Outer-sphere contributions to the electronic structure of type zero copper proteins

Analysis of a Cu-Doped Metal-Organic Framework, MFM-520(Zn1-x Cux ), for NO2 Adsorption

MFM-520(Zn) confines dimers of NO2 with a high adsorption of 4.52 mmol g-1 at 1 bar at 298 K. The synthesis and the incommensurate structure of Cu-doped MFM-520(Zn) are reported. The introduction of paramagnetic Cu2+ sites allows investigation of the electronic and geometric structure of metal site by in situ electron paramagnetic resonance (EPR) spectroscopy upon adsorption of NO2 . By combining continuous wave and electron-nuclear double resonance spectroscopy, an unusual reverse Berry distorted coordination geometry of the Cu2+ centers is observed. Interestingly, Cu-doped MFM-520(Zn0.95 Cu0.05 ) shows enhanced adsorption of NO2 of 5.02 mmol g-1 at 1 bar at 298 K. Whereas MFM-520(Zn) confines adsorbed NO2 as N2 O4 , the presence of monomeric NO2 at low temperature suggests that doping with Cu2+ centers into the framework plays an important role in tuning the dimerization of NO2 molecules in the pore via the formation of specific host-guest interactions.

Profiling charge transport: A new computational approach

To maintain life, charge transfer processes must be efficient to allow electrons to migrate across distances as large as 30-50 Å within a timescale from picoseconds to milliseconds, and the free-energy cost should not exceed one electron volt. By employing local ionization and local affinity energies, we calculated the pathway for electron and electron-hole transport, respectively. The pathway is then used to calculate both the driving force and the activation energy. The electronic coupling is calculated using configuration interaction procedure. When the charge acceptor is not known, as in oxidative stress, the charge transport terminals are found using Monte-Carlo simulation. These parameters were used to calculate the rate described by Marcus theory. Our approach has been elaborately explained using the famous androstane example and then applied to two proteins: electron transport in azurin protein and hole-hopping migration route from the heme center of cytochrome c peroxidase to its surface. This model gives an effective method to calculate the charge transport pathway and the free-energy profile within 0.1 eV from the experimental measurements and electronic coupling within 3 meV.

On the roles of methionine and the importance of its microenvironments in redox metalloproteins

The amino acid residue methionine (Met) is commonly thought of as a ligand in redox metalloproteins, for example in cytochromes c and in blue copper proteins. However, the roles of Met can go beyond a simple ligand. The thioether functional group of Met allows it to be considered as a hydrophobic residue as well as one that is capable of weak dipolar interactions. In addition, the lone pairs on sulphur allow Met to interact with other groups, inluding the aforementioned metal ions. Because of its properties, Met can play diverse roles in metal coordination, fine tuning of redox reactions, or supporting protein structures. These roles are strongly influenced by the nature of the surrounding medium. Herein, we describe several common interactions between Met and surrounding aromatic amino acids and how they affect the physical properties of both copper and iron metalloproteins. While the importance of interactions between Met and other groups is established in biological systems, less is known about their roles in redox metalloproteins and our view is that this is an area that is ready for greater attention.

Converged Structural and Spectroscopic Properties for Refined QM/MM Models of Azurin

Blue copper proteins continue to challenge experiment and theory with their electronic structure and spectroscopic properties that respond sensitively to the coordination environment of the copper ion. In this work, we report state-of-the art electronic structure studies for geometric and spectroscopic properties of the archetypal "Type I" copper protein azurin in its Cu(II) state. A hybrid quantum mechanics/molecular mechanics (QM/MM) approach is used, employing both density functional theory (DFT) and coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) methods for the QM region, the latter method making use of the domain-based local pair natural orbital (DLPNO) approach. Models of increasing QM size are employed to investigate the convergence of critical geometric parameters. It is shown that convergence is slow and that a large QM region is critical for reproducing the short experimental Cu-SCys112 distance. The study of structural convergence is followed by investigation of spectroscopic parameters using both DFT and DLPNO-CC methods and comparing these to the experimental spectrum using simulations. The results allow us to examine for the first time the distribution of spin densities and hyperfine coupling constants at the coupled cluster level, leading us to revisit the experimental assignment of the 33S hyperfine splitting. The wavefunction-based approach to obtain spin-dependent properties of open-shell systems demonstrated here for the case of azurin is transferable and applicable to a large array of bioinorganic systems.

Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase

Biocatalytic copper centers are generally involved in the activation and reduction of dioxygen, with only few exceptions known. Here we report the discovery and characterization of a previously undescribed copper center that forms the active site of a copper-containing enzyme thiocyanate dehydrogenase (suggested EC 1.8.2.7) that was purified from the haloalkaliphilic sulfur-oxidizing bacterium of the genus Thioalkalivibrio ubiquitous in saline alkaline soda lakes. The copper cluster is formed by three copper ions located at the corners of a near-isosceles triangle and facilitates a direct thiocyanate conversion into cyanate, elemental sulfur, and two reducing equivalents without involvement of molecular oxygen. A molecular mechanism of catalysis is suggested based on high-resolution three-dimensional structures, electron paramagnetic resonance (EPR) spectroscopy, quantum mechanics/molecular mechanics (QM/MM) simulations, kinetic studies, and the results of site-directed mutagenesis.

Mechanical Deformation and Electronic Structure of a Blue Copper Azurin in a Solid-State Junction

Protein-based electronics is an emerging field which has attracted considerable attention over the past decade. Here, we present a theoretical study of the formation and electronic structure of a metal-protein-metal junction based on the blue-copper azurin from pseudomonas aeruginosa. We focus on the case in which the protein is adsorbed on a gold surface and is contacted, at the opposite side, to an STM (Scanning Tunneling Microscopy) tip by spontaneous attachment. This has been simulated through a combination of molecular dynamics and density functional theory. We find that the attachment to the tip induces structural changes in the protein which, however, do not affect the overall electronic properties of the protein. Indeed, only changes in certain residues are observed, whereas the electronic structure of the Cu-centered complex remains unaltered, as does the total density of states of the whole protein.

Magnetic circular dichroism spectra of transition metal complexes calculated from restricted active space wavefunctions

Multiconfigurational restricted active space (RAS) self-consistent field (SCF) or configuration interaction (CI) approaches, augmented with a treatment of spin–orbit coupling by state interaction, were used to calculate the magnetic circular dichroism , , and/or for closed- and open-shell transition metal complexes.

Clarifying the Copper Coordination Environment in a de Novo Designed Red Copper Protein

Cupredoxins are copper-dependent electron-transfer proteins that can be categorized as blue, purple, green, and red depending on the spectroscopic properties of the Cu(II) bound forms. Interestingly, despite significantly different first coordination spheres and nuclearity, all cupredoxins share a common Greek Key β-sheet fold. We have previously reported the design of a red copper protein within a completely distinct three-helical bundle protein, α3DChC2. (1) While this design demonstrated that a β-barrel fold was not requisite to recapitulate the properties of a native cupredoxin center, the parent peptide α3D was not sufficiently stable to allow further study through additional mutations. Here we present the design of an elongated protein GRANDα3D (GRα3D) with Δ Gu = -11.4 kcal/mol compared to the original design's -5.1 kcal/mol. Diffraction quality crystals were grown of GRα3D (a first for an α3D peptide) and solved to a resolution of 1.34 Å. Examination of this structure suggested that Glu41 might interact with the Cu in our previously reported red copper protein. The previous bis(histidine)(cysteine) site (GRα3DChC2) was designed into this new scaffold and a series of variant constructs were made to explore this hypothesis. Mutation studies around Glu41 not only prove the proposed interaction, but also enabled tuning of the constructs' hyperfine coupling constant from 160 to 127 × 10-4 cm-1. X-ray absorption spectroscopy analysis is consistent with these hyperfine coupling differences being the result of variant 4p mixing related to coordination geometry changes. These studies not only prove that an Glu41-Cu interaction leads to the α3DChC2 construct's red copper protein like spectral properties, but also exemplify the exact control one can have in a de novo construct to tune the properties of an electron-transfer Cu site.

Accurate Quantum Mechanical/Molecular Mechanical Calculations of Reduction Potentials in Azurin Variants

Understanding the regulation mechanism and molecular determinants of the reduction potential of metalloprotein is a major challenge. An ab initio quantum mechanical/molecular mechanical (QM/MM) method combining the minimum free energy path (MFEP) and fractional number of electron (FNE) approaches has been developed in our group to simulate the redox processes of large systems. The FNE scheme provides an efficient unique description for the redox process, while the MFEP method provides improved conformational sampling on complex environments such as protein in the QM/MM calculations. The reduction potentials of wild-type and seven mutants of azurin, a type 1 copper metalloprotein, were simulated with the QM/MM-MFEP+FNE approach in this paper. A range of 350 mV for the variations of the reduction potentials of these azurin proteins was reproduced faithfully with relative errors around 20 mV. The correlation between structural interactions and reduction potentials observed in simulations provides in-depth insight into the regulation of reduction potentials, which potentially can also be very useful to the engineering of metalloprotein-based electrocatalysts in artificial photosynthesis. The excellent accuracy and efficiency of the QM/MM-MFEP+FNE approach demonstrate the potential for simulations of many electron transfer processes in condensed phases and biochemical systems.

Engineering a bifunctional copper site in the cupredoxin fold by loop-directed mutagenesis

Copper sites in proteins are designed to perform either electron transfer or redox catalysis. Type 1 and CuA sites are electron transfer hubs bound to a rigid protein fold that prevents binding of exogenous ligands and side reactions. Here we report the engineering of two Type 1 sites by loop-directed mutagenesis within a CuA scaffold with unique electronic structures and functional features. A copper-thioether axial bond shorter than the copper-thiolate bond is responsible for the electronic structure features, in contrast to all other natural or chimeric sites where the copper thiolate bond is short. These sites display highly unusual features, such as: (1) a high reduction potential despite a strong interaction with the axial ligand, which we attribute to changes in the hydrogen bond network and (2) the ability to bind exogenous ligands such as imidazole and azide. This strategy widens the possibility of using natural protein scaffolds with functional features not present in nature.

Ab initio electronic structure calculations of entire blue copper azurins

We present a theoretical study of the blue-copper azurin extracted from Pseudomonas aeruginosa and several of its single amino acid mutants.

A new series of tetrahedral Co(ii) complexes [CoLX2] (X = NCS, Cl, Br, I) manifesting single-ion magnet features

The influence of ligand field strength on the magnetic anisotropy of a series of isostructural tetrahedral Co^II complexes has been investigated by using a combined experimental and theoretical approach.

Magnetic circular dichroism of UCl6− in the ligand-to-metal charge-transfer spectral region

We present a combined ab initio theoretical and experimental study of the magnetic circular dichroism (MCD) spectrum of the octahedral UCl₆⁻ complex ion in the UV-Vis spectral region.

Modular Artificial Cupredoxins

Cupredoxins are electron-transfer proteins that have active sites containing a mononuclear Cu center with an unusual trigonal monopyramidal structure (Type 1 Cu). A single Cu-Scys bond is present within the trigonal plane that is responsible for its unique physical properties. We demonstrate that a cysteine-containing variant of streptavidin (Sav) can serve as a protein host to model the structure and properties of Type 1 Cu sites. A series of artificial Cu proteins are described that rely on Sav and a series of biotinylated synthetic Cu complexes. Optical and EPR measurements highlight the presence of a Cu-Scys bond, and XRD analysis provides structural evidence. We further provide evidence that changes in the linker between the biotin and Cu complex within the synthetic constructs allows for small changes in the placement of Cu centers within Sav that have dramatic effects on the structural and physical properties of the resulting artificial metalloproteins. These findings highlight the utility of the biotin-Sav technology as an approach for simulating active sites of metalloproteins.

Reversible S-nitrosylation in an engineered azurin

S-Nitrosothiols are known as reagents for NO storage and transportation and as regulators in many physiological processes. Although the S-nitrosylation catalysed by haem proteins is well known, no direct evidence of S-nitrosylation in copper proteins has been reported. Here, we report reversible insertion of NO into a copper-thiolate bond in an engineered copper centre in Pseudomonas aeruginosa azurin by rational design of the primary coordination sphere and tuning its reduction potential by deleting a hydrogen bond in the secondary coordination sphere. The results not only provide the first direct evidence of S-nitrosylation of Cu(II)-bound cysteine in metalloproteins, but also shed light on the reaction mechanism and structural features responsible for stabilizing the elusive Cu(I)-S(Cys)NO species. The fast, efficient and reversible S-nitrosylation reaction is used to demonstrate its ability to prevent NO inhibition of cytochrome bo3 oxidase activity by competing for NO binding with the native enzyme under physiologically relevant conditions.

Asn47 and Phe114 modulate the inner sphere reorganization energies of type zero copper proteins

The geometric structures and electron transfer properties of type 1 Cu proteins are reasonably understood at the molecular level (E. I. Solomon and R. G. Hadt, Coord. Chem. Rev., 2011, 255, 774-789, J. J. Warren, K. M. Lancaster, J. H. Richards and H. B. Gray, J. Inorg. Biochem., 2012, 115, 119-126). Much understanding of type 1 copper electron transfer reactivity has come from site directed mutagenesis studies. For example, artificial "type zero" Cu-centres constructed in cupredoxin-azurin have showcased the capacity of outer-sphere hydrogen bonding networks to enhance Cu II/I electron transfer reactivity. In this paper, we have elaborated on earlier kinetics and electronic structural studies of type zero Cu by calculating the inner sphere reorganization energies of type 1, type 2, and type zero Cu proteins using density functional theory (DFT). Although the choice of density functionals for copper systems is not straightforward, we have benchmarked the density functionals against the recently reported ESI-PES data for two synthetic copper models (S. Niu, D.-L. Huang, P. D. Dau, H.-T. Liu, L.-S. Wang and T. J. Ichiye, Chem. Theory Comput., 2014, 10, 1283). For the Cu proteins, our calculations predict that changes in the coordination number upon metal reduction lead to large inner sphere reorganization energies for type 2 Cu sites, whereas retention in the coordination number is observed for type zero Cu sites. These variations in the coordination number are modulated by the outer-sphere coordinating residues Asn47 and Phe114, which are involved in hydrogen bonding with the Asp112 side chain.

Synthesis, structural and theoretical studies of dithiodiglycolamide compounds of palladium(II)

The reaction of palladium(ii) halide with dithiodiglycolamide ligands yielded compounds of the type [PdX2L] (where X = Cl, L = (CH2SCH2CON(i)Pr2)2 (1); L = (CH2SCH2CON(i)Bu2)2 (2); L = (CH2SCH2CONBu2)2 (3); L = C7H6(SCH2CON(i)Bu2)2 (4); X = Br, L = (CH2SCH2CON(i)Bu2)2 (5); X = I, L = (CH2SCH2CON(i)Bu2)2 (6)), whereas palladium(ii) nitrate yielded compounds of the type [PdL2](NO3)2 (where L = (CH2SCH2CON(i)Pr2)2 (7); L = (CH2SCH2CON(i)Bu2)2 (8)). All compounds were characterized by using IR, (1)H NMR spectral techniques and CHN analyses. The structures of compounds 4, 5 and 7 have been determined by using X-ray diffraction methods. The structures show that the ligands bond through the thioether group to the metal centre in all compounds. They show further that the palladium(ii) ion is surrounded by four atoms (two halogens and two thio groups in 4 and 5 and four thio groups in 7) in a square planar arrangement. The dithiodiglycolamide ligand acts as a bidentate chelating ligand and bonds through both the thioether groups to the metal centre, leaving the carbamoyl groups uncoordinated. Theoretical studies reveal that the 1 : 2 compound is energetically more stable and nicely correlates with the IR carbamoyl stretching frequencies as compared to the 1 : 1 compound in which the ligand acts as a tetradentate ligand.

Molecular dynamics simulations of apocupredoxins: insights into the formation and stabilization of copper sites under entatic control

Cupredoxins perform copper-mediated long-range electron transfer (ET) in biological systems. Their copper-binding sites have evolved to force copper ions into ET-competent systems with decreased reorganization energy, increased reduction potential, and a distinct electronic structure compared with those of non-ET-competent copper complexes. The entatic or rack-induced state hypothesis explains these special properties in terms of the strain that the protein matrix exerts on the metal ions. This idea is supported by X-ray structures of apocupredoxins displaying "closed" arrangements of the copper ligands like those observed in the holoproteins; however, it implies completely buried copper-binding atoms, conflicting with the notion that they must be exposed for copper loading. On the other hand, a recent work based on NMR showed that the copper-binding regions of apocupredoxins are flexible in solution. We have explored five cupredoxins in their "closed" apo forms through molecular dynamics simulations. We observed that prearranged ligand conformations are not stable as the X-ray data suggest, although they do form part of the dynamic landscape of the apoproteins. This translates into variable flexibility of the copper-binding regions within a rigid fold, accompanied by fluctuations of the hydrogen bonds around the copper ligands. Major conformations with solvent-exposed copper-binding atoms could allow initial binding of the copper ions. An eventual subsequent incursion to the closed state would result in binding of the remaining ligands, trapping the closed conformation thanks to the additional binding energy and the fastening of noncovalent interactions that make up the rack.

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes

In this study, a set of 50 transition-metal complexes of Cu(I) and Cu(II), were used in the evaluation of 18 density functionals in geometry determination. In addition, 14 different basis sets were considered, including four commonly used Pople's all-electron basis sets; four basis sets including popular types of effective-core potentials: Los Alamos, Steven-Basch-Krauss, and Stuttgart-Dresden; and six triple-ζ basis sets. The results illustrate the performance of different methodological alternatives for the treatment of geometrical properties in relevant copper complexes, pointing out Double-Hybrid (DH) and Long-range Correction (LC) Generalized Gradient Approximation (GGA) methods as better descriptors of the geometry of the evaluated systems. These however, are associated with a computational cost several times higher than some of the other methods employed, such as the M06 functional, which has also demonstrated a comparable performance. Regarding the basis sets, 6-31+G(d) and 6-31+G(d,p) were the best performing approaches. In addition, the results show that the use of effective-core potentials has a limited impact, in terms of the accuracy in the determination of metal-ligand bond-lengths and angles in our dataset of copper complexes. Hence, these could become a good alternative for the geometrical description of these systems, particularly CEP-121G and SDD basis sets, if one is considering larger copper complexes where the computational cost could be an issue.

Electron self-exchange of cytochrome c measured via13C detected protonless NMR

The use of protonless 13C′–13C′ EXSY (COCO-EXSY) is proposed here to measure electron self-exchange rates. The experiment is compared to the commonly employed 1H and 15N EXSY experiments using as a reference system human cytochrome c. In COCO-EXSY, the exchange peaks are stronger than in the other experiments with respect to the self peaks and their intensity is less dependent on the choice of the EXSY mixing time. The use of 13C directed detection may be essential for all those cases where T2 relaxation is detrimental, as in the case of proteins containing highly paramagnetic metal centers, or rotating slowly in solution, or where the amide signals are difficult to detect due to chemical or conformational exchange. The proposed experiment has a general applicability and can be used to monitor exchange phenomena different from electron self-exchange.

Inner- and outer-sphere metal coordination in blue copper proteins

Blue copper proteins (BCPs) comprise classic cases of Nature's profound control over the electronic structures and chemical reactivity of transition metal ions. Early studies of BCPs focused on their inner coordination spheres, that is, residues that directly coordinate Cu. Equally important are the electronic and geometric perturbations to these ligands provided by the outer coordination sphere. In this tribute to Hans Freeman, we review investigations that have advanced the understanding of how inner-sphere and outer-sphere coordination affects biological Cu properties.

Spin delocalization over type zero copper

Hard-ligand, high-potential copper sites have been characterized in double mutants of Pseudomonas aeruginosa azurin (C112D/M121X (X = L, F, I)). These sites feature a small A(zz)(Cu) splitting in the EPR spectrum together with enhanced electron transfer activity. Due to these unique properties, these constructs have been called "type zero" copper sites. In contrast, the single mutant, C112D, features a large A(zz)(Cu) value characteristic of the typical type 2 Cu(II). In general, A(zz)(Cu) comprises contributions from Fermi contact, spin dipolar, and orbital dipolar terms. In order to understand the origin of the low A(zz)(Cu) value of type zero Cu(II), we explored in detail its degree of covalency, as manifested by spin delocalization over its ligands, which affects A(zz)(Cu) through the Fermi contact and spin dipolar contributions. This was achieved by the application of several complementary EPR hyperfine spectroscopic techniques at X- and W-band (∼9.5 and 95 GHz, respectively) frequencies to map the ligand hyperfine couplings. Our results show that spin delocalization over the ligands in type zero Cu(II) is different from that of type 2 Cu(II) in the single C112D mutant. The (14)N hyperfine couplings of the coordinated histidine nitrogens are smaller by about 25-40%, whereas that of the (13)C carboxylate of D112 is about 50% larger. From this comparison, we concluded that the spin delocalization of type zero copper over its ligands is not dramatically larger than in type 2 C112D. Therefore, the reduced A(zz)(Cu) value of type zero Cu(II) is largely attributable to an increased orbital dipolar contribution that is related to its larger g(zz) value, as a consequence of the distorted tetrahedral geometry. The increased spin delocalization over the D112 carboxylate in type zero mutants compared to type 2 C112D suggests that electron transfer paths involving this residue are enhanced.