Rational De Novo Design of a Cu Metalloenzyme for Superoxide Dismutation

Superoxide dismutases (SODs) are highly efficient enzymes for superoxide dismutation and the first line of defense against oxidative stress. These metalloproteins contain a redox-active metal ion in their active site (Mn, Cu, Fe, Ni) with a tightly controlled reduction potential found in a close range around the optimal value of 0.36 V versus the normal hydrogen electrode (NHE). Rationally designed proteins with well-defined three-dimensional structures offer new opportunities for obtaining functional SOD mimics. Here, we explore four different copper-binding scaffolds: H₃ (His₃), H₄ (His₄), H₂DH (His₃Asp with two His and one Asp in the same plane) and H₃D (His₃Asp with three His in the same plane) by using the scaffold of the de novo protein GRα₃D. EPR and XAS analysis of the resulting copper complexes demonstrates that they are good Cu^II-bound structural mimics of Cu-only SODs. Furthermore, all the complexes exhibit SOD activity, though three orders of magnitude slower than the native enzyme, making them the first de novo copper SOD mimics.     

EPR and ligand field studies of iron superoxide dismutases and iron-substituted manganese superoxide dismutases: relationships between electronic structure of the active site and activity

The problem of metal selectivity of iron/manganese superoxide dismutases (SODs) is addressed through the electronic structures of active sites using electron paramagnetic resonance and ligand field calculations. Studies of wild-type iron(III) SOD (FeSOD) from Escherichia coli and from Methanobacterium thermoautotrophicum and iron-substituted manganese(III) SOD (Fe(sub)MnSOD) from E. coli and from Serratia marcescens are reported. EPR spectroscopy of wild-type enzymes shows transitions within all three Kramers doublets identified by their g values. From the temperature dependence of the observed transitions, the zero-field splitting is found to be negative, D = -2 +/- 0.2 cm-1. The electronic structure is typical of a distorted trigonal bipyramid, all the EPR features being reproduced by ligand field analysis. This unique and necessary electronic structure characterizes wild-type enzymes whatever their classification from the amino acid sequence into iron or manganese types, as E. coli FeSOD or M. thermoautotrophicum FeSOD. In iron-substituted manganese SODs, reduced catalytic activity is found. We describe how inhomogeneity of all reported substituted MnSODs might explain the activity decrease. EPR spectra of substituted enzymes show several overlapping components. From simulation of these spectra, one component is identified which shares the same electronic structure of the wild-type FeSODs, with the proportion depending on pH. Ligand field calculations were performed to investigate distortions of the active site geometry which induce variation of the excitation energy of the lowest quartet state. The corresponding coupling between the ground state and the excited state is found to be maximum in the geometry of the native SODs. We conjecture that such coupling should be considered in the electron-transfer process and in the contribution of the typical electronic structure of FeSOD to the activity.     

Manganese(II) zero-field interaction in cambialistic and manganese superoxide dismutases and its relationship to the structure of the metal binding site

The Mn(II) high-magnetic-field electron paramagnetic resonance (HFEPR) spectra of five different superoxide dismutases (SODs) were measured at 190 and 285 GHz. The native E. coli manganese SOD was found to be distinct from the other SODs by virtue of its large zero-field E-value. The two wild-type cambialistic proteins from Porphyromonas gingivalis and Rhodobacter capsulatus were also distinct. However, the Gly155Thr mutant of the P. gingivalis SOD changed the Mn(II) spectrum so that it closely resembled the spectrum of manganese reconstituted E. coli iron SOD. This observation paralleled enzyme activity measurements that show that this mutation causes the loss of activity with manganese and enhanced activity with iron indicating a conversion from a cambialistic to an iron-specific protein. The Mn(II) magnetic parameters were determined by simultaneously fitting the multifrequency data. Simulations were carried out by numerically diagonalizing the spin Hamiltonian and explicitly calculating all possible transition probabilities. The relationship between the Mn(II) zero-field interaction and structure of the metal binding site is also discussed.     

Resolution of three forms of superoxide dismutase by immobilised metal affinity chromatography.

A new method for separation of three forms of superoxide dismutase (SOD) using immobilised metal affinity chromatography (IMAC) is reported. Fe-, Mn- and Cu/Zn-SODs were eluted sequentially from Cu(2+)-IMAC column with an increasing gradient of a counter ion (NH+4) run in combination with an increasing pH gradient (6.8-7.8). The combined gradient elution method resulted in separation of SODs with high resolution, the three proteins being eluted in electrophoretically homogeneous forms. Similar preparation could not be achieved by either increasing gradient of a counter ion or decreasing pH gradients used separately. The described methodology has been successfully applied for separation of three SODs from a protozoan parasite, indicating that this combined gradient elution system for IMAC offers new possibilities for the high-resolution separation of proteins exhibiting only minor differences in their amino acid composition and structure.     

Stability of Cu–Mn bimetal catalysts based on different zeolites for NOx removal from diesel engine exhaust

Cu–Mn bimetal catalysts were prepared to remove nitrogen oxides (NO_x) from diesel engine exhaust at low temperatures. At a Cu/Mn ratio of 3:2, the NO_x conversions at 200 °C reached 65% and 90% on Cu–Mn/ZSM-5 and Cu–Mn/SAPO-34, respectively. After a hydrothermal treatment and reaction in the presence of C₃H₆, the activity of Cu–Mn/SAPO-34 was more stable than that of Cu–Mn/ZSM-5. No obvious variations in the crystal structure or dealumination were observed, whereas the physical structure was best maintained in Cu–Mn/SAPO-34. The atomic concentration of Cu on the surface of Cu–Mn/SAPO-34 was quite stable, and the consumption of octahedrally coordinated Cu²⁺ could be recovered. Conversely, the proportion of octahedrally coordinated Cu²⁺ on the surface of Cu–Mn/ZSM-5 significantly decreased. Therefore, besides the structure, the redox cycle between Cu⁺ and octahedrally coordinated Cu²⁺ played an important role in the stability of the catalysts.     

Tuning the redox properties of manganese(II) and its implications to the electrochemistry of manganese and iron superoxide dismutases

Superoxide dismutases (SODs) catalyze the disproportionation of superoxide to dioxygen and hydrogen peroxide. The active metal sites of iron and manganese superoxide dismutases are structurally indistinguishable from each other. Despite the structural homology, these enzymes exhibit a high degree of metal selective activity suggesting subtle redox tuning of the active site. The redox tuning model, however, up to now has been challenged by the existence of so-called cambialistic SODs that function with either metal ion. We have prepared and investigated two sets of manganese complexes in which groups of varying electron-withdrawing character, as measured by their Hammett constants sigma Para, have been introduced into the ligands. We observed that the Mn(III)/Mn(II) reduction potential for the series based on 4'-X-terpyridine ligands together with the corresponding values for the iron-substituted 4'-X-terpyridine complexes changed linearly with sigma Para. The redox potential of the iron and manganese complexes could be varied by as much as 600 mV by the 4'-substitution with the manganese complexes being slightly more sensitive to the substitution than iron. The difference was such that in the case where the 4'-substituent was a pyrrolidine group both the manganese and the iron complex were thermodynamically competent to catalytically disproportionate superoxide, making this particular ligand "cambialistic". Taking our data and those available from the literature together, it was found that in addition to the electron-withdrawing capacity of the 4'-substituents the overall charge of the Mn(II) complexes plays a major role in tuning the redox potential, about 600 mV per charge unit. The ion selectivity in Mn and FeSODs and the occurrence of cambialistic SODs are discussed in view of these results. We conclude that the more distant electrostatic contributions may be the source of metal specific enzymatic activity.     

The generic geometry of helices and their close-packed structures

The formation of helices is an ubiquitous phenomenon for molecular structures whether they are biological, organic, or inorganic, in nature. Helical structures have geometrical constraints analogous to close-packing of three-dimensional crystal structures. For helical packing the geometrical constraints involve parameters such as the radius of the helical cylinder, the helical pitch angle, and the helical tube radius. In this communication, the geometrical constraints for single helix, double helix, and for double helices with minor and major grooves are calculated. The results are compared with values from the literature for helical polypeptide backbone structures, the α-, π-, 3₁₀-, and γ-helices. The α-helices are close to being optimally packed in the sense of efficient use of space, i.e. close-packed. They are also more densely packed than the other three types of helices. For double helices comparisons are made to the A, B, and Z forms of DNA. The helical geometry of the A form is nearly close-packed. The packing density for the B and Z forms of DNA are found to be approximately equal to each other.     

Selective inhibition of Fe- versus Cu/Zn-superoxide dismutases by 2,3-dihydroxybenzoic acid derivatives

A series of catechol derivatives were synthesised and tested for their ability to inactivate the iron-containing superoxide dismutase (Fe-SOD) from Escherichia coli and the bovine erythrocytes Cu/Zn-SOD. Incubation of catechols with Fe- or Cu/Zn SODs resulted in a time-dependent loss of enzyme activity with highly selective inhibition for the iron-dependent enzyme. Catechol-induced inactivation of SODs was correlated with the auto-oxidation of the catechol compounds to their corresponding ortho-quinone derivatives, which was found to be non-dependent on the presence of enzymes. Mass electrospray experiments on catechol-incubated Fe-SOD provided evidence for the irreversible nature of the inhibition process, yielding to a complex mixture of modified proteins.     

The far infrared spectra of metal chloride complexes of pyridine in relation to their structures

The infrared spectra of the complexes [M(py)₂Cl₂] (py = pyridine; M = Mn, Fe, Co, Ni, Cu, Zn) have been determined within the range 650–150 cm^?1. Assignments of the metal—nitrogen and metal—halogen stretching frequencies (vM—N and vM—Cl) are made on the basis of the band shifts induced by deuteration of the pyridine ring and by varying the coordinated metal ion. If the band of lowest frequency is assigned to a bending mode, the number of vM—N and vM—Cl bands observed agrees with the number required by symmetry considerations based on the known structures of the complexes. On the basis of this work, some earlier assignments have been revised.     

Synthesis of trans,trans,cis-fused tetracyclic skeleton via radical domino cyclization

Limonoids are characterized by a polycyclic structure and show a wide variety of bioactivities. In particular, mesendanin L, 12-hydroxyamoorastatone, and meliatoosenin F have unique structures containing a trans-A/B/C and cis-C/D-fused tetracyclic skeleton. We synthesized the core structure of these limonoids via Mn(OAc)₃ and Cu(OAc)₂-mediated radical domino cyclization of an acyclic tetraene precursor having a terminal β-keto ester. To the best of our knowledge, this is the first example of the radical-mediated construction of a 6/6/6/5-membered tetracyclic skeleton.     

From an inactive prokaryotic SOD homologue to an active protein through site-directed mutagenesis

It is known that several prokaryotic protein sequences, characterized by high homology with the eukaryotic Cu,ZnSODs, lack some of the metal ligands. In the present work, we have stepwise reintroduced the two missing copper ligands in the SOD-like protein of Bacillus subtilis, through site-directed mutagenesis. The mutant with three out of the four His that bind copper is not active, whereas the fully reconstituted mutant displays an activity of about 10% that of human Cu,ZnSOD. The mutated proteins have been characterized in solution and in the solid state. In solution, the proteins experience conformational disorder, which is believed to be partly responsible for the decreased enzymatic activity and sheds light on the tendency of several human SOD mutants to introduce mobility in the protein frame. In the crystal, on the contrary, the protein has a well-defined conformation, giving rise to dimers through the coordination of an exogenous zinc ion. The catalytic properties of the double mutant, which might be regarded as a step in an artificial evolution from a nonactive SOD to a fully functioning enzyme, are discussed on the basis of the structural and dynamical properties.     

二价金属离子激活铜超氧化物歧化酶断裂DNA的活性

以铜超氧化物歧化酶(CunSOD, n＝1—4)作为野生型CuZnSOD突变体的一种模型, 研究了其在二价金属离子(Mg2+, Mn2+)存在下由非氧化途径断裂DNA的活性, 并与CuZnSOD和脱辅基SOD(apoSOD)进行了比较. 结果表明, 在Mg2+或Mn2+存在下, CunSOD断裂DNA的活性高于CuZnSOD和apoSOD, 并且DNA的断裂活性受二价金属离子浓度、pH及酶浓度等因素影响. 相对活性及动力学参数的测定结果表明, CunSOD断裂DNA的相对能力按Cu1SOD2SOD≈Cu4SOD3SOD的顺序变化.     

Single stranded helical supramolecular architecture with a left handed helical water chain in ternary copper(II) tryptophan/diamine complexes

The ternary copper(II) complexes [Cu(l-trp)(bpy)](ClO₄) (1) and [Cu(l-trp)(phen)] (ClO₄) · 3H₂O (2) (where l-trp = l-tryptophan, bpy = bipridyl, phen = phenanthroline) have been synthesized. The single crystal X-ray structures for these complexes revealed that the monocationic Cu^II-units are interlinked through Cu–OCO–Cu connectivity and exist as helical coordination polymers. The two different helical strands composed with Cu1 and Cu2 independently, possess a similar pitch distance of 7.713 Å in complex 1. For complex 2, existing in the hydrated form, the Cu(II) polymeric strand and the hydrated water molecules have gained a supramolecular helical architecture with a similar pitch distance of 8.133 Å. The two helical strands in complex 1 are associated with right handed (PP) supramolecular chirality, while the helical water chain and the Cu^II-strand in 2 are self assembled into left handed (MM) helicity in the solid state. The solid state CD recorded for 1 and the dehydrated form of 2 exhibit a positive optical sign at their respective d–d band [λ_max = 667 nm, 1; λ_max = 630 nm, 2], the solution state CD for both these complexes are found to be inverted into a negative optical sign, which could be attributed to inversion of their associated supramolecular helicity. The TGA curve illustrates two distinct weight losses at 60 °C and 87 °C, equivalent to one and two water molecules, respectively. The PXRD pattern for the hydrated and dehydrated forms of 2 indicated a change, on comparison with the simulated diffractograph. The fluorescence properties of both these complexes, possessing tryptophan and bipy/phen, were investigated.     

SOD模拟及其抗氧化和抗炎症功能的研究进展*

超氧化物歧化酶(superoxide dismutase, 简称SOD) 作为生物体内超氧离子自由基的清除剂, 具备有效抗氧化、抗炎症、抗衰老之功效, 并用于临床, 其化学模拟引起了人们的广泛研究兴趣。本文将简要介绍近年来SOD 人工模拟酶及其生物医学活性研究所取得的重要进展, 特别是Cu,Zn-SOD 模拟物结构与功能的相互关系、Mn-SOD 模拟物的生物活性及其医学应用。     

Spectroscopic and computational investigation of second-sphere contributions to redox tuning in Escherichia coli iron superoxide dismutase

In Fe- and Mn-dependent superoxide dismutases (SODs), second-sphere residues have been implicated in precisely tuning the metal ion reduction potential to maximize catalytic activity (Vance, C. K.; Miller, A.-F. J. Am. Chem. Soc. 1998, 120, 461-467). In the present study, spectroscopic and computational methods were used to characterize three distinct Fe-bound SOD species that possess different second-coordination spheres and, consequently, Fe(3+/2+)reduction potentials that vary by approximately 1 V, namely, FeSOD, Fe-substituted MnSOD (Fe(Mn)SOD), and the Q69E FeSOD mutant. Despite having markedly different metal ion reduction potentials, FeSOD, Fe(Mn)SOD, and Q69E FeSOD exhibit virtually identical electronic absorption, circular dichroism, and magnetic circular dichroism (MCD) spectra in both their oxidized and reduced states. Likewise, variable-temperature, variable-field MCD data obtained for the oxidized and reduced species do not reveal any significant electronic, and thus geometric, variations within the Fe ligand environment. To gain insight into the mechanism of metal ion redox tuning, complete enzyme models for the oxidized and reduced states of all three Fe-bound SOD species were generated using combined quantum mechanics/molecular mechanics (QM/MM) geometry optimizations. Consistent with our spectroscopic data, density functional theory computations performed on the corresponding active-site models predict that the three SOD species share similar active-site electronic structures in both their oxidized and reduced states. By using the QM/MM-optimized active-site models in conjunction with the conductor-like screening model to calculate the proton-coupled Fe(3+/2+) reduction potentials, we found that different hydrogen-bonding interactions with the conserved second-sphere Gln (changed to Glu in Q69E FeSOD) greatly perturb the p K of the Fe-bound solvent ligand and, thus, drastically affect the proton-coupled metal ion reduction potential.     

Synthesis,characterization and X-ray crystal structures of two non-molecular coordination polymers of manganese(II) and copper(II) with <Emphasis Type="Italic">N</Emphasis>-(2-pyridylmethyl)-<Emphasis Type="SmallCaps">l</Emphasis>-alanine and isothiocyanato ligands

The reduced Schiff base, N-(2-pyridylmethyl)-l-alanine (Pyala), has been prepared and used as a ligand for the synthesis of two new non-centrosymmetrical isothiocyanate mixed-ligand coordination polymers, [MnPyalaSCN] _n and [CuPyalaSCN] _n . Pyala and the metal complexes were characterized by physico-chemical and spectroscopic methods. The single-crystal X-ray structures of the complexes reveal both compounds to be non-molecular coordination polymers which crystallize in the orthorhombic system. The ligand acts as a bridge between two metal centres in both compounds, forming two six-membered rings around each Mn atom and two five-membered rings around each Cu centre. The 1D chains are assembled via N–H?O, N–H?S hydrogen bonds and S–S interactions building 3D helical supramolecular networks in both compounds. Packing of the polymers of both compounds along the b-axis gives chiral channels.     

Synthesis and magnetic properties of copper (II)-manganese (II) compounds with N,N′-ethylenedisalicylamidatocuprate(II)

By the reaction of sodium N,N′-ethylenedisalicylamidatocuprate ( I ) pentahydrate, Na₂[Cu(samen)]·5H₂O, with a manganese ( I ) salt and 2,2′-dipyridyl (bpy) or 1,10-phenanthroline (phen), the binuclear metal complexes [Cu(samen) Mn(L)₂] (L ? bpy, phen) have been synthesized. Based on IR, elemental analyses and electronic spectra, the complexes are proposed to consist of a four-coordinated Cu( I ) in a distorted planar environment and Mn( I ) in a distorted octahedron. The complexes have been characterized with variable-temperature magnetic susceptibility (4.2—300 K) and the susceptibility data were least-squares fit to susceptibility equation derived from the spin Hamiltonian including single-ion zero-field interaction for Mn²⁺ ion, H?—2JS₁·S₂—DS, where D is the axial zero-field splitting parameter for the Mn(II) ion. The exchange integral, J, was found to be —34.6 and —28.8 cm^?1 for [Cu(samen)Mn(bpy)₂] and [Cu(samen)Mn(phen)₂] respectively. The weak antiferromagnetic spin-exchange interaction can be interpreted by considering σ-π exchange pathway.     

Novel inhibitors to <Emphasis Type="Italic">Taenia solium</Emphasis> Cu/Zn superoxide dismutase identified by virtual screening

We describe in this work a successful virtual screening and experimental testing aimed to the identification of novel inhibitors of superoxide dismutase of the worm Taenia solium (TsCu/Zn–SOD), a human parasite. Conformers from LeadQuest^® database of drug-like compounds were selected and then docked on the surface of TsCu/Zn–SOD. Results were screened looking for ligand contacts with receptor side-chains not conserved in the human homologue, with a subsequent development of a score optimization by a set of energy minimization steps, aimed to identify lead compounds for in vitro experiments. Six out of fifty experimentally tested compounds showed μM inhibitory activity toward TsCu/Zn–SOD. Two of them showed species selectivity since did not inhibit the homologous human enzyme when assayed in vitro.     

OXIDATIVE ETHOXYCARBONYLATION OF ANILINE TO ETHYL PHENYLCARBAMATE CATALYZED BY SILICA- SUPPORTED POLY-γ-AMINOPROPYLSILOXANEMETAL COMPLEXES

Several silica-supported poly-γ-aminopropylsiloxane-monometal and bimetal complexes (Si-NH_2-M,M = Cu or Co ; Si-NH_2-Cu-M', M' =Co, Sn, Mn, Ni or Fe) have been prepared. Their catalytic properties for oxidative ethoxycarbonylation of aniline to ethyl phenylcarbamate have been investigated.The catalytic reaction was carried out under relatively mild conditions. The catalyst Si-NH_2-Cu-CO had high activity and selectivity, and the turn-over number (molar of aniline converted/molar of metal in Si-NH_2-Cu-CO added) could amount to 450 under the conditions: 150℃, 4 MPa (CO/O_2 =3) and 40 hours.The results of XPS and IR indicated that the coordination bonds were formed between nitrogen and metals in Si-NH2-Cu, Si-NH_2-Co and Si-NH_2-Cu-Co, and the coordination pattern was not single. In the oxidative ethoxycarbonylation of aniline to ethyl phenylcarbamate, the catalytic property of Si-NH_2-Cu-CO bimetallic complex was better than Si-NH_2-Cu or Si-NH_2-Co monometatlic complex. This indicated that there was synergistic action between different metals in the bimetallic complex.     

Packing of chiral molecules of metal TRIS-acetylacetonates

The Cambridge Crystallographic Data Centre (CCDC) is searched to organize packings of metal tris-acetylacetonates M(aa)₃ (about 70 structures over the last 50 years). In all structures, planes with a hexagonal molecular environment are found. Three types of the nearest hexagonal environment are revealed in these planes with allowance for the chirality of molecules. Different superposition of these planes produces five types of packing of metal tris-acetylacetonates: α, β, γ, jg, and pg. Spectrally pure Al(aa)₃, Cr(aa)₃, Mn(aa)₃, and Fe(aa)₃ complexes are synthesized and their solid solutions are studied. The effect of impurities on crystallization is established. A temperature range of 210 K to 100 K, in which we have previously detected thermochromism of metal β-diketonates is distinguished. In the same range, a symmetry change was previously found for Al(aa)₃ and Mn(aa)₃, however, Cr(aa)₃ symmetry did not change in this temperature range. The ratios of components in solid solutions, at which low temperature symmetry change is observed in the complexes, are found experimentally. The relation between thermochromism and the symmetry change is discussed.