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1.
Inorg Chem ; 62(51): 20913-20918, 2023 Dec 25.
Article in English | MEDLINE | ID: mdl-38047903

ABSTRACT

The novel dinuclear complex related to the [FeFe]-hydrogenases active site, [Fe2(µ-pdt)(κ2-dmpe)2(CO)2] (1), is highly reactive toward chlorinated compounds CHxCl4-x (x = 1, 2) affording selectively terminal or bridging chloro diiron isomers through a C-Cl bond activation. DFT calculations suggest a cooperative mechanism involving a formal concerted regioselective chloronium transfer depending on the unrotated or rotated conformation of two isomers of 1.


Subject(s)
Hydrogenase , Iron-Sulfur Proteins , Hydrogenase/chemistry , Iron-Sulfur Proteins/chemistry , Isomerism , Catalytic Domain , Density Functional Theory
2.
Inorg Chem ; 62(41): 16842-16853, 2023 Oct 16.
Article in English | MEDLINE | ID: mdl-37788376

ABSTRACT

The salt [K(18-crown-6)]2[Ru(CN)2(CO)3] ([K(18-crown-6)]2[1]) was generated by the reaction of Ru(C2H4)(CO)4 with [K(18-crown-6)]CN. An initial thermal reaction gives [Ru(CN)(CO)4]-, which, upon ultraviolet (UV) irradiation, reacts with a second equiv of CN-. Protonation of [1]2- gave [HRu(CN)2(CO)3]- ([H1]-), which was isolated as a single isomer with mutually trans cyanide ligands. The complex cis,cis,cis-[Ru(pdt)(CN)2(CO)2]2- ([2]2-) was prepared by the UV-induced reaction of [1]2- with propanedithiol (pdtH2). The corresponding iron complex cis,cis,cis-[Fe(pdt)(CN)2(CO)2]2- ([3]2-) was prepared similarly. The pdt complexes [2]2- and [3]2- were treated with Fe(benzylideneacetone)(CO)3 to give, respectively, [RuFe (µ-pdt)(CN)2(CO)4]2- ([5]2-) and [Fe2(µ-pdt)(CN)2(CO)4]2- ([4]2-). The pathway from [3]2- to Fe2 complex [4]2- implicates intermetallic migration of CN-. In contrast, the formation of [5]2- leaves the Ru(CN)2(CO) center intact, as confirmed by X-ray crystallography. The structure of [5]2- features a "rotated" square-pyramidal Fe(CO)2(µ-CO) site. NMR measurements indicate that the octahedral Ru site is stereochemically rigid, whereas the Fe site dynamically undergoes turnstile rotation. 57Fe Mössbauer spectral parameters are very similar for rotated [5]2- and unrotated Fe2 complex [4]2-, indicating the insensitivity of that technique to both the geometry and the oxidation state of the Fe site. According to cyclic voltammetry, [5]2- oxidizes at E1/2 ∼ -0.8 V vs Fc+/0. Electron paramagnetic resonance (EPR) measurements show that 1e- oxidation of [5]2- gives an S = 1/2 rhombic species, consistent with the formulation Ru(II)Fe(I), related to the Hox state of the [FeFe] hydrogenases. Density functional theory (DFT) studies reproduce the structure, 1H NMR shifts, and infrared (IR) spectra observed for [5]2-. Related homometallic complexes with both cyanides on a single metal are predicted to not adopt rotated structures. These data suggest that [5]2- is best described as Ru(II)Fe(0). This conclusion raises the possibility that for some reduced states of the [FeFe]-hydrogenases, the [2Fe]H site may be better described as Fe(II)Fe(0) than Fe(I)Fe(I).

3.
Molecules ; 28(16)2023 Aug 11.
Article in English | MEDLINE | ID: mdl-37630271

ABSTRACT

Flavodoxins are enzymes that contain the redox-active flavin mononucleotide (FMN) cofactor and play a crucial role in numerous biological processes, including energy conversion and electron transfer. Since the redox characteristics of flavodoxins are significantly impacted by the molecular environment of the FMN cofactor, the evaluation of the interplay between the redox properties of the flavin cofactor and its molecular surroundings in flavoproteins is a critical area of investigation for both fundamental research and technological advancements, as the electrochemical tuning of flavoproteins is necessary for optimal interaction with redox acceptor or donor molecules. In order to facilitate the rational design of biomolecular devices, it is imperative to have access to computational tools that can accurately predict the redox potential of both natural and artificial flavoproteins. In this study, we have investigated the feasibility of using non-equilibrium thermodynamic integration protocols to reliably predict the redox potential of flavodoxins. Using as a test set the wild-type flavodoxin from Clostridium Beijerinckii and eight experimentally characterized single-point mutants, we have computed their redox potential. Our results show that 75% (6 out of 8) of the calculated reaction free energies are within 1 kcal/mol of the experimental values, and none exceed an error of 2 kcal/mol, confirming that non-equilibrium thermodynamic integration is a trustworthy tool for the quantitative estimation of the redox potential of this biologically and technologically significant class of enzymes.


Subject(s)
Clostridium beijerinckii , Flavodoxin , Thermodynamics , Flavoproteins , Electron Transport
4.
Int J Mol Sci ; 24(7)2023 Mar 28.
Article in English | MEDLINE | ID: mdl-37047341

ABSTRACT

Molecular modeling techniques have become indispensable in many fields of molecular sciences in which the details related to mechanisms and reactivity need to be studied at an atomistic level. This review article provides a collection of computational modeling works on a topic of enormous interest and urgent relevance: the properties of metalloenzymes involved in the degradation and valorization of natural biopolymers and synthetic plastics on the basis of both circular biofuel production and bioremediation strategies. In particular, we will focus on lytic polysaccharide monooxygenase, laccases, and various heme peroxidases involved in the processing of polysaccharides, lignins, rubbers, and some synthetic polymers. Special attention will be dedicated to the interaction between these enzymes and their substrate studied at different levels of theory, starting from classical molecular docking and molecular dynamics techniques up to techniques based on quantum chemistry.


Subject(s)
Plastics , Polysaccharides , Plastics/metabolism , Molecular Docking Simulation , Oxidation-Reduction , Polysaccharides/metabolism , Lignin/metabolism , Oxidative Stress , Biopolymers/metabolism
5.
Chemistry ; 29(38): e202300569, 2023 Jul 06.
Article in English | MEDLINE | ID: mdl-37015870

ABSTRACT

Three hexacarbonyl diiron dithiolate complexes [Fe2 (CO)6 (µ-(SCH2 )2 X)] with different substituted bridgeheads (X=CH2 , CEt2 , CBn2 (Bn=CH2 C6 H5 )), have been studied under the same experimental conditions by cyclic voltammetry in dichloromethane [NBu4 ][PF6 ] 0.2 M. DFT calculations were performed to rationalize the mechanism of reduction of these compounds. The three complexes undergo a two-electron transfer whose the mechanism depends on the bulkiness of the dithiolate bridge, which involves a different timing of the structural changes (Fe-S bond cleavage, inversion of conformation and CO bridging) vs redox steps. The introduction of a bulky group in the dithiolate linker has obviously an effect on normally ordered (as for propanedithiolate (pdt)) or inverted (pdtEt2 , pdtBn2 ) reduction potentials. Et→Bn replacement is not theoretically predicted to alter the geometry and energy of the most stable mono-reduced and bi-reduced forms but such a replacement alters the kinetics of the electron transfer vs the structural changes.


Subject(s)
Hydrogenase , Iron-Sulfur Proteins , Hydrogenase/chemistry , Iron-Sulfur Proteins/chemistry , Biomimetics , Electron Transport , Oxidation-Reduction
6.
Molecules ; 27(15)2022 Jul 22.
Article in English | MEDLINE | ID: mdl-35897863

ABSTRACT

The behaviour of triazolylidene ligands coordinated at a {Fe2(CO)5(µ-dithiolate)} core related to the active site of [FeFe]-hydrogenases have been considered to determine whether such carbenes may act as redox electron-reservoirs, with innocent or non-innocent properties. A novel complex featuring a mesoionic carbene (MIC) [Fe2(CO)5(Pmpt)(µ-pdt)] (1; Pmpt = 1-phenyl-3-methyl-4-phenyl-1,2,3-triazol-5-ylidene; pdt = propanedithiolate) was synthesized and characterized by IR, 1H, 13C{1H} NMR spectroscopies, elemental analyses, X-ray diffraction ,and cyclic voltammetry. Comparison with the spectroscopic characteristics of its analogue [Fe2(CO)5(Pmbt)(µ-pdt)] (2; Pmbt = 1-phenyl-3-methyl-4-butyl-1,2,3-triazol-5-ylidene) showed the effect of the replacement of a n-butyl by a phenyl group in the 1,2,3-triazole heterocycle. A DFT study was performed to rationalize the electronic behaviour of 1, 2 upon the transfer of two electrons and showed that such carbenes do not behave as redox ligands. With highly perfluorinated carbenes, electronic communication between the di-iron site and the triazole cycle is still limited, suggesting low redox properties of MIC ligands used in this study. Finally, although the catalytic performances of 2 towards proton reduction are weak, the protonation process after a two-electron reduction of 2 was examined by DFT and revealed that the protonation process is favoured by S-protonation but the stabilized diprotonated intermediate featuring a {Fe-H⋯H-S} interaction does not facilitate the release of H2 and may explain low efficiency towards HER (Hydrogen Evolution Reaction).


Subject(s)
Hydrogenase , Iron-Sulfur Proteins , Hydrogenase/chemistry , Iron/chemistry , Iron-Sulfur Proteins/chemistry , Ligands , Protons , Triazoles
7.
Chem Sci ; 13(17): 4863-4873, 2022 May 04.
Article in English | MEDLINE | ID: mdl-35655865

ABSTRACT

Despite the high levels of interest in the synthesis of bio-inspired [FeFe]-hydrogenase complexes, H2 oxidation, which is one specific aspect of hydrogenase enzymatic activity, is not observed for most reported complexes. To attempt H-H bond cleavage, two disubstituted diiron dithiolate complexes in the form of [Fe2(µ-pdt)L2(CO)4] (L: PMe3, dmpe) have been used to play the non-biomimetic role of a Lewis base, with frustrated Lewis pairs (FLPs) formed in the presence of B(C6F5)3 Lewis acid. These unprecedented FLPs, based on the bimetallic Lewis base partner, allow the heterolytic splitting of the H2 molecule, forming a protonated diiron cation and hydrido-borate anion. The substitution, symmetrical or asymmetrical, of two phosphine ligands at the diiron dithiolate core induces a strong difference in the H2 bond cleavage abilities, with the FLP based on the first complex being more efficient than the second. DFT investigations examined the different mechanistic pathways involving each accessible isomer and rationalized the experimental findings. One of the main DFT results highlights that the iron site acting as a Lewis base for the asymmetrical complex is the {Fe(CO)3} subunit, which is less electron-rich than the {FeL(CO)2} site of the symmetrical complex, diminishing the reactivity towards H2. Calculations relating to the different mechanistic pathways revealed the presence of a terminal hydride intermediate at the apical site of a rotated {Fe(CO)3} site, which is experimentally observed, and a semi-bridging hydride intermediate from H2 activation at the Fe-Fe site; these are responsible for a favourable back-reaction, reducing the conversion yield observed in the case of the asymmetrical complex. The use of two equivalents of Lewis acid allows for more complete and faster H2 bond cleavage due to the encapsulation of the hydrido-borate species by a second borane, favouring the reactivity of each FLP, in agreement with DFT calculations.

8.
Chem Commun (Camb) ; 57(41): 5079-5081, 2021 May 21.
Article in English | MEDLINE | ID: mdl-33890601

ABSTRACT

The reaction of Fe2S2(CO)6 and PPh3 affords Fe2S2(CO)4(PPh3)2 by an unprecedented mechanism involving the intermediacy of SPPh3 and Fe2S(CO)6(PPh3)2.

9.
Inorg Chem ; 60(6): 3917-3926, 2021 Mar 15.
Article in English | MEDLINE | ID: mdl-33650855

ABSTRACT

Density functional theory (DFT) calculations on Fe2S2(CO)6-2n(PMe3)2n for n = 0, 1, and 2 reveal that the most electron-rich derivatives (n = 2) exist as diferrous disulfides lacking an S-S bond. The thermal interconversion of the FeII2(S)2 and FeI2(S2) valence isomers is symmetry-forbidden. Related electron-rich diiron complexes [Fe2S2(CN)2(CO)4]2- of an uncertain structure are implicated in the biosynthesis of [FeFe]-hydrogenases. Several efforts to synthesize electron-rich derivatives of Fe2(µ-S2)(CO)6 (1) are described. First, salts of iron persulfido cyanides [Fe2(µ-S2)(CO)5(CN)]- and [Fe2(µ-S2)(CN)(CO)4(PPh3)]- were prepared by the reactions of NaN(tms)2 with 1 and Fe2(µ-S2)(CO)5(PPh3), respectively. Alternative approaches to electron-rich diiron disulfides targeted Fe2(µ-S2)(CO)4(diphosphine). Whereas the preparation of Fe2(µ-S2)(CO)4(dppbz) was straightforward, that of Fe2(µ-S2)(CO)4(dppv) required an indirect route involving the oxidation of Fe2(µ-SH)2(CO)4(dppv) (dppbz = C6H4-1,2-(PPh2)2, dppv = cis-C2H2(PPh2)2). DFT calculations indicate that the oxidation of Fe2(µ-SH)2(CO)4(dppv) produces singlet diferrous disulfide Fe2(µ-S)2(CO)4(dppv), which is sufficiently long-lived as to be trapped by ethylene. The reaction of 1 and dppv mainly afforded Fe2(µ-SCH=CHPPh2)(µ-SPPh2)(CO)5, implicating a S-centered reaction.

10.
Organometallics ; 40(19): 3306-3312, 2021 Oct 11.
Article in English | MEDLINE | ID: mdl-37933322

ABSTRACT

One of the more active areas in bioorganometallic chemistry is the preparation and reactivity studies of active site mimics of the [NiFe]-hydrogenases. One area of particular recent progress involves reactions that interconvert Ni(µ-X)Fe centers for X = OH, H, CO, as described by Song et al. Such reactions illustrate new ways to access intermediates related to the Ni-R and Ni-SI states of the enzyme. Most models are derivatives of the type (diphosphine)Ni(SR)2Fe(CO)3-n(PR'3)n. In recent work, the methodology has been generalized to include FeII(diphosphine) derivatives of Ni(N2S2), where N2S22- is the tetradentate diamine-dithiolate (CH2N(CH3)CH2CH2S-)2. Indeed, models based on Ni(N2S2) have proven valuable, but these studies also highlight challenges in working with heterobimetallic complexes, specifically the tendency of some such Ni-Fe complexes to convert to homometalliic Ni-Ni derivatives. This kind of problem is not readily detected by X-ray crystallography. With this caution in mind, we argue that one series of complexes recently described in this journal are almost certainly misassigned.

11.
Int J Mol Sci ; 21(23)2020 Nov 28.
Article in English | MEDLINE | ID: mdl-33260658

ABSTRACT

Palmitoylethanolamide (PEA) belongs to the class of N-acylethanolamine and is an endogenous lipid potentially useful in a wide range of therapeutic areas; products containing PEA are licensed for use in humans as a nutraceutical, a food supplement, or food for medical purposes for its analgesic and anti-inflammatory properties demonstrating efficacy and tolerability. However, the exogenously administered PEA is rapidly inactivated; in this process, fatty acid amide hydrolase (FAAH) plays a key role both in hepatic metabolism and in intracellular degradation. So, the aim of the present study was the design and synthesis of PEA analogues that are more resistant to FAAH-mediated hydrolysis. A small library of PEA analogues was designed and tested by molecular docking and density functional theory calculations to find the more stable analogue. The computational investigation identified RePEA as the best candidate in terms of both synthetic accessibility and metabolic stability to FAAH-mediated hydrolysis. The selected compound was synthesized and assayed ex vivo to monitor FAAH-mediated hydrolysis and to confirm its anti-inflammatory properties. 1H-NMR spectroscopy performed on membrane samples containing FAAH in integral membrane protein demonstrated that RePEA is not processed by FAAH, in contrast with PEA. Moreover, RePEA retains PEA's ability to inhibit LPS-induced cytokine release in both murine N9 microglial cells and human PMA-THP-1 cells.


Subject(s)
Amides/chemistry , Amides/metabolism , Ethanolamines/chemistry , Ethanolamines/metabolism , Fatty Acids/chemistry , Models, Molecular , Palmitic Acids/chemistry , Palmitic Acids/metabolism , Animals , Cell Shape , Cell Survival , Humans , Hydrolysis , Interleukin-1beta/metabolism , Interleukin-6/metabolism , Ligands , Mice , Microglia/metabolism , NF-kappa B/metabolism , PPAR alpha/metabolism , Proton Magnetic Resonance Spectroscopy , Substrate Specificity , THP-1 Cells , Thermodynamics , Tumor Necrosis Factor-alpha/metabolism
12.
Metallomics ; 12(11): 1765-1780, 2020 11 01.
Article in English | MEDLINE | ID: mdl-33052996

ABSTRACT

Oxidative stress and metal dyshomeostasis are considered as crucial factors in the pathogenesis of Alzheimer's disease (AD). Indeed, transition metal ions such as Cu(ii) can generate Reactive Oxygen Species (ROS) via O2 Fenton-like reduction, catalyzed by Cu(ii) coordinated to the Amyloid beta (Aß) peptide. Despite intensive effort, the mechanisms of ROS-induced molecular damage remain poorly understood. In the present paper, we investigate on the basis of molecular modelling computations the mechanism of OH radical propagation toward the Aß peptide, starting from the end-product of OH radical generation by Cu(ii)·Aß. We evaluate (i) the OH oxidative capacity, as well as the energetics of the possible Aß oxidation target residues, by quantum chemistry Density Functional Theory (DFT) on coordination models of Cu(ii)/OH/Aß and (ii) the motion of the OH˙ approaching the Aß target residues by classical Molecular Dynamics (MD) on the full peptide Cu(ii)/OH/Aß(1-16). The results show that the oxidative capacity of OH coordinated Cu(ii)Aß is significantly lower than that of the free OH radical and that propagation toward Aß Asp and His residues is favoured over Tyr residues. These results are discussed on the basis of the recent literature on in vitro Aß metal-catalyzed oxidation and on the possible implications for the AD oxidative stress mechanism.


Subject(s)
Amyloid beta-Peptides/metabolism , Hydroxyl Radical/metabolism , Models, Molecular , Amino Acids/chemistry , Amyloid beta-Peptides/chemistry , Copper , Homeostasis , Molecular Dynamics Simulation , Oxidation-Reduction , Oxidative Stress
13.
Chemphyschem ; 21(20): 2279-2292, 2020 10 16.
Article in English | MEDLINE | ID: mdl-32815583

ABSTRACT

It was recently discovered that some redox proteins can thermodynamically and spatially split two incoming electrons towards different pathways, resulting in the one-electron reduction of two different substrates, featuring reduction potential respectively higher and lower than the parent reductant. This energy conversion process, referred to as electron bifurcation, is relevant not only from a biochemical perspective, but also for the ground-breaking applications that electron-bifurcating molecular devices could have in the field of energy conversion. Natural electron-bifurcating systems contain a two-electron redox centre featuring potential inversion (PI), i. e. with second reduction easier than the first. With the aim of revealing key factors to tailor the span between first and second redox potentials, we performed a systematic density functional study of a 26-molecule set of models with the general formula Fe2 (µ-PR2 )2 (L)6 . It turned out that specific features such as i) a Fe-Fe antibonding character of the LUMO, ii) presence of electron-donor groups and iii) low steric congestion in the Fe's coordination sphere, are key ingredients for PI. In particular, the synergic effects of i)-iii) can lead to a span between first and second redox potentials larger than 700 mV. More generally, the "molecular recipes" herein described are expected to inspire the synthesis of Fe2 P2 systems with tailored PI, of primary relevance to the design of electron-bifurcating molecular devices.

14.
Chemistry ; 26(72): 17536-17545, 2020 Dec 23.
Article in English | MEDLINE | ID: mdl-32722853

ABSTRACT

The electrochemical reduction of complexes [Fe2 (CO)4 (κ2 -phen)(µ-xdt)] (phen=1,10-phenanthroline; xdt=pdt (1), adtiPr (2)) in MeCN-[Bu4 N][PF6 ] 0.2 m is described as a two-reduction process. DFT calculations show that 1 and its monoreduced form 1- display metal- and phenanthroline-centered frontier orbitals (LUMO and SOMO) indicating the non-innocence of the phenanthroline ligand. Two energetically close geometries were found for the doubly reduced species suggesting an intriguing influence of the phenanthroline ligand leading to the cleavage of a Fe-S bond as proposed generally for this type of complex or retaining the electron density and avoiding Fe-S cleavage. Extension of calculations to other complexes with edt, adtiPr bridge and even virtual species [Fe2 (CO)4 (κ2 -phen)(µ-adtR )] (R=CH(CF3 )2 , H) or [Fe2 (CO)4 (κ2 -phen)(µ-pdtR )] (R=CH(CF3 )2 , iPr) showed that the relative stability between both two-electron-reduced isomers depends on the nature of the bridge and the possibility to establish a remote anagostic interaction between the iron center {Fe(CO)3 } and the group carried by the bridged-head atom of the dithiolate group.


Subject(s)
Hydrogenase , Iron-Sulfur Proteins , Biomimetics , Crystallography, X-Ray , Electrons , Hydrogenase/metabolism , Iron-Sulfur Proteins/metabolism , Oxidation-Reduction
15.
Comput Struct Biotechnol J ; 18: 1137-1152, 2020.
Article in English | MEDLINE | ID: mdl-32489527

ABSTRACT

Chromosomal DNA double-strand breaks (DSBs) are potentially lethal DNA lesions that pose a significant threat to genome stability and therefore need to be repaired to preserve genome integrity. Eukaryotic cells possess two main mechanisms for repairing DSBs: non-homologous end-joining (NHEJ) and homologous recombination (HR). HR requires that the 5' terminated strands at both DNA ends are nucleolytically degraded by a concerted action of nucleases in a process termed DNA-end resection. This degradation leads to the formation of 3'-ended single-stranded DNA (ssDNA) ends that are essential to use homologous DNA sequences for repair. The evolutionarily conserved Mre11-Rad50-Xrs2/NBS1 complex (MRX/MRN) has enzymatic and structural activities to initiate DSB resection and to maintain the DSB ends tethered to each other for their repair. Furthermore, it is required to recruit and activate the protein kinase Tel1/ATM, which plays a key role in DSB signaling. All these functions depend on ATP-regulated DNA binding and nucleolytic activities of the complex. Several structures have been obtained in recent years for Mre11 and Rad50 subunits from archaea, and a few from the bacterial and eukaryotic orthologs. Nevertheless, the mechanism of activation of this protein complex is yet to be fully elucidated. In this review, we focused on recent biophysical and structural insights on the MRX complex and their interplay.

16.
Nucleic Acids Res ; 48(5): 2424-2441, 2020 03 18.
Article in English | MEDLINE | ID: mdl-31879780

ABSTRACT

The cellular response to DNA double-strand breaks (DSBs) is initiated by the Mre11-Rad50-Xrs2 (MRX) complex that has structural and catalytic functions. MRX association at DSBs is counteracted by Rif2, which is known to interact with Rap1 that binds telomeric DNA through two tandem Myb-like domains. Whether and how Rap1 acts at DSBs is unknown. Here we show that Rif2 inhibits MRX association to DSBs in a manner dependent on Rap1, which binds to DSBs and promotes Rif2 association to them. Rap1 in turn can negatively regulate MRX function at DNA ends also independently of Rif2. In fact, a characterization of Rap1 mutant variants shows that Rap1 binding to DNA through both Myb-like domains results in formation of Rap1-DNA complexes that control MRX functions at both DSBs and telomeres primarily through Rif2. By contrast, Rap1 binding to DNA through a single Myb-like domain results in formation of high stoichiometry complexes that act at DNA ends mostly in a Rif2-independent manner. Altogether these findings indicate that the DNA binding modes of Rap1 influence its functional properties, thus highlighting the structural plasticity of this protein.


Subject(s)
DNA, Fungal/metabolism , Multiprotein Complexes/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Telomere Homeostasis , Telomere-Binding Proteins/metabolism , Telomere/metabolism , Transcription Factors/metabolism , Alleles , DNA Breaks, Double-Stranded , DNA Damage , Models, Biological , Mutation/genetics , Protein Binding , Saccharomyces cerevisiae/cytology , Shelterin Complex , Transcription, Genetic
17.
Inorg Chem ; 58(4): 2430-2443, 2019 Feb 18.
Article in English | MEDLINE | ID: mdl-30707014

ABSTRACT

Described are the syntheses of several Ni(µ-SR)2Fe complexes, including hydride derivatives, in a search for improved models for the active site of [NiFe]-hydrogenases. The nickel(II) precursors include (i) nickel with tripodal ligands: Ni(PS3)- and Ni(NS3)- (PS33- = tris(phenyl-2-thiolato)phosphine, NS33- = tris(benzyl-2-thiolato)amine), (ii) traditional diphosphine-dithiolates, including chiral diphosphine R,R-DIPAMP, (iii) cationic Ni(phosphine-imine/amine) complexes, and (iv) organonickel precursors Ni( o-tolyl)Cl(tmeda) and Ni(C6F5)2. The following new nickel precursor complexes were characterized: PPh4[Ni(NS3)] and the dimeric imino/amino-phosphine complexes [NiCl2(PCH═NAn)]2 and [NiCl2(PCH2NHAn)]2 (P = Ph2PC6H4-2-). The iron(II) reagents include [CpFe(CO)2(thf)]BF4, [Cp*Fe(CO)(MeCN)2]BF4, FeI2(CO)4, FeCl2(diphos)(CO)2, and Fe(pdt)(CO)2(diphos) (diphos = chelating diphosphines). Reactions of the nickel and iron complexes gave the following new Ni-Fe compounds: Cp*Fe(CO)Ni(NS3), [Cp(CO)Fe(µ-pdt)Ni(dppbz)]BF4, [( R,R-DIPAMP)Ni(µ-pdt)(H)Fe(CO)3]BArF4, [(PCH═NAn)Ni(µ-pdt)(Cl)Fe(dppbz)(CO)]BF4, [(PCH2NHAn)Ni(µ-pdt)(Cl)Fe(dppbz)(CO)]BF4, [(PCH═NAn)Ni(µ-pdt)(H)Fe(dppbz)(CO)]BF4, [(dppv)(CO)Fe(µ-pdt)]2Ni, {H[(dppv)(CO)Fe(µ-pdt)]2Ni]}BF4, and (C6F5)2Ni(µ-pdt)Fe(CO)2(dppv) (DIPAMP = (CH2P(C6H4-2-OMe)2)2; BArF4- = [B(C6H3-3,5-(CF3)2]4-)) Within the context of Ni-(SR)2-Fe complexes, these new complexes feature new microenvironments for the nickel center: tetrahedral Ni, chirality, imine, and amine coligands, and Ni-C bonds. In the case of {H[(dppv)(CO)Fe(µ-pdt)]2Ni}+, four low-energy isomers are separated by ≤3 kcal/mol, one of which features a biomimetic HNi(SR)4 site, as supported by density functional theory calculations.

18.
Nucleic Acids Res ; 47(7): 3550-3567, 2019 04 23.
Article in English | MEDLINE | ID: mdl-30698745

ABSTRACT

Activation of the checkpoint protein Tel1 requires the Mre11-Rad50-Xrs2 (MRX) complex, which recruits Tel1 at DNA double-strand breaks (DSBs) through direct interaction between Tel1 and Xrs2. However, in vitro Tel1 activation by MRX requires ATP binding to Rad50, suggesting a role also for the MR subcomplex in Tel1 activation. Here we describe two separation-of-functions alleles, mre11-S499P and rad50-A78T, which we show to specifically affect Tel1 activation without impairing MRX functions in DSB repair. Both Mre11-S499P and Rad50-A78T reduce Tel1-MRX interaction leading to poor Tel1 association at DSBs and consequent loss of Tel1 activation. The Mre11-S499P variant reduces Mre11-Rad50 interaction, suggesting an important role for MR complex formation in Tel1 activation. Molecular dynamics simulations show that the wild type MR subcomplex bound to ATP lingers in a tightly 'closed' conformation, while ADP presence leads to the destabilization of Rad50 dimer and of Mre11-Rad50 association, both events being required for MR conformational transition to an open state. By contrast, MRA78T undertakes complex opening even if Rad50 is bound to ATP, indicating that defective Tel1 activation caused by MRA78T results from destabilization of the ATP-bound conformational state.


Subject(s)
DNA-Binding Proteins/genetics , Endodeoxyribonucleases/genetics , Exodeoxyribonucleases/genetics , Intracellular Signaling Peptides and Proteins/genetics , Protein Serine-Threonine Kinases/genetics , Saccharomyces cerevisiae Proteins/genetics , Transcriptional Activation/genetics , Adenosine Triphosphate/genetics , Ataxia Telangiectasia Mutated Proteins/genetics , DNA Damage/genetics , DNA Repair/genetics , DNA, Fungal/genetics , Molecular Conformation , Multiprotein Complexes/genetics , Protein Binding/genetics , Protein Multimerization/genetics , Saccharomyces cerevisiae/genetics , Signal Transduction/genetics
19.
Chemistry ; 25(5): 1227-1241, 2019 Jan 24.
Article in English | MEDLINE | ID: mdl-30475417

ABSTRACT

Catalytic H2 oxidation has been dissected by means of DFT into the key steps common to the Fe2 unit of both the [FeFe]-hydrogenase cofactor and selected biomimics. The aim was to elucidate the molecular details underlying the very different performances of the two systems. We found that the better enzyme performance is based on a single iron atom that is maintained electron-poor, favoring H2 binding, although embedded within a highly electron-rich cofactor, ensuring a facile oxidation of the Fe2 -H2 adduct. This is due to 1) CN- coordinating to both iron atoms, due to their amphipathic Lewis acid/base properties, and 2) the 4Fe4S subunit further withdrawing electrons from the Fe2 core. Preserving a moderate electron deficiency at a single iron also helps the cofactor preserve hydride affinity, which favors H2 cleavage. Such valuable characteristics allow the biocatalyst to turnover close to equilibrium conditions. All previous biomimicry has shown, in contrast, the impossibility to properly balance the two apparently contrasting aforementioned requisites, although evident progress has been made by the H2 -ase community. Disclosure of the differences identified could inspire the design of novel biomimics, for instance, reconsidering the use of CN- in the catalyst architecture. Indeed, in the presence of bases normally employed in oxidative catalysis, undesired stable protonation at coordinated CN- , which affects the opposite process (proton reduction), could be overcome.

20.
Metallomics ; 10(11): 1618-1630, 2018 11 14.
Article in English | MEDLINE | ID: mdl-30345437

ABSTRACT

Alzheimer's disease (AD) involves a number of factors including an anomalous interaction of copper with the amyloid peptide (Aß), inducing oxidative stress with radical oxygen species (ROS) production through a three-step cycle in which O2 is gradually reduced to superoxide, oxygen peroxide and finally OH radicals. The purpose of this work has been to investigate the reactivity of 14 different Cu(ii)-Aß coordination models with the aim of identifying on an energy basis (Density Functional Theory (DFT) and classical Molecular Dynamics (MD)) the redox competent form(s). Accordingly, we have specifically focused on the first three steps of the cycle, i.e. ascorbate binding to Cu(ii), Cu(ii) → Cu(i) reduction and O2 reduction to O2-. Compared to the recent literature, our results broaden the set of possible redox competent metallopeptide forms responsible for ROS production. Indeed, in addition to the three-coordinated species containing one His ligand, a N-terminal amine group and the carboxylate side chain of the Asp1 residue of Aß already proposed, we found two other Cu-Aß coordination modes involving two histidines.


Subject(s)
Amyloid beta-Peptides/metabolism , Coordination Complexes/metabolism , Copper/metabolism , Models, Molecular , Oxidative Stress , Oxygen/chemistry , Amyloid beta-Peptides/chemistry , Coordination Complexes/chemistry , Copper/chemistry , Humans , Ligands , Oxidation-Reduction
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