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Three decades of studies on the multifunctional 6-deoxyerythronolide B synthase have laid a foundation for understanding the chemistry and evolution of polyketide antibiotic biosynthesis by a large family of versatile enzymatic assembly lines. Recent progress in applying chemical and structural biology tools to this prototypical assembly-line polyketide synthase (PKS) and related systems has highlighted several features of their catalytic cycles and associated protein dynamics. There is compelling evidence that multiple mechanisms have evolved in this enzyme family to channel growing polyketide chains along uniquely defined sequences of 10–100 active sites, each of which is used only once in the overall catalytic cycle of an assembly-line PKS. Looking forward, one anticipates major advances in our understanding of the mechanisms by which the free energy of a repetitive Claisen-like reaction is harnessed to guide the growing polyketide chain along the assembly line in a manner that is kinetically robust yet evolutionarily adaptable. [ABSTRACT FROM AUTHOR]

The thermal effect of a model oxo-transfer reaction with the participation of a tungsten-containing synthetic analog of the enzyme active site, [WO2(mnt)2]2− (mnt = maleonitriledithiolate), has been determined for the first time. The value of the thermal effect indicates that the driving force of the oxo-transfer is the enthalpy factor. To determine the thermal effect of oxo-transfer, the dissolution enthalpies of the reaction participants in acetonitrile were determined: Δ H sol 0 PPh 3 = 24.9 ± 0.8 kJ mol−1, Δ H sol 0 OPPh 3 = 18.9 ± 0.6 kJ mol−1, and Δ H sol 0 ([Bu4N]2[WO2(mnt)2]) = (70.8 ± 1.9) kJ mol−1. In this study, the thermal effect of the transfer process of an oxygen atom from the tungsten complex [WO2(mnt)2]2− to the PPh3 substrate was determined at different ratios of reagents: ΔrH0 = (− 109 ± 4) kJ mol−1. The catalytic cycle of PPh3 oxidation with oxygen in the presence of [WO2(mnt)2]2− in acetonitrile solution was described calorimetrically. The absence of the reduced form of tungsten in the solution after the oxo-transfer reaction was shown spectroscopically, which confirms the role of the tungsten complex in the PPh3 oxidation as the catalyst. [ABSTRACT FROM AUTHOR]

We have studied the reduction reactions of two cytosolic human peroxiredoxins (Prx) in their disulfide form by three thioredoxins (Trx; two human and one bacterial), with the aim of better understanding the rate and mechanism of those reactions, and their relevance in the context of the catalytic cycle of Prx. We have developed a new methodology based on stopped‐flow and intrinsic fluorescence to study the bimolecular reactions, and found rate constants in the range of 105–106 m−1 s−1 in all cases, showing that there is no marked kinetic preference for the expected Trx partner. By combining experimental findings and molecular dynamics studies, we found that the reactivity of the nucleophilic cysteine (CN) in the Trx is greatly affected by the formation of the Prx–Trx complex. The protein–protein interaction forces the CN thiolate into an unfavorable hydrophobic microenvironment that reduces its hydration and results in a remarkable acceleration of the thiol‐disulfide exchange reactions by more than three orders of magnitude and also produces a measurable shift in the pKa of the CN. This mechanism of activation of the thiol disulfide exchange may help understand the reduction of Prx by alternative reductants involved in redox signaling. [ABSTRACT FROM AUTHOR]

Previous studies have revealed the extraordinarily large catalytic efficiency of some enzymes. High catalytic proficiency is an essential accomplishment of biological evolution. Natural selection led to the increased turnover number, kcat, and enzyme efficiency, kcat/KM, of uni–uni enzymes, which convert a single substrate into a single product. We added or multiplied random noise with chosen rate constants to explore the correlation between dissipation and catalytic efficiency for ten enzymes: beta-galactosidase, glucose isomerase, β-lactamases from three bacterial strains, ketosteroid isomerase, triosephosphate isomerase, and carbonic anhydrase I, II, and T200H. Our results highlight the role of biological evolution in accelerating thermodynamic evolution. The catalytic performance of these enzymes is proportional to overall entropy production—the main parameter from irreversible thermodynamics. That parameter is also proportional to the evolutionary distance of β-lactamases PC1, RTEM, and Lac-1 when natural or artificial evolution produces the optimal or maximal possible catalytic efficiency. De novo enzyme design and attempts to speed up the rate-limiting catalytic steps may profit from the described connection between kinetics and thermodynamics. [ABSTRACT FROM AUTHOR]

[Display omitted] The cross-coupling reaction of chlorobenzene and phenylboronic acid, catalyzed by the [R 3 Si–IPr]Pd0 species (generated upon activation of {[R 3 Si–IPr]Pd(173-allyl)Cl} pre-catalyst complexes) in the presence of hydroxide ion as a base, was studied in details by the quantum chemical calculations. Each step of the whole process, including pre- catalyst activation, oxidative addition, transmetalation and reductive elimination, were computationally probed to locate reaction intermediates and transition states along the reaction coordinate. Accordingly, transmetalation was found to be a limiting step of the catalytic cycle (involving oxidative addition, transmetalation and reductive elimination), whereas pre-catalyst activation was revealed as a limiting step of the whole catalytic process. [ABSTRACT FROM AUTHOR]

The special electronic configuration of phosphorus atoms endows organophosphorus reagents with unique chemical properties, which enable them to be used to catalyze various organic reactions, such as the Wittig reaction, Staudinger reaction, Appel reaction and Mitsunobu reaction. However, the catalytic process will be accompanied by the generation of large amounts of phosphine oxide waste, resulting in the reduction of atom utilization of the reaction, and it is difficult to separate the product. Therefore, it is essential to explore a greener and more sustainable organic synthesis route based on the catalytic cycle of phosphine oxide as a model. This paper summarizes the catalytic cycle and recycling of phosphorus with or without reducing agents and reviews the related developments in recent decades: from the addition of stoichiometric strong reducing agents, to the design of ring phosphines with specific structures, to the development of new energy inputs (electrochemistry), to the addition of a series of compounds to activate the P(V)O double bond, driving the catalytic cycle of phosphine oxide through chemical transformation. This review also points out the development potential of this field in the future, which will promote its development and progress in a greener direction.

While the use of l-proline-derived peptides has been proven similarly successful with respect to enantioselectivity, the physico-chemical and conformational properties of these organocatalysts are not fully compatible with transition state and intermediate structures previously suggested for l-proline catalysis. l-Proline or l-4-hydroxyproline catalysis is assumed to involve proton transfers mediated by the carboxylic acid group, whereas a similar mechanism is unlikely for peptides, which lack a proton donor. Herein, we prepared an array of hydroxyproline-based dipeptides through amide coupling of Boc-protected cis- or trans-4-l-hydroxyproline (cis- or trans-4-Hyp) to benzylated glycine (Gly-OBn) and l-valine (l-Val-OBn) and used these dipeptides as catalysts for a model aldol reaction. Despite the lack of a proton donor in the catalytic site, we observed good stereoselectivities for the R-configured aldol product both with dipeptides formed from cis- or trans-4-Hyp at moderate conversions after 24 h. To explain this conundrum, we modeled reaction cycles for aldol additions in the presence of cis-4-Hyp, trans-4-Hyp, and cis- and trans-configured 4-Hyp-peptides as catalysts by calculation of free energies of conformers of intermediates and transition states at the density functional theory level (B3LYP/6-31G(d), DMSO PCM as solvent model). While a catalytic cycle as previously suggested with l-proline is also plausible for cis- or trans-4-Hyp, with the peptides, the energy barrier of the first reaction step would be too high to allow conversions at room temperature. Calculations on modeled transition states suggest an alternative pathway that would explain the experimental results: here, the catalytic cycle is entered by the acetone self-adduct 4-hydroxy-4-methylpentan-2-one, which forms spontaneously to a small extent in the presence of a base, leading to considerably reduced calculated free energy levels of transition states of reaction steps that are considered rate-determining.

Type IIA DNA topoisomerases are complex molecular nanomachines that manage topological states of the DNA molecule in the cell and play a crucial role in cellular processes such as cell division and transcription. They are also established targets of cancer chemotherapy. Starting from the available crystal structure of a fully catalytic topoisomerase IIA homodimer from Saccharomyces cerevisiae, we constructed three states of this molecular motor primarily changing the configurations of the DNA segment bound in the DNA gate and performed μs-long all-atom molecular simulations. A comprehensive analysis revealed a sliding motion within the DNA gate and a teamwork between the N-gate and DNA gate that may be associated with the necessary molecular events that allow passage of the T-segment of DNA. The observed movement of the ATPase dimer relative to the DNA domain was reflected in different interaction patterns between the K-loops of the transducer domain and the B-A-B form of the bound DNA. Based on the obtained results, we mapped simulated configurations to the structures in the proposed catalytic cycle through which type IIA topoisomerases exert their function and discussed the possible transition events. The results extend our understanding of the mechanism of action of type IIA topoisomerases and provide an atomistic interpretation of some of the observed features of these molecular motors.

While the use of l-proline-derived peptides has been proven similarly successful with respect to enantioselectivity, the physico-chemical and conformational properties of these organocatalysts are not fully compatible with transition state and intermediate structures previously suggested for l-proline catalysis. l-Proline or l-4-hydroxyproline catalysis is assumed to involve proton transfers mediated by the carboxylic acid group, whereas a similar mechanism is unlikely for peptides, which lack a proton donor. Herein, we prepared an array of hydroxyproline-based dipeptides through amide coupling of Boc-protected cis- or trans-4-l-hydroxyproline (cis- or trans-4-Hyp) to benzylated glycine (Gly-OBn) and l-valine (l-Val-OBn) and used these dipeptides as catalysts for a model aldol reaction. Despite the lack of a proton donor in the catalytic site, we observed good stereoselectivities for the R-configured aldol product both with dipeptides formed from cis- or trans-4-Hyp at moderate conversions after 24 h. To explain this conundrum, we modeled reaction cycles for aldol additions in the presence of cis-4-Hyp, trans-4-Hyp, and cis- and trans-configured 4-Hyp-peptides as catalysts by calculation of free energies of conformers of intermediates and transition states at the density functional theory level (B3LYP/6-31G(d), DMSO PCM as solvent model). While a catalytic cycle as previously suggested with l-proline is also plausible for cis- or trans-4-Hyp, with the peptides, the energy barrier of the first reaction step would be too high to allow conversions at room temperature. Calculations on modeled transition states suggest an alternative pathway that would explain the experimental results: here, the catalytic cycle is entered by the acetone self-adduct 4-hydroxy-4-methylpentan-2-one, which forms spontaneously to a small extent in the presence of a base, leading to considerably reduced calculated free energy levels of transition states of reaction steps that are considered rate-determining. [ABSTRACT FROM AUTHOR]

Neisseria gonorrhoeae is an obligate human pathogenic bacterium responsible for gonorrhea, a sexually transmitted disease. The bacterial peroxidase, an enzyme present in the periplasm of this bacterium, detoxifies the cells against hydrogen peroxide and constitutes one of the primary defenses against exogenous and endogenous oxidative stress in this organism. The 38 kDa heterologously produced bacterial peroxidase was crystallized in the mixed-valence state, the active state, at pH 6.0, and the crystals were soaked with azide, producing the first azide-inhibited structure of this family of enzymes. The enzyme binds exogenous ligands such as cyanide and azide, which also inhibit the catalytic activity by coordinating the P heme iron, the active site, and competing with its substrate, hydrogen peroxide. The inhibition constants were estimated to be 0.4 ± 0.1 µM and 41 ± 5 mM for cyanide and azide, respectively. Imidazole also binds and inhibits the enzyme in a more complex mechanism by binding to P and E hemes, which changes the reduction potential of the latest heme. Based on the structures now reported, the catalytic cycle of bacterial peroxidases is revisited. The inhibition studies and the crystal structure of the inhibited enzyme comprise the first platform to search and develop inhibitors that target this enzyme as a possible new strategy against N. gonorrhoeae. [ABSTRACT FROM AUTHOR]

For a more resource-efficient production of amines the homogeneously catalyzed tandem hydroaminomethylation reaction is of large relevance. The kinetics of the sulfoxantphos‑rhodium-catalyzed hydroaminomethylation of 1-decene were studied exploiting a thermomorphic solvent system. Focus was a mechanistic kinetic description of the enamine hydrogenation as the final step in the tandem reaction. Based on proposing a catalytic cycle and applying the Christiansen mathematics, a mechanistic rate model was derived and parameterized. The mechanistic model was able to describe the experimental observations in a broad range of operation conditions including pressure and temperature perturbations providing the basis for process design and optimization.

ABCG2 is an exporter-type ABC protein that can expel numerous chemically unrelated xeno- and endobiotics from cells. When expressed in tumor cells or tumor stem cells, ABCG2 confers multidrug resistance, contributing to the failure of chemotherapy. Molecular details orchestrating substrate translocation and ATP hydrolysis remain elusive. Here, we present methods to concomitantly investigate substrate and nucleotide binding by ABCG2 in cells. Using the conformation-sensitive antibody 5D3, we show that the switch from the inward-facing (IF) to the outward-facing (OF) conformation of ABCG2 is induced by nucleotide binding. IF-OF transition is facilitated by substrates, and hindered by the inhibitor Ko143. Direct measurements of 5D3 and substrate binding to ABCG2 indicate that the high-to-low affinity switch of the drug binding site coincides with the transition from the IF to the OF conformation. Low substrate binding persists in the post-hydrolysis state, supporting that dissociation of the ATP hydrolysis products is required to reset the high substrate affinity IF conformation of ABCG2.

Distinct isoforms of FAD-containing ferredoxin-NADP+ oxidoreductase (FNR) and ferredoxin (Fd) are involved in photosynthetic and non-photosynthetic electron transfer systems. The FNR (FAD)-Fd [2Fe-2S] redox pair complex switches between one- and two-electron transfer reactions in steps involving FAD semiquinone intermediates. In cyanobacteria and some algae, one-electron carrier Fd serves as a substitute for low-potential FMN-containing flavodoxin (Fld) during growth under low-iron conditions. This complex evolves into the covalent FNR (FAD)-Fld (FMN) pair, which participates in a wide variety of NAD(P)H-dependent metabolic pathways as an electron donor, including bacterial sulfite reductase, cytochrome P450 BM3, plant or mammalian cytochrome P450 reductase and nitric oxide synthase isoforms. These electron transfer systems share the conserved Ser-Glu/Asp pair in the active site of the FAD module. In addition to physiological electron acceptors, the NAD(P)H-dependent diflavin reductase family catalyzes a one-electron reduction of artificial electron acceptors such as quinone-containing anticancer drugs. Conversely, NAD(P)H: quinone oxidoreductase (NQO1), which shares a Fld-like active site, functions as a typical two-electron transfer antioxidant enzyme, and the NQO1 and UDP-glucuronosyltransfease/sulfotransferase pairs function as an antioxidant detoxification system. In this review, the roles of the plant FNR-Fd and FNR-Fld complex pairs were compared to those of the diflavin reductase (FAD-FMN) family. In the final section, evolutionary aspects of NAD(P)H-dependent multi-domain electron transfer systems are discussed. [ABSTRACT FROM AUTHOR]

New theoretical relationships for a complex catalytic reaction accompanied by deactivation are obtained, using as an example the two-step catalytic mechanism (Temkin–Boudart mechanism) with irreversible reactions and irreversible deactivation. In the domain of small concentrations, A lim = N S k 1 C A k d , where A lim is the limit of the integral consumption of the gas substance, N S is the number of active sites per unit of catalyst surface; k 1 and k d , are kinetic coefficients which relate to two reactions which compete for the free active site Z. C A is the gas concentration. One reaction belongs to the catalytic cycle. The other reaction with kinetic coefficient k d is irreversible deactivation. The catalyst lifetime, τ cat = 1 C Z ′ 1 k d , where C Z ′ is the dimensionless steady-state concentration of free active sites. The main conclusion was formulated as follows: the catalyst lifetime can be enhanced by decreasing the steady-state (quasi-steady-state) concentration of free active sites. In some domains of parameters, it can also be achieved by increasing the steady-state (quasi-steady-state) reaction rate of the fresh catalyst. We can express this conclusion as follows: under some conditions, an elevated fresh catalyst activity protects the catalyst from deactivation. These theoretical results are illustrated with the use of computer simulations. [ABSTRACT FROM AUTHOR]

The expertise of protein kinases lies in their dynamic structure, wherein they are able to modulate cellular signaling by their phosphotransferase activity. Only a few hundreds of protein kinases regulate key processes in human cells, and protein kinases play a pivotal role in health and disease. The present study dwells on understanding the working of the protein kinase-molecular switch as an allosteric network of "communities" composed of congruently dynamic residues that make up the protein kinase core. Girvan-Newman algorithm-based community maps of the kinase domain of cAMP-dependent protein kinase A allow for a molecular explanation for the role of protein conformational entropy in its catalytic cycle. The community map of a mutant, Y204A, is analyzed vis-à-vis the wild-type protein to study the perturbations in its dynamic profile such that it interferes with transfer of the γ-phosphate to a protein substrate. Conventional biochemical measurements are used to ascertain the effect of these dynamic perturbations on the kinetic profiles of both proteins. These studies pave the way for understanding how mutations far from the kinase active site can alter its dynamic properties and catalytic function even when major structural perturbations are not obvious from static crystal structures.

Studying phospholipases A2 (PLA2s) is a challenging task since they act on membrane-like aggregated substrates and not on monomeric phospholipids. Multidisciplinary approaches that include hydrogen/deuterium exchange mass spectrometry (DXMS) and computational techniques have been employed with great success in order to address important questions about the mode of interactions of PLA2 enzymes with membranes, phospholipid substrates and inhibitors. Understanding the interactions of PLA2s is crucial since these enzymes are the upstream regulators of the eicosanoid pathway liberating free arachidonic acid (AA) and other polyunsaturated fatty acids (PUFA). The liberation of AA by PLA2 enzymes sets off a cascade of molecular events that involves downstream regulators such as cyclooxygenase (COX) and lipoxygenase (LOX) metabolites leading to inflammation. Aspirin and other nonsteroidal anti-inflammatory drugs (NSAIDs) work by inhibiting COX, while Zileuton inhibits LOX and both rely on PLA2 enzymes to provide them with AA. That means PLA2 enzymes can potentially also be targeted to diminish inflammation at an earlier point in the process. In this review we describe extensive efforts reported in the past to define the interactions of PLA2 enzymes with membranes, substrate phospholipids and inhibitors using DXMS, molecular docking, and molecular dynamics (MD) simulations.

ATP binding cassette (ABC) proteins are present in all phyla of life and form one of the largest protein families. The Bacillus subtilis ABC transporter BmrA is a functional homodimer that can extrude many different harmful compounds out of the cell. Each BmrA monomer is composed of a transmembrane domain (TMD) and a nucleotide binding domain (NBD). While the TMDs of ABC transporters are sequentially diverse, the highly conserved NBDs harbor distinctive conserved motifs that enable nucleotide binding and hydrolysis, interdomain communication and that mark a protein as a member of the ABC superfamily. In the catalytic cycle of an ABC transporter, the NBDs function as the molecular motor that fuels substrate translocation across the membrane via the TMDs and are thus pivotal for the entire transport process. For a better understanding of the structural and dynamic consequences of nucleotide interactions within the NBD at atomic resolution, we determined the 1H, 13C and 15N backbone chemical shift assignments of the 259 amino acid wildtype BmrA-NBD in its post-hydrolytic, ADP-bound state. [ABSTRACT FROM AUTHOR]

Distinct isoforms of FAD-containing ferredoxin-NADP+ oxidoreductase (FNR) and ferredoxin (Fd) are involved in photosynthetic and non-photosynthetic electron transfer systems. The FNR (FAD)-Fd [2Fe-2S] redox pair complex switches between one- and two-electron transfer reactions in steps involving FAD semiquinone intermediates. In cyanobacteria and some algae, one-electron carrier Fd serves as a substitute for low-potential FMN-containing flavodoxin (Fld) during growth under low-iron conditions. This complex evolves into the covalent FNR (FAD)-Fld (FMN) pair, which participates in a wide variety of NAD(P)H-dependent metabolic pathways as an electron donor, including bacterial sulfite reductase, cytochrome P450 BM3, plant or mammalian cytochrome P450 reductase and nitric oxide synthase isoforms. These electron transfer systems share the conserved Ser-Glu/Asp pair in the active site of the FAD module. In addition to physiological electron acceptors, the NAD(P)H-dependent diflavin reductase family catalyzes a one-electron reduction of artificial electron acceptors such as quinone-containing anticancer drugs. Conversely, NAD(P)H: quinone oxidoreductase (NQO1), which shares a Fld-like active site, functions as a typical two-electron transfer antioxidant enzyme, and the NQO1 and UDP-glucuronosyltransfease/sulfotransferase pairs function as an antioxidant detoxification system. In this review, the roles of the plant FNR-Fd and FNR-Fld complex pairs were compared to those of the diflavin reductase (FAD-FMN) family. In the final section, evolutionary aspects of NAD(P)H-dependent multi-domain electron transfer systems are discussed.

Carbohydrate degradation is crucial for living organisms due to their essential functions in providing energy and composing various metabolic pathways. Nevertheless, in the catalytic cycle of polysaccharide degradation, the details of how the substrates bind and how the products release need more case studies. Here, we choose an inulin fructotransferase ( Sp IFTase) as a model system, which can degrade inulin into functionally difructose anhydride I. At first, the crystal structures of Sp IFTase in the absence of carbohydrates and complex with fructosyl-nystose (GF4), difructose anhydride I, and fructose are obtained, giving the substrate trajectory and product path of Sp IFTase, which are further supported by steered molecular dynamics simulations (MDSs) along with mutagenesis. Furthermore, structural topology variations at the active centers of inulin fructotransferases are suggested as the structural base for product release, subsequently proven by substitution mutagenesis and MDSs. Therefore, this study provides a case in point for a deep understanding of the catalytic cycle with substrate trajectory and product path.

The human multidrug transporter ABCG2 is required for physiological detoxification and mediates anticancer drug resistance. Here, we identify pivotal residues in the first intracellular loop (ICL1), constituting an intrinsic part of the transmission interface. The architecture includes a triple helical bundle formed by the hot spot helix of the nucleotide‐binding domain, the elbow helix, and ICL1. We show here that the highly conserved ICL1 residues G462, Y463, and Y464 are essential for the proper cross talk of the closed nucleotide‐binding domain dimer with the transmembrane domains. Hence, ICL1 acts as a molecular spring, triggering the conformational switch of ABCG2 before substrate extrusion. These data suggest that the ABCG2 transmission interface may offer therapeutic options for the treatment of drug‐resistant malignancies. [ABSTRACT FROM AUTHOR]

We have used experimental studies and DFT calculations to investigate the IrIII‐catalyzed isomerization of allylic alcohols into carbonyl compounds, and the regiospecific isomerization–chlorination of allylic alcohols into α‐chlorinated carbonyl compounds. The mechanism involves a hydride elimination followed by a migratory insertion step that may take place at Cβ but also at Cα with a small energy‐barrier difference of 1.8 kcal mol−1. After a protonation step, calculations show that the final tautomerization can take place both at the Ir center and outside the catalytic cycle. For the isomerization–chlorination reaction, calculations show that the chlorination step takes place outside the cycle with an energy barrier much lower than that for the tautomerization to yield the saturated ketone. All the energies in the proposed mechanism are plausible, and the cycle accounts for the experimental observations. [ABSTRACT FROM AUTHOR]

Peroxiredoxin (Prx) is a thiol-based peroxidase that eliminates reactive oxygen species to avoid oxidative damage. Alkyl hydroperoxide reductase Ahp1 is a novel and specific typical 2-cysteine Prx. Here, we present the crystal structure of sulfonic Ahp1 complexed with thioredoxin Trx2 at 2.12 Å resolution. This structure implies that the transient Ahp1-Trx2 complex during the catalytic cycle already have an ability to decompose the peroxides. Structural analysis reveals that the segment glutamine23–lysine32 juxtaposed to the resolving cysteine (C R) of Ahp1 moves inward to generate a compact structure upon peroxidatic cysteine (C P) overoxidation, resulting in the breakdown of several conserved hydrogen bonds formed by Ahp1-Trx2 complex interaction. Structural comparisons suggest that the structure of sulfonic Ahp1 represents a novel conformation of Ahp1, which can mimic a conformational intermediate between the reduced and oxidized forms. Therefore, this study may provide a new structural insight into the intermediate state in which the segment glutamine23–lysine32 juxtaposed to the cysteine31 (C R) undergoes a conformational change upon cysteine62 (C P) oxidation to prepare for the formation of an intermolecular C P -C R disulfide bond during Ahp1 catalytic cycle. • 2.12 Å resolution crystal structure of sulfonic Ahp1 in complex with Trx2 is provided. • Transient Ahp1-Trx2 complex already possess an ability to decompose the peroxides. • Segment Gln23–Lys32 of Ahp1 moves inward upon peroxidatic cysteine overoxidation. • Conserved hydrogen bonds breakdown of Ahp1-Trx2 caused by movement of Gln23–Lys32. • Provided structure can mimic an Ahp1 intermediate between reduced and oxidized forms. [ABSTRACT FROM AUTHOR]

A general framework by which dynamic interactions within a protein will promote the necessary series of structural changes, or "conformational cycle," required for function is proposed. It is suggested that the free‐energy landscape of a protein is biased toward this conformational cycle. Fluctuations into higher energy, although thermally accessible, conformations drive the conformational cycle forward. The amino acid interaction network is defined as those intraprotein interactions that contribute most to the free‐energy landscape. Some network connections are consistent in every structural state, while others periodically change their interaction strength according to the conformational cycle. It is reviewed here that structural transitions change these periodic network connections, which then predisposes the protein toward the next set of network changes, and hence the next structural change. These concepts are illustrated by recent work on tryptophan synthase. Disruption of these dynamic connections may lead to aberrant protein function and disease states. [ABSTRACT FROM AUTHOR]

The potential energy surface (PES) of the elementary catalytic cycle of hydrogenation of magnesium clusters doped with transition metals (L = Ti, V, Cr, Mn, Fe, Co), Mg17L + H2, has been calculated by the density functional theory method. Stationary points of the PES corresponding to local minima of intermediates and transition states along the minimum energy reaction path have been determined. The energies, geometries, and spectroscopic parameters of the stationary points have been calculated. Trends in the catalytic activity of dopants in the series of 3d metals have been studied. The results are compared with the data of previous DFT calculations of the catalytic cycle of hydrogenation Al12L + H2 for similar reactions of aluminum clusters with the same dopants L. [ABSTRACT FROM AUTHOR]

Background: Topoisomerase IIα (topIIα) maintains the topology of DNA in order to ensure the proper functioning of numerous DNA processes. Inhibition of topIIα leads to the killing of cancer cells thus constituting such inhibitors as useful tools in cancer therapeutics. Triazolo[3,4-b]thiadiazole derivatives are known for their wide range of pharmacological activities while previous studies have documented their in vitro anticancer activity. The purpose of the current study was to investigate if these chemical compounds can act as topIIα inhibitors in cell-free and cell-based systems. Materials and Methods: The MTT assay was performed in DLD-1, HT-29, and LoVo cancer cells so as to evaluate the antiproliferative activity of KA25, KA26, and KA39 triazolo[3,4-b]thiadiazole derivatives. The KA39 compound was tested as a potential topIIα inhibitor using the plasmid-based topoisomerase II drug screening kit. The inhibitory effect of the three derivatives on topIIα phosphorylation was studied in HT-29 and LoVo cancer cells according to Human Phospho-TOP2A/Topoisomerase II Alpha Cell-Based Phosphorylation ELISA Kit. Moreover, flow cytometry was utilized in order to explore apoptotic induction and cell cycle growth arrest, upon treatment with KA39, in DLD-1 and HT-29 cells, respectively. In silico studies were also carried out for further investigation. Results: All three triazolo[3,4-b]thiadiazole derivatives showed an in vitro antiproliferative effect with the KA39 compound being the most potent one. Our results indicated that KA39 induced both early and late apoptosis as well as cell cycle growth arrest in S phase. In addition, the compound blocked the relaxation of supercoiled DNA while it also inhibited topIIα phosphorylation (upon treatment; P< 0.001). Conclusion: Among the three triazolo[3,4-b]thiadiazole derivatives, KA39 was shown to be the most potent anticancer agent and catalytic inhibitor of topIIα phosphorylation as well. [ABSTRACT FROM AUTHOR]

Type IIA DNA topoisomerases are molecular nanomachines responsible for controlling topological states of DNA molecules. Here, we explore the dynamic landscape of yeast topoisomerase IIA during key stages of its catalytic cycle, focusing in particular on the events preceding the passage of the T-segment. To this end, we generated six configurations of fully catalytic yeast topo IIA, strategically inserted a T-segment into the N-gate in relevant configurations, and performed all-atom simulations. The essential motion of topo IIA protein dimer was characterized by rotational gyrating-like movement together with sliding motion within the DNA-gate. Both appear to be inherent properties of the enzyme and an inbuilt feature that allows passage of the T-segment through the cleaved G-segment. Coupled dynamics of the N-gate and DNA-gate residues may be particularly important for controlled and smooth passage of the T-segment and consequently the prevention of DNA double-strand breaks. QTK loop residue Lys367, which interacts with ATP and ADP molecules, is involved in regulating the size and stability of the N-gate. The unveiled features of the simulated configurations provide insights into the catalytic cycle of type IIA topoisomerases and elucidate the molecular choreography governing their ability to modulate the topological states of DNA topology. [Display omitted] • The dynamics of topoisomerase IIA configurations prior to T-segment passage evaluated by molecular simulations. • Impact of inserted T-segment on structural and dynamic properties of topoisomerase IIA. • Rotational gyrating-like movement and a sliding motion within the DNA-gate identified as inherent properties. • ATPase domain ensures controlled and smooth passage of the T-segment and thus prevents DNA double-strand breaks. • Hydrolysis of ATP to ADP influences the size of the N-gate and facilitates the passage of the T-segment. [ABSTRACT FROM AUTHOR]

In this work, the quinone based 3,3′,5,5′-tetra-tert-butyl-4,4′-stilbenequinone was tested as a catalyst in the sulfide oxidation in aqueous medium. On the basis of the obtained experimental results, the catalytic cycle of sulfide oxidation in the presence of stilbenequinone has been established. The research results also point out that a considerable amount of hydrogen peroxide is formed during catalyst regeneration. Application of the catalyst based on stilbenequinone was made to industrial wastewater treatments. According to Fenton reaction, a new catalytic system composed of ferrous iron and stillbenequinone has been developed for the sulfide oxidation. [ABSTRACT FROM AUTHOR]

Terminal oxidases of aerobic respiratory chains catalyze the transfer of electrons from the respiratory substrate, cytochrome c or quinol, to O2 with the formation of two H2O molecules. There are two known families of these membrane oxidoreductases: heme-copper oxidase superfamily and bd-type oxidase family (cytochromes bd) found in prokaryotes only. The redox reaction catalyzed by these enzymes is coupled to the generation of proton motive force used by the cell to synthesize ATP and to perform other useful work. Due to the presence of the proton pump, heme-copper oxidases create the membrane potential with a greater energy efficiency than cytochromes bd. The latter, however, play an important physiological role that enables bacteria, including pathogenic ones, to survive and reproduce under adverse environmental conditions. This review discusses the features of organization and molecular mechanisms of functioning of terminal oxidases from these two families in the light of recent experimental data. [ABSTRACT FROM AUTHOR]

The reaction of the synthesis of benzylbutyl ether via the intermolecular dehydration of benzyl and n-butyl alcohols under the action of copper-containing catalysts is studied by mathematical means. The mechanism of the reaction was proposed, and the values of kinetic parameters are determined. A comparative analysis of the activation energies of possible stages of chemical conversions is performed, and possible routes of the reactions and the catalytic cycles of reactions are determined. Variations in stage rates and the concentrations of all substances participating in the reaction are analyzed. [ABSTRACT FROM AUTHOR]

We carried out a DFT computational investigation on the mechanism of the copper(II) catalyzed C–N, C–O cross coupling reaction involving isatin and phenylglyoxylic acid recently reported by Gogoi. The mechanistic hypothesis proposed by this author is overall confirmed. Our computations demonstrated that the initial decarboxylation is an exergonic reaction (–15.3 kcal mol–1). This process, which can occur rather easily under the used experimental conditions (95 °C for 24 hours), triggers the catalytic cycle with the formation of the initial active organometallic complex (I1). A copper acetate ligand deprotonates the isatin nitrogen. This enhances its nucleophilic character and makes possible the attack of nitrogen on the Cu atom. A reversible transformation connects the initial encounter complex between isatin and the active intermediate I1 and the intermediate where the metal atom inserts into the amide bond. The decarbonylation step represents the rate‐determining step of the entire process (activation free energy = 23.3 kcal mol–1). Copper does not change its oxidation state (II) in the course of the catalytic reaction. The mechanism never involves directly the isatin benzene ring: this is consistent with the fact that only slight changes in the reaction yield are observed when substituents are inserted at different positions of the aromatic ring. [ABSTRACT FROM AUTHOR]

2-Hydroxyisobutyric acid (2-HIBA) is a biomarker of adiposity and associated metabolic diseases such as diabetes mellitus. It is also formed in the bacterial degradation pathway of the fuel oxygenate methyl tert -butyl ether (MTBE), requiring thioesterification with CoA prior to isomerization to 3-hydroxybutyryl-CoA by B 12 -dependent acyl-CoA mutases. Here, we identify the adenylating enzymes superfamily member 2-HIBA-CoA ligase (HCL) in the MTBE-degrading bacterium Aquincola tertiaricarbonis L108 by knockout experiments. To characterize this central enzyme of 2-HIBA metabolism, ligase activity kinetics of purified HCL and its X-ray crystal structures were studied. We analyzed the enzyme in three states, which differ in the orientation of the two enzyme domains. A 154° rotation of the C-terminal domain accompanies the switch from the adenylate- into the thioester-forming state. Furthermore, a third conformation was obtained, which differs by 50° and 130° from the adenylation and thioesterification states, respectively. Phylogenetic and structural analysis reveals that HCL defines a new subgroup within phenylacetate-CoA ligases (PCLs) thus far described to exclusively accept aromatic acyl substrates. In contrast, kinetic characterization clearly demonstrated that HCL catalyzes CoA activation of several aliphatic short-chain carboxylic acids, preferentially 2-HIBA. Compared to the classical PCL representatives PaaK1 and PaaK2 of Burkholderia cenocepacia J2315, the acyl binding pocket of HCL is significantly smaller and more polar, due to unique active-site residues Y164 and S239 forming H-bonds with the OH-group of the acyl substrate moiety. Furthermore, HCL and PaaK topologies illustrate the evolutionary steps leading from a homodimeric to the fused monomeric core fold found in other ligases. Unlabelled Image • ANL enzymes form a large superfamily with a characteristic domain motion in catalysis. • We identify a new superfamily member as a 2-hydroxyisobutyric acid-CoA ligase (HCL). • In addition to the adenylation and thioesterification states, a third conformation is analyzed. • The unique active-site residues Y164 and S239 determine specificity for the 2-OH-group. • The HCL structure sheds light on the evolutionary steps leading to the canonical ANL core fold. [ABSTRACT FROM AUTHOR]

• Reaction mechanism of Hg° oxidation on RuO 2 /TiO 2 (110) was studied using DFT method. • HgCl molecule serves as an intermediate connecting reactant state to product state. • The dominant reaction channel of Hg° catalytic oxidation is a four-step process. • Catalytic cycle consists of HCl activation, Hg oxidation and surface reoxidation. RuO 2 -based catalysts have attracted great attention in mercury emission control region due to their outstanding catalytic activity and long-term stability. Quantum chemistry calculation was performed to uncover the atomic-scale reaction mechanism of Hg0 oxidation by HCl over RuO 2 /TiO 2 catalyst. The results indicate that Hg0 adsorption on RuO 2 /TiO 2 (110) surface is controlled by a weak chemisorption mechanism. The 5-fold coordinated surface Ru atom is identified as the active center for Hg0 adsorption. HgCl molecule serves as an intermediate connecting reactant state to product state. The weak interaction between HgCl 2 and catalyst surface is favorable for product desorption. HCl activation is an O-assisted surface reaction process in which HCl is oxidized into active Cl atom for Hg0 oxidation. The heterolytic cleavage of HCl molecule occurs without noticeable activation energy barrier. Hg0 oxidation by HCl over RuO 2 /TiO 2 catalyst proceeds through two independent reaction channels. The dominant reaction channel of Hg0 oxidation is identified as a four-step process. Finally, a complete catalytic cycle that can produce the correct stoichiometry was proposed to understand the heterogeneous reaction mechanism of Hg0 oxidation over RuO 2 /TiO 2 catalyst. The catalytic cycle consists of HCl activation, mercury oxidation and surface reoxidation. Mercury oxidation is the rate-determining step of the catalytic cycle. [ABSTRACT FROM AUTHOR]

Abstract The chemistry of low-temperature ignition in propane/air mixtures is analyzed using a recently developed pathway representation of the chemical kinetics. The "Sum Over Histories Representation" allows time-dependent kinetic observables to be computed using an expansion over global chemical pathways that follow chemical moieties as they move through a complex reaction network. This methodology assigns probabilities to complete chemical pathways through which specific intermediate or product species are generated. The growth of the radical pool during the ignition process is analyzed by enumerating chemical pathways that constitute catalytic cycles, in particular the catalyzed production of the highly reactive OH-radical. In addition to the well-known reaction route followed in low-temperature ignition of hydrocarbons which involves the QOOH and keto-hydroperoxide species, we have explicitly identified several other cycles that are responsible for most of the remaining OH-production. [ABSTRACT FROM AUTHOR]