spin state (13) by carrying out independent total energy calculations for several uncoupled spin configurations (14,15). Such approaches allow the calculation of the exchange coupling constant J directly and have been proven to perform particularly well for binuclear homovalent clusters in static calculations (16, 17).…”

mentioning

confidence: 99%

Dynamical magnetostructural properties of Anabaena ferredoxin

Schreiner

Nair

Pollet

et al. 2007

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

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A mixed quantum/classical investigation of the dynamical magnetostructural properties, that is, ''magnetodynamics,'' of oxidized Anabaena PCC7119 ferredoxin is carried out at room temperature in two distinct conformational states. This protein hosts a [2Fe-2S] cluster in which two iron centers are antiferromagnetically coupled to an overall low-spin electronic ground state that has a genuine multireference character. To study the magnetodynamics of this prosthetic group, an approximate spin projection method is formulated in the framework of density functional theory that allows for multideterminant ab initio molecular dynamics simulations to be carried out efficiently. By using this scheme, the influence of both thermal fluctuations and conformational motion on the structure of the [2Fe-2S] cluster and on the dynamics of the antiferromagnetic coupling constant, J(t), has been investigated. In addition to demonstrating how sensitively the shape of the [2Fe-2S] core itself is affected by hydrogen bonding, the analyses reveal a complex dynamical coupling of J to both local vibrations and large-amplitude motion. It is shown that this interplay can be understood in terms of specific vibrational modes and distinct hydrogen-bonding patterns between the iron-sulfur cluster and the protein backbone, respectively. This implies going beyond the Goodenough-Kanamori rules for angular magnetostructural correlations of oxidized iron-sulfur prosthetic groups.exchange coupling ͉ extended broken-symmetry ͉ hydrogen bonding ͉ iron-sulfur protein ͉ multideterminant hybrid molecular dynamics I ron-sulfur clusters are among the most ubiquitous, functionally versatile, and ancient prosthetic groups in proteins (1-4). One of the major classes of mobile electron carriers in contemporary biology is ferredoxin (Fd). Its fourfold cysteine-coordinated [2Fe-2S] core mediates electron transfer from photosystem I to ferredoxin-NADP ϩ -oxidoreductase, which reduces NADP ϩ to NADPH. A particularly interesting system is Fd from cyanobacterium Anabaena PCC7119 whose crystal structure was recently obtained at 1.3 and 1.17 Å resolution in the oxidized and the reduced forms (5), respectively. Most interestingly, it was found that two alternative conformations of Cys-46 exist, which is one of the four cysteinyl ligands of the [2Fe-2S] cluster (5). In the oxidized state Cys-46 adopts the so-called CO-in conformation, where the peptide oxygen points in the direction of the cluster, whereas, on reduction, the backbone flips to the CO-out conformation.Spin Coupling in Iron-Sulfur Clusters. In the ground state of the oxidized form of bioinorganic [mFe-nS] clusters, the Fe 3ϩ metal centers are typically in a local high-spin d 5 configuration [i.e., S Fe ϭ 5/2 for ferric Fe(III) centers], whereas they themselves are antiferromagnetically coupled to yield an overall low-spin state due to dominant superexchange interactions (6). In particular, the electronic ground state of [2Fe-2S] clusters in Fd has genuine multireference character and makes computational ...

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Insights into properties and energetics of iron–sulfur proteins from simple clusters to nitrogenase

Cited by 130 publications

References 73 publications

Variations ofg-tensor principal values in reduced [2Fe−2S] cluster of iron-sulfur proteins

Variations ofg-tensor principal values in reduced [2Fe−2S] cluster of iron-sulfur proteins

Electrostatics of Proteins: Principles, Models and Applications

Dynamical magnetostructural properties of Anabaena ferredoxin

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