Electronic structure of the oxidized and reduced blue copper sites: contributions to the electron transfer pathway, reduction potential, and geometry (original) (raw)
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Electronic structure contributions to function in bioorganic chemistry: The blue copper active site
Pure and Applied Chemistry, 1998
The blue copper site has a unique electronic structure which contributes to its electron transfer function and is reflected in unique spectral properties. The HOMO in the oxidized blue Cu site exhibits high anisotripic covalency which enhances intra-and inter-protein electron transfer rates. The electronic structure of the reduced dlo blue Cu centers is developed using a combination of variable energy photoelectron spectroscopy and density functional calculations. These studies establish the change in electronic structure that occurs upon oxidation of the blue Cu center and permit an evaluation of whether the reduced geometry is imposed on the oxidized site by the protein (i.e. the entatidrack state). Studies of the perturbed blue Cu site in nitrite reductase demonstrate that a tetragonal distortion is the origin of the perturbed spectral features of this site. This distortion derives from a Jahn-Teller force along an -E(u) mode not present in the classic blue copper proteins and reflects differences in protein contributions to active site structure.
Electronic Structures of Active Sites in Copper Proteins and Their Contributions to Reactivity
Advances in chemistry series, 1996
Contents I. Introduction I I. Normal Cupric Complexes I I I. Blue Copper Proteins A. Nature of the Ligand-Metal Bonding Interactions B. Nature of the Ground-State Wave Function A. Origin of Excited-State Spectral Features B. Electronic Structure of Oxyhemocyanin C. Molecular Mechanism of Tyrosinase A. Coupled Binuciear/T3 Copper Site B. Trinuclear Copper Cluster Site C. Oxygen Reactivity and Intermediates IV. Coupled Binuclear Copper Proteins V. Multicopper Oxidases Comparison VI. Future Directions V I I. Abbreviations V I I I. References 52 1 52 1
Electronic structure and its relation to function in copper proteins
Current Opinion in Chemical Biology, 2002
Spectroscopic and theoretical investigations of the geometric and electronic structures of mononuclear and binuclear copper sites in proteins help in understanding the contributions of these proteins to biological electron transfer. Spectroscopically calibrated density functional theory calculations, which give reasonable bonding descriptions in both ground- and excited-states, define the role of the protein in determining the geometric and electronic structure of the active site.
Springer eBooks, 1993
Contents I. Introduction I I. Normal Cupric Complexes I I I. Blue Copper Proteins A. Nature of the Ligand-Metal Bonding Interactions B. Nature of the Ground-State Wave Function A. Origin of Excited-State Spectral Features B. Electronic Structure of Oxyhemocyanin C. Molecular Mechanism of Tyrosinase A. Coupled Binuciear/T3 Copper Site B. Trinuclear Copper Cluster Site C. Oxygen Reactivity and Intermediates IV. Coupled Binuclear Copper Proteins V. Multicopper Oxidases Comparison VI. Future Directions V I I. Abbreviations V I I I. References 52 1 52 1
The Journal of Chemical Physics, 2010
Structural and energetic reorganizations in redox reaction of type 1 copper proteins are studied by density functional and ab initio molecular orbital calculations. Model complexes of the active site with varying number of ligands, from Cu͑SCH 3 ͒ 0/+ to Cu͑SCH 3 ͒͑Im͒ 2 ͑S͑CH 3 ͒ 2 ͒ 0/+ , where Im denotes imidazole, are investigated. Following the findings of structural instability in Cu͑I͒ ϫ͑SCH 3 ͒͑Im͒ 2 and its stabilization by the addition of the axial methionine ͑Met͒ ligand model, the structure and energetics are examined as functions of the Cu-S Met distance in the range of 2.1-3.3 Å. The reorganization energies in both redox states exhibit a minimum at the Cu-S Met distance of ϳ2.4 Å, whereas the ionization potential increases monotonically. The changes of reorganization energies correlate well with one of the Cu-N His distances rather than the Cu-S Cys distance. The estimated Arrhenius factor for oxidation of plastocyanin by P700 + ͑in photosystem I͒ changes by an order of magnitude when the Cu-S Met distance fluctuates between 2.4 and 3.0 Å, whereas the factor for reduction of plastocyanin by cytochrome f is nearly constant. Together with the data from our previous classical molecular dynamics simulation of solvated protein, we argue that the electron transfer rate is affected, and thus may be controlled, by the fluctuation of a weakly bound axial Met ligand. We also present the assessment of various exchange-correlation functionals, including those with the long-range correction, against the CCSD͑T͒ reference and on the basis of a perturbative adiabatic connection model. For Cu͑SCH 3 ͒ and Cu͑SCH 3 ͒͑Im͒, simple correlations have been found between the reorganization energies and the amount of Hartree-Fock exchange.
Quantum chemical calculations of the reorganization energy of blue-copper proteins
Protein Science - PROTEIN SCI, 1998
The inner-sphere reorganization energy for several copper complexes related to the active site in blue-copper protein has been calculated with the density functional B3LYP method. The best model of the blue-copper proteins, Cu(Im),(SCH3)(S(CH3),)0/+, has a self-exchange inner-sphere reorganization energy of 62 kJ/mol, which is at least 120 k.J/mol lower than for Cu(HZO);/*+. This lowering of the reorganization energy is caused by the soft ligands in the blue-copper site, especially the cysteine thiolate and the methionine thioether groups. Soft ligands both make the potential surfaces of the complexes flatter and give rise to oxidized structures that are quite close to a tetrahedron (rather than tetragonal). Approximately half of the reorganization energy originates from changes in the copper-ligand bond lengths and half of this contribution comes from the Cu-Scys bond. A tetragonal site, which is present in the rhombic type 1 blue-copper proteins, has a slightly higher (16 kJ/mol) inner-sphere reorganization energy than a trigonal site, present in the axial type 1 copper proteins. A site with the methionine ligand replaced by an amide group, as in stellacyanin, has an even higher reorganization energy, about 90 kJ/mol.
Inorganica Chimica Acta, 1996
We investigate with semi-empirical extended Hilckel theory calculations the tunneling matrix element for electron transfer in three ruthenium-modified blue copper azurin molecules from the bacterium Pseudomonas aeruginosa which have been recently synthesized and studied experimentally by Gray and co-workers. All of the atoms in the protein can be included in the calculations with the method of transition amplitudes that has been developed recently. Our particular focus here, however, is to develop procedures that create a truncated protein much smaller than the initial 2000 atom one, the aim being to retain only those amino acids that are important to the electron tunneling mechanism. Such a procedure, which we refer to as 'pruning', is useful, first because it reduces the size of the problem, perhaps allowing for more accurate techniques to be used on the truncated protein, and second because it allows for the identification of the regions in the protein in which the tunneling electron is localized. The pruning procedures enable us to reduce the number of atoms required in an extended H0ekel theory analysis of the tunneling mechanism by approximately a factor of 10 over that in the original protein.
The Journal of Physical Chemistry B, 2013
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.
Advanced Science, 2015
Electron transfer (ET) reactions are central to a wide range of biological processes, notably those of energy conversion such as the respiratory and photosynthetic chains. These employ mostly proteins, between which electrons are shuttled from one electron mediator to another by a redox process, driven by a free energy difference (driving force) between or within the mediators. The separation distance over which an electron is transferred within proteins can reach in some cases around 2.5 nm. One of the most intensively studied group of ET proteins is the blue copper proteins (e.g., plastocyanin, azurin, and the family of multi-copper oxidases). [ 1 ] The copper binding sites were shown to confer unique spectroscopic and thermodynamic properties on the copper ions. [ 2 ] These properties attracted studies aiming at understanding their role in the ET via proteins. Here we focus on the bacterial blue copper protein azurin (Az), functioning as an electron mediator in certain bacterial respiratory chains. [ 3 ] Most of the studies of the ET process in Az were done in solution, using spectroscopy, mainly fl ash-quench [ 4 ] or pulse-radiolysis [ 5 ] techniques. A common denominator of these studies is monitoring the ET process between the Cu ion of Az and an intramolecular donor/acceptor. In another experimental approach for measuring intramolecular ET process in Az, the protein is bound to a conductive electrode and ET can be measured between the Cu ion and the electrode as a rate-determining step of an electrochemical redox process in an electrochemical cell. [ 6 ] In contrast, electronic transport (ETp) via the protein has more recently been studied by measuring conductance across Az, trapped between two electrodes in a solid-state confi guration. [ 7 ] One pronounced difference between measuring ET in solution by spectroscopy or electrochemistry and measuring the ETp in a solid-state confi guration is that while the former requires a redox process to occur and, thus, the presence of a redox-active center (such as the Cu ion, a disulphide bond or a bound external Ru complex), the latter does not. Electron transfer (ET) proteins are biomolecules with specifi c functions, selected by evolution. As such they are attractive candidates for use in potential bioelectronic devices. The blue copper protein azurin (Az) is one of the most-studied ET proteins. Traditional spectroscopic, electrochemical, and kinetic methods employed for studying ET to/from the protein's Cu ion have been complemented more recently by studies of electrical conduction through a monolayer of Az in the solid-state, sandwiched between electrodes. As the latter type of measurement does not require involvement of a redox process, it also allows monitoring electronic transport (ETp) via redox-inactive Az-derivatives. Here, results of macroscopic ETp via redox-active and-inactive Az derivatives, i.e., Cu(II) and Cu(I)-Az, apo-Az, Co(II)-Az, Ni(II)-Az, and Zn(II)-Az are reported and compared. It is found that earlier reported temperature independence of ETp via Cu(II)-Az (from 20 K until denaturation) is unique, as ETp via all other derivatives is thermally activated at temperatures >≈200 K. Conduction via Cu(I)-Az shows unexpected temperature dependence >≈200 K, with currents decreasing at positive and increasing at negative bias. Taking all the data together we fi nd a clear compensation effect of Az conduction around the Az denaturation temperature. This compensation can be understood by viewing the Az binding site as an electron trap, unless occupied by Cu(II), as in the native protein, with conduction of the native protein setting the upper transport effi ciency limit. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.