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A Single-Event MicroKinetic (SEMK) model has been extended towards the simulation of Steady State Isotopic Transient Kinetic Analysis (SSITKA) data for Co catalyzed Fischer-Tropsch Synthesis (FTS). The extended model considers two types of sites and both direct and H-assisted CO dissociation. Regression of the model parameters to the data obtained from 17 steady state and 11 SSITKA experiments resulted in physicochemically meaningful estimates for the activation energies and atomic chemisorption enthalpies. The application of the phenomenological UBI-QEP method allows to physically interpret the nature of the two site types considered in the model, i.e., terrace and step sites. A reaction path analysis shows that over 80 percent of the CO reacts on the step sites. Furthermore, chain growth exclusively occurs on these sites. The terrace sites are less reactive for CO dissociation and are identified as responsible for methane production. A fraction of the alkenes, produced on the step sites, is hydrogenated to alkanes on the terrace sites. Based on model simulations, the metal particle size effect, i.e., a lower TOF, higher methane selectivity and increasing alkane to alkene ratio with decreasing metal particle size, is attributed to an increasing relative importance of the terrace sites on the reaction kinetics.

Here, we disclose a new copper(i)-Schiff base complex series for selective oxidation of primary alcohols to aldehydes under benign conditions. The catalytic protocol involves 2,2,6,6-tetramethylpiperidine-N-oxyl (TEMPO), N-methylimidazole (NMI), ambient air, acetonitrile, and room temperature. This system provides a straightforward and rapid pathway to a series of Schiff bases, particularly, the copper(i) complexes bearing the substituted (furan-2-yl)imine bases N-(4-fluorophenyl)-1-(furan-2-yl)methanimine (L2) and N-(2-fluoro-4-nitrophenyl)-1-(furan-2-yl)methanimine (L4) have shown excellent yields. Both benzylic and aliphatic alcohols were converted to aldehydes selectively with 99% yield (in 1-2 h) and 96% yield (in 16 h). The mechanistic studies via kinetic analysis of all components demonstrate that the ligand type plays a key role in reaction rate. The basicity of the ligand increases the electron density of the metal center, which leads to higher oxidation reactivity. The Hammett plot shows that the key step does not involve H-abstraction. Additionally, a generalized additive model (GAM, including random effect) showed that it was possible to correlate reaction composition with catalytic activity, ligand structure, and substrate behavior. This can be developed in the form of a predictive model bearing in mind numerous reactions to be performed or in order to produce a massive data-set of this type of oxidation reaction. The predictive model will act as a useful tool towards understanding the key steps in catalytic oxidation through dimensional optimization while reducing the screening of statistically poor active catalysis.

Protein bioconjugates are in high demand for applications in biomedicine, diagnostics, chemical biology and bionanotechnology. Proteins are large and sensitive molecules containing multiple different functional groups and in particular nucleophilic groups. In bioconjugation reactions it can therefore be challenging to obtain a homogeneous product in high yield. Numerous strategies for protein conjugation have been developed, of which a vast majority target lysine, cysteine and to a lesser extend tyrosine. Likewise, several methods that involve recombinantly engineered protein tags have been reported. In recent years a number of methods have emerged for chemical bioconjugation to other amino acids and in this review, we present the progress in this area.

Funding Information: ACKNOWLEDGMENTS. This work was funded by the Knut and Alice Wallenberg Foundation (2019.0251 and 2019.0043 to V.R.I.K.). V.R.I.K. also acknowledges support from the German Research Foundation (DFG) via the Collaborative Research Centre (SFB1078) as Mercator Fellow. Computational resources were provided by Funding Information: the Swedish National Infrastructure for Computing (SNIC 2021/1-40, SNIC 2022/1-29) at the Center of High-Performance Computing (PDC), and by the Leibniz-Rechenzentrum. M.W. was supported by the Institute of Biotechnology, University of Helsinki. Funding Information: This work was funded by the Knut and Alice Wallenberg Foundation (2019.0251 and 2019.0043 to V.R.I.K.). V.R.I.K. also acknowledges support from the German Research Foundation (DFG) via the Collaborative Research Centre (SFB1078) as Mercator Fellow. Computational resources were provided by the Swedish National Infrastructure for Computing (SNIC 2021/1-40, SNIC 2022/1-29) at the Center of High-Performance Computing (PDC), and by the Leibniz-Rechenzentrum. M.W. was supported by the Institute of Biotechnology, University of Helsinki. Publisher Copyright: Copyright © 2022 the Author(s). Published by PNAS. Aerobic life is powered by membrane-bound enzymes that catalyze the transfer of electrons to oxygen and protons across a biological membrane. Cytochrome c oxidase (CcO) functions as a terminal electron acceptor in mitochondrial and bacterial respiratory chains, driving cellular respiration and transducing the free energy from O2 reduction into proton pumping. Here we show that CcO creates orientated electric fields around a nonpolar cavity next to the active site, establishing a molecular switch that directs the protons along distinct pathways. By combining large-scale quantum chemical density functional theory (DFT) calculations with hybrid quantum mechanics/ molecular mechanics (QM/MM) simulations and atomistic molecular dynamics (MD) explorations, we find that reduction of the electron donor, heme a, leads to dissociation of an arginine (Arg438)-heme a3 D-propionate ion-pair. This ion-pair dissociation creates a strong electric field of up to 1 V A21 along a water-mediated proton array leading to a transient proton loading site (PLS) near the active site. Protonation of the PLS triggers the reduction of the active site, which in turn aligns the electric field vectors along a second, "chemical," proton pathway. We find a linear energy relationship of the proton transfer barrier with the electric field strength that explains the effectivity of the gating process. Our mechanism shows distinct similarities to principles also found in other energy-converting enzymes, suggesting that orientated electric fields generally control enzyme catalysis.

In the biosynthesis of the iron-guanylylpyridinol (FeGP) cofactor, 6-carboxymethyl-5-methyl-4-hydroxy-2-pyridinol (1) is 3-methylated to form 2, then 4-guanylylated to form 3, and converted into the full cofactor. HcgA-G proteins catalyze the biosynthetic reactions. Herein, we report the function of two radical S-adenosyl methionine enzymes, HcgA and HcgG, as uncovered by in vitro complementation experiments and the use of purified enzymes. In vitro biosynthesis using the cell extract from the Methanococcus maripaludis Delta hcgA strain was complemented with HcgA or precursors 1, 2 or 3. The results suggested that HcgA catalyzes the biosynthetic reaction that forms 1. We demonstrated the formation of 1 by HcgA using the 3 kDa cell extract filtrate as the substrate. Biosynthesis in the Delta hcgG system was recovered by HcgG but not by 3, which indicated that HcgG catalyzes the reactions after the biosynthesis of 3. The data indicated that HcgG contributes to the formation of CO and completes biosynthesis of the FeGP cofactor.

The azoreductase AzoA from the alkali-tolerant Bacillus wakoensis A01 has been studied to reveal its structural and mechanistic details. For this, a recombinant expression system was developed which yields impressive amounts of fully active enzyme. The purified holo enzyme is remarkably solvent-tolerant and thermostable with an apparent melting temperature of 71 °C. The dimeric enzyme contains FMN as a prosthetic group and is strictly NADH dependent. While AzoA shows a negligible ability to use molecular oxygen as an electron acceptor, it is efficient in reducing various azo dyes and quinones. The kinetic and catalytic mechanism has been studied in detail using steady state kinetic analyses and stopped-flow studies. The data show that AzoA performs quinone and azo dye reductions via a two-electron transfer. Moreover, quinones were shown to be much better substrates (kcat values of 100-400 s-1 for several naphtoquinones) when compared with azo dyes. This suggests that the physiological role of AzoA and sequence-related microbial reductases is linked to quinone reductions and that they can better be annotated as quinone reductases. The structure of AzoA has been determined in complex with FMN at 1.8 Å resolution. AzoA displays unique features in the active site providing clues for explaining its catalytic and thermostability features. An uncommon loop, when compared with sequence-related reductases, forms an active site lid with Trp60 acting as an anchor. Several Trp60 mutants have been analyzed disclosing an important role of this residue in the stability of AzoA, while they retained activity. Structural details are discussed in relation to other azo and quinone reductases. This study provides new insights into the molecular functioning of AzoA and sequence-related reductases.

In the FeGP cofactor of [Fe]-hydrogenase, low-spin Fe-II is in complex with two CO ligands and a pyridinol derivative; the latter ligates the iron with a 6-acylmethyl substituent and the pyridinol nitrogen. A guanylylpyridinol derivative, 6-carboxymethyl-3,5-dimethyl-4-guanylyl-2-pyridinol (3), is produced by the decomposition of the FeGP cofactor under irradiation with UV-A/blue light and is also postulated to be a precursor of FeGP cofactor biosynthesis. HcgC and HcgB catalyze consecutive biosynthesis steps leading to 3. Here, we report an in vitro biosynthesis assay of the FeGP cofactor using the cell extract of the Delta hcgB Delta hcgC strain of Methanococcus maripaludis, which does not biosynthesize 3. We chemically synthesized pyridinol precursors 1 and 2, and detected the production of the FeGP cofactor from 1, 2 and 3. These results indicated that 1, 2 and 3 are the precursors of the FeGP cofactor, and the carboxy group of 3 is converted to the acyl ligand.

The oxido-bridged diiron(III) complex [Fe-2(mu-O)(mu-OAc)(DPEAMP)(2)](OCH3) (1), based on a new unsymmetrical ligand with an N4O donor set, viz. [2-((bis(pyridin-2-ylmethyl)amino)methyl)-6-((ethylamino)methyl)-4-meth-ylphenol (HDPEAMP)], has been prepared and characterized by spectroscopic methods and X-ray crystallog-raphy. The crystal structure of the complex reveals that each Fe(III) ion is coordinated by three nitrogen and three oxygen donors, two of which are the bridging oxido and acetate ligands. Employing H2O2 as a terminal oxidant, 1 is capable of oxidizing a number of alkanes and alkenes with high activity. The catalytic oxidation of 1,2-dimethylcyclohexane results in excellent retention of configuration. Monitoring of the reaction of 1 with H2O2 and acetic acid in the absence of substrate, using low-temperature UV-Vis spectroscopy, suggests the in situ formation of a transient Fe(III)(2)-peroxido species. While the selectivity and nature of oxidation products implicate a high-valent iron-oxido complex as a key intermediate, the low alcohol/ketone ratios suggest a simultaneous radical-based process.

Doped-ZnO nanoparticles, capped with dioctylphosphinate ligands, are synthesised by the controlled hydrolysis of a mixture of organometallic precursors. Substitutional doping of the wurtzite ZnO nanoparticles with 5 mol% Mg(II), Al(III) and Cu(I) is achieved by the addition of sub-stoichiometric amounts of the appropriate dopant [(n-butyl)(sec-butyl)magnesium, triethylaluminium or mesitylcopper] to diethylzinc in the precursor mixture. After hydrolysis, the resulting colloidal nanoparticles (sizes of 2–3 nm) are characterised by powder X-ray crystallography, transmission electron microscopy, inductively-coupled plasma optical emission spectrometry and X-ray photoelectron spectroscopy. A solution of the doped-ZnO nanoparticles and colloidal Cu(0) nanoparticles [M:ZnO : Cu = 1 : 1] are applied as catalysts for the hydrogenation of CO2 to methanol in a liquid-phase continuous flow stirred tank reactor [210 °C, 50 bar, CO2 : H2 = 1 : 3, 150 mL min−1, mesitylene, 20 h]. All the catalyst systems display higher rates of methanol production and better stability than a benchmark heterogeneous catalyst, Cu–ZnO–Al2O3 [480 μmol mmolmetal−1 h−1], with approximately twice the activity for the Al(III)-doped nanocatalyst. Despite outperforming the benchmark catalyst, Mg(II) doping is detrimental towards methanol production in comparison to undoped ZnO. X-Ray photoelectron spectroscopy and transmission electron microscopy analysis of the most active post-catalysis samples implicate the migration of Al(III) to the catalyst surface, and this surface enrichment is proposed to facilitate stabilisation of the catalytic ZnO/Cu interfaces.

Innovative and efficient hit‐identification techniques are required to accelerate drug discovery. Protein‐templated fragment ligations represent a promising strategy in early drug discovery, enabling the target to assemble and select its binders from a pool of building blocks. Development of new protein‐templated reactions to access a larger structural diversity and expansion of the variety of targets to demonstrate the scope of the technique are of prime interest for medicinal chemists. Herein, we present our attempts to use a protein‐templated reductive amination to target protein‐protein interactions (PPIs), a challenging class of drug targets. We address a flexible pocket, which is difficult to achieve by structure‐based drug design. After careful analysis we did not find one of the possible products in the kinetic target‐guided synthesis (KTGS) approach, however subsequent synthesis and biochemical evaluation of each library member demonstrated that all the obtained molecules inhibit MDM2. The most potent library member (K i=0.095 μm) identified is almost as active as Nutlin‐3, a potent inhibitor of the p53‐MDM2 PPI., Templated potential: Herein, we present our attempts to use a protein‐templated reductive amination to target protein–protein interactions (PPIs). After careful analysis, we did not find one of the possible products in the kinetic target‐guided synthesis (KTGS) approach. Subsequent synthesis and biochemical evaluation of each library member demonstrated that all the obtained molecules inhibit MDM2. The most potent library member (K i=0.095 μm) identified is almost as active as Nutlin‐3, a potent inhibitor of the p53‐MDM2 PPI.

The ability of one enzyme to catalyse multiple, mechanistically distinct transformations likely played a crucial role in organisms' abilities to adapt to changing external stimuli in the past and can still be observed in extant enzymes. Given the importance of catalytic promiscuity in nature, enzyme designers have recently begun to create catalytically promiscuous enzymes in order to expand the canon of transformations catalysed by proteins. This article aims to both critically review different strategies for the design of enzymes that display catalytic promiscuity for new-to-nature reactions and highlight the successes of subsequent directed-evolution efforts to fine-tune these novel reactivities. For the former, we put a particular emphasis on the creation, stabilization and repurposing of reaction intermediates, which are key for unlocking new activities in an existing or designed active site. For the directed evolution of the resulting catalysts, we contrast approaches for enzyme design that make use of components found in nature and those that achieve new reactivities by incorporating synthetic components. Following the critical analysis of selected examples that are now available, we close this Review by providing a set of considerations and design principles for enzyme engineers, which will guide the future generation of efficient artificial enzymes for synthetically useful, abiotic transformations.

The ability of one enzyme to catalyse multiple, mechanistically distinct transformations likely played a crucial role in organisms’ abilities to adapt to changing external stimuli in the past and can still be observed in extant enzymes. Given the importance of catalytic promiscuity in nature, enzyme designers have recently begun to create catalytically promiscuous enzymes in order to expand the canon of transformations catalysed by proteins. This article aims to both critically review different strategies for the design of enzymes that display catalytic promiscuity for new-to-nature reactions and highlight the successes of subsequent directed-evolution efforts to fine-tune these novel reactivities. For the former, we put a particular emphasis on the creation, stabilization and repurposing of reaction intermediates, which are key for unlocking new activities in an existing or designed active site. For the directed evolution of the resulting catalysts, we contrast approaches for enzyme design that make use of components found in nature and those that achieve new reactivities by incorporating synthetic components. Following the critical analysis of selected examples that are now available, we close this Review by providing a set of considerations and design principles for enzyme engineers, which will guide the future generation of efficient artificial enzymes for synthetically useful, abiotic transformations. Enzyme designers can exploit catalytic promiscuity to unlock activities unknown to nature. This Review discusses how repurposing versatile reaction intermediates and creating new ones installs abiological activities into existing, designed and hybrid enzymes, and how directed-evolution strategies readily improve catalysts for these new-to-nature activities.

The hemocyanin protein binds and transports molecular oxygen via two copper atoms at its core. The singlet state of the $${{\rm{Cu}}}_{2}{{\rm{O}}}_{2}$$ Cu 2 O 2 core is thought to be stabilised by a superexchange pathway, but detailed in situ computational analysis is complicated by the multi-reference character of the electronic ground state. Here, electronic correlation effects in the functional site of hemocyanin are investigated using a novel approach, treating the localised copper 3d electrons with cluster dynamical mean field theory. This enables us to account for dynamical and multi-reference quantum mechanics, capturing valence and spin fluctuations of the 3d electrons. Our approach explains the stabilisation of the experimentally observed di-Cu singlet for the butterflied $${{\rm{Cu}}}_{2}{{\rm{O}}}_{2}$$ Cu 2 O 2 core, with localised charge and incoherent scattering processes across the oxo-bridge that prevent long-lived charge excitations. This suggests that the magnetic structure of hemocyanin is largely influenced by the many-body corrections.

Crystal structure analyses at atomic resolution and FTIR spectroscopic studies of cytochrome c oxidase have yet not revealed protonation or deprotonation of key sites of proton transfer in a time-resolved mode. Here, a sensitive technique to detect protolytic transitions is employed. In this work, probing a proton-loading site of cytochrome c oxidase from Paracoccus denitrificans with time-resolved Fourier transform infrared spectroscopy is presented for the first time. For this purpose, variants with single-site mutations of N131V, D124N, and E278Q, the key residues in the D-channel, were studied. The reaction of mutated CcO enzymes with oxygen was monitored and analyzed. Seven infrared bands in the &ldquo, fast&rdquo, kinetic spectra were found based on the following three requirements: (1) they are present in the &ldquo, phases of N131V and D124N mutants, (2) they have reciprocal counterparts in the &ldquo, slow&rdquo, kinetic spectra in these mutants, and (3) they are absent in &ldquo, kinetic spectra of the E278Q mutant. Moreover, the double-difference spectra between the first two mutants and E278Q revealed more IR bands that may belong to the proton-loading site protolytic transitions. From these results, it is assumed that several polar residues and/or water molecule cluster(s) share a proton as a proton-loading site. This site can be propionate itself (holding only a fraction of H+), His403, and/or water cluster(s).

Thiosulfate sulfurtransferase (TST, EC 2.8.1.1), also known as Rhodanese, is a mitochondrial enzyme which catalyzes the transfer of sulfur in several molecular pathways. After its initial identification as a cyanide detoxification enzyme, it was found that its functions also include sulfur metabolism, modification of iron-sulfur clusters and the reduction of antioxidants glutathione and thioredoxin. TST deficiency was shown to be strongly related to the pathophysiology of metabolic diseases including diabetes and obesity. This review summarizes research related to the enzymatic properties and functions of TST, to then explore the association between the effects of TST on mitochondria and development of diseases such as diabetes and obesity.

Carbonic anhydrase (CA) mimics are often studied with a focus on the hydration of CO2 for atmospheric carbon capture. Consequently, the reverse reaction (dehydration of HCO3–) has received minimal attention, so much so that the rate-limiting step of the dehydration reaction in CA mimics is currently unknown. The rate-limiting step of the hydration reaction is reported to be the bicarbonate-bound intermediate step, and thus is susceptible to product inhibition. It is not, however, clear if this inhibition is a consequence of an increase in the rate of the competing dehydration reaction or resulting from the strong affinity of bicarbonate to the mimic. To address this, insight into the dehydration reaction kinetics is needed. We therefore report the most comprehensive study of a CA mimic to date. The dehydration profile of the fastest small-molecule CA mimic, ZnL1S, was characterized, and consequently evidence for the rate-limiting step for the dehydration reaction was seen to be the bicarbonate-bound intermediate step, much like the hydration reaction. This experimental validation of the rate-limiting step was achieved through a variety of methods including NMR experiments and the effect of inhibitors, substrate concentration, and metal center on activity. With this understanding, an improvement in the favorability of the rate-limiting step was achieved, resulting in decreased bicarbonate inhibition. Thus, an increase in the mimic’s kcat for both reactions was observed, resulting in the largest rate constants of any small-molecule CA mimic reported to date (28 093 and 579 M–1 s–1 for hydration and dehydration, respectively). Enzyme-like kcat/km values were obtained for ZnL1S (5.9 × 105 M–1 s–1 for CO2 hydration), and notably there is only a difference of 2.5 orders of magnitude from the enzyme, the closest of any CA mimic reported in the literature. The results from this work can be applied to the development and improvement of future and existing mimics toward attaining increased activities.

Two [Cu2O]2+ cores have been identified as the active sites of low temperature methane hydroxylation in the zeolite Cu-MOR. These cores have similar geometric and electronic structures, yet different reactivity with CH4: one reacts with a much lower activation enthalpy. In the present study, we couple experimental reactivity and spectroscopy studies to DFT calculations to arrive at structural models of the Cu-MOR active sites. We find that the more reactive core is located in a constricted region of the zeolite lattice. This leads to close van der Waals contact between the substrate and the zeolite lattice in the vicinity of the active site. The resulting enthalpy of substrate adsorption drives the subsequent H atom abstraction step-a manifestation of the "nest" effect seen in hydrocarbon cracking on acid zeolites. This defines a mechanism to tune the reactivity of metal active sites in microporous materials. ispartof: Journal Of The American Chemical Society vol:140 issue:29 pages:9236-9243 ispartof: location:United States status: published

Due to volatile sugar prices, the food vs fuel debate, and recent increases in the supply of natural gas, methanol has emerged as a promising feedstock for the bio-based economy. However, attempts to engineer Escherichia coli to metabolize methanol have achieved limited success. Here, we provide a rigorous systematic analysis of several potential pathway bottlenecks. We show that regeneration of ribulose 5-phosphate in E. coli is insufficient to sustain methanol assimilation, and overcome this by activating the sedoheptulose bisphosphatase variant of the ribulose monophosphate pathway. By leveraging the kinetic isotope effect associated with deuterated methanol as a chemical probe, we further demonstrate that under these conditions overall pathway flux is kinetically limited by methanol dehydrogenase. Finally, we identify NADH as a potent kinetic inhibitor of this enzyme. These results provide direction for future engineering strategies to improve methanol utilization, and underscore the value of chemical biology methodologies in metabolic engineering., United States. Advanced Research Projects Agency-Energy (Award DE-AR0000433), National Science Foundation (U.S.). Graduate Research Fellowship (Grant No. 1122374), Research Foundation-Flander

Lytic Polysaccharide Monooxygenases (LPMOs) oxidatively cleave recalcitrant polysaccharides. The mechanism involves (i) reduction of the Cu, (ii) polysaccharide binding, (iii) binding of different oxygen species, and (iv) glycosidic bond cleavage. However, the complete mechanism is poorly understood and may vary across different families and even within the same family. Here, we have investigated the protonation state of a secondary co-ordination sphere histidine, conserved across AA9 family LPMOs that has previously been proposed to be a potential proton donor. Partial unrestrained refinement of newly obtained higher resolution data for two AA9 LPMOs and re-refinement of four additional data sets deposited in the PDB were carried out, where the His was refined without restraints, followed by measurements of the His ring geometrical parameters. This allowed reliable assignment of the protonation state, as also validated by following the same procedure for the His brace, for which the protonation state is predictable. The study shows that this histidine is generally singly protonated at the Nε2 atom, which is close to the oxygen species binding site. Our results indicate robustness of the method. In view of this and other emerging evidence, a role as proton donor during catalysis is unlikely for this His.

Melanin is the main pigment responsible for the color of human skin, hair and eye. Its biosynthesis requires three melanogenic enzymes, tyrosinase (TYR), and the tyrosinase-related proteins TYRP1 and TYRP2. The difficulty of isolating pure and homogeneous proteins from endogenous sources has hampered their study, and resulted in many contradictory findings regarding their physiological functions. In this review, we summarize recent advances on the structure and function of TYR and TYRPs by virtue of the crystal structure of human TYRP1, which is the first available structure of a mammalian melanogenic enzyme. This structure, combined with tyrosinase structures from other lower eukaryotes and mutagenesis studies of key active site residues, sheds light on the mechanism of TYR and TYRPs. Furthermore, a TYRP1-based homology model of TYR provides a high-quality platform to map and analyze albinism-related mutations, as well as the design of specific antimelanogenic compounds. Finally, we provide perspectives for future structure/function studies of TYR and TYRPs.

Melanin is the main pigment responsible for the color of human skin, hair and eye. Its biosynthesis requires three melanogenic enzymes, tyrosinase (TYR), and the tyrosinase-related proteins TYRP1 and TYRP2. The difficulty of isolating pure and homogeneous proteins from endogenous sources has hampered their study, and resulted in many contradictory findings regarding their physiological functions. In this review, we summarize recent advances on the structure and function of TYR and TYRPs by virtue of the crystal structure of human TYRP1, which is the first available structure of a mammalian melanogenic enzyme. This structure, combined with tyrosinase structures from other lower eukaryotes and mutagenesis studies of key active site residues, sheds light on the mechanism of TYR and TYRPs. Furthermore, a TYRP1-based homology model of TYR provides a high-quality platform to map and analyze albinism-related mutations, as well as the design of specific antimelanogenic compounds. Finally, we provide perspectives for future structure/function studies of TYR and TYRPs.

We introduce LytU, a short member of the lysostaphin family of zinc-dependent pentaglycine endopeptidases. It is a potential antimicrobial agent for S. aureus infections and its gene transcription is highly upregulated upon antibiotic treatments along with other genes involved in cell wall synthesis. We found this enzyme to be responsible for the opening of the cell wall peptidoglycan layer during cell divisions in S. aureus. LytU is anchored in the plasma membrane with the active part residing in the periplasmic space. It has a unique Ile/Lys insertion at position 151 that resides in the catalytic site-neighbouring loop and is vital for the enzymatic activity but not affecting the overall structure common to the lysostaphin family. Purified LytU lyses S. aureus cells and cleaves pentaglycine, a reaction conveniently monitored by NMR spectroscopy. Substituting the cofactor zinc ion with a copper or cobalt ion remarkably increases the rate of pentaglycine cleavage. NMR and isothermal titration calorimetry further reveal that, uniquely for its family, LytU is able to bind a second zinc ion which is coordinated by catalytic histidines and is therefore inhibitory. The pH-dependence and high affinity of binding carry further physiological implications.

Previous studies have shown that prolyl oligopeptidase (PREP) negatively regulates autophagy and increases the aggregation of alpha-synuclein (alpha Syn), linking it to the pathophysiology of Parkinson's disease. Our earlier results have revealed that the potent small molecular PREP inhibitor KYP-2047 is able to increase autophagy and decrease dimerization of alpha Syn but other PREP inhibitors have not been systematically studied for these two protein-protein interaction mediated biological functions of PREP. In this study, we characterized these effects for 12 known PREP inhibitors with IC50-values ranging from 0.2 nM to 1010 nM. We used protein-fragment complementation assay (PCA) to assess alpha Syn dimerization and Western Blot of microtubule-associated protein light chain 3B II (LC3B-II) and a GFP-LC3-RFP expressing cell line to study autophagy. In addition, we tested selected compounds in a cell-free alpha Syn aggregation assay, native gel electrophoresis, and determined the compound concentration inside the cell by LC-MS. We found that inhibition of the proteolytic activity of PREP did not predict decreased alpha Syn dimerization or increased autophagy, and we also confirmed that this result did not simply reflect concentration differences of the compounds inside the cell. Thus, PREP ligands regulate the effect of PREP on autophagy and alpha Syn aggregation through a conformational stabilization of the enzyme that is not equivalent to inhibiting its proteolytic activity.

The biodegradation of the nylon-6 precursor caprolactam by a strain of Pseudomonas jessenii proceeds via ATP-dependent hydrolytic ring-opening to 6-aminohexanoate. This non-natural ω-amino acid is converted to 6-oxohexanoic acid by an aminotransferase (PjAT) belonging to the fold type I PLP enzymes. To understand the structural basis of 6-aminohexanoatate conversion, we solved different crystal structures and determined the substrate scope with a range of aliphatic and aromatic amines. Comparison with the homologous aminotransferases from Chromobacterium violaceum (CvAT) and Vibrio fluvialis (VfAT) showed that the PjAT enzyme has the lowest KM values (highest affinity) and highest specificity constant (kcat /KM ) with the caprolactam degradation intermediates 6-aminohexanoate and 6-oxohexanoic acid, in accordance with its proposed in vivo function. Five distinct three-dimensional structures of PjAT were solved by protein crystallography. The structure of the aldimine intermediate formed from 6-aminohexanoate and the PLP cofactor revealed the presence of a narrow hydrophobic substrate-binding tunnel leading to the cofactor and covered by a flexible arginine, which explains the high activity and selectivity of the PjAT with 6-aminohexanoate. The results suggest that the degradation pathway for caprolactam has recruited an aminotransferase that is well adapted to 6-aminohexanoate degradation. This article is protected by copyright. All rights reserved.

Thiosulfate sulfurtransferase (TST, EC 2.8.1.1), also known as Rhodanese, is a mitochondrial enzyme which catalyzes the transfer of sulfur in several molecular pathways. After its initial identification as a cyanide detoxification enzyme, it was found that its functions also include sulfur metabolism, modification of iron-sulfur clusters and the reduction of antioxidants glutathione and thioredoxin. TST deficiency was shown to be strongly related to the pathophysiology of metabolic diseases including diabetes and obesity. This review summarizes research related to the enzymatic properties and functions of TST, to then explore the association between the effects of TST on mitochondria and development of diseases such as diabetes and obesity.

A novel nickel pincer cofactor was recently discovered in lactate racemase. Reported here are three synthetic nickel pincer complexes that are both structural and functional models of the pincer cofactor in lactate racemase. DFT computations suggest the ipso-carbon atom of the pyridinium pincer ligands act as a hydride acceptor for lactate isomerization, whereas an organometallic pathway involving nickel-mediated beta-hydride elimination is less favored.

We developed an artificial hydrolase based on the symmetrical Pizza6 β-propeller protein for the metal-free hydrolysis of 4-nitrophenyl acetate and butyrate. Through site-specific mutagenesis and crystallisation studies, the catalytic mechanism was investigated and found to be dependent on a threonine-histidine dyad. The mutant with additional histidine residues generated the highest kcat values, forming a His-His-Thr triad and matched previously reported metalloenzymes. The highly symmetrical β-propeller artificial enzymes and their protein-metal complexes have potential to be utilised in bioinorganic and supramolecular chemistry, as well as being developed further into 2D/3D catalytic materials. ispartof: CHEMICAL COMMUNICATIONS vol:55 issue:60 pages:8880-8883 ispartof: location:England status: published

The Fe III/Fe II redox potentials for [Fe(tpen)] 2+/3+, [Fe(tpena)] +/2+, and [Fe(tpenO)] +/2+ ( N-R- N, N' ,N'-tris(2-pyridylmethyl)ethane-1,2-diamine, where R = CH 2C 6H 4N, CH 2COO -, CH 2CH 2O -, respectively) span 470 mV with the oxidation potentials following the order [Fe II(tpenO)] + (MeOH) < [Fe II(tpena)] + (MeCN) < [Fe II(tpen)] 2+ (MeCN). In their +3 oxidation states the complexes react with 1 equiv of H 2O 2 to give the purple [Fe III(OOH)(HL)] n+ ( n = 2 for L = tpena, tpenO; n = 3 for L = tpen). A pyridine arm is decoordinated in these complexes, furnishing a second coordination sphere base which is protonated at ambient pH. The lifetimes of these transient species depend on how readily the substrate (sometimes the solvent) is oxidized and reflect the trend in both the O-O bond lability and oxidizing potency of the putative iron-based oxidant derived from the iron(III) peroxides. In methanol solution, [Fe III(tpenO)] 2+ and [Fe III(tpena)] 2+ exist in their Fe(III) states and hence the formation of [Fe III(OOH)(Htpena)] 2+ and [Fe III(OOH)(HtpenO)] 2+ is instantaneous. This is in contrast to the short lag time that occurs before adduct formation between [Fe II(tpen)] 2+ and H 2O 2 due to the requisite prior oxidation of the solution-state iron(II) complex to its iron(III) state. Stabilization of the +3 iron oxidation state in the resting state catalysts affords complexes that activate H 2O 2 more readily with the consequence of higher yields in the oxidation of the C-H bonds using H 2O 2 as terminal oxidant. The presence of a cis monodentate carboxylato donor increases the rate of oxidation by hydrogen atom transfer in comparison to the systems with an alkoxo or pyridine in this position. Competing with substrate oxidation is the oxidative modification of the alkoxido group in [Fe III(tpenO)] 2+, converting it to a carboxylato group in the presence of H 2O 2: in effect, transforming tpenO to tpena.

We report here new copper(I)-Schiff base complexes for the selective oxidation of primary alcohols to aldehydes under ambient conditions (with 2,2,6,6-tetramethylpiperdine-N-oxyl (TEMPO), N-methylimidazole (NMI), ambient air, acetonitril and RT). Particularly, the copper(I) complex bearing N-(4-fluorophenyl)-1-(furan-2-yl)methanimine (L2) showed high activity in the series and gave near- quantitative yields in the oxidations of benzyl alcohol (99% yield in 1 h) and 1-octanol (96% yield in 24 h). Based on the X-ray structure determination, the complex has a square pyramidal coordination accomplished by two L2 ligands and bromide as a counter anion. The oxidation reactions were monitored with UV vis and in situ ATR-IR spectroscopy to study the changes in the catalytic structure and to elucidate the catalytic properties and the mechanistic details. Accordingly, detachment of one of the L2 ligands from the complexes is related to the oxidation activity.

The new di- and tetranuclear Fe(III) μ-oxido complexes [Fe 4 (μ-O) 4 (PTEBIA) 4 ](CF 3 SO 3 ) 4 (CH 3 CN) 2 ] (1a), [Fe 2 (μ-O)Cl 2 (PTEBIA) 2 ](CF 3 SO 3 ) 2 (1b), and [Fe 2 (μ-O)(HCOO) 2 (PTEBIA) 2 ](ClO 4 ) 2 (MeOH) (2) were prepared from the sulfur-containing ligand (2-((2,4-dimethylphenyl)thio)-N,N-bis ((1-methyl-benzimidazol-2-yl)methyl)ethanamine (PTEBIA). The tetrairon complex 1a features four μ-oxido bridges, while in dinuclear 1b, the sulfur moiety of the ligand occupies one of the six coordination sites of each Fe(III) ion with a long Fe-S distance of 2.814(6) A. In 2, two Fe(III) centers are bridged by one oxido and two formate units, the latter likely formed by methanol oxidation. Complexes 1a and 1b show broad sulfur-to-iron charge transfer bands around 400-430 nm at room temperature, consistent with mononuclear structures featuring Fe-S interactions. In contrast, acetonitrile solutions of 2 display a sulfur-to-iron charge transfer band only at low temperature (228 K) upon addition of H 2 O 2 /CH 3 COOH, with an absorption maximum at 410 nm. Homogeneous oxidative catalytic activity was observed for 1a and 1b using H 2 O 2 as oxidant, but with low product selectivity. High valent iron-oxo intermediates could not be detected by UV-vis spectroscopy or ESI mass spectrometry. Rather, evidence suggest preferential ligand oxidation, in line with the relatively low selectivity and catalytic activity observed in the reactions.

Changes in prolyl oligopeptidase (PREP) expression levels, protein distribution, and activity correlate with aging and are reported in many neurodegenerative conditions. Together with decreased neuropeptide levels observed in aging and neurodegeneration, and PREP's ability to cleave only small peptides, PREP was identified as a druggable target. Known PREP non-enzymatic functions were disregarded or attributed to PREP enzymatic activity, and several potent small molecule PREP inhibitors were developed during early stages of PREP research. These showed a lot of potential but with variable results in experimental memory models, however, the initial excitement was short-lived and all of the clinical trials were discontinued in either Phase I or II clinical trials for unknown reasons. Recently, PREP's ability to form protein-protein interactions, alter cell proliferation and autophagy has gained more attention than earlier recognized catalytical activity. Of new findings, particularly the aggregation of alpha-synuclein (aSyn) that is seen in the presence of PREP is especially interesting because PREP inhibitors are capable of altering aSyn-PREP interaction in a manner that reduces the aSyn dimerization process. Therefore, it is possible that PREP inhibitors that are altering interactions could have different characteristics than those aimed for strong inhibition of catalytic activity. Moreover, PREP co-localization with aSyn, tau, and amyloid-beta hints to PREP's possible role not only in the synucleinopathies but in other neurodegenerative diseases as well. This commentary will focus on less well-acknowledged non-enzymatic functions of PREP that may provide a better approach for the development of PREP inhibitors for the treatment of neurodegenerative disorders.

Because arginine residues in proteins are expected to be in their protonated form almost without exception, reports demonstrating that a protein arginine residue is charge-neutral are rare and potentially controversial. Herein, we present a (13) C-detected NMR experiment for probing individual arginine residues in proteins notwithstanding the presence of chemical and conformational exchange effects. In the experiment, the (15) N(η) and (15) N(ϵ) chemical shifts of an arginine head group are correlated with that of the directly attached (13) C(ζ) . In the resulting spectrum, the number of protons in the arginine head group can be obtained directly from the (15) N-(1) H scalar coupling splitting pattern. We applied this method to unambiguously determine the ionization state of the R52 side chain in the photoactive yellow protein from Halorhodospira halophila. Although only three H(η) atoms were previously identified by neutron crystallography, we show that R52 is predominantly protonated in solution.

Thermobifida fusca is a well-known cellulose-degrading actinomycete, which produces various glycoside hydrolases for this purpose. However, despite the presence of putative chitinase genes in its genome, T. fusca has not been reported to grow on chitin as sole carbon source. In this study, a gene encoding a putative membrane anchored GH18 chitinase (Tfu0868) from T. fusca has been cloned and overexpressed in Escherichia coli. The protein was produced as SUMO fusion protein and, upon removal of the SUMO domain, soluble pure TfChi18A was obtained with yields typically amounting to 150 mg per litre of culture. The enzyme was found to be relatively thermostable (apparent T-m = 57.5 degrees C) but not particularly thermoactive, the optimum temperature being 40-45 degrees C. TfChi18A bound to alpha- and beta-chitin and degraded both these substrates. Interestingly, activity towards colloidal chitin was minimal and in this case, substrate inhibition was observed. TfChi18A also cleaved soluble chitooligosaccharides and showed a clear preference for substrates having five sugars or more. While these results show that TfChi18A is a catalytically competent GH18 chitinase, the observed catalytic rates were low compared to those of well-studied GH18 chitinases. This suggests that TfChi18A is not a true chitinase and not likely to endow T. fusca with the ability to grow on chitin. (C) 2016 Elsevier B.V. All rights reserved.

Sulfur is an essential element for the growth and development of plants, which synthesize cysteine and methionine from the reductive assimilation of sulfate. Besides its incorporation into proteins, cysteine is the building block for the biosynthesis of numerous sulfur-containing molecules and cofactors. The required sulfur atoms are extracted either directly from cysteine by cysteine desulfurases or indirectly after its catabolic transformation to 3-mercaptopyruvate, a substrate for sulfurtransferases (STRs). Both enzymes are transiently persulfidated in their reaction cycle, i.e. the abstracted sulfur atom is bound to a reactive cysteine residue in the form of a persulfide group. Trans-persulfidation reactions occur when sulfur atoms are transferred to nucleophilic acceptors such as glutathione, proteins, or small metabolites. STRs form a ubiquitous, multigenic protein family. They are characterized by the presence of at least one rhodanese homology domain (Rhd), which usually contains the catalytic, persulfidated cysteine. In this review, we focus on Arabidopsis STRs, presenting the sequence characteristics of all family members as well as their biochemical and structural features. The physiological functions of particular STRs in the biosynthesis of molybdenum cofactor, thio-modification of cytosolic tRNAs, arsenate tolerance, cysteine catabolism, and hydrogen sulfide formation are also discussed.

A mutated KRAS protein is frequently observed in human cancers. Traditionally, the oncogenic properties of KRAS missense mutants at position 12 (G12X) have been considered as equal. Here, by assessing the probabilities of occurrence of all KRAS G12X mutations and KRAS dynamics we show that this assumption does not hold true. Instead, our findings revealed an outstanding mutational bias. We conducted a thorough mutational analysis of KRAS G12X mutations and assessed to what extent the observed mutation frequencies follow a random distribution. Unique tissue-specific frequencies are displayed with specific mutations, especially with G12R, which cannot be explained by random probabilities. To clarify the underlying causes for the nonrandom probabilities, we conducted extensive atomistic molecular dynamics simulations (170 μs) to study the differences of G12X mutations on a molecular level. The simulations revealed an allosteric hydrophobic signaling network in KRAS, and that protein dynamics is altered among the G12X mutants and as such differs from the wild-type and is mutation-specific. The shift in long-timescale conformational dynamics was confirmed with Markov state modeling. A G12X mutation was found to modify KRAS dynamics in an allosteric way, which is especially manifested in the switch regions that are responsible for the effector protein binding. The findings provide a basis to understand better the oncogenic properties of KRAS G12X mutants and the consequences of the observed nonrandom frequencies of specific G12X mutations., Author summary The oncogene KRAS is frequently mutated in various cancers. When the amino acid glycine 12 is mutated, KRAS protein acquires oncogenic properties that result in tumor cell-growth and cancer progression. These mutations prevail especially in the pancreatic ductal adenocarcinoma, which is a cancer with an exceptionally dismal prognosis. To date, there is a limited understanding of the different mutations at the position 12, also regarding whether the different mutations would have different consequences. These discrepancies could have major implications for the future drug therapies targeting KRAS mutant harboring tumors. In this study, we made a critical assessment of the observed frequency of KRAS G12X mutations and the underlying causes for these frequencies. We also assessed KRAS G12X mutant discrepancies on an atomistic level by utilizing state-of-the-art molecular dynamics simulations. We found that the dynamics of the mutants does not only differ from the wild-type protein, but there is also a profound difference among the different mutants. These results emphasize that the different KRAS G12X mutations are not equal, and thereby they suggest that the future research related to mutant KRAS biology should account for these observations.

Nine GtfB-like 4,6-α-glucanotransferases (4,6-α-GTs) (represented by GtfX of L. aviarius subsp. aviarius DSM 20655) were identified to show distinct characteristics in conserved motifs I-IV. In particular, the "fingerprint" Tyr in motif III of these nine GtfB-type 4,6-α-GTs was found to be replaced by a Trp. In L. aviarius subsp. aviarius DSM20655, a second GtfB-like protein (GtfY), containing the canonical GtfB Tyr residue in motif III, was located directly upstream of GtfX. Biochemical characterization revealed that both GtfX and GtfY showed GtfB-like 4,6-α-GT activity, cleaving (α1→4) linkages and catalyzing the synthesis of (α1→6) linkages. Nonetheless, they differ in product specificity; GtfY only synthesizes consecutive (α1→6) linkages, yielding linear α-glucan products, but GtfX catalyzes the synthesis of (α1→6) linkages predominantly at branch points (22%) rather than in linear segments (10%). The highly branched α-glucan produced by GtfX from amylose V is resistant to digestion by α-amylase, offering great potential as dietary fibers.

Heme is essential and synthesised via highly-regulated processes. For this reason, most organisms strive to recycle it or acquire it from their environment. When heme is bound to proteins non-covalently, degradation of the polypeptide is sufficient to release it. However, in some hemoproteins, such as c-type cytochromes, heme is covalently bound to the protein backbone. We use the heme auxotroph Caenorhabditis elegans to investigate if cytochromes c can be a heme source, and we show that this organism must encode a novel system, which specifically cleaves the thioether bonds of c-type cytochromes. We also find that at limiting heme concentrations, while somatic tissues develop normally the germline fails to proliferate, suggesting the presence of a heme-sensing checkpoint in C. elegans.

The quinone-dependent alcohol dehydrogenase (PQQ-ADH, E.C. 1.1.5.2) from the Gram-negative bacterium Pseudogluconobacter saccharoketogenes IFO 14464 oxidizes primary alcohols (e.g. ethanol, butanol), secondary alcohols (monosaccharides), as well as aldehydes, polysaccharides, and cyclodextrins. The recombinant protein, expressed in Pichia pastoris, was crystallized, and three-dimensional (3D) structures of the native form, with PQQ and a Ca2+ ion, and of the enzyme in complex with a Zn2+ ion and a bound substrate mimic were determined at 1.72 angstrom and 1.84 angstrom resolution, respectively. PQQ-ADH displays an eight-bladed beta-propeller fold, characteristic of Type I quinone-dependent methanol dehydrogenases. However, three of the four ligands of the Ca2+ ion differ from those of related dehydrogenases and they come from different parts of the polypeptide chain. These differences result in a more open, easily accessible active site, which explains why PQQ-ADH can oxidize a broad range of substrates. The bound substrate mimic suggests Asp333 as the catalytic base. Remarkably, no vicinal disulfide bridge is present near the PQQ, which in other PQQ-dependent alcohol dehydrogenases has been proposed to be necessary for electron transfer. Instead an associated cytochrome c can approach the PQQ for direct electron transfer.

Cytochrome P450 2E1 (CYP2E1) expression and activity in the liver is associated with the degree of liver damage in patients with alcoholic steatohepatitis (ASH) as well as non-alcoholic steatohepatitis (NASH). CYP2E1 is known to generate reactive oxygen species, which leads to oxidative stress, one of the hallmarks of both diseases. Apart from ROS, toxic metabolites can be formed by CYP2E1 metabolism, further potentiating liver injury. Therefore, CYP2E1 is implicated in the pathogenesis of ASH and NASH. The aim of this study was to determine the chemical characteristics of compounds that are important to inhibit CYP2E1. To this end, structurally related analogues that differed in their lipophilic, steric and electronic properties were tested. In addition, homologues series of aliphatic primary alcohols, secondary alcohols, aldehydes, ketones and carboxylic acids were tested. It was found that inhibition of the CYP2E1 activity is primarily governed by lipophilicity. The optimal log D7.4 (octanol/water distribution coefficient at pH 7.4) value for inhibition of CYP2E1 was approximately 2.4. In the carboxylic acids series the interaction of the carboxylate group with polar residues lining the CYP2E1 active site also has to be considered. This study sketches the basic prerequisites in the search for inhibitors of CYP2E1, which would strengthen our therapeutic armamentarium against CYP2E1 associated diseases, such as ASH and NASH.

International audience; Natural organic matter (NOM) generated in all niches of the environment constitutes a large fraction of the global pool of organic carbon while magnesium is one of the most abundant elements that has multiple roles in both biotic and abiotic processes. Although interactions between Mg2+ and NOM have been recognized to affect many environmental processes, little is understood about relevant mechanisms and equilibria. This study addressed this deficiency and quantified Mg2+-NOM interactions using differential absorbance spectroscopy (DAS) in combination with the NICA-Donnan speciation model. DAS data were obtained for varying total Mg concentrations, pHs from 5.0 to 11.0 and ionic strengths from 0.001 to 0.3 mol L-1. DAS results demonstrated the existence Of strong interactions between magnesium and NOM at all examined conditions and demonstrated that the binding of Mg2+ by NOM was accompanied by the replacement of protons in the protonation-active phenolic and carboxylic groups. The slope of the log-transformed absorbance spectra of NOM in the range of wavelength 350-400 nm was found to be indicative of the extent of Mg2+-NOM binding. The differential and absolute values of the spectral slopes were strongly correlated with the amount of NOM-bound Mg2+ ions and with the concentrations of NOM-bound protons.