Probing the role of the fully conserved Cys126 in triosephosphate isomerase by site-specific mutagenesis - distal effects on dimer stability

Cys126 is a completely conserved residue in triosephosphate isomerase that is proximal to the active site but has been ascribed no specific role in catalysis. A previous study of the C126S and C126A mutants of yeast TIM reported substantial catalytic activity for the mutant enzymes, leading to the suggestion that this residue is implicated in folding and stability [Gonzalez-Mondragon E et al. (2004) Biochemistry43, 3255–3263]. We re-examined the role of Cys126 with the Plasmodium falciparum enzyme as a model. Five mutants, C126S, C126A, C126V, C126M, and C126T, were characterized. Crystal structures of the 3-phosphoglycolate-bound C126S mutant and the unliganded forms of the C126S and C126A mutants were determined at a resolution of 1.7–2.1 Å. Kinetic studies revealed an approximately five-fold drop in kcat for the C126S and C126A mutants, whereas an approximately 10-fold drop was observed for the other three mutants. At ambient temperature, the wild-type enzyme and all five mutants showed no concentration dependence of activity. At higher temperatures (> 40 °C), the mutants showed a significant concentration dependence, with a dramatic loss in activity below 15 μm. The mutants also had diminished thermal stability at low concentration, as monitored by far-UV CD. These results suggest that Cys126 contributes to the stability of the dimer interface through a network of interactions involving His95, Glu97, and Arg98, which form direct contacts across the dimer interface.

Mutations in beta ` subunit of Escherichia coli RNA polymerase perturb the activator polymerase functional interaction required for promoter clearance

P>Transcription activator C employs a unique mechanism to activate mom gene of bacteriophage Mu. The activation process involves, facilitating the recruitment of RNA polymerase (RNAP) by altering the topology of the promoter and enhancing the promoter clearance by reducing the abortive transcription. To understand the basis of this multi-step activation mechanism, we investigated the nature of the physical interaction between C and RNAP during the process. A variety of assays revealed that only DNA-bound C contacts the beta' subunit of RNAP. Consistent to these results, we have also isolated RNAP mutants having mutations in the beta' subunit which were compromised in C-mediated activation. Mutant RNAPs show reduced productive transcription and increased abortive initiation specifically at the C-dependent mom promoter. Positive control (pc) mutants of C, defective in interaction with RNAP, retained the property of recruiting RNAP to the promoter but were unable to enhance promoter clearance. These results strongly suggest that the recruitment of RNAP to the mom promoter does not require physical interaction with C, whereas a contact between the beta' subunit and the activator, and the subsequent allosteric changes in the active site of the enzyme are essential for the enhancement of promoter clearance.

Studies in crystal engineering: Crystal packing, topological photodimerization and structure-reactivity correlations in fluoro-substituted styrylcoumarins

In continuation of our studies on the influence of fluoro substitution on the solid state photobehaviour and packing pattern of styrylcoumarins, the results obtained for 4-(3-fluorostyryl)coumarin 1, 4-styryl-6-fluorocoumarin 2 and 4-styryl-7-fluorocoumarin 3 are presented. The configuration of the dimers was established on the basis of crystal packing of 1 and 2 (alpha-packed). A rationale for the significantly lower dimer yield in the crystal for 2 is proposed. In the observed centrosymmetric arrangement of the reactants the C=O ...pi (phenyl) contacts seem to provide additional attractive interactions. C-H ... O and C-H ... F hydrogen bonding seems to provide stability in these structures.

Role of Hetero-Halogen (F center dot center dot center dot X, X = Cl, Br, and I) or Homo-Halogen (X center dot center dot center dot X, X = F, Cl, Br, and I) Interactions in Substituted Benzanilides

A series of halogen-substituted benzanilides have been synthesized and characterized, and crystallization studies directed toward generation of polymorphs have been performed to delineate the importance of interactions involving halogens. The effect of halogen substitution on the molecular conformation and supramolecular packing has been investigated. The N-H center dot center dot center dot O H-bond is a key structure-directing element acting in conjunction with C-H center dot center dot center dot O and C-H center dot center dot center dot pi interactions. In addition, it is of importance to note that organic fluorine prefers Type I F center dot center dot center dot F contacts, whereas Cl, Br, and I prefer Type II contacts. Hetero-halogen center dot center dot center dot halogen interactions on the other hand are predominately of Type II geometry, and this is due to the greater polarizability of the electron density associated with the heavier halogens. It is of importance to evaluate the contributing role of these interactions in crystal structure packing and the co-operativity associated with such interactions in the solid state.

Amino acid interaction preferences in helical membrane proteins

Membrane proteins are involved in a number of important biological functions. Yet, they are poorly understood from the structure and folding point of view. The external environment being drastically different from that of globular proteins, the intra-protein interactions in membrane proteins are also expected to be different. Hence, statistical potentials representing the features of inter-residue interactions based exclusively on the structures of membrane proteins are much needed. Currently, a reasonable number of structures are available, making it possible to undertake such an analysis on membrane proteins. In this study we have examined the inter-residue interaction propensities of amino acids in the membrane spanning regions of the alpha-helical membrane (HM) proteins. Recently we have shown that valuable information can be obtained on globular proteins by the evaluation of the pair-wise interactions of amino acids by classifying them into different structural environments, based on factors such as the secondary structure or the number of contacts that a residue can make. Here we have explored the possible ways of classifying the intra-protein environment of HM proteins and have developed scoring functions based on different classification schemes. On evaluation of different schemes, we find that the scheme which classifies amino acids to different intra-contact environment is the most promising one. Based on this classification scheme, we also redefine the hydrophobicity scale of amino acids in HM proteins.

Epitaxial LaNiO3 thin films: A normal metal barrier for SNS junction

Epitaxial LaNiO3 thin films have been grown on SrTiO3 and several other substrates by pulsed laser deposition. The films are observed to be metallic down to 15 K, and the temperature dependence of resistivity is similar to that of bulk LaNiO3. Epitaxial, c-axis oriented YBa2Cu3O7-x films with good superconducting properties have been grown on the LaNiO3 (100) films. I-V characteristics of the YBa2Cu3O7-x-LaNiO3 junction are linear, indicating ohmic contact between them.

Lubricant Degradation and Related Wear of a Steel Pin in Lubricated Sliding Against a Steel Disc

In lubricated sliding contacts, components wear out and the lubricating oil ages with time. The present work explores the interactive influence between lubricant aging and component wear. The flat face of a steel pin is slid against a rotating steel disk under near isothermal conditions while the contact is immersed in a reservoir of lubricant (hexadecane). The chemical changes in the oil with time are measured by vibrational spectroscopy and gas chromatography. The corresponding chemistry of the pin surface is recorded using X-ray photoelectron spectroscopy while the morphology of the worn pins; surface and subsurface, are observed using a combination of focused ion beam milling and scanning electron 5 microscopy. When compared to thermal auto-oxidation of the lubricant alone, steel on steel friction and wear are found to accentuate the decomposition of oil and to reduce the beneficial impact of antioxidants. The catalytic action of nascent iron, an outcome of pin wear and disk wear, is shown to contribute to this detrimental effect. Over long periods of sliding, the decomposition products of lubricant aging on their own, as well as in conjunction with their products of reaction with iron, generate a thick tribofilm that is highly protective in terms of friction and wear.

Nature and strength of C-H center dot center dot center dot O interactions involving formyl hydrogen atoms: computational and experimental studies of small aldehydes

Structural and electronic properties of C-H center dot center dot center dot O contacts in compounds containing a formyl group are investigated from the perspective of both hydrogen bonding and dipole-dipole interactions, in a systematic and graded approach. The effects of a-substitution and self-association on the nature of the formyl H-atom are studied with the NBO and AIM methodologies. The relative dipole-dipole contributions in formyl C-H center dot center dot center dot O interactions are obtained for aldehyde dimers. The stabilities and energies of aldehyde clusters (dimer through octamer) have been examined computationally. Such studies have an implication in crystallization mechanisms. Experimental X-ray crystal structures of formaldehyde, acrolein and N-methylformamide have been determined in order to ascertain the role of C-H center dot center dot center dot O interactions in the crystal packing of formyl compounds.

An Investigation into the Dependence of the Arc Voltage on the Parameters of the Short-Circuit Current and the Design of the Vacuum Interrupter

The vacuum interrupter is extensively employed in the medium voltage switchgear for the interruption of the short-circuit current. The voltage across the arc during current interruption is termed as the arc voltage. The nature and magnitude of this arc voltage is indicative of the performance of the contacts and the vacuum interrupter as a whole. Also, the arc voltage depends on the parameters like the magnitude of short-circuit current, the arcing time, the point of opening of the contacts, the geometry and area of the contacts and the type of magnetic field. This paper investigates the dependency of the arc voltage on some of these parameters. The paper also discusses the usefulness of the arc voltage in diagnosing the performance of the contacts.

Electrochemical phase formation. Time-dependent nucleation and growth rates

The theory of phase formation is generalised for any arbitrary time dependence of nucleation and growth rates. Some sources of this time dependence are time-dependent potential inputs, ohmic drop and the ingestion effect. Particular cases, such as potentiostatic and, especially, linear potential sweep, are worked out for the two limiting cases of nucleation, namely instantaneous and progressive. The ohmic drop is discussed and a procedure for this correction is indicated. Recent results of Angerstein-Kozlowska, Conway and Klinger are critically investigated. Several earlier results are deduced as special cases. Evans' overlap formula is generalised for the time-dependent case and the equivalence between Avrami's and Evans' equations established.

Recent Research in Structural Health Monitoring

Roctest Group believes in the importance of maintaining a close contact with the scientific community active in fields close to our activities domains, in particular smart structures, structural engineering, sensing and fiber optic sensors. These contacts allow Roctest SMARTEC Telemac to remain at the front of scientific progress and to contribute to the diffusion of the monitoring culture worldwide. Our research and development team actively contributes in the research community, attending conferences and regularly publishing in the scientific literature. we support academic research by participating in joint research projects and by regularly welcoming graduate and undergraduate students for stages and exchange programs.

Low‐voltage varistors based on zinc antimony spinel Zn7Sb2O12

It is possible to prepare low‐voltage varistors from the zinc antimony spinel Zn7Sb2O12 with breakdown voltages in the range of 3–20 V and nonlinearity coefficient α=7–15. The varistor property is due to the formation of high ohmic potential barriers at the grain boundary regions on low‐ohmic n‐type grain interiors of the polycrystalline samples. The method of preparation of the spinel, synthesized by coprecipitation followed by annealing under restricted partial pressures of oxygen, controls the mixed valence states for antimony, namely, Sb3+ and Sb5+. This is critical in attaining high nonlinearity and lower breakdown voltages.

Growth and characterization of SrBi2Nb2O9 thin films by pulsed-laser ablation

Polycrystalline films of SrBi2Nb2O9 were grown using pulsed-laser ablation. The ferroelectric properties were achieved by low-temperature deposition followed by a subsequent annealing process. The lower switching voltage was obtained by lowering the thickness, which did not affect the insulating nature of the films. The hysteresis results showed an excellent square-shaped loop with results (Pr = 6 μC/cm2, Ec = 100 kV/cm) in good agreement with earlier reports. The films also exhibited a dielectric constant of 250 and a dissipation factor of 0.02. The transport studies indicated an ohmic behavior, while higher voltages induced a bulk space charge.

Effect of surface on the conductance characteristics of Au‐Bi2Sr2CaCu2O8+δ (single crystal) point contact junctions

We report the effect of surface treatments on the dynamic conductance curves (G=dI/dV‐V) of Au‐Bi2Sr2CaCu2O8+δ (single crystal) point contact junctions of variable junction conductances (100 mS≳G≳100 μS). We find that if the crystal surface is cleaved freshly just prior to making contacts, all irreproducible sharp multiple features often observed in tunneling data of Bi(2212) oxide superconductors disappear. If the cleaved crystal surfaces are left under ambient conditions for a few days and the tunneling experiments are repeated, these multiple features reappear. We also find that if the current in the junction is made to pass predominantly through the bulk (and not along the surface), gap features are sharper. The observed conductance curves are fitted to a modified model [G. E. Blonder et al., Phys. Rev. B 25, 4515 (1982)] and estimated gap values are Δ≂28 to 30 meV corresponding to the ratio 2Δ/kBTc ≂ 7.5 with lifetime broadening Γ/Δ≂0.2. We conclude that the sharp multiple features observed in Bi(2212) tunneling curves has no intrinsic origin in the bulk and they arise from the surface only.

Thermodynamics of Al(1-x)Ga(x)N solid solution: Inclination for phase separation and ordering

Although Al(1-x)Ga(x)N semiconductors are used in lighting, displays and high-power amplifiers, there is no experimental thermodynamic information on nitride solid solutions. Thermodynamic data are useful for assessing the intrinsic stability of the solid solution with respect to phase separation and extrinsic stability in relation to other phases such as metallic contacts. The activity of GaN in Al(1-x)Ga(x)N solid solution is determined at 1100 K using a solid-state electrochemical cell: Ga + Al(1-x)Ga(x)N/Fe, Ca(3)N(2)//CaF(2)//Ca(3)N(2), N(2) (0.1 MPa), Fe. The solid-state cell is based on single crystal CaF(2) as the electrolyte and Ca(3)N(2) as the auxiliary electrode to convert the nitrogen chemical potential established by the equilibrium between Ga and Al(1-x)Ga(x)N solid solution into an equivalent fluorine potential. Excess Gibbs free energy of mixing of the solid solution is computed from the results. Results suggest an unusual mixing behavior: a mild tendency for ordering at three discrete compositions (x = 0.25, 0.5 and 0.75) superimposed on predominantly positive deviation from ideality. The lattice parameters exhibit slight deviation from Vegard's law, with the a-parameter showing positive and the c-parameter negative deviation. Although the solid solution is stable in the full range of compositions at growth temperatures, thermodynamic instability is indicated at temperatures below 410 K in the composition range 0.26 <= x <= 0.5. At 355 K, two biphasic regions appear, with terminal solid solutions stable only for 0 <= x <= 0.26 and 0.66 <= x <= 1. The range of terminal solid solubility reduces with decreasing temperature. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.