Molecular orbital analysis of active site of oxidized azurin: Dependency of electronic properties on molecular structure

Shuku, Tomofumi; Sugimori, Kimikazu; Sugiyama, Ayumu; Nagao, Hidemi; Sakurai, Takeshi; Nishikawa, Kiyoshi

doi:10.1016/j.poly.2005.03.141

Cited by 13 publications

(11 citation statements)

References 14 publications

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“…More interestingly, the difference ranges of some compounds with same or similar ligands are very close, even though those compounds may belong to different types. Similarly, the ranges for the copper nucleases in A1-bpy/dione/dpq/dppz are comparable with the previously reported results [22,29,[114][115][116].…”

Section: Force Field Parameters Of Different Nucleasessupporting

confidence: 91%

“…This could be related to the five-membered ring of Cu1-N2-N3-C8-C9, together with the two aromatic rings in bpy group, resulting more stable for the rigid aromatic part, so when changing the angle (Cu1-N2-C8/Cu1-N3-C9) within the rigid 5-membered ring, the effect of the N^O ligand at the other side of copper center should be less. But for the remaining bond and angle, the values of these parameters appear to be more random, i.e., the ranges of 81-108, 67-100, 124-144 kcal mol -1 Å -2 for bonds Cu1-N2, Cu1-N5 and Cu1-O4, which are mostly in the reported ranges of 59-204, 33-242, 36-250 kcal mol -1 -rad -2 [22,29,[114][115][116], and the ranges of 81-106, 81-103, 49-72 kcal mol -1 rad -2 for angles Cu1-N3-C7, Cu1-O4-C10 and N3-Cu1-O4 in A1-/A2-/A3-/A4-bpy, respectively. Especially for A2-bpy, the differences for bond parameters are large than those of other structures, for example, the parameter for Cu1-N2/Cu1-N3/Cu1-N5 is 107 Å -2 in A4-bpy, which may be caused by the long polar group (-CH 2 CH 2 CH 2 CH 2 NH 3 ) in A2-bpy.…”

Section: Force Field Parameters Of Different Nucleasesmentioning

confidence: 99%

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Evaluations of AMBER force field parameters by MINA approach for copper-based nucleases

et al. 2016

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We describe the development of the AMBER force field parameters for 46 nucleases involving most kinds of copper nucleases with high DNA affinities and specificities by MINA approach that could evaluate accurate force constants for batch bonds/angles on the basis of energies of three adjacent lengths/angles geometries. The molecular mechanics (MM) and molecular dynamic simulations on adducts of the 21 representative copper-based nucleases with DNA are in excellent agreement with those of experimental results. Furthermore, to validate the evaluated parameters, the studied structures performed frequency analysis together with normal mode calculations in quantum mechanics and MM calculations. The force field parameters evaluated in this work provide an extension of AMBER force field, and the results of molecular dynamics simulations of adduct of copper nuclease and duplex DNA illustrate the potential utility of these parameters.

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Section: Force Field Parameters Of Different Nucleasessupporting

confidence: 91%

Section: Force Field Parameters Of Different Nucleasesmentioning

confidence: 99%

Evaluations of AMBER force field parameters by MINA approach for copper-based nucleases

et al. 2016

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“…As has been shown by Shuku et al, the Cu-S(Cys) distance influences the spin-density distribution decisively. 74 In stellacyanin, the axial glutamine ligand is much more strongly bound than the glycine in azurin, and the Cu-S(Cys) bond length is intermediate between azurin and plastocyanin ( Figure 1). Interestingly, the spin density of stellacyanin is the most metal-centered one of the three systems.…”

Section: Resultsmentioning

confidence: 99%

Density Functional Study of EPR Parameters and Spin-Density Distribution of Azurin and Other Blue Copper Proteins

2007

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Modern density functional methods have been used to study spin-density distribution, g tensors, as well as Cu and ligand hyperfine tensors for azurin models, for two more blue copper proteins plastocyanin and stellacyanin, and for small model complexes. The aim was to establish a consistent computational protocol that provides a realistic description of the EPR parameters as probes of the spin-density distribution between metal and coordinated ligands in copper proteins. In agreement with earlier conclusions for plastocyanin, hybrid functionals with appreciable exact-exchange admixtures, roughly around 50%, provide the best overall agreement with all parameters. Then the bulk of the spin density is almost equally shared by the copper atom and the sulfur atom of the equatorial cysteine ligand, and the best values are obtained for copper, histidine nitrogen, and cysteine beta-proton hyperfine couplings, as well as for g(parallel). Spin-orbit effects on the EPR parameters may be appreciable and have to be treated carefully to obtain agreement with experiment. Most notably, spin-orbit effects on the (65)Cu hyperfine coupling tensors in blue copper sites are unusually large compared to more regularly coordinated Cu(II) complexes with similar spin density on copper. In addition to the often emphasized high covalency of the Cu-S(Cys) bond, the characteristically small A(parallel) component of blue copper proteins is shown to derive to a large part from a near-cancellation between negative first-order (Fermi contact and dipolar) and unusually large positive second-order (spin-orbital) contributions. The large spin-orbit effects relate to the distorted tetrahedral structures. Square planar dithiolene complexes with similar spin density on copper exhibit much more negative A(parallel) values, as the cancellation between nonrelativistic and spin-orbit contributions is less complete. Calculations on a selenocysteine-substituted variant of azurin have provided further insight into the relations between bonding and EPR parameters.

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“…Next, from the geometry‐optimized structure of model c, the force field parameters are also calculated. We evaluate force field parameters by harmonic potential functions written as Because the force field parameters of azurin have already been evaluated in our previous studies 5, 16, and have also been prepared in the official database for the porphyrin ring, we calculate the remaining force field parameters, e.g., Fe–S(Met) and S(Cys)–C(porphyrin). The parameter fitting is carried out using calculated energy profiles.…”

Section: Methodsmentioning

confidence: 99%

Docking stability and electronic structure of azurin–cytochrome c₅₅₁ complex system

Sugiyama¹,

Takamatsu²,

Nishikawa³

et al. 2006

Int J of Quantum Chemistry

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ABSTRACT:We investigate the docking structure between cytochrome c 551 and azurin proteins by quantum mechanical calculation and molecular dynamics (MD). A model for the docking structure of the cytochrome-azurin complex is presented. We calculate the charge distribution around the active site for each protein and force field parameters to simulate the complex system by MD. We estimate some physical properties, such as binding free energy and the dynamical cross-correlation map. We discuss the stability of the cytochrome c 551 -azurin complex system.

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Molecular orbital analysis of active site of oxidized azurin: Dependency of electronic properties on molecular structure

Cited by 13 publications

References 14 publications

Evaluations of AMBER force field parameters by MINA approach for copper-based nucleases

Evaluations of AMBER force field parameters by MINA approach for copper-based nucleases

Density Functional Study of EPR Parameters and Spin-Density Distribution of Azurin and Other Blue Copper Proteins

Docking stability and electronic structure of azurin–cytochrome c₅₅₁ complex system

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Molecular orbital analysis of active site of oxidized azurin: Dependency of electronic properties on molecular structure

Cited by 13 publications

References 14 publications

Evaluations of AMBER force field parameters by MINA approach for copper-based nucleases

Evaluations of AMBER force field parameters by MINA approach for copper-based nucleases

Density Functional Study of EPR Parameters and Spin-Density Distribution of Azurin and Other Blue Copper Proteins

Docking stability and electronic structure of azurin–cytochrome c551 complex system

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Docking stability and electronic structure of azurin–cytochrome c₅₅₁ complex system