Azorhizobium caulinodans chemotaxis is controlled by an unusual phosphorelay network

Azorhizobium caulinodans is a nitrogen-fixing bacterium that forms root nodules on its host legume, Sesbania rostrata . This agriculturally significant symbiotic relationship is important in lowland rice cultivation, and allows for nitrogen fixation under flood conditions. Chemotaxis plays an important role in bacterial colonization of the rhizosphere. Plant roots release chemical compounds that are sensed by bacteria, triggering chemotaxis along a concentration gradient toward the roots. This gives motile bacteria a significant competitive advantage during root surface colonization. Although plant-associated bacterial genomes often encode multiple chemotaxis systems, A. caulinodans appears to encode only one. The che cluster on the A. caulinodans genome contains cheA , cheW , cheY2 , cheB , and cheR . Two other chemotaxis genes, cheY1 and cheZ , are located independently from the che operon. Both CheY1 and CheY2 are involved in chemotaxis, with CheY1 being the predominant signaling protein. A. caulinodans CheA contains an unusual set of C-terminal domains: a CheW-like/Receiver pair (termed W2-Rec), follows the more common single CheW-like domain. W2-Rec impacts both chemotaxis and CheA function. We found a preference for transfer of phosphoryl groups from CheA to CheY2, rather than to W2-Rec or CheY1, which appears to be involved in flagellar motor binding. Furthermore, we observed increased phosphoryl group stabilities on CheY1 compared to CheY2 or W2-Rec. Finally, CheZ enhanced dephosphorylation of CheY2 substantially more than CheY1, but had no effect on the dephosphorylation rate of W2-Rec. This network of phosphotransfer reactions highlights a previously uncharacterized scheme for regulation of chemotactic responses. IMPORTANCE Chemotaxis allows bacteria to move towards nutrients and away from toxins in their environment. Chemotactic movement provides a competitive advantage over non-specific motion. CheY is an essential mediator of the chemotactic response with phosphorylated and unphosphorylated forms of CheY differentially interacting with the flagellar motor to change swimming behavior. Previously established schemes of CheY dephosphorylation include action of a phosphatase and/or transfer of the phosphoryl group to another receiver domain that acts as a sink. Here, we propose A. caulinodans uses a concerted mechanism in which the Hpt domain of CheA, CheY2, and CheZ function together as a dual sink system to rapidly reset chemotactic signaling. To the best of our knowledge, this mechanism is unlike any that have previously been evaluated. Chemotaxis systems that utilize both receiver and Hpt domains as phosphate sinks likely occur in other bacterial species.

Adsorption and Dehydration Reaction of Ethanol to Ethylene on Isomorphous B, Al, and Ga Substitution of H-ZSM-5 Zeolite: An Embedded ONIOM Study

Dehydration reactions are important in the petroleum and petrochemical industries, especially for the feedstock production. In this work, the catalytic activity of zeolites with different acidities for the dehydration of ethanol to ethylene was investigated by calculations on cluster models of three isomorphous B, Al, and Ga substitution of H-ZSM-5 zeolites. Detailed reaction profiles for the dehydration reaction, assuming either a stepwise or a concerted mechanism, were calculated by using the ONIOM(MP2:M06-2X) + SCREEP method. The adsorption energies of ethanol are -21.6, -28.1 and -27.7 kcal/mol on H-[B]-ZSM-5, H-[Al]-ZSM-5, H-[Ga]-ZSM-5 zeolites, respectively. The stepwise mechanism was preferred on all isomorphous zeolites. The activation energies for the ethoxy formation as the rate-determining step are in range of 40.0 to 42.3 kcal/mol. The results indicated that the order of catalytic activity were H-[Al]-ZSM-5 > H-[Ga]-ZSM-5 > H-[B]-ZSM-5 for catalyzing the dehydration of ethanol to ethylene. Besides the acid strength, the zeolite framework affected the reaction by stabilizing the reaction intermediates leading to more stable adsorption complexes and lower activation barriers.

Crystal structures of human MGST2 reveal synchronized conformational changes regulating catalysis

Microsomal glutathione S-transferase 2 (MGST2) produces leukotriene C4, key for intracrine signaling of endoplasmic reticulum (ER) stress, oxidative DNA damage and cell death. MGST2 trimer restricts catalysis to only one out of three active sites at a time, but the molecular basis is unknown. Here, we present crystal structures of human MGST2 combined with biochemical and computational evidence for a concerted mechanism, involving local unfolding coupled to global conformational changes that regulate catalysis. Furthermore, synchronized changes in the biconical central pore modulate the hydrophobicity and control solvent influx to optimize reaction conditions at the active site. These unique mechanistic insights pertain to other, structurally related, drug targets.

Effect of the Supporting Electrolyte on Chloroform Reduction at a Silver Electrode in Aqueous Solutions

Herein, we report, for the first time, a comparative study on the electrocatalytic reduction of chloroform on silver in different aqueous supporting electrolytes. Cyclic voltammetry measurements were performed at a wide range of scan rates and concentrations of CHCl3 using 0.05 M NaClO4, NaH2PO4, and Na2HPO4 as supporting electrolytes. We observed that a type of supporting electrolyte anion strongly influences both the potential as well as the current density of the chloroform reduction peak, mainly due to the presence of OH− in an alkaline Na2HPO4 solution, which is a specifically interacting anion. Moreover, the highest sensitivity of the Ag electrode toward CHCl3 reduction was observed in a neutral NaClO4 aqueous solution. It was found that the electroreduction of chloroform at the silver surface occurs via a concerted mechanism regardless of the type of the studied supporting electrolyte.

On the Question of Zwitterionic Intermediates in the [3+2] Cycloaddition Reactions: A Critical Review

New discoveries require a fundamental revision of the view on the mechanism of the 32CAreaction (according to the older nomenclature defined as 1,3-dipolar cycloaddition reactions). The view of the one-step, “concerted” mechanism of such processes developed in the 20-century is very popular today, both in academic literature and among organic chemists who do not specialize in such transformations. Meanwhile, more and more reports bring examples of reactions that clearly cannot be treated as processes without intermediates. However, these examples are documented very differently. In addition to comprehensive studies using many complementary research techniques, there are also reports in which the presence of intermediates in the cycloaddition environment is postulated on the basis of very unreliable premises. This review is an attempt at a critical analysis and systematization of data in the presented area.

The desensitization pathway of GABAA receptors, one subunit at a time

GABAA receptors mediate most inhibitory synaptic transmission in the brain of vertebrates. Following GABA binding and fast activation, these receptors undergo a slower desensitization, the conformational pathway of which remains largely elusive. To explore the mechanism of desensitization, we used concatemeric α1β2γ2 GABAA receptors to selectively introduce gain-of-desensitization mutations one subunit at a time. A library of twenty-six mutant combinations was generated and their bi-exponential macroscopic desensitization rates measured. Introducing mutations at the different subunits shows a strongly asymmetric pattern with a key contribution of the γ2 subunit, and combining mutations results in marked synergistic effects indicating a non-concerted mechanism. Kinetic modelling indeed suggests a pathway where subunits move independently, the desensitization of two subunits being required to occlude the pore. Our work thus hints towards a very diverse and labile conformational landscape during desensitization, with potential implications in physiology and pharmacology.

Hypervalent Iodine-Mediated Styrene Hetero- and Homodimerization Initiation Proceeds with Two-Electron Reductive Cleavage

<p><a>A mechanistic insight into </a>the hetero- and homodimerizations (HETD and HOMD) of styrenes promoted by hypervalent iodine reagents (HVIRs; <b>DMP</b> and <b>PIDA</b>) and facilitated by HFIP to yield all <i>trans</i> cyclobutanes is reported using density functional theory (DFT) calculations. The initialization involving direct bimolecular one-electron transfer is found to be highly unfavored, especially for the <b>PIDA</b> system. At this point, we suggest that the reaction is initiated with an overall two-electron reductive cleavage of two I─O bond cleavages, affording I(III) (iodinane) and I(I) (iodobenzene) product with DMP and PIDA as oxidant, respectively. The resulting acetate groups are stabilized by the solvent HFIP through strong hydrogen bonding interaction, which promotes the electron transfer process. The nature of the electron transfer is studied in detail and found that the overall two-electron transfer occurs within tri-molecular complex organized by π-stacking interactions and as a stepwise and concerted mechanism for I(III) and I(V) oxidants, respectively. The reaction rate is determined by the initialization step: for I(III), the initiation is thermodynamically endergonic, whereas the endergonicity for I(V) is modest. Upon initialization, the reaction proceeds through a stepwise [2+2] pathway, involving a radical-cationic π-π stacked intermediate, either hetero- or homodimerized. DFT results supported by quasiclassical molecular dynamics simulations show that HOMD is dynamically competing pathway to HETD although the latter is relatively faster, in accordance with experimental observations. </p>

Hypervalent Iodine-Mediated Styrene Hetero- and Homodimerization Initiation Proceeds with Two-Electron Reductive Cleavage

<p><a>A mechanistic insight into </a>the hetero- and homodimerizations (HETD and HOMD) of styrenes promoted by hypervalent iodine reagents (HVIRs; <b>DMP</b> and <b>PIDA</b>) and facilitated by HFIP to yield all <i>trans</i> cyclobutanes is reported using density functional theory (DFT) calculations. The initialization involving direct bimolecular one-electron transfer is found to be highly unfavored, especially for the <b>PIDA</b> system. At this point, we suggest that the reaction is initiated with an overall two-electron reductive cleavage of two I─O bond cleavages, affording I(III) (iodinane) and I(I) (iodobenzene) product with DMP and PIDA as oxidant, respectively. The resulting acetate groups are stabilized by the solvent HFIP through strong hydrogen bonding interaction, which promotes the electron transfer process. The nature of the electron transfer is studied in detail and found that the overall two-electron transfer occurs within tri-molecular complex organized by π-stacking interactions and as a stepwise and concerted mechanism for I(III) and I(V) oxidants, respectively. The reaction rate is determined by the initialization step: for I(III), the initiation is thermodynamically endergonic, whereas the endergonicity for I(V) is modest. Upon initialization, the reaction proceeds through a stepwise [2+2] pathway, involving a radical-cationic π-π stacked intermediate, either hetero- or homodimerized. DFT results supported by quasiclassical molecular dynamics simulations show that HOMD is dynamically competing pathway to HETD although the latter is relatively faster, in accordance with experimental observations. </p>