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Human osteocalcin (OC) undergoes reversible, vitamin K-dependent gamma-carboxylation at three glutamic acid residues, modulating its release from bones and its hormonal roles. A complete understanding of OC roles and structure-activity relationships is still lacking, as only uncarboxylated and few differently carboxylated variants have been considered so far. To fill this lack of knowledge, a comprehensive experimental and computational investigation of the structural properties and calcium-binding activity of all the OC variants is reported here. Such a comparative study indicates that the carboxylation sites are not equivalent and differently affect the OC structure and interaction with calcium, properties that are relevant for the modulation of OC functions. This study also discloses cooperative effects and provides structural and mechanistic interpretation. The disclosed peculiar features of each carboxylated proteoform strongly suggest that considering all eight possible OC variants in future studies may help rationalize some of the conflicting hypotheses observed in the literature.

Societal Impact Statement: The legume crop cowpea is grown worldwide, but 90% of the world's total share is produced in Africa. It is a promising species due to its resilience properties, balance of macro and micronutrients and presence of health-promoting bioactive compounds. In African countries, cowpea has a crucial role in guaranteeing food security as a subsistence crop for families and commercial income for small farmers. The discovery of compounds with high nutraceutical value and bioactive properties supports socio-economic policies to improve health and nutrition, especially in low- and middle-income countries. In turn, this encourages biodiversity protection and crop enhancement programmes. Summary: Bowman–Birk protease inhibitors (BBIs) are a restricted group of small proteins in plants mainly involved in defence mechanisms against pests. BBIs are demonstrated to be active components capable of reducing the viabilities of different cancer cell lines. BBI bioactivity is directly linked to the inhibition capacity, but the variability and the efficiency against the physiological targets of different BBI isoforms remain still unexplored. We analysed the natural genetic diversity of two main genes encoding BBI trypsin-trypsin (BBI-TT) and trypsin-chymotrypsin (BBI-TC) in wild and domesticated cowpea samples mainly spread in Sub-Saharan Africa. We analysed DNA sequences and respective amino acidic isoforms/isoproteins to explore signs of natural selection and haplotype relationships. Moreover, we calculated the binding energy between BBIs and their biological targets to identify which are the most efficient inhibitors and their geographical locations. We found a high level of haplotype diversity for both genes, almost exclusively in wild accessions and detected positive and negative selection signals in the amino acid sequences. Furthermore, in the wild diversity pool, some BBI-TT and BBI-TC mature proteins were potentially better interactors with the physiolog

The electron rich Fe2(pdt)(RNC)6 1 (pdt=CH2(CH2S−)2) has been used as starting point for a DFT multi-functional study to assess the feasibility of designing a stable inverted (or rotated) disposition of the two FeL3 pyramidal moieties in the dimetallic core, a key feature of [FeFe]-hydrogenase cofactor. The choice of 1 was motivated by the presence of a rotated form in solution, slightly less stable than the unrotated stereoisomer. Aimed to find an upgraded version of 1, featuring the rotated isomer as ground state, various combinations of factors have been tested, for their effect on the relative stability of rotated vs unrotated isomers. The general result is that combining coordination asymmetry, electron donor presence and isocyanides R substituents able to establish intramolecular interactions is effective in stabilizing the rotated isomer. Our DFT study may inspire the design of synthetic biomimetics, with improved resemblance to the natural system.

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.

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.

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.

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.

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.

FeIFeI Fe2(S2C3H6)(CO)6(µ-CO) (1a–CO) and its FeIFeII cationic species (2a+–CO) are the simplest model of the CO-inhibited [FeFe] hydrogenase active site, which is known to undergo CO photolysis within a temperature-dependent process whose products and mechanism are still a matter of debate. Using density functional theory (DFT) and time-dependent density functional theory (TDDFT) computations, the ground state and low-lying excited-state potential energy surfaces (PESs) of 1a–CO and 2a+–CO have been explored aimed at elucidating the dynamics of the CO photolysis yielding Fe2(S2C3H6)(CO)6 (1a) and [Fe2(S2C3H6)(CO)6]+ (2a+), two simple models of the catalytic site of the enzyme. Two main results came out from these investigations. First, a–CO and 2a+–CO are both bound with respect to any CO dissociation with the lowest free energy barriers around 10 kcal mol−1, suggesting that at least 2a+–CO may be synthesized. Second, focusing on the cationic form, we found at least two clear excited-state channels along the PESs of 2a+–CO that are unbound with respect to equatorial CO dissociation.

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 ecacy 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.

This perspective aims at illustrating a computational viewpoint on some specific issues concerning structure–activity relationships related to [FeFe]-hydrogenase ([FeFe]-H2ase) biomimicry. Most of the research outlined herein has been addressed by means of density functional theory (DFT) based tools, in some cases in conjunction with experimental techniques. The number of computational, experimental and mixed approach studies on the “hydrogenase models” topic is extraordinarily high. Accordingly, several comprehensive reviews have been published over the last twenty years. Moreover, the number of iron compounds of increasing nuclearity that have been considered as “biomimetic models” of [FeFe]-H2ase has grown exponentially over time. Additionally, the issues regarding some mismatches existing between the natural system and related synthetic analogues, are quite variegated. As a consequence of the countless examples that could be considered as related to “hydrogenase mimicry”, the intent of the present contribution is to provide an account of a limited number of recent study cases, in which DFT has been employed to elucidate redox properties, reactivity issues of selected examples of diiron biomimicry. Herein the treated topics have been explicitly chosen to show how DFT has allowed us to rationalize and complement experimental observations, with a special focus on electrocatalysis aspects. Finally, the specific purpose of this perspective is to show how mutually intertwined are the various issues concerning a fascinating branch of biomimetic research.

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.

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.

Carminic acid, a natural hydrophilic dye extensively used in the food and cosmetic industries, is converted in hydrophobic dyes by acetylation or pivaloylation. These derivatives are successfully used as biocolourants for rubber objects. In this paper, spectroscopic properties of the carminic acid derivatives in dimethyl sulfoxide and in polybutylacrylate are studied by means of photoluminescence and time-resolved photoluminescence decays, revealing a hypsochromic effect due to the presence of bulky substituents as the acetyl or pivaloyl groups. Molecular mechanics and density functional theory calculations confirm the disruption of planarity between the sugar ring and the anthraquinoid system determined by the esterification

Homologous recombination is triggered by nucleolytic degradation (resection) of DNA double-strand breaks (DSBs). DSB resection requires the Mre11-Rad50-Xrs2 (MRX) complex, which promotes the activity of Exo1 nuclease through a poorly understood mechanism. Here, we describe the Mre11-R10T mutant variant that accelerates DSB resection compared to wild-type Mre11 by potentiating Exo1-mediated processing. This increased Exo1 resection activity leads to a decreased association of the Ku complex to DSBs and an enhanced DSB resection in G1, indicating that Exo1 has a direct function in preventing Ku association with DSBs. Molecular dynamics simulations show that rotation of the Mre11 capping domains is able to induce unwinding of double-strand DNA (dsDNA). The R10T substitution causes altered orientation of the Mre11 capping domain that leads to persistent melting of the dsDNA end. We propose that MRX creates a specific DNA end structure that promotes Exo1 resection activity by facilitating the persistence of this nuclease on the DSB ends, uncovering a novel MRX function in DSB resection

The synthesis and redox properties are presented for the electron-rich bis(monothiolate)s Fe2(SR)2(CO)2(dppv)2 for R = Me ([1]0), Ph ([2]0), CH2Ph ([3]0). Whereas related derivatives adopt C2-symmetric Fe2(CO)2P4 cores, [1]0-[3]0 have Cs symmetry resulting from the unsymmetrical steric properties of the axial vs equatorial R groups. Complexes [1]0-[3]0 undergo 1e- oxidation upon treatment with ferrocenium salts to give the mixed valence cations [Fe2(SR)2(CO)2(dppv)2]+. As established crystallographically, [3]+ adopts a rotated structure, characteristic of related mixed valence diiron complexes. Unlike [1]+ and [2]+ and many other [Fe2(SR)2L6]+ derivatives, [3]+ undergoes C-S bond homolysis, affording the diferrous sulfido-thiolate [Fe2(SCH2Ph)(S)(CO)2(dppv)2]+ ([4]+). According to X-ray crystallography, the first coordination spheres of [3]+ and [4]+ are similar, but the Fe-sulfido bonds are short in [4]+. The conversion of [3]+ to [4]+ follows first-order kinetics, with k = 2.3 × 10-6 s-1 (30 °C). When the conversion is conducted in THF, the organic products are toluene and dibenzyl. In the presence of TEMPO, the conversion of [3]+ to [4]+ is accelerated about 10×, the main organic product being TEMPO-CH2Ph. DFT calculations predict that the homolysis of a C-S bond is exergonic for [Fe2(SCH2Ph)2(CO)2(PR3)4]+ but endergonic for the neutral complex as well as less substituted cations. The unsaturated character of [4]+ is indicated by its double carbonylation to give [Fe2(SCH2Ph)(S)(CO)4(dppv)2]+ ([5]+), which adopts a bioctahedral structure.

The biological reduction of dinitrogen (N2) 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 N2followed 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-Mo molybdenum cofactor, FeMo-co) allow substrates to persist even in the resting state. Reported here is a 1.70 Ã crystal structure of a nitrogenase MoFe protein alfa-96Arg -> 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.

The photochemistry of the [FeFe] hydrogenases model [Fe-2(edt)(CO)(4)(PMe3)(2)] (edt=1-2 ethane-dithiolate, (1) is investigated at Time-Dependent Density Functional Theory (TDDFT) level, focusing on the effect of the phosphine ligands on the early stages of the photodynamic of the system compared to that of the all CO model Fe-2(pdt)(CO)(6) (2) (pdt=1-3 propanedithiolate). We observed a role of the FeS charge transfer for the lower energy singlet transitions, unveiling a photoisomerization pathway between the lowest energy forms while the higher energy excitations are likely involved in the CO dissociation pathways. TDDFT shows that the average Fe-CO bond elongation in 1 is shorter than that observed in 2, providing the electronic structure rationale on the observation that diiron dithiolates are more photo-stable with respect to the CO photolysis than the all CO model. This is relevant for catalyst photo-stability and is an advantageous and thus desirable feature for practical applications of photo-hydrogen evolution

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

Recently a growing interest in the photochemical aspects of [FeFe] hydrogenases catalytic site and their biomimetic models has emerged. The photochemical aspects investigated range from the CO photolysis of the CO inhibited form of the enzyme to the excited state properties of the H-cluster models. [1] Regarding this last point, many efforts have been devoted to the investigation of the photochemical properties of simple diiron models of the [FeFe] hydrogenases catalytic site. The present contribution is focused on the Time-Dependent Density Functional theory (TDDFT) investigation of CO photolysis and photoisomerization of the trimetilphosphine (PMe3) derivative Fe2(S2C2H4)(CO)4(PMe3)2 starting from the recent ultrafast time-resolved infrared spectroscopy measurements [2,3]. By exploring the potential energy surfaces of low energy singlet excited states [4,5] the photoisomerization pathways has been characterized. Our calculation also show that the nature of this mechanism depends on the type of ligands coordinated to the iron atoms. The photoinduced CO dissociation involved excited states at higher excitation energy with the formation of a solvent adduct

It is well known that transition metal ions are often bound to proteins, conveying very specific functional properties. In fact, metalloproteins play crucial biological roles in the transport and activation of small molecules such as H-2, O-2, and N-2, as well as in several other biochemical processes. However, even if the presence of transition metals in the active site of proteins allows a very rich biochemistry, the experimental disclosure of structure-activity relationships in metalloproteins is generally difficult exactly because of the presence of transition metals, which are intrinsically characterized by a very versatile and often elusive chemistry. For this reason, computational methods are becoming very popular tools in the characterization of metalloproteins. In particular, since computing power is becoming less and less expensive, due to the continuous technological development of CPUs, the computational tools suited to investigate metalloproteins are becoming more accessible and therefore more commonly used also in molecular biology and biochemistry laboratories. Here, we present the main procedures and computational methods based on quantum mechanics, which are commonly used to study the structural, electronic, and reactivity properties of metalloproteins and related bioinspired compounds, with a specific focus on the practical and technical aspects that must be generally tackled to properly study such biomolecular systems.

Bromoperoxidase catalytic activity exerted by oxidated amavadin [V(HIDPA)(2)](-) (HIDPA = 2,2'-(hydroxyimino) dipropionate) in mono- and bis-protonated forms has been investigated by DFT. Possible reaction pathways for formation of peroxido/hydroperoxido complexes and subsequent bromide oxidation have been systematically dissected. The effect of increasing [H+] on catalytically active species and on halogenide oxidation has been also studied. Similarly to vanadium haloperoxidase (VHPO), the results point to a hydroperoxido amavadin adduct as the most reactive species toward bromide oxidation. However, comparison of the reactivity of amavadin and VHPO reveals also crucial differences in the catalytic mechanism of such natural V complexes.