Autoinhibitory mechanism and activity-related structural changes in a mycobacterial adenylyl cyclase

An adenylyl cyclase from Mycobacterium avium, Mal 120, is a functional orthologue of a pseudogene Rv1120c from Mycobacterium tuberculosis. We report the crystal structure of Mal 120 in a monomeric form and its truncated construct as a dimer. Mal 120 exists as a monomer in solution and crystallized as a monomer in the absence of substrate or inhibitor. An additional alpha-helix present at the N-terminus of the monomeric structure blocks the active site by interacting with the substrate binding residues and occupying the dimer interface region. However, the enzyme has been found to be active in solution, indicating the movement of the helix away from the interface to facilitate the formation of active dimers in conditions favourable for catalysis. Thus, the N-terminal helix of Ma1120 keeps the enzyme in an autoinhibited state when it is not active. Deletion of this helix enabled us to crystallize the molecule as an active homodimer in the presence of a P-site inhibitor 2',5'-dideoxy-3'-ATP, or pyrophosphate along with metal ions. The substrate specifying lysine residue plays a dual role of interacting with the substrate and stabilizing the dimer. The dimerization loop region harbouring the second substrate specifying residue, an aspartate, shows significant differences in conformation and position between the monomeric and dimeric structures. Thus, this study has not only revealed that significant structural transitions are required for the interconversion of the inactive and the active forms of the enzyme, but also provided precise nature of these transitions. (C) 2015 Elsevier Inc. All rights reserved.

Smaller is Plastic: Polymorphic Structures and Mechanism of Deformation in Nanoscale hcp Metals

Using first-principles calculations, we establish the existence of highly-stable polymorphs of hcp metals (Ti, Mg, Be, La and Y) with nanoscale structural periodicity. They arise from heterogeneous deformation of the hcp structure occurring in response to large shear stresses localized at the basal planes separated by a few nanometers. Through Landau theoretical analysis, we show that their stability derives from nonlinear coupling between strains at different length scales. Such multiscale hyperelasticity and long-period structures constitute a new mechanism of size-dependent plasticity and its enhancement in nanoscale hcp metals.

High Catalytic Activity of Amorphous Ir-Pi for Oxygen Evolution Reaction

Large-scale production of hydrogen gas by water electrolysis is hindered by the sluggish kinetics of oxygen evolution reaction (OER) at the anode. The development of a highly active and stable catalyst for OER is a challenging task. Electrochemically prepared amorphous metal-based catalysts have gained wide attention after the recent discovery of a cnbalt-phosphate (Co-Pi) catalyst: Herein, an amorphous iridium-phosphate (Ir-Pi) is investigated as an oxygen evolution catalyst. The catalyst is prepared by the anodic polarization of carbon paper electrodes in neutral phosphate buffer solutions containing IrCl3. The Ir-Pi film deposited on the substrate has significant amounts of phosphate and It centers in an oxidation state higher than +4. Phosphate plays a significant role in the deposition of the catalyst and also in its activity toward OER. The onset potential of OER on the Ir-Pi is about 150 mV lower in comparison with the Co-Pi under identical experimental conditions. Thus, Ir-Pi is a promising catalyst for electrochemical oxidation of water.

Broadcast Control Mechanism for Positional Consensus in Multiagent Systems

In this paper, a strategy for controlling a group of agents to achieve positional consensus is presented. The problem is constrained by the requirement that every agent must be given the same control input through a broadcast communication mechanism. Although the control command is computed using state information in a global framework, the control input is implemented by the agents in a local coordinate frame. We propose a novel linear programming (LP) formulation that is computationally less intensive than earlier proposed methods. Moreover, a random perturbation input in the control command that helps the agents to come close to each other even for a large number of agents, which was not possible with an existing strategy in the literature, is introduced. The method is extended to achieve positional consensus at a prespecified location. The effectiveness of the approach is illustrated through simulation results. A comparison between the LP approach and the existing second-order cone programming-based approach is also presented. The algorithm was successfully implemented on a robotic platform with three robots.

Molecular mechanism of water permeation in a helium impermeable graphene and graphene oxide membrane

Layers of graphene oxide (GO) are found to be good for the permeation of water but not for helium (Science, 2012, 335(6067), 442-444) suggesting that the GO layers are dynamic in the formation of a permeation route depending on the environment they are in (i.e., water or helium). To probe the microscopic origin of this observation we calculate the potential of mean force (PMF) of GO sheets (with oxidized and reduced parts), with the inter-planar distance as a reaction coordinate in helium and water. Our PMF calculation shows that the equilibrium interlayer distance between the oxidized part of the GO sheets in helium is at 4.8 angstrom leaving no space for helium permeation. In contrast, the PMF of the oxidized part of the GO in water shows two minima, one at 4.8 angstrom and another at 6.8 angstrom, corresponding to no water and a water filled region, thus giving rise to a permeation path. The increased electrostatic interaction between water with the oxidized part of the sheet helps the sheet open up and pushes water inside. Based on the entropy calculations for water trapped between graphene sheets and oxidized graphene sheets at different inter-sheet spacings, we also show the thermodynamics of filling.

Structures of substrate- and nucleotide-bound propionate kinase from Salmonella typhimurium: substrate specificity and phosphate-transfer mechanism

Kinases are ubiquitous enzymes that are pivotal to many biochemical processes. There are contrasting views on the phosphoryl-transfer mechanism in propionate kinase, an enzyme that reversibly transfers a phosphoryl group from propionyl phosphate to ADP in the final step of non-oxidative catabolism of L-threonine to propionate. Here, X-ray crystal structures of propionate- and nucleotide-bound Salmonella typhimurium propionate kinase are reported at 1.8-2.0 angstrom resolution. Although the mode of nucleotide binding is comparable to those of other members of the ASKHA superfamily, propionate is bound at a distinct site deeper in the hydrophobic pocket defining the active site. The propionate carboxyl is at a distance of approximate to 5 angstrom from the -phosphate of the nucleotide, supporting a direct in-line transfer mechanism. The phosphoryl-transfer reaction is likely to occur via an associative S(N)2-like transition state that involves a pentagonal bipyramidal structure with the axial positions occupied by the nucleophile of the substrate and the O atom between the - and the -phosphates, respectively. The proximity of the strictly conserved His175 and Arg236 to the carboxyl group of the propionate and the -phosphate of ATP suggests their involvement in catalysis. Moreover, ligand binding does not induce global domain movement as reported in some other members of the ASKHA superfamily. Instead, residues Arg86, Asp143 and Pro116-Leu117-His118 that define the active-site pocket move towards the substrate and expel water molecules from the active site. The role of Ala88, previously proposed to be the residue determining substrate specificity, was examined by determining the crystal structures of the propionate-bound Ala88 mutants A88V and A88G. Kinetic analysis and structural data are consistent with a significant role of Ala88 in substrate-specificity determination. The active-site pocket-defining residues Arg86, Asp143 and the Pro116-Leu117-His118 segment are also likely to contribute to substrate specificity.

Introduction of a catalytic triad increases the glutathione peroxidase-like activity of diaryl diselenides

Reactive oxygen species (ROS)-mediated diseased states are of major concern in modern day life. Under oxidative stress conditions, the cellular antioxidants deplete, leading to several biological disorders. Small molecule mimics of different antioxidant enzymes are found to be useful in supplementing the biological systems to detoxify ROS. In this study, we have synthesized a series of amine or amide-based diselenides containing an additional amino group as glutathione peroxidase (GPx) mimetics. These diselenides act as a catalytic triad model of the native GPx featuring two basic amino groups near the selenium centre. A comparison of the catalytic activities reveals that the additional amino group increases the activity significantly in the presence of aromatic thiols. Deprotonation of thiol by an additional amine either stabilizes the selenolate intermediate or facilitates the nucleophilic attack of thiol in other intermediates. The Se-77 NMR experiments and DFT calculations show that the amino group does not have any significant effect on the catalytic intermediates. Although the amino moiety increases the nucleophilicity of the thiol, it does not prevent the thiol exchange reactions that take place in the selenenyl sulfide intermediates.

Catalytic Enantioselective 1,4-lodofunctionalizations of Conjugated Dienes

The first catalytic enantioselective 1,4-iodofunctionalizations of conjugated dienes have been developed. Starting from beta,gamma,delta,epsilon-unsaturated oximes and 4-Ns hydrazones, these N-iodosuccinimide-mediated reactions are catalyzed by newly modified tertiary aminothiourea derivatives and furnish Delta(2)-isoxazoline and Delta(2)-pyrazoline derivatives, respectively, containing an (E)-allyl iodide group at the quaternary stereogenic center generally in high yield and with excellent enantioselectivity (up to 98.5:1.5 er).

ABSOLUTE/CONVECTIVE INSTABILITY TRANSITION IN A BACKWARD FACING STEP COMBUSTOR: FUNDAMENTAL MECHANISM AND INFLUENCE OF DENSITY GRADIENT

Hydrodynamic instabilities of the flow field in lean premixed gas turbine combustors can generate velocity perturbations that wrinkle and distort the flame sheet over length scales that are smaller than the flame length. The resultant heat release oscillations can then potentially result in combustion instability. Thus, it is essential to understand the hydrodynamic instability characteristics of the combustor flow field in order to understand its overall influence on combustion instability characteristics. To this end, this paper elucidates the role of fluctuating vorticity production from a linear hydrodynamic stability analysis as the key mechanism promoting absolute/convective instability transitions in shear layers occurring in the flow behind a backward facing step. These results are obtained within the framework of an inviscid, incompressible, local temporal and spatio-temporal stability analysis. Vorticity fluctuations in this limit result from interaction between two competing mechanisms - (1) production from interaction between velocity perturbations and the base flow vorticity gradient and (2) baroclinic torque in the presence of base flow density gradients. This interaction has a significant effect on hydrodynamic instability characteristics when the base flow density and velocity gradients are co-located. Regions in the space of parameters characterizing the base flow velocity profile, i.e. shear layer thickness and ratio of forward to reverse flow velocity, corresponding to convective and absolute instability are identified. The implications of the present results on prior observations of flow instability in other flows such as heated jets and bluff-body stabilized flames is discussed.

Iridium-decorated multiwall carbon nanotubes and its catalytic activity with Shell 405 in hydrazine decomposition

Iridium-functionalized multiwalled carbon nanotubes (Ir-MWNT) are the future catalyst support material for hydrazine fuel decomposition. The present work demonstrates decoration of iridium particle on iron-encapsulated multiwalled carbon nanotubes (MWNT) by wet impregnation method in the absence of any stabilizer. Electron microscopy studies reveal the coated iridium particle size in the range of 5-10 nm. Elemental analysis by energy dispersive X-ray diffraction confirms 21 wt% of Ir coated over MWNT. X-ray photoelectron spectroscopy (XPS) shows 4f(5/2) and 4f(7/2) lines of iridium and confirms the metallic nature. The catalytic activity of Ir-MWNT/Shell 405 combination is performed in 1 N hydrazine micro-thrusters. The thruster performance shows increase in chamber pressure and decrease in chamber temperature when compared to Shell 405 alone. This enhanced performance is due to high thermal conducting nature of MWNTs and the presence of Ir active sites over MWNTs.

Novel pppGpp binding site at the C-terminal region of the Rel enzyme from Mycobacterium smegmatis

Mycobacterium tuberculosis elicits the stringent response under unfavorable growth conditions, such as those encountered by the pathogen inside the host. The hallmark of this response is production of guanosine tetra-and pentaphosphates, collectively termed (p)ppGpp, which have pleiotropic effects on the bacterial physiology. As the stringent response is connected to survival under stress, it is now being targeted for developing inhibitors against bacterial persistence. The Rel enzyme in mycobacteria has two catalytic domains at its N-terminus that are involved in the synthesis and hydrolysis of (p)ppGpp, respectively. However, the function of the C-terminal region of the protein remained unknown. Here, we have identified a binding site for pppGpp in the C-terminal region of Rel. The binding affinity of pppGpp was quantified by isothermal titration calorimetry. The binding site was determined by crosslinking using the nucleotide analog azido-pppGpp, and examining the crosslink product by mass spectrometry. Additionally, mutations in the Rel protein were created to confirm the site of pppGpp binding by isothermal titration calorimetry. These mutants showed increased pppGpp synthesis and reduced hydrolytic activity. We believe that binding of pppGpp to Rel provides a feedback mechanism that allows the protein to detect and adjust the (p)ppGpp level in the cell. Our work suggests that such sites should also be considered while designing inhibitors to target the stringent response.

Detailed mechanism and kinetic study of CO oxidation on cobalt oxide surfaces

Co3O4 catalysts were prepared by combustion synthesis using different fuels glycine (G), ODH (O) and urea (U). Morphological changes of the materials were observed by using different fuels. The prepared catalysts were characterized by XRD, XPS, SEM, TEM, BET and DRIFTS analysis. All compounds showed 100% conversion of CO below 175C. The prepared catalysts exhibited very high stability and conversions did not decrease even after 50 h of continuous operation. The oxygen storage capacity (OSC) of materials was measured by H-2-TPR analysis. Co3O4-O is having high OSC among the synthesized catalysts. The activation energies of these catalysts were found to be in the range of 42.3-64.8 kJ mol(-1). With DRIFTS analysis, the surface carbonates, superoxide anions, adsorbed CO, O-2 species on the catalyst surface were found and this information was used to develop a detailed reaction pathway. A kinetic model was developed with the help of proposed mechanism and used to fit the data. (C) 2014 Elsevier B.V. All rights reserved.

Catalytic Aldol-Cyclization Cascade of 3-Isothiocyanato Oxindoles with alpha-Ketophosphonates for the Enantioselective Synthesis of beta-Amino-alpha-hydroxyphosphonates

A cascade aldol cyclization reaction between 3-isothiocyanato oxindoles and alpha-ketophosphonates has been developed for the synthesis of beta-amino-alpha-hydroxyphosphonate derivatives. Catalyzed by a quinine-based tertiary amino-thiourea derivative, this reaction delivers 2-thioxooxazolidinyl phosphonates based on a spirooxindole scaffold bearing two contiguous quaternary stereogenic centers in high yields with excellent diastereo- (up to >20:1 dr) and enantioselectivities (up to >99:1 er).