Structural and electrochemical studies of novel bis(mu-methoxo)diiron complexes: observation of Fe(III)Fe(IV) and Fe(IV)Fe(IV) states resonating with phenoxyl radicals

Novel diiron complexes with an Fe2(mu-OMe)2 core were studied as models of the active site of nonheme iron-containing enzymes. X-ray crystal structures of the complexes showed the existence of two types of ligand folding-parallel and twisted-both of which have four virtually equivalent phenolato groups sticking out from the Fe2O2 rhombic plane. Cyclic voltammetry measurements revealed two or more distinct redox waves in a region of relatively high potential, in addition to known Fe(II)/Fe(III) redox waves in a region of lower potential. These new peaks were assigned to the high-valence state of iron atoms, that is, Fe(III)Fe(IV) and Fe(IV)Fe(IV), resonating with the phenoxyl radical(s). The split width of the redox waves ranged from 0.14 to 0.20 eV, which may be a measure of the electronic interaction of the phenolate groups through the Fe2(mu-OMe)2 core.     

Theoretical Aspects of Hydrolysis of Peptide Bonds by Zinc Metalloenzymes

Activation and reaction energies for four model systems capturing the essential physicochemical features of the hydrolysis of the peptide bond have been calculated at various level of theory, including the presumably accurate CCSD(T) calculations. The models studied covered a part of the spectrum encountered in biological systems: the hydrolysis in the absence of metal ions (represented by formamide and Ala–Ala) and the hydrolysis in the presence of one and two zinc(II) ions, mimicking the active sites of mono‐ and dizinc metallopeptidases, respectively (by using thermolysin and glutamate carboxypeptidase II as the model catalytic systems and formamide as the model substrate). The results obtained using CCSD(T)/def2‐TZVP and CCSD(T)/aug‐cc‐pVTZ calculations were used as the benchmark values to which the set of cheaper methods, such as (RI‐)DFT, (RI‐)MP2, and SCS‐MP2, were referenced. It was shown that deviations of 3–5 kcal mol^?1 (translating to 2–3 orders in reaction constants) with respect to the reference CCSD(T) barriers are frequently encountered for many correlated methods and most of studied DFT functionals. It has been concluded that from the set of wave‐function methods, both MP2 and SCS‐MP2 methods can be recommended for smaller models (measured by the mean absolute deviation of the activation barriers over the four systems studied), whereas among the popular DFT functionals, B3LYP and especially M06‐2X are likely to be reasonable choices for calculating the activation barriers of zinc metallopeptidases. Finally, with the model of glutamate carboxypeptidase II, issues related to the convergence of the calculated barriers with the size of the model system used as the representative of the enzyme active site were addressed. The intricacies related to system truncation are demonstrated, and suggest that the correlated wave‐function methods may suffer from problems, such as intramolecular BSSE, which make their usage for the larger system questionable. Altogether, the presented data should contribute to efforts to understand enzymatic catalysis more deeply and to gain control of the accuracy and deficiencies of the available theoretical methods and computational approaches.     

Machine Learning Approaches for Metalloproteins

Metalloproteins are a family of proteins characterized by metal ion binding, whereby the presence of these ions confers key catalytic and ligand-binding properties. Due to their ubiquity among biological systems, researchers have made immense efforts to predict the structural and functional roles of metalloproteins. Ultimately, having a comprehensive understanding of metalloproteins will lead to tangible applications, such as designing potent inhibitors in drug discovery. Recently, there has been an acceleration in the number of studies applying machine learning to predict metalloprotein properties, primarily driven by the advent of more sophisticated machine learning algorithms. This review covers how machine learning tools have consolidated and expanded our comprehension of various aspects of metalloproteins (structure, function, stability, ligand-binding interactions, and inhibitors). Future avenues of exploration are also discussed.     

Electrochemical Studies of CO2-Reducing Metalloenzymes

Only two enzymes are capable of directly reducing CO₂: CO dehydrogenase, which produces CO at a [NiFe₄S₄] active site, and formate dehydrogenase, which produces formate at a mononuclear W or Mo active site. Both metalloenzymes are very rapid, energy-efficient and specific in terms of product. They have been connected to electrodes with two different objectives. A series of studies used protein film electrochemistry to learn about different aspects of the mechanism of these enzymes (reactivity with substrates, inhibitors…). Another series focused on taking advantage of the catalytic performance of these enzymes to build biotechnological devices, from CO₂-reducing electrodes to full photochemical devices performing artificial photosynthesis. Here, we review all these works.     

Vanadium Chloroperoxidases: The Missing Link in the Formation of Chlorinated Compounds and Chloroform in the Terrestrial Environment?

It is well established that the majority of chlorinated organic substances found in the terrestrial environment are produced naturally. The presence of these compounds in soils is not limited to a single ecosystem. Natural chlorination is also a widespread phenomenon in grasslands and agricultural soils typical for unforested areas. These chlorinated compounds are formed from chlorination of natural organic matter consisting of very complex chemical structures, such as lignin. Chlorination of several lignin model compounds results in the intermediate formation of trichloroacetyl‐containing compounds, which are also found in soils. These decay, in general, through a haloform‐type reaction mechanism to CHCl₃. Upon release into the atmosphere, CHCl₃ will produce chlorine radicals through photolysis, which will, in turn, lead to natural depletion of ozone. There is evidence that fungal chloroperoxidases able to produce HOCl are involved in the chlorination of natural organic matter. The objective of this review is to clarify the role and source of the various chloroperoxidases involved in the natural formation of CHCl₃.     

Application of 57Co emission Mössbauer spectroscopy to studying biocomplexes in frozen solutions

Emission Mössbauer spectroscopy with the ⁵⁷Co isotope was used to study very dilute rapidly frozen aqueous solutions of cobalt(II) complexes with low-molecular-weight biomolecules (aromatic amino acids – anthranilic acid and L-tryptophan) and within a sophisticated biopolymer, bacterial glutamine synthetase, a key enzyme of nitrogen metabolism. The appearance of after-effects of the ⁵⁷Co→⁵⁷Fe nuclear transformation as well as the coordination properties of the cation and the ligands in the complexes are discussed on the basis of their Mössbauer parameters.     

Ring‐Closing and Cross‐Metathesis with Artificial Metalloenzymes Created by Covalent Active Site‐Directed Hybridization of a Lipase

A series of Grubbs‐type catalysts that contain lipase‐inhibiting phosphoester functionalities have been synthesized and reacted with the lipase cutinase, which leads to artificial metalloenzymes for olefin metathesis. The resulting hybrids comprise the organometallic fragment that is covalently bound to the active amino acid residue of the enzyme host in an orthogonal orientation. Differences in reactivity as well as accessibility of the active site by the functionalized inhibitor became evident through variation of the anchoring motif and substituents on the N‐heterocyclic carbene ligand. Such observations led to the design of a hybrid that is active in the ring‐closing metathesis and the cross‐metathesis of N,N‐diallyl‐p‐toluenesulfonamide and allylbenzene, respectively, the latter being the first example of its kind in the field of artificial metalloenzymes.     

Stability and structure of mixed-ligand metal ion complexes that contain Ni2+, Cu2+, or Zn2+, and Histamine, as well as adenosine 5'-triphosphate (ATP4-) or uridine 5'-triphosphate (UTP(4-): an intricate network of equilibria

With a view on protein–nucleic acid interactions in the presence of metal ions we studied the “simple” mixed‐ligand model systems containing histamine (Ha), the metal ions Ni²⁺, Cu²⁺, or Zn²⁺ (M²⁺), and the nucleotides adenosine 5′‐triphosphate (ATP^4?) or uridine 5′‐triphosphate (UTP^4?), which will both be referred to as nucleoside 5′‐triphosphate (NTP^4?) . The stability constants of the ternary M(NTP)(Ha)^2? complexes were determined in aqueous solution by potentiometric pH titrations. We show for both ternary‐complex types, M(ATP)(Ha)^2? and M(UTP)(Ha)^2?, that intramolecular stacking between the nucleobase and the imidazole residue occurs and that the stacking intensity is approximately the same for a given M²⁺ in both types of complexes: The formation degree of the intramolecular stacks is estimated to be 20 to 50 %. Consequently, in protein–nucleic acid interactions imidazole–nucleobase stacks may well be of relevance. Furthermore, the well‐known formation of macrochelates in binary M²⁺ complexes of purine nucleotides, that is, the phosphate‐coordinated M²⁺ interacts with N7, is confirmed for the M(ATP)^2? complexes. It is concluded that upon formation of the mixed‐ligand complexes the M²⁺? N7 bond is broken and the energy needed for this process corresponds to the stability differences determined for the M(UTP)(Ha)^2? and M(ATP)(Ha)^2? complexes. It is, therefore, possible to calculate from these stability differences of the ternary complexes the formation degrees of the binary macrochelates: The closed forms amount to (65±10) %, (75±8) %, and (31±14) % for Ni(ATP)^2?, Cu(ATP)^2?, and Zn(ATP)^2?, respectively, and these percentages agree excellently with previous results obtained by different methods, confirming thus the internal validity of the data and the arguments used in the evaluation processes. Based on the overall results it is suggested that M(ATP)^2? species, when bound to an enzyme, may exist in a closed macrochelated form only, if no enzyme groups coordinate directly to the metal ion.