Spectroscopic and Geometric Variations in Perturbed Blue Copper Centers:  Electronic Structures of Stellacyanin and Cucumber Basic Protein

LaCroix, Louis B.; Randall, David; Nersissian, Aram M.; Hoitink, Carla W. G.; Canters, Gerard W.; Valentine, Joan Selverstone; Solomon, Edward I.

doi:10.1021/ja980606b

Cited by 139 publications

(263 citation statements)

References 37 publications

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“…[5][6][7] Closely related blue copper sites, such as cucumber basic protein, pseudoazurin and nitrite reductase, each have a slightly distorted active site compared to plastocyanin and exhibit remarkably different spectral features, in particular an increased intensity of the higher energy band. 4,8 Furthermore, recent studies have shown that a closely related protein, nitrosocyanin, adsorbs in the red. 9 This results from a change in the nature of the intense transition from an excitation from a cysteine-Cu p-like orbital to a s -like one.…”

Section: Introductionmentioning

confidence: 99%

Theoretical Study of the Electronic Spectra of Small Molecules That Incorporate Analogues of the Copper–Cysteine Bond

Besley

2012

J. Phys. Chem. A

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The copper-sulphur bond which binds cysteinate to the metal centre is a key factor in the spectroscopy of blue copper proteins. We present theoretical calculations describing the electronically excited states of small molecules, including CuSH, CuSCH 3 , (CH 3 ) 2 SCuSH, (imidazole)-CuSH and (imidazole) 2 -CuSH, derived from the active site of blue copper proteins that contain the copper-sulphur bond in order to identify small molecular systems that have electronic structure that is analogous to the active site of the proteins. Both neutral and cationic forms are studied, since these represent the reduced and oxidised forms of the protein, respectively. For CuSH and CuSH + , excitation energies from time-dependent density functional theory with the B97-1 exchange-correlation functional agree well with the available experimental data and multireference configuration interaction calculations. For the positive ions, the singly occupied molecular orbital is formed from an antibonding combination of a 3d orbital on copper and a 3p p orbital on sulphur, which is analogous to the protein. This leads several of the molecules to have qualitatively similar electronic spectra to the proteins. For the neutral molecules, changes in the nature of the low lying virtual orbitals leads the predicted electronic spectra to vary substantially between the different molecules. In particular, addition of a ligand bonded directly to copper results in the low-lying excited states observed in CuSH and CuSCH 3 to be absent or shifted to higher energies.

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Section: Introductionmentioning

confidence: 99%

Theoretical Study of the Electronic Spectra of Small Molecules That Incorporate Analogues of the Copper–Cysteine Bond

Besley

2012

J. Phys. Chem. A

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“…The long thioether bond reduces its donor interaction with the copper which is compensated by the thiolate leading to the short Cu-S(Cys) bond of 2.1 Å in the blue copper sites. This long thioether/short thiolate would eliminate all orbital degeneracy of the oxidized site; thus, there would be no Jahn-Teller distortion from the tetrahedral to a tetragonal structure.The above ''coupled distortion'' model provided an explanation for a series of blue copper related proteins (i.e., same Cys, Met, 2His ligand set) which changed from blue to green in color in going from plastocyanin to nitrite reductase (NiR) (5,22,23). In the latter protein the Cu-S(Met) bond has decreased to 2.45 Å, the Cu-S(Cys) bond has elongated to 2.21 Å, and the S-Cu-S plane has rotated relative to the N-Cu-N plane to a more tetragonal structure (24).…”

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confidence: 99%

Thermodynamic equilibrium between blue and green copper sites and the role of the protein in controlling function

Ghosh

Xie

Dey

et al. 2009

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

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A combination of spectroscopies and density functional theory calculations indicate that there are large temperature-dependent absorption spectral changes present in green nitrite reductases (NiRs) due to a thermodynamic equilibrium between a green and a blue type 1 (T1) copper site. The axial methionine (Met) ligand is unconstrained in the oxidized NiRs, which results in an enthalpically favored (⌬H Ϸ4.6 kcal/mol) Met-bound green copper site at low temperatures, and an entropically favored (T⌬S Ϸ4.5 kcal/mol, at room temperature) Met-elongated blue copper site at elevated temperatures. In contrast to the NiRs, the classic blue copper sites in plastocyanin and azurin show no temperature-dependent behavior, indicating that a single species is present at all temperatures. For these blue copper proteins, the polypeptide matrix opposes the gain in entropy that would be associated with the loss of the weak axial Met ligand at physiological temperatures by constraining its coordination to copper. The potential energy surfaces of Met binding indicate that it stabilizes the oxidized state more than the reduced state. This provides a mechanism to tune down the reduction potential of blue copper sites by >200 mV.electron transfer ͉ reduction potential ͉ thermodynamics ͉ DFT calculation ͉ spectroscopy B lue copper (also called type 1, T1 copper) (1) active sites are found in a variety of proteins including plastocyanins and azurins that undergo rapid electron transfer (ET) (2-5). The first crystal structures were available for plastocyanin from poplar leaves, which showed an unusual active-site geometry that was a distorted tetrahedron with a short Cu-S(Cys) bond at 2.1 Å, a long Cu-S(Met) bond at 2.8-2.9 Å, and two Cu-N(His) bonds at Ϸ2.0 Å (6-8). Normally, Cu 2ϩ complexes are square planar because of the Jahn-Teller effect (9), and it was thought that the protein constrained the copper site structure to be in between that of Cu ϩ (tetrahedral) and Cu 2ϩ (square planar) to facilitate ET. This concept of the protein constraint on the copper site was referred to as an entatic or rack-induced state (10-12). Associated with this unusual active-site structure were novel spectral features relative to normal tetrahedral Cu 2ϩ complexes (1, 13-15). In particular, the blue copper site exhibited an intense lower-energy thiolate to Cu charge transfer (CT) transition (and a weak higher-energy CT transition) reflecting a bonding interaction of the thiolate with the Cu 2ϩ of the blue copper center ( ground state, Scheme 1A) (16,17). Normal tetragonal cupric complexes have ligand-metal bonds that result in an intense higher-energy and a weak lower-energy ligand to metal CT transition ( ground state, Scheme 1B) (5). However, the idea of protein constraint on the oxidized site was questioned both in calculations and spectroscopic studies. Total energy calculations were used to argue that the blue copper ligand set gives a structure similar to the protein site on geometry optimization (18). Photoemission spectroscopic studies on models (19...

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“…This leads to a small geometry change on reduction from Cu(II) to Cu(I), 3,4 resulting in a small reorganization energy and high rate of electron transfer. 5 The oxidised forms of blue copper proteins have a d 9 electronic configuration that results in distinctive absorption spectra, [6][7][8][9] with an intense band at about 2.1 eV (16 700 cm 1 ). This band is often referred to as arising from a ligand to metal charge transfer (LMCT) transition, which corresponds to an excitation from the Cys p orbital to the singly occupied orbital (SOMO).…”

Section: Introductionmentioning

confidence: 99%

“…10 Blue copper proteins have also been studied with electronic circular dichroism (CD) spec-troscopy. 6,7 There are more distinct bands in the CD spectra compared to the absorption spectra.…”

Section: Introductionmentioning

confidence: 99%

“…In particular, the intensity of the band arising from the LMCT excitation is reduced relative to the ligand field bands. 6,7 In addition to experimental work, a number of theoretical studies have investigated the structure or spectroscopy of the oxidised form of blue copper proteins. [11][12][13][14][15][16][17][18][19][20]22,[24][25][26] Calculations confirm that the intense band observed in the absorption spectrum arises from an excitation from the orbital comprising a bonding mixture of the Cu 3d x 2 y 2 and S cys 3p p orbitals to the SOMO.…”

Section: Introductionmentioning

confidence: 99%

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Computational Study of the Structure and Electronic Circular Dichroism Spectroscopy of Blue Copper Proteins

Deeth

Besley

2013

J. Phys. Chem. B

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The calculation of the electronic circular dichroism (CD) spectra of the oxidised form of the blue copper proteins plastocyanin and cucumber basic protein and the relationship between the observed spectral features and the structure of the active site of the protein is investigated.Excitation energies and transition strengths are computed using multi reference configuration interaction, and it is shown that computed spectra based on coordinates from the crystal structure or a single structure optimised in quantum mechanics/molecular mechanics (QM/MM) or ligand field molecular mechanics (LFMM) are qualitatively incorrect. In particular, the rotational strength of the ligand to metal charge transfer band is predicted to be too small or have the incorrect sign. By considering calculations on active site models with modified structures it is shown that the intensity of this band is sensitive to the non-planarity of the histidine and cysteine ligands coordinated to copper. Calculation of the ultraviolet absorption and CD spectra based upon averaging over many structures drawn from a LFMM molecular dynamics simulation are in good agreement with experiment, and superior to analogous calculations based upon structures from a classical molecular dynamics simulation. This provides evidence that the LFMM force field provides an accurate description of the molecular dynamics of these proteins.

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Spectroscopic and Geometric Variations in Perturbed Blue Copper Centers: Electronic Structures of Stellacyanin and Cucumber Basic Protein

Cited by 139 publications

References 37 publications

Theoretical Study of the Electronic Spectra of Small Molecules That Incorporate Analogues of the Copper–Cysteine Bond

Theoretical Study of the Electronic Spectra of Small Molecules That Incorporate Analogues of the Copper–Cysteine Bond

Thermodynamic equilibrium between blue and green copper sites and the role of the protein in controlling function

Computational Study of the Structure and Electronic Circular Dichroism Spectroscopy of Blue Copper Proteins

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