Electronic Structures of Metal Sites in Proteins and Models:  Contributions to Function in Blue Copper Proteins

Solomon, Edward I.; Szilágyi, Róbert K.; DeBeer, Serena; Basumallick, Lipika

doi:10.1021/cr0206317

Cited by 800 publications

(986 citation statements)

References 167 publications

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“…CuCl 2À 4 The electronic structure of the CuCl 2À 4 ion is a model for the electronic structure of the active site of oxidised blue copper proteins. The absorption spectrum of CuCl 2À 4 with a D 4h configuration has been reported, 7 and this provides a useful system to explore the accuracy of the DFT based techniques. Table 1 shows the computed excitation energies and oscillator strengths for transitions in the UV region with TDDFT and View Online MOM approaches.…”

Section: Resultsmentioning

confidence: 99%

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Modelling the spectroscopy and dynamics of plastocyanin

Robinson

Besley

2010

Phys. Chem. Chem. Phys.

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The electronic absorption, electronic circular dichroism and X-ray absorption spectroscopy of the blue copper protein plastocyanin is studied with density functional theory, time-dependent density functional theory and multireference configuration interaction in conjunction with classical molecular dynamics simulations. A strong correlation is observed between the excitation energy of the intense ligand to metal charge transfer band and the copper-cysteine sulfur bond length. The results suggest that the copper-cysteine sulfur bond length in the crystal structure of plastocyanin is too short and should be closer to the corresponding bond lengths in related blue copper proteins. Averaging over many structural conformations is required to reproduce the major features of the experimental circular dichroism spectra. A correlation between the rotational strength of the ligand to metal charge transfer band and the distortion of the copper atom from the plane of the cysteine sulfur and histidine nitrogen atoms is found. X-ray absorption calculations show a smaller sulfur p orbital character in the singly occupied molecular orbital of cucumber basic protein compared to plastocyanin.

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Section: Resultsmentioning

confidence: 99%

“…In addition, core excitations can provide information on the oxidation state, coordination number and nature of the ground state wavefunction of the metal centre. 7 Plastocyanin represents a classic example of a blue copper protein. The active site of plastocyanin is shown in Fig.…”

Section: Introductionmentioning

confidence: 99%

Modelling the spectroscopy and dynamics of plastocyanin

Robinson

Besley

2010

Phys. Chem. Chem. Phys.

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“…These orbitals are described best as s Ã SÀH and s Ã CÀS consistent with earlier assignment. 52 Two distinct peaks are evident in the experimental spectrum of Si(CH 3 ) 3 Cl. The first peak has been assigned to a Sið1sÞ !…”

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confidence: 99%

“…The computed spectra is evaluated with the SRC-1 functional, which was optimized for the first row excitations. Furthermore, sulfur and silicon K-edge spectra are shown for 1-propanthiol and Si(CH 3 ) 3 Cl, computed with the SRC-1 functional parameterized for the second row excitations. The computed spectra agree well with the experimental spectra, and it is not necessary to apply any shift to the excitation energies.…”

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confidence: 99%

“…Experiments have shown the pre-edge features in the copper and sulfur X-ray absorption spectra to lie at 8978 and 2469 eV. 3,[53][54][55] Using a model of the active site ( Fig. 5) and the SRC-1 functional optimized for the second row nuclei with the 6-31(2+,2+)G** basis set, Cu(1s) -3d and S(1s) -3d excitation energies are predicted to be 8977.8 eV and 2469.2 eV, once corrected for relativity.…”

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confidence: 99%

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Time-dependent density functional theory calculations of near-edge X-ray absorption fine structure with short-range corrected functionals

Besley

Peach

Tozer

2009

Phys. Chem. Chem. Phys.

201

304

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We report calculations of core excitation energies and near-edge X-ray absorption fine structure (NEXAFS) spectra computed with time-dependent density functional theory (TDDFT). TDDFT with generalized gradient approximation and standard hybrid exchange-correlation functionals is known to underestimate core excitation energies. This failure is shown to be associated with the self-interaction error at short interelectronic distances. Short-range corrected hybrid functionals are shown to reduce the error in the computed core excitation energies for first and second row nuclei in a range of molecules to a level approaching that observed in more traditional excited states calculations in the ultraviolet region. NEXAFS spectra computed with the new functionals agree well with experiment and the pre-edge features in the NEXAFS spectra of plastocyanin are correctly predicted.

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Copper Proteins: Oxidases

Stoj¹,

Kosman²

2005

Encyclopedia of Inorganic Chemistry

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Oxidases are enzymes that use dioxygen as the electron acceptor in oxido‐reduction reactions. Many members of this enzyme class (EC 1.) rely on the Cu 1+ /Cu 2+ redox cycle of copper prosthetic group(s) in their catalysis of the electron transfer from reducing substrate to O 2 . Those copper oxidases that catalyze the four‐electron reduction of O 2 to 2H 2 O are known as multicopper oxidases (MCO) because each member of this group contains at least four copper atoms of three distinct electronic and spectral types. These three types are: type 1 or ‘blue’ Cu(II), so‐called because of its distinguishing strong absorbance at ∼600 nm; type 2 Cu(II), comparable in electronic structure to that found in square‐planar copper complexes; and type 3 Cu(II), a Cu(II)Cu(II) pair bridged by O(H) and thus diamagnetic. With four 1e − metal redox sites, MCOs are the all‐copper equivalent of the copper‐heme respiratory terminal oxidases. However, MCOs are true oxidases in that all members can use as electron acceptors common (di)phenolic, and aromatic (di)amine substrates, for example, hydroquinone, ascorbic acid, and phenylenediamine. The laccases and ascorbate oxidase are examples of these MCOs (EC 1.10.3). Members of a separate MCO class (EC 1.16.3) also use lower valent metal ions as substrates, for example, Fe 2+ , Cu 1+ , and/or Mn 2+ . These are thereby designated metallo‐oxidases; the most widely studied activity of this class has been towards Fe 2+ giving rise to the common enzyme name, ferroxidase. The typical MCO structure consists of three ‘cuprodoxin’ domains, a Greek‐key beta‐fold that characterizes a family of mononuclear copper electron‐transfer factors. Among MCOs are both soluble and type 1 membrane proteins. Functionally, MCOs are known to play essential roles in biodegradation and transformation, cell redox balance, and metal metabolism. This article summarizes current knowledge of this class of copper oxidase enzymes.

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Electronic Structures of Metal Sites in Proteins and Models: Contributions to Function in Blue Copper Proteins

Cited by 800 publications

References 167 publications

Modelling the spectroscopy and dynamics of plastocyanin

Modelling the spectroscopy and dynamics of plastocyanin

Time-dependent density functional theory calculations of near-edge X-ray absorption fine structure with short-range corrected functionals

Copper Proteins: Oxidases

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