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FeFe hydrogenases catalyze H2 oxidation and production using an "H-cluster", where two Fe ions are bound by an aza-dithiolate (adt) ligand. Various hypotheses have been proposed (by us and others) to explain that the enzyme reversibly inactivates under oxidizing, anaerobic conditions: intramolecular binding of the N atom of adt, formation of the so-called "Hox/inact" state or nonproductive binding of H2 to isomers of the H-cluster. Here, we show that none of the above explains the new finding that the anaerobic, oxidative, H2-dependent reversible inactivation is strictly dependent on the presence of Cl- or Br-. We provide experimental evidence that chloride uncompetitively inhibits the enzyme: it reversibly binds to catalytic intermediates of H2 oxidation (but not to the resting "Hox" state), after which oxidation locks the active site into a stable, saturated, inactive form, the structure of which is proposed here based on DFT calculations. The halides interact with the amine group of the H-cluster but do not directly bind to iron. It should be possible to stabilize the inhibited state in amounts compatible with spectroscopic investigations to explore further this unexpected reactivity of the H-cluster of hydrogenase. [ABSTRACT FROM AUTHOR]

The biological reduction of dinitrogen (N 2 ) to ammonia is catalyzed by the complex metalloenzyme nitrogenase. Structures of the nitrogenase component proteins, Iron (Fe) protein and Molybdenum‑iron (MoFe) protein, and the stabilized complexes these component proteins, have been determined, providing a foundation for a number of fundamental aspects of the complicated catalytic mechanism. The reduction of dinitrogen to ammonia is a complex process that involves the binding of N 2 followed by reduction with multiple electrons and protons. Electron transfer into nitrogenase is typically constrained to the unique electron donor, the Fe protein. These constraints have prevented structural characterization of the active site with bound substrate. Recently it has been realized that selected amino acid substitutions in the environment of the active site metal cluster (Iron‑molybdenum cofactor, FeMo-co) allow substrates to persist even in the resting state. Reported here is a 1.70 Å crystal structure of a nitrogenase MoFe protein α-96 Arg ➔ Gln variant with the alternative substrate acetylene trapped in a channel in close proximity to FeMo-co. Complementary theoretical calculations support the validity of the acetylene interaction at this site and is also consistent with more favorable interactions in the variant MoFe protein compared to the native MoFe protein. This work represents the first structural evidence of a substrate trapped in the nitrogenase MoFe protein and is consistent with earlier assignments of proposed substrate pathways and substrate binding sites deduced from biochemical, spectroscopic, and theoretical studies. [ABSTRACT FROM AUTHOR]

The angiogenin protein (Ang) is a member of the vertebrate-specific secreted ribonucleases and one of the most potent angiogenic factors known. Ang is a normal constituent of human plasma and its concentration increases under some physiological and pathological conditions to promote neovascularization. Ang was originally identified as an angiogenic tumour factor, but its biological activity has been found to extend from inducing angiogenesis to promoting cell survival in different neurodegenerative diseases. Ang exhibits weak ribonucleolytic activity, which is critical for its biological functions. The RNase catalytic sites are two histidine residues, His-13 and His-114, and the lysine Lys-40. Copper is also an essential cofactor in angiogenesis and influences angiogenin's biological properties. The main Cu(ii) anchoring site of Ang is His-114, where metal binding inhibits RNase activity of the protein. To reveal the Cu(ii) coordination environment in the C-terminal domain of the Ang protein, we report on the characterization, by means of potentiometric, voltammetric, and spectroscopic (CD, UV-Vis and EPR) methods and DFT calculations, of Cu(ii) complexes formed with a peptide fragment including the Ang sequence 112–117 (PVHLDQ). Potentiometric titrations indicated that [CuLH−2] is the predominant species at physiological pH. EPR, voltammetric data and DFT calculations are consistent with a CuN3O2 coordination mode in which a distorted square pyramidal arrangement of the peptide was observed with the equatorial positions occupied by the nitrogen atoms of the deprotonated amides of the Asp and Leu residues, the δ-N atom of histidine and the oxygen atom of the aspartic carboxylic group. Moreover, two analogous peptides encompassing the PVHLNQ and LVHLDQ sequences were also characterized by using thermodynamic, spectroscopic and DFT studies to reveal the role they play in Cu(ii) complex formation by the carboxylate side chain of the Asp and Pro residues, a known breaking-point in metal coordination. [ABSTRACT FROM AUTHOR]

The article presents a study on the quantum refinement calculation of hydrogenase to determine the nature of the dithiolate ligand. It mentions that the study was conducted through the analysis of the quantum-mechanical energies of CH2, NH2+, NHdown, NHup, O, and crystal states. It reveals that quantum refinement calculation does not affirm that dithiolate ligand should be O(CH2S-)2.

The Mo/Cu-dependent CO dehydrogenase from Oligotropha carboxidovorans is an enzyme that is able to catalyze CO oxidation to CO2; moreover, it can also oxidize H2, thus eliciting a characteristic EPR signal. Interestingly, the Ag-substituted enzyme form proved unable to catalyze H2 oxidation. In the present contribution, we characterized the reactivity of the enzyme with H2 by quantumchemical calculations. It was found that dihydrogen binding to the wild-type enzyme requires significant structural rearrangements of the active site Theoretical EPR spectra for plausible H2-bound models of the partially reduced, paramagnetic active site are also presented and compared with the experimental counterpart. Finally, density functional theory modeling shows that Ag substitution impairs H2 binding at the active site. [ABSTRACT FROM AUTHOR]

It is successfully shown that photocatalytic proton reduction to dihydrogen in the presence of a sacrificial electron donor, such as trimethylamine (TEA) and ascorbate, can be driven by compact sensitizer-catalyst dyads, that is, dithiolate-bridged [FeFe] hydrogenase models tethered to organic sensitizers, such as fluorenes and silafluorenes ( 1 a- 4 a). The sensitizer-catalyst dyads 1 a- 4 a show remarkable and promising catalytic activities as well as enhanced stabilities during photocatalysis performed under UV-light irradiation. The photocatalysis was carried out both in non-aqueous and aqueous media. The latter experiments were performed by solubilizing the photocatalysts within micelles formed by either sodium dodecyl sulfate (SDS) or cetyltrimethylammonium bromide (CTAB). In this study a turnover number of 539 (7 h) is achieved under optimized conditions, which corresponds to an exceptionally high turnover frequency of 77 h−1. Theoretical investigations as well as emission decay experiments were performed to understand the observed phenomena together with the mechanisms of photocatalytic H2 generation. [ABSTRACT FROM AUTHOR]

[NiFe]-hydrogenases catalyse the relevant H → 2H + 2e reaction. Aerobic oxidation or anaerobic oxidation of this enzyme yields two inactive states called Ni-A and Ni-B. These states differ for the reactivation kinetics which are slower for Ni-A than Ni-B. While there is a general consensus on the structure of Ni-B, the nature of Ni-A is still controversial. Indeed, several crystallographic structures assigned to the Ni-A state have been proposed, which, however, differ for the nature of the bridging ligand and for the presence of modified cysteine residues. The spectroscopic characterization of Ni-A has been of little help due to small differences of calculated spectroscopic parameters, which does not allow to discriminate among the various forms proposed for Ni-A. Here, we report a DFT investigation on the nature of the Ni-A state, based on systematic explorations of conformational and configurational space relying on accurate energy calculations, and on comparisons of theoretical geometries with the X-ray structures currently available. The results presented in this work show that, among all plausible isomers featuring various protonation patterns and oxygenic ligands, the one corresponding to the crystallographic structure recently reported by Volbeda et al. (J Biol Inorg Chem 20:11-22, 19)-featuring a bridging hydroxide ligand and the sulphur atom of Cys64 oxidized to bridging sulfenate-is the most stable. However, isomers with cysteine residues oxidized to terminal sulfenate are very close in energy, and modifications in the network of H-bond with neighbouring residues may alter the stability order of such species. [ABSTRACT FROM AUTHOR]

Aim of this contribution is to review some recent quantum mechanical approaches used to compute the redox potentials of transition metal complexes, with the emphasis on copper and iron species, which are particularly relevant in inorganic biochemistry and in synthetic chemistry of bio-mimetic compounds. The paper presents also new DFT results obtained on Cu and Fe aquo ions in the framework of the Thermodynamic Integration and Grand Canonical Ensemble approaches. Such results show that without explicit inclusion of water molecules in the external solvation shells (even using a continuum solvation model) also very advanced methodologies fail to predict the redox potential in an acceptable manner. This is a confirmation of some previous studies which however never addressed this specific problem along the aforementioned approaches. Better results are obtained, on the contrary, on a series of Cu(II) complexes with Gly, Ala, en, Im, and water ligands with coordination type [ABSTRACT FROM AUTHOR]

FeFe hydrogenases catalyze H2 oxidation and formation at an inorganic active site (the "H-cluster"), which consists of a [Fe2(CO)3(CN)2(dithiomethylamine)] subcluster covalently attached to a Fe4S4 subcluster. This active site is photosensitive: visible light has been shown to induce the release of exogenous CO (a reversible inhibitor of the enzyme), shuffle the intrinsic CO ligands, and even destroy the H-cluster. These reactions must be understood because they may negatively impact the use of hydrogenase for the photoproduction of H2. Here, we explore in great detail the reactivity of the excited states of the H-cluster under catalytic conditions by examining, both experimentally and using TDDFT calculations, the simplest photochemical reaction: the binding and release of exogenous CO. A simple dyad model can be used to predict which excitations are active. This strategy could be used for probing other aspects of the photoreactivity of the H-cluster. [ABSTRACT FROM AUTHOR]

The serine–threonine protein kinase Akt, also known as protein kinase B, is a key component of the phosphoinositide 3-kinase (PI3K)–Akt–mTOR axis. Deregulated activation of this pathway is frequent in human tumors and Akt-dependent signaling appears to be critical in cell survival. PI3K activation generates 3-phosphorylated phosphatidylinositols that bind Akt pleckstrin homology (PH) domain. The blockage of Akt PH domain/phosphoinositides interaction represents a promising approach to interfere with the oncogenic potential of over-activated Akt. In the present study, phosphatidyl inositol mimics based on a β-glucoside scaffold have been synthesized as Akt inhibitors. The compounds possessed one or two lipophilic moieties of different length at the anomeric position of glucose, and an acidic or basic group at C-6. Docking studies, ELISA Akt inhibition assays, and cellular assays on different cell models highlighted 1- O -octadecanoyl-2- O -β- d -sulfoquinovopyranosyl- sn -glycerol as the best Akt inhibitor among the synthesized compounds, which could be considered as a lead for further optimization in the design of Akt inhibitors. [ABSTRACT FROM AUTHOR]

The complement system is an innate immunity effector mechanism; its action is antagonized by a wide array of pathogens and complement evasion determines the virulence of several infections. We investigated the evolutionary history of the complement system and of bacterial-encoded complement-interacting proteins. Complement components targeted by several pathogens evolved under strong selective pressure in primates, with selection acting on residues at the contact interface with microbial/viral proteins. Positively selected sites in CFH and C4 BPA account for the human specificity of gonococcal infection. Bacterial interactors, evolved adaptively as well, with selected sites located at interaction surfaces with primate complement proteins. These results epitomize the expectation under a genetic conflict scenario whereby the host's and the pathogen's genes evolve within binding avoidance-binding seeking dynamics. In silico mutagenesis and protein-protein docking analyses supported this by showing that positively selected sites, both in the host's and in the pathogen's interacting partner, modulate binding. [ABSTRACT FROM AUTHOR]

To learn from Nature how to create an efficient hydrogen-producing catalyst, much attention has been paid to the investigation of structural and functional biomimics of the active site of [FeFe]-hydrogenase. To understand their catalytic activities, the μ-S atoms of the dithiolate bridge have been considered as possible basic sites during the catalytic processes. For this reason, a series of [FeFe]-H2ase mimics have been synthesized and characterized. Different [FeFe]-hydrogenase model complexes containing bulky Si-heteroaromatic systems or fluorene directly attached to the dithiolate moiety as well as their mono-PPh3-substituted derivatives have been prepared and investigated in detail by spectroscopic, electrochemical, X-ray diffraction, and computational methods. The assembly of the herein reported series of complexes shows that the μ-S atoms can be a favored basic site in the catalytic process. Small changes in the (hetero)-aromatic system of the dithiolate moiety are responsible for large differences in their structures. This was elucidated in detail by DFT calculations, which were consistent with the experimental results. [ABSTRACT FROM AUTHOR]

Protein structure and dynamics are crucial for protein function. Thus, the study of conformational properties can be very informative for characterizing new proteins and to rationalize how residue substitutions at specific protein sites affect its dynamics, activity and thermal stability. Here, we investigate the structure and dynamics of the recently isolated cold-adapted acylaminoacyl peptidase from Sporosarcina psychrophila (SpAAP) by the integration of simulations, circular dichroism, mass spectrometry and other experimental data. Our study notes traits of cold-adaptation, such as lysine-to-arginine substitutions and a lack of disulphide bridges. Cold-adapted enzymes are generally characterized by a higher number of glycine residues with respect to their warm-adapted counterparts. Conversely, the SpAAP glycine content is lower than that in the warm-adapted variants. Nevertheless, glycine residues are strategically located in proximity to the functional sites in SpAAP, such as the active site and the linker between the two domains.. In particular, G457 reduces the steric hindrance around the nucleophile elbow. Our results suggest a local weakening of the intramolecular interactions in the cold-adapted enzyme. This study offers a basis for the experimental mutagenesis of SpAAP and related enzymes. The approaches employed in this study may also provide a more general framework to characterize new protein structures in the absence of X-ray or NMR data. [ABSTRACT FROM AUTHOR]

[FeFe]-hydrogenases are the most efficient biological catalysts available for the H 2 evolution reaction. Their active site – the H-cluster – features a diiron subsite which has the peculiar characteristic of bearing cyanide groups hydrogen-bonded to the apoprotein as well as carbonyl ligands. Notably, one of the CO ligands is disposed in bridging position between the metal centers. This allows one of the Fe ions to retain a square pyramidal coordination – which determines the assumption of the so-called “rotated structure” – with a vacant coordination site in trans to the μ-CO group, ready to bind protons when the active site is in the Fe I Fe I state. Many Fe I Fe I biomimetic models have been synthesized and characterized so far, but most of them fail to reproduce the orientation of the diatomic ligands that is observed in the enzyme active site. In the present contribution we carried out a density functional theory investigation, with the aim of evaluating whether the establishment of hydrogen bonding at the level of cyanides is sufficient to favor rotation of ligands around one of the Fe centers, in analogy with the reduced H-cluster. To this end, we carried out an investigation of the potential energy surface of an isolated Fe 2 S 2 model bearing CN and CO groups, as well as of the supramolecular complex formed by the diiron model and a porphyrin derivative hydrogen-bonded to the former. As far as the isolated Fe 2 S 2 species are concerned, the sole μ-CO models individuated in the course of our potential energy surface scans are the ones in which both cyanides are bound to same iron center, while no CO-bridged minima could be found in the case of models having one CN group bound to each of the metal ions. The latter represents a major difference with respect to the coordination geometry of the reduced diiron subcluster in the enzyme. However, perturbation of the diiron model by a porphyrin ring designed to donate hydrogen bonds to the cyanide groups – thus, at least partially, reproducing the network of H-bond between the H-cluster and the apoprotein in [FeFe]-hydrogenases – significantly changes the picture in this regard. Therefore, possible strategies to modulate the disposition of ligands around the metal centers of biomimetic [FeFe]-hydrogenases models are discussed in light of computed geometries and relative stabilities of the supramolecular complexes. [ABSTRACT FROM AUTHOR]

Nature is a valuable source of inspiration in the design of catalysts, and various approaches are used to elucidate the mechanism of hydrogenases, the enzymes that oxidize or produce H2. In FeFe hydrogenases, H2 oxidation occurs at the H-cluster, and catalysis involves H2 binding on the vacant coordination site of an iron centre. Here, we show that the reversible oxidative inactivation of this enzyme results from the binding of H2 to coordination positions that are normally blocked by intrinsic CO ligands. This flexibility of the coordination sphere around the reactive iron centre confers on the enzyme the ability to avoid harmful reactions under oxidizing conditions, including exposure to O2. The versatile chemistry of the diiron cluster in the natural system might inspire the design of novel synthetic catalysts for H2 oxidation. [ABSTRACT FROM AUTHOR]

Abstract: RIG-I-like receptors (RLRs) are nucleic acid sensors that activate antiviral innate immune response. These molecules recognize diverse non-self RNA substrates and are antagonized by several viral inhibitors. We performed an evolutionary analysis of RLR genes (RIG-I, MDA5, and LGP2) in mammals. Results indicated that purifying selection had a dominant role in driving the evolution of RLRs. However, application of maximum-likelihood analyses identified several positions that evolved adaptively. Positively selected sites are located in all domains of MDA5 and RIG-I, whereas in LGP2 they are confined to the helicase domain. In both MDA5 and RIG-I, the linkers separating the caspase activation and recruitment domain and the helicase domain represented preferential targets of positive selection. Independent selective events in RIG-I and LGP2 targeted the corresponding site (Asp421 and Asp179, respectively) within a protruding α-helix that grips the V-shaped structure formed by the pincer. Most of the positively selected sites in MDA5 are in regions unique to this RLR, including a characteristic insertion within the helicase domain. Additional selected sites are located at the contact interface between MDA5 monomers, in spatial proximity to a positively selected human polymorphism (Arg843His) and immediately external to the parainfluenza virus 5 V protein binding region. Structural analyses suggested that the positively selected His834 residue is involved in parainfluenza virus 5 V protein binding. Data herein suggest that RLRs have been engaged in host-virus genetic conflict leading to diversifying selection and indicate parallel evolution at the same site in RIG-I and LGP2, a position likely to be of central importance in antiviral responses. [Copyright &y& Elsevier]

The antigenic repertoire presented by MHC molecules is generated by the antigen processing and presentation (APP) pathway. We analyzed the evolutionary history of 45 genes involved in APP at the inter- and intra-species level. Results showed that 11 genes evolved adaptively in mammals. Several positively selected sites involve positions of fundamental importance to the protein function (e.g. the TAP1 peptide-binding domains, the sugar binding interface of langerin, and the CD1D trafficking signal region). In CYBB, all selected sites cluster in two loops protruding into the endosomal lumen; analysis of missense mutations responsible for chronic granulomatous disease (CGD) showed the action of different selective forces on the very same gene region, as most CGD substitutions involve aminoacid positions that are conserved in all mammals. As for ERAP2, different computational methods indicated that positive selection has driven the recurrent appearance of protein-destabilizing variants during mammalian evolution. Application of a population-genetics phylogenetics approach showed that purifying selection represented a major force acting on some APP components (e.g. immunoproteasome subunits and chaperones) and allowed identification of positive selection events in the human lineage. We also investigated the evolutionary history of APP genes in human populations by developing a new approach that uses several different tests to identify the selection target, and that integrates low-coverage whole-genome sequencing data with Sanger sequencing. This analysis revealed that 9 APP genes underwent local adaptation in human populations. Most positive selection targets are located within noncoding regions with regulatory function in myeloid cells or act as expression quantitative trait loci. Conversely, balancing selection targeted nonsynonymous variants in TAP1 and CD207 (langerin). Finally, we suggest that selected variants in PSMB10 and CD207 contribute to human phenotypes. Thus, we used evolutionary information to generate experimentally-testable hypotheses and to provide a list of sites to prioritize in follow-up analyses. [ABSTRACT FROM AUTHOR]

Abstract: Polynucleotide phosphorylase (PNPase) reversibly catalyzes RNA phosphorolysis and polymerization of nucleoside diphosphates. Its homotrimeric structure forms a central channel where RNA is accommodated. Each protomer core is formed by two paralogous RNase PH domains: PNPase1, whose function is largely unknown, hosts a conserved FFRR loop interacting with RNA, whereas PNPase2 bears the putative catalytic site, ∼20 Å away from the FFRR loop. To date, little is known regarding PNPase catalytic mechanism. We analyzed the kinetic properties of two Escherichia coli PNPase mutants in the FFRR loop (R79A and R80A), which exhibited a dramatic increase in K m for ADP/Pi binding, but not for poly(A), suggesting that the two residues may be essential for binding ADP and Pi. However, both mutants were severely impaired in shifting RNA electrophoretic mobility, implying that the two arginines contribute also to RNA binding. Additional interactions between RNA and other PNPase domains (such as KH and S1) may preserve the enzymatic activity in R79A and R80A mutants. Inspection of enzyme structure showed that PNPase has evolved a long-range acting hydrogen bonding network that connects the FFRR loop with the catalytic site via the F380 residue. This hypothesis was supported by mutation analysis. Phylogenetic analysis of PNPase domains and RNase PH suggests that such network is a unique feature of PNPase1 domain, which coevolved with the paralogous PNPase2 domain. [Copyright &y& Elsevier]

Summary: T cell activation plays a central role in immune response and in the maintenance of self-tolerance. We analyzed the evolutionary history of T cell regulatory molecules. Nine genes involved in triggering T cell activation or in regulating the ensuing response evolved adaptively in mammals. Several positively selected sites overlap with positions interacting with the binding partner or with cellular components. Population genetic analysis in humans revealed a complex scenario of local (FASLG, CD40LG, HAVCR2) and worldwide (FAS, ICOSLG) adaptation and H. sapiens-to-Neandertal gene flow (gene transfer between populations). Disease variants in these genes are preferential targets of pathogen-driven selection, and a Crohn’s disease risk polymorphism targeted by bacterial-driven selection modulates the expression of ICOSLG in response to a bacterial superantigen. Therefore, we used evolutionary information to generate experimentally testable hypotheses concerning the function of specific genetic variants and indicate that adaptation to infection underlies the maintenance of autoimmune risk alleles. [Copyright &y& Elsevier]

Acyl aminoacyl peptidases are two-domain proteins composed by a C-terminal catalytic α/β-hydrolase domain and by an N-terminal β-propeller domain connected through a structural element that is at the N-terminus in sequence but participates in the 3D structure of the C-domain. We investigated about the structural and functional interplay between the two domains and the bridge structure (in this case a single helix named α1-helix) in the cold-adapted enzyme from Sporosarcina psychrophila (SpAAP) using both protein variants in which entire domains were deleted and proteins carrying substitutions in the α1-helix. We found that in this enzyme the inter-domain connection dramatically affects the stability of both the whole enzyme and the β-propeller. The α1-helix is required for the stability of the intact protein, as in other enzymes of the same family; however in this psychrophilic enzyme only, it destabilizes the isolated β-propeller. A single charged residue (E10) in the α1-helix plays a major role for the stability of the whole structure. Overall, a strict interaction of the SpAAP domains seems to be mandatory for the preservation of their reciprocal structural integrity and may witness their co-evolution. [ABSTRACT FROM AUTHOR]

This investigation examines the protonation of diiron dithiolates, exploiting the new family of exceptionally electron-rich complexes Fe2(xdt)(CO)2(PMe3)4, where xdt is edt (ethanedithiolate, 1), pdt (propanedithiolate, 2), and adt (2-aza-1,3-propanedithiolate, 3), prepared by the photochemical substitution of the corresponding hexacarbonyls. Compounds 1-3 oxidize near -950 mV vs Fc+/0. Crystallographic analyses confirm that 1 and 2 adopt C2-symmetric structures (Fe-Fe = 2.616 and 2.625 Å, respectively). Low-temperature protonation of 1 afforded exclusively [μ-H1]+, establishing the non-intermediacy of the terminal hydride ([t-H1]+). At higher temperatures, protonation afforded mainly [t-H1]+. The temperature dependence of the ratio [t-H1]+/[μ-H1]+ indicates that the barriers for the two protonation pathways differ by ∼4 kcal/mol. Low-temperature 31P{1H} NMR measurements indicate that the protonation of 2 proceeds by an intermediate, proposed to be the S-protonated dithiolate [Fe2(Hpdt)(CO)2(PMe3)4]+ ([S-H2]+). This intermediate converts to [t-H2]+ and [μ-H2]+ by first-order and second-order processes, respectively. DFT calculations support transient protonation at sulfur and the proposal that the S-protonated species (e.g., [S-H2]+) rearranges to the terminal hydride intramolecularly via a low-energy pathway. Protonation of 3 affords exclusively terminal hydrides, regardless of the acid or conditions, to give [t-H3]+, which isomerizes to [t-H3′]+, wherein all PMe3 ligands are basal. [ABSTRACT FROM AUTHOR]

DFT/BP86/TZVP and DFT/B3LYP/TZVP have been used to investigate systematically the reaction pathways associated with the H-transfer step, which is the rate-determining step of the reaction HCOO- ⇆ CO2 + H+ + 2e-, as catalyzed by metalloenzyme formate dehydrogenase (FDH). Actually, the energetics associated with the transfer from formate to all H (proton or hydride) acceptors that are present within the FDH active site have been sampled. This study points to a viable intimate mechanism in which the metal center mediates H transfer from formate to the final acceptor, i.e. a selenocysteine residue. The Mo-based reaction pathway, consisting of a β-H elimination to metal with concerted decarboxylation, turned out to be favored over previously proposed routes in which proton transfer occurs directly from HCOO- to selenocysteine. The proposed reaction pathway is reminiscent of the key step of metal-based catalysis of the water-gas shift reaction. [ABSTRACT FROM AUTHOR]

Abstract: E2 ubiquitin-conjugating enzymes are key elements of the ubiquitin (Ub) pathway, since they influence processivity and topology of the Ub chain assembly and, as a consequence, the fate of the target substrates. E2s are multi-domain proteins, with accessory N-terminal or C-terminal domains that can contribute to the specificity for the cognate Ub-like molecules, or even the E3. In this context, the thorough structural characterization of E2 accessory domains is mandatory, in particular when they are associated to specific functions. We here provide, by computational and comparative studies, the first evidence of an acidic domain (AD) conserved in the E2 sub-family 3R. It is an intrinsically disordered domain, in which elements for Ub or E3 recognition are maintained. This conserved acidic domain (AD) shows propensity for α-helix structures (185–192 and 204–218) in the proximity of the sites for interaction with the Ub or the cognate E3. Moreover, our results also suggest that AD can explore conformations with tertiary contacts mainly driven by aromatic and hydrophobic interactions, in absence of its interaction partners. The globular states are likely to be regulated by multiple phosphorylation events, which can trigger conformational changes toward more extended conformations, as judged by MD simulations of the phospho-variants. The extended conformations, in turn, promote the accessibility of the interaction sites for Ub and the E3. We also trace a parallel between this new and natively unfolded structural motif for Ub-recognition and the natively folded ubiquitin associated domain (UBA) typical of family 1 of E2 enzymes, which includes Ubc1. In fact, according to our calculations, Ubc1 maps at the interface between the space of the natively unfolded and folded proteins, as well as it shares common features with the acidic domain of family 3 members. [Copyright &y& Elsevier]

Networks and clusters of intramolecular interactions, as well as their "communication" across the three-dimensional architecture have a prominent role in determining protein stability and function. Special attention has been dedicated to their role in thermal adaptation. In the present contribution, seven previously experimentally characterized mutants of a cold-adapted a-amylase, featuring mesophilic-like behavior, have been investigated by multiple molecular dynamics simulations, essential dynamics and analyses of correlated motions and electrostatic interactions. Our data elucidate the molecular mechanisms underlying the ability of single and multiple mutations to globally modulate dynamic properties of the cold-adapted a-amylase, including both local and complex unpredictable distal effects. Our investigation also shows, in agreement with the experimental data, that the conversion of the cold-adapted enzyme in a warm-adapted variant cannot be completely achieved by the introduction of few mutations, also providing the rationale behind these effects. Moreover, pivotal residues, which are likely to mediate the effects induced by the mutations, have been identified from our analyses, as well as a group of suitable candidates for protein engineering. In fact, a subset of residues here identified (as an isoleucine, or networks of mesophilic-like salt bridges in the proximity of the catalytic site) should be considered, in experimental studies, to get a more efficient modification of the features of the cold-adapted enzyme. [ABSTRACT FROM AUTHOR]

E2 ubiquitin-conjugating enzymes are crucial mediators of protein ubiquitination, which strongly influence the ultimate fate of the target substrates. Recently, it has been shown that the activity of several enzymes of the ubiquitination pathway is finely tuned by phosphorylation, an ubiquitous mechanism for cellular regulation, which modulates protein conformation. In this contribution, we provide the first rationale, at the molecular level, of the regulatory mechanism mediated by casein kinase 2 (CK2) phosphorylation of E2 Cdc34-like enzymes. In particular, we identify two co-evolving signature elements in one of the larger families of E2 enzymes: an acidic insertion in b4a2 loop in the proximity of the catalytic cysteine and two conserved key serine residues within the catalytic domain, which are phosphorylated by CK2. Our investigations, using yeast Cdc34 as a model, through 2.5 μs molecular dynamics simulations and biochemical assays, define these two elements as an important phosphorylation-controlled switch that modulate opening and closing of the catalytic cleft. The mechanism relies on electrostatic repulsions between a conserved serine phosphorylated by CK2 and the acidic residues of the b4a2 loop, promoting E2 ubiquitin charging activity. Our investigation identifies a new and unexpected pivotal role for the acidic loop, providing the first evidence that this loop is crucial not only for downstream events related to ubiquitin chain assembly, but is also mandatory for the modulation of an upstream crucial step of the ubiquitin pathway: the ubiquitin charging in the E2 catalytic cleft. [ABSTRACT FROM AUTHOR]

Carbon monoxide is often described as a competitive inhibitor of FeFe hydrogenases, and it is used for probing H2 binding to synthetic or in silico models of the active site H-cluster. Yet it does not always behave as a simple inhibitor. Using an original approach which combines accurate electrochemical measurements and theoretical calculations, we elucidate the mechanism by which, under certain conditions, CO binding can cause permanent damage to the H-cluster. Like in the case of oxygen inhibition, the reaction with CO engages the entire H-cluster, rather than only the Fe2 subsite. [ABSTRACT FROM AUTHOR]

Abstract: Tyrosinase (Ty) is a copper-containing enzyme ubiquitously distributed in nature. In recent years, Ty has attracted interest as a potential detoxifying agent for xenobiotic compounds with phenolic structure. Among these, chlorophenols are particularly relevant pollutants, commonly found in waste waters. The activity of Streptomyces antibioticus tyrosinase toward isomeric monochlorophenols was studied. Tyrosinase oxidizes both 3- and 4-chlorophenol to the same product, 4-chloro-1,2-ortho-quinone, which subsequently undergoes a nucleophilic substitution reaction at the chlorine atom by excess phenol to give the corresponding phenol-quinone adduct. By contrast, 2-chlorophenol is not reactive and acts as a competitive inhibitor. Docking calculations suggest that the substrates point to one of the copper atoms of the dinuclear center (copper B) and appear to interact preferentially with one of the two coordinated oxygen atoms. The approach of the substrate toward the active site is favored by a π-stacking interaction with one of the copper-coordinated histidines (His194) and by a hydrogen bonding interaction with the O1 oxygen. With this study, we provide the first characterization of the early intermediates in the biotechnologically relevant reaction of Ty with chlorophenols. Additionally, combining experimental evidences with molecular modeling simulations, we propose a detailed reaction scheme for Ty-mediated oxidation of monochlorophenols. [ABSTRACT FROM AUTHOR]

Abstract: Reacting a bidentate ligand H 2 L, 2-(2-methoxybenzyl)-2-methylpropane-1,3-dithiol, with Fe3(CO)12 formed a diiron hexacarbonyl complex (1Me) from which a diiron hexacarbonyl complex (1H) pendant with a phenolic group was derived via in-situ demethylation. Further deprotonation of complex 1H gave a diiron pentacarbonyl species (1) in which a rare bond between the soft metal FeI and the relatively hard base phenolate formed, FeI-OR (R = phenolic moiety). This bonding may be a suitable mimic of the bonding feature, {FeIFeI}R-OH/OH2 found in the [FeFe]-hydrogenase. [Copyright &y& Elsevier]

Abstract: Natriuretic peptides (NPs) are a family of structurally related hormone/paracrine factors (ANP, BNP and CNP), which mediate a broad array of physiological effects by interacting with specific guanylyl cyclase receptors (NPR) and have promising therapeutic and clinical applications. NPs are specific for different NPRs and share a common ring structure in which a disulfide bond between two conserved cysteine residues is formed. Residues within the cyclic loop are largely responsible for receptor selectivity. Structural features of free NPs in solution have not been investigated in details even if their characterization would be very useful in order to identify important aspects related to NPs function and receptor selectivity. In light of the above scenario, we carried out a 0.1μs molecular dynamics investigation of NPs with the aim of providing a high-resolution atomistic view of specific of their conformational ensemble in solution. Our results clearly indicate that NP receptor-bound conformations are not stable solution structure and that induced-fit mechanisms are involved in the formation of NP-NPR complexes. Moreover, in agreement with the current view on strictly relationship between protein dynamics and protein function and activity, it turns out that differences in activity and NPR specificity of CNP and ANP/BNP might be correlated to different amino acid composition of the cyclic loop, propensity to form β-sheet structures, flexibility patterns, dynamics properties and free conformations explored during the simulations. [Copyright &y& Elsevier]

Abstract: We have studied the accessibility of the structural calcium ion in the Burkholderia glumae lipase and the consequences of its removal on the protein conformation by different biophysical techniques (circular dichroism, fluorimetry, and mass spectrometry) and by molecular-dynamics simulations. We show that, in the native protein, calcium is not accessible unless specific flexible loops are displaced, for example, by a temperature increase. Such movements concern the whole calcium-binding pocket and particularly the environment of the coordinating aspartate residue 241. As a consequence of metal depletion the protein unfolds irreversibly and undergoes aggregation. The removal of the metal ion causes major structural transitions and leads to an increase in β-structure, in particular in protein regions that are largely unstructured in the native protein and encompass the calcium coordination residues. [Copyright &y& Elsevier]

Abstract: Mutation of RAS genes is a critical event in the pathogenesis of different human tumors and in some developmental disorders. Here we present an arabinose-derived bicyclic compound displaying selective cytotoxicity in human colorectal cancer cells expressing K-RasG13D , that shows high intrinsic nucleotide exchange rate. We characterize binding of bicyclic compounds by docking and NMR experiments and their inhibitory activity on GEF-mediated nucleotide exchange on wild-type and mutant Ras proteins. We demonstrate that the in vitro inhibition of Ras nucleotide exchange depends on the molar ratio between Ras and its GEF activator, suggesting that the observed in vivo selective effect may depend on biochemical parameters and actual intracellular concentration of the Ras protein and its regulators. [Copyright &y& Elsevier]

Abstract: Reaction of a trithiol ligand, 2-(mercaptomethyl)-2-methylpropane-1,3-dithiol (H3L), with tri-iron dodecacarbonyl in toluene produces two hexa-iron clusters (1 and 2). The two clusters are characterised crystallographically and spectroscopically. NMR spectroscopy reveals that the cluster 2 exists in two conformations in equilibrium 2 anti ⇔ 2 syn and the equilibrium constant K eq =0.55 under CO atmosphere. In the cluster 2, the central {Fe2S2(CO)6} sub-unit is flanked by two identical {Fe2S2(CO)6} satellite sub-units through thiolate linkages whereas one of the thiolate linkages can further form Fe–S bond with the proximal Fe atom in one of the two satellite sub-units to produce the cluster 1 by expelling one CO. This conversion can be entirely reversed by continuously purging CO through the solution of the cluster 1. As suggested by DFT calculations, the conversion features a key step, the rotation of the Feprox(CO)3 to expose a vacant site for exogenic ligand binding (the S atom from the central sub-unit in this case) with concomitant switch for one of the three CO ligands in the unit of Feprox(CO)3 from terminal to bridging orientation. The conversion from the clusters 1–2 involving one CO uptake is much faster than its reverse process since the latter is an endergonic process characterised by large reaction barriers, as revealed by the DFT calculations. [Copyright &y& Elsevier]

Abstract: In the present contribution, a density functional theory (DFT) investigation is described regarding a recently synthesized Fe6S6 complex – see C. Tard, X. Liu, S.K. Ibrahim, M. Bruschi, L. De Gioia, S.C. Davies, X. Yang, L.-S. Wang, G. Sawers, C.J. Pickett, Nature 433 (2005) 610 – that is structurally and functionally related to the [FeFe]-hydrogenases active site (the so-called H-cluster, which includes a binuclear subsite directly involved in catalysis and an Fe4S4 cubane). The analysis of relative stabilities and atomic charges of different isomers evidenced that the structural and redox properties of the synthetic assembly are significantly different from those of the enzyme active site. A comparison between the hexanuclear cluster and simpler synthetic diiron models is also described; the results of such a comparison indicated that the cubane moiety can favour the stabilization of the cluster in a structure closely resembling the H-cluster geometry when the synthetic Fe6S6 complex is in its dianionic state. However, the opposite effect is observed when the synthetic cluster is in its monoanionic form. [Copyright &y& Elsevier]

Oxidation of the electron-rich (E1/2 = -175 vs Ag/AgCI) ethanedithiolato complex Fe2(S2C2H4)-(CO)2(dppv)2 (1) under a CO atmosphere yielded [Fe2(S2C2H4)(μ-CO)(CO)2(dppv)2]+ ([1(CO)]+), a model for the HoxCO state of the [FeFe]-hydrogenases. This complex exists as two isomers: a kinetically favored unsymmetrical derivative, unsym-[1(CO)]+, and a thermodynamically favored isomer, sym-[1(CO)]+, wherein both diphosphines span apical and basal sites. Crystallographic characterization of sym-[1(CO)]+ confirmed a C2-symmetric structure with a bridging CO ligand and an elongated Fe-Fe bond of 2.7012(14) Å, as predicted previously. Oxidation of sym-[1(CO)f+ and unsym-[1(CO)]+ again by 1e- oxidation afforded the respective diamagnetic diferrous derivatives where the relative stabilities of the sym and unsym isomers are reversed. DFT calculations indicate that the stabilities of sym and unsym isomers are affected differently by the oxidation state of the diiron unit: the mutually trans CO ligands in the sym isomer are more destabilizing in the mixed-valence state than in the diferrous state. EPR analysis of mixed-valence complexes revealed that, for [1)+, the unpaired spin is localized on a single iron center, whereas for unsym/sym-[1(CO)]+, the unpaired spin was delocalized over both iron centers, as indicated by the magnitude of the hyperfine coupling to the phosphine ligands trans to the Fe-Fe vector. Oxidation of 1 by 2 equiv of acetylferrocenium afforded the dication [1]2+, which, on the basis of low-temperature IR spectrum, is structurally similar to [1]+. Treatment of [1]2+ with CO gives unsym-[1(CO)]2+. [ABSTRACT FROM AUTHOR]

Density functional theory has been used to investigate the reaction between H2 and [Ni(NHPnPr3)-(`S3')] or [Pd(NHPnPr3)('S3')], where `S3' = bis(2-sulfanylphenyl)sulfide(2-), which are among the few synthetic complexes featuring a metal coordination environment similar to that observed in the [NiFe] hydrogenase active site and capable of catalyzing H2 heterolytic cleavage. Results allowed us to unravel the reaction mechanism, which is consistent with an oxidative addition—hydrogen migration pathway for [Ni(NHPnPr3)('S3')], whereas metathesis is also possible with [Pd(NHPnPr3)('S3')]. Unexpectedly, H2 binding and activation implies structural reorganization of the metal coordination environment. It turns out that the structural rearrangement in [Ni(NHPnPr3)('S3')] and [Pd(NHPnPr3)('S3')) can take place due to the peculiar structural features of the Ni and Pd ligands, explaining the remarkable catalytic properties. However, the structural reorganization is the most unfavorable step along the H2 cleavage pathway (ΔG > 100 kJ mol-1), an observation that is relevant for the design and synthesis of novel biomimetic catalysts. [ABSTRACT FROM AUTHOR]

Abstract: Density functional theory (DFT) has been recently used to explore the chemistry of models of the active site of [NiFe] and [Fe] hydrogenases, which are enzymes that catalyse the reversible oxidation of H2. Results from recent theoretical investigations aimed at characterizing relevant intermediate species in the catalytic cycle of hydrogenases, clarifying the structural and electronic properties of the bimetallic cofactors, as well as the key factors responsible for H2 activation, are reviewed. The role of theoretical contributions in the investigation of synthetic models related to the enzymatic metal cofactors is also discussed, showing how ‘in silico’ coordination chemistry can nicely complement experimental studies in the characterization of relevant species. [Copyright &y& Elsevier]

Density functional theory has been used to investigate structural, electronic and reactivity properties of complexes related to the peroxo forms of vanadium haloperoxidases (VHPO). In particular, the reactivity of the cofactor as a function of protonation state and environment, which are two factors thought to be crucial in modulating the activity of the enzyme, has been examined. In full agreement with experimental data, results highlight the role of protonation in the activation of the peroxo-vanadium complexes and show that the oxo-transfer step involves the unprotonated axial peroxo oxygen atom, which is easily accessible to substrates in the peroxo form of the enzyme. The role of Lys353, which in the X-ray structure of the peroxide-bound form of vanadium chloroperoxidase is hydrogen bonded to the equatorial oxygen atom of the peroxo group, has been also explored. It is concluded that Lys353 can play a role similar to a H+ in the activation of the peroxo form of the cofactor. [ABSTRACT FROM AUTHOR]

[Display omitted] • Coordination models of bioinorganic compounds. • Density Functional Theory approaches in bioinorganic chemistry. • Co, Fe and Cu-mediated small molecules activation. • The cultural and research legacy of professor Renato Ugo. A few bio-inorganic systems have been studied by means of modern quantum chemistry (QM) methods, such as the Density Functional Theory (DFT) in connection with a large set of basis functions. At this level, DFT has proven to give reliable (semi-quantitative) description of several properties of transition metals complexes which are either relevant part of a natural enzyme or ad hoc built to mimic the behaviour of enzymes. The first example considered is the N,N'-ethylenebis(acetylacetonatiminato)Co(II) (Coacacen) , a very famous synthetic oxygen carrier. We report results of a DFT investigation of Coacacen in its free form as well as in penta-coordinated form with a suitable axial ligand and, finally, in hexa -coordinated form bound to dioxygen. The problems related to the electronic structure of Coacacen derivatives are very old, and have been investigated (mainly experimentally) for several years. Coacacen has been the first bio-inorganic system investigated in the group of Renato Ugo in the 1970s. In addition, a short review will be presented concerning the "modern" problems of the bio-inorganics, as they are presently investigated in our research group based at the University of Milano-Bicocca (Italy): the catalytic cycle characteristic of Fe-Fe hydrogenases and the model compounds describing the interaction between copper and amyloid β-peptides. [ABSTRACT FROM AUTHOR]

The article focuses on [FeFe]-hydrogenases, hydrogen-evolving enzymes that are able to catalyze H2 production at very low overpotentials under mild conditions. The components of the active site of [FeFe]-hydrogenases include an Fe6S6 complex, known as the H-cluster, which is further composed of a classical Fe4S4 cubane cluster. Three CO and two CN- ligands and a bidentate chelating ligand coordinate the Fe atoms of the binuclear subcluster.

The art of designing coupling systems to drive reactions for endergonic synthesis is a subject of great interest in the scientific community, but it still presents major challenges. The aim of this kinetic study was to run simulations in COPASI 4.39 to test the behavior of hypothetical models for a system that couples two independent reactions, one exergonic and the other endergonic. In our computational study, we unraveled the qualitative and quantitative conditions that allow and benefit coupling, considering all possible reaction pathways within the network. Optimal conditions were reached by assigning favorable directionalities and low activation energies to six reaction steps within a network that featured twenty reaction steps. Moreover, different models were designed and tested in order to investigate the availability of coupling with different reaction steps.

Laccases that oxidize low-density polyethylene (LDPE) represent a promising strategy for bioremediation purposes. To rationalize or optimize their PE-oxidative activity, two fundamental factors must be considered: the enzyme's redox potential and its binding affinity/mode towards LDPE. Indeed, a stable laccase-PE complex may facilitate a thermodynamically unfavorable electron transfer, even without redox mediators. In this study, we compared the redox potential and the LDPE-binding properties of three different PE-oxidizing laccases: a fungal high-redox potential laccase from Trametes versicolor, a bacterial low-redox potential laccase from Bacillus subtilis, and the recently characterized LMCO2 from Rhodococcus opacus R7. First we found that LMCO2 is a low-potential laccase (E°=413 mV), as reported in other bacterial variants. Using computational tools, we simulated the interactions of these laccases with a large LDPE model and highlighted the key role of hydrophobic residues surrounding the T1 site. Notably, a methionine-rich loop in LMCO2 appears to enhance the formation of a stable complex with LDPE, potentially facilitating electron transfer. This study underscores the necessity for comprehensive computational strategies to analyze enzyme-polymer interactions beyond simplistic models, uncovering critical binding determinants and informing future mutagenesis experiments, in order to enhance laccase performance and rationalize variations in enzymatic activity., (© 2025 Wiley-VCH GmbH.)