X-ray absorption spectroscopic studies of the blue copper site: metal and ligand K-edge studies to probe the origin of the EPR hyperfine splitting in plastocyanin

Shadle, Susan E.; Penner‐Hahn, James E.; Schugar, Harvey J.; Hedman, Britt; Hodgson, Keith O.; Solomon, Edward I.

doi:10.1021/ja00055a057

Cited by 284 publications

(420 citation statements)

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“…A variety of spectroscopic techniques have been applied to study these proteins, predominantly by Solomon and co-workers. [10][11][12][13] Also of interest are model systems, such as CuCl 2À 4 , which have been used to inform the interpretation of the protein spectra. 7 In the ultraviolet (UV) and visible regions of the spectrum, ligand field and charge transfer excitations occur, arising from d ' d and d ' ligand excitations, respectively.…”

Section: Introductionmentioning

confidence: 99%

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: Introductionmentioning

confidence: 99%

Modelling the spectroscopy and dynamics of plastocyanin

Robinson

Besley

2010

Phys. Chem. Chem. Phys.

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“…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%

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.

194

309

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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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“…In particular, the metal sites of blue copper proteins are characterized by a short coppersulfur bond. This unusual geometry is believed to be the main reason for the strong covalency of the metal site (10,16,17) and, thus, responsible for the rapid and long-range electron transfer reactivity (18-22) that characterizes the blue copper proteins. Detailed knowledge of the geometric and electronic metal site structures of the blue copper proteins is, therefore, imperative for understanding the function of the proteins at the molecular level.…”

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confidence: 99%

“…So far, the geometric structure of the metal site in blue copper proteins (12)(13)(14) has been determined primarily by x-ray crystallography and extended x-ray absorption fine structure (3,23,24), whereas the electronic structure of the blue copper site has been determined theoretically from quantum chemical calculations (5,(25)(26)(27) and experimentally by x-ray absorption spectroscopy (16,17), and more recently by nuclear paramagnetic relaxation (28)(29)(30)(31). These structures have formed the basis for a detailed understanding of the biological function of the proteins by elucidating the interplay between the electronic and geometric structure of the metal site (8,15,(32)(33)(34).…”

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confidence: 99%

“…Because the paramagnetic restraints are derived from the relaxation rates of nuclei close to the metal site, the point dipole approximation of the electron spin fails and a description of the paramagnetic relaxation that takes the electron delocalization into account must be used (37). Therefore, the approach requires knowledge of the distribution of the unpaired electron spin, which can be obtained experimentally by x-ray absorption spectroscopy (16,17), electron nuclear double resonance (38), paramagnetic NMR (28-31) spectroscopy, or theoretically by quantum chemical calculations (5,(25)(26)(27). The blue copper protein, plastocyanin from Anabaena variabilis (A.v.…”

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Determination of the geometric structure of the metal site in a blue copper protein by paramagnetic NMR

Hansen

Led

2006

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

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The biological function of metalloproteins is closely tied to the geometric and electronic structures of the metal sites. Here, we show that the geometric structure of the metal site of a metalloprotein in solution can be determined from experimentally measured electron-nuclear spin-spin interactions obtained by NMR. Thus, the geometric metal site structure of plastocyanin from Anabaena variabilis was determined by including the paramagnetic relaxation enhancement of protons close to the copper site as restraints in a conventional NMR structure determination, together with the distribution of the unpaired electron onto the ligand atoms. Also, the interproton distances (nuclear Overhauser enhancements) and dihedral angles (scalar nuclear spin-spin couplings) normally used in NMR structure determinations were included as restraints. The structure calculations were carried out with the program X-PLOR and a module that takes into account the specific characteristics of the paramagnetic restraints. A well defined metal site structure was obtained with the structural characteristics of the blue copper site, including a distorted tetrahedral geometry, a short Cu-Cys S ␥ bond, and a long Cu-Met S ␦ bond. Overall, the agreement of the obtained metal site structure of Anabaena variabilis plastocyanin with those of other plastocyanins obtained by x-ray crystallography confirms the reliability of the approach.metal site structure ͉ metalloproteins ͉ paramagnetic nuclear relaxation T he biological function of many metalloproteins stems from the geometric and electronic structures of the metal sites imposed by the protein environment. In the blue copper proteins, such as plastocyanins, amicyanins, and azurins, the geometry of the copper site is unusual as compared with smallmolecule copper complexes (1-15). In particular, the metal sites of blue copper proteins are characterized by a short coppersulfur bond. This unusual geometry is believed to be the main reason for the strong covalency of the metal site (10,16,17) and, thus, responsible for the rapid and long-range electron transfer reactivity (18-22) that characterizes the blue copper proteins. Detailed knowledge of the geometric and electronic metal site structures of the blue copper proteins is, therefore, imperative for understanding the function of the proteins at the molecular level.So far, the geometric structure of the metal site in blue copper proteins (12-14) has been determined primarily by x-ray crystallography and extended x-ray absorption fine structure (3,23,24), whereas the electronic structure of the blue copper site has been determined theoretically from quantum chemical calculations (5, 25-27) and experimentally by x-ray absorption spectroscopy (16, 17), and more recently by nuclear paramagnetic relaxation (28-31). These structures have formed the basis for a detailed understanding of the biological function of the proteins by elucidating the interplay between the electronic and geometric structure of the metal site (8,15,(32)(33)(34). However, the geomet...

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X-ray absorption spectroscopic studies of the blue copper site: metal and ligand K-edge studies to probe the origin of the EPR hyperfine splitting in plastocyanin

Cited by 284 publications

References 1 publication

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

Determination of the geometric structure of the metal site in a blue copper protein by paramagnetic NMR

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