Differential stability of beta-sheets and alpha-helices in beta-lactamase: a high temperature molecular dynamics study of unfolding intermediates

Beta-Lactamase, which catalyzes beta-lactam antibiotics, is prototypical of large alpha/beta proteins with a scaffolding formed by strong noncovalent interactions. Experimentally, the enzyme is well characterized, and intermediates that are slightly less compact and having nearly the same content of secondary structure have been identified in the folding pathway. In the present study, high temperature molecular dynamics simulations have been carried out on the native enzyme in solution. Analysis of these results in terms of root mean square fluctuations in cartesian and [phi, psi] space, backbone dihedral angles and secondary structural hydrogen bonds forms the basis for an investigation of the topology of partially unfolded states of beta-lactamase. A differential stability has been observed for alpha-helices and beta-sheets upon thermal denaturation to putative unfolding intermediates. These observations contribute to an understanding of the folding/unfolding processes of beta-lactamases in particular, and other alpha/beta proteins in general.

Effects of thermal annealing on the properties of zirconia films prepared by ion-assisted deposition

The effect of thermal annealing in the range 300–800 °C on the properties of zirconia films prepared by ion assisted deposition was studied. It was found that at low temperature the cubic phase is formed. This phase is stable up to 700 °C. All the films exhibit a monophasic monoclinic structure at 800 °C. The stress, estimated from X-ray patterns, shows a transition from tensile to compressive with increasing ion fluence. The refractive index and extinction coefficient do not seem to change appreciably up to 700 °C, showing a marked degradation thereafter. Single step annealing to the highest temperature was found to result in better stability than multistep annealing.

New flame-retardant poly(pyromellitic imide aryl phosphoramide-ester)s

Flame-retardant poly(pyromellitic imide aryl phosphoramide-ester)s were synthesized by interfacial polycondensation of N,N?-bis(p-hydroxyphenyl)pyromellitic diimide with aryl phosphoramidic dichlorides. The polymers were characterized by IR and 1H-NMR spectroscopy. The molecular composition was confirmed by elemental analysis. The thermal stability and flammability of the polymers were studied by thermogravimetry and limiting oxygen index, respectively. Durch Grenzflächen-Polykondensation von N,N?-bis(4-hydroxyphenyl)pyromellitsäurediimid mit Dichloriden verschiedener Phosphoramide wurden flammhemmende Polymere erhalten. Diese wurden mittels IR- und 1H-NMR-Spektroskopie und Elementaranalyse charakterisiert. Thermische Stabilität und Entflammbarkeit wurden thermogravimetrisch bzw. durch Bestimmung des Sauerstoff-Indexes untersucht.

Oxidative copolymerization: microstructure analysis of the terpolymer of styrene, methyl methacrylate, and oxygen

This paper reports the first study of the microstructure of a copolyperoxide by nuclear magnetic resonance spectroscopy. The copolyperoxides of styrene and methyl methacrylate (MMA) of various compositions have been synthesized. An analysis of the resonance signal of the backbone methylene protons gave the diad sequence probabilities which led to the calculation of the oxidative copolymerization reactivity ratios for styrene and MMA and the microstructural parameters like average chain length of the repeat unit sequences, run number, etc. The results point to the tendency of the SO1 and MO:! units to alternate in the chain. Compared to poly(styrene peroxide), the aromatic C1 seems to be stereosensitive in the terpolymers.

Tropical Clays .1. Index Properties And Microstructural Aspects

Soils showing changes in plasticity characteristics upon driving form an important group in tropical soils. These changes are attributed to the grouping of particles into aggregates either due to mineralogy or presence of cementing agents and/or pore fluid characteristics. These changes are found to be permanent. In this paper, the effect of these changes leading to changes in index properties is discussed. The coefficient of permeability has been found to be comparable at liquid limit water content for different soils of varying liquid limit values. Permeability is an indirect reflection of microstructure and indicates the flow rate, which depends upon pore geometry. Other mechanical properties like compressibility and shear strength also depend upon pore geometry. These microstructural aspects of liquid limit as a reference state for the analysis of engineering behavior of tropical soils are examined in detail.

Crystallography of solid-liquid interface and evolution of texture during directional solidification of Tb0.3Dy0.7Fe1.95 alloy

The effect of growth texture on the magnetostriction of ternary Tb0.3Dy0.7Fe1.95 was studied by conducting unidirectional solidification experiments using a zoning set-up. Detailed texture evolutions were studied using X-ray diffraction on samples obtained by varying growth rates from 18 to 72 cm/h, under a temperature gradient of 100 degrees C/cm. The estimated texture co-efficient and pole figures of the samples indicate that during the onset of the solidification, < 110 > and < 331 >/'rotated < 110 >' texture components nucleate and grow in all the samples. However, as the solidification progresses, < 112 > texture component becomes dominant at higher growth rate. This results in an improvement of magnetostriction from 1000 to 1300 microstrains for samples grown at growth rates of 18 and 72 cm/h respectively. The transition of preferred growth direction occurs through intermediate orientations < 123 >. An attempt has been made in this paper to explain the occurrence of different growth texture by considering the stability of growing interface, its planar packing fraction and atomic stacking sequence of several low index planes. (C) 2010 Elsevier Ltd. All rights reserved.

Analysis of Hydrogen Bonding and Stability of Protein Secondary Structures in Molecular Dynamics Simulation

Molecular Dynamics (MD) simulations provide an atomic level account of the molecular motions and have proven to be immensely useful in the investigation of the dynamical structure of proteins. Once an MD trajectory is obtained, specific interactions at the molecular level can be directly studied by setting up appropriate combinations of distance and angle monitors. However, if a study of the dynamical behavior of secondary structures in proteins becomes important, this approach can become unwieldy. We present herein a method to study the dynamical stability of secondary structures in proteins, based on a relatively simple analysis of backbone hydrogen bonds. The method was developed for studying the thermal unfolding of beta-lactamases, but can be extended to other systems and adapted to study relevant properties.

A simplified kinetic model for oxidative dehydrogenation of ethylbenzene over Pd-NaBr/Al2O3 catalyst

The oxidative dehydrogenation of ethylbenzene is gaining considerable importance in recent years as a promising alternative for styrene production. This vapour phase reaction has been studied over Pd-NaBr/Al2O3 catalyst in the temperature range 623-793 K in a fixed bed reactor. Kinetic analysis of this reaction has been done using a recursion procedure developed in this work from first principles. The advantage of this method is the absence of any restriction on the conversion level as it uses an integrated rate equation. The rate of styrene formation was found to follow a linear relationship with concentration of ethylbenzene and shows a Langmuir type dependence on the concentration of oxygen.

Edge-sharing bioctahedral diruthenium(III) complexes containing methoxy and carboxylate bridges:x-ray structures, redox behavior, and core stability

Edge-sharing bioctahedral (ESBO) complexes [Ru-2(OMe)(O2CC6H4-p-X)3(1-MeIm)(4)](ClO4)2 (X = OMe (1a), Me (1b)) and [Ru-2(O2CC6H4-P-X)(4)(1-MeIm)(4)](ClO4)(2) (X = OMe (2a), Me (2b)) are prepared by reacting Ru2Cl(O(2)CR)(4) with 1-methylimidazole (1-MeIm) in methanol followed by treatment with NaClO4. Complex 2a and the PF6- salt (1a') of 1a have been structurally characterized. Crystal data for 1a.1.5MeCN. 0.5Et(2)O: triclinic, P (1) over bar, a = 13.125(2) Angstrom, b = 15.529(3) Angstrom, c 17.314(5) Angstrom, a; 67.03(2)degrees, beta 68.05(2)degrees, gamma = 81.38(1)degrees, V 3014(1) Angstrom(3), Z = 2. Crystal data for 2a: triclinic, P (1) over bar, a 8.950(1) Angstrom, b = 12.089(3) Angstrom, c = 13.735(3) Angstrom, alpha 81.09(2)degrees, beta = 72.27(1)degrees, gamma = 83.15(2)degrees, V = 1394(1) Angstrom(3), Z = 1. The complexes consist of a diruthenium(III) unit held by two monoatomic and two three-atom bridging ligands. The 1-MeIm ligands are at the terminal sites of the [Ru-2(mu-L)(eta(1):mu-O(2)CR)(eta(1):eta(1):mu-O(2)CR)(2)](2+) core having a Ru-Ru single bond (L = OMe or eta(1)-O(2)CR). The Ru-Ru distance and the Ru-O-Ru angle in the core of 1a' and 2a are 2.49 Angstrom and similar to 76 degrees. The complexes undergo one-electron oxidation and reduction processes in MeCN-0.1 M TBAP to form mixed-valence diruthenium species with Ru-Ru bonds of orders 1.5 and 0.5, respectively.

Heterogeneous permanganate oxidations: Synthesis of medium ring keto-lactones via substituent directed oxidative cyclisation

Homoallyl alcohols 4a-b and 5a-b undergo smooth oxidative cyclisation to give the corresponding ring enlarged keto-lactones under heterogeneous permanganate oxidation conditions.

High-temperature stability of Ca2ZrSi4O12

The standard Gibbs free energy of formation of orthorhombic Ca2ZrSi4O12 from component oxides ZrO2 (monoclinic), CaO (rock salt), and SiO2 (quartz) has been determined in the temperature range 973 to 1273 K using a solid-state cell incorporating single-crystal CaF2 as the electrolyte: Delta G(f) degrees = -219930 + 11.77T (+/- 1500) J.mol(-1) This is the only quantitative information now available on the stability of Ca2ZrSi4O12.

Interactions of L-serine at the active site of serine hydroxymethyltransferases: induction of thermal stability

Serine hydroxymethyltransferase (SHMT), EC 2.1.2.1, exhibits broad substrate and reaction specificity. In addition to cleaving many 3-hydroxyamino acids to glycine and an aldehyde, the enzyme also catalyzed the decarboxylation, transamination and racemization of several substrate analogues of amino acids. To elucidate the mechanism of interaction of substrates, especially L-serine with the enzyme, a comparative study of interaction of L-serine with the enzyme from sheep liver and Escherichia coli, was carried out. The heat stability of both the enzymes was enhanced in the presence of serine, although to different extents. Thermal denaturation monitored by spectral changes indicated an alteration in the apparent T, of sheep liver and E. coli SHMTs from 55 +/- 1 degrees C to 72 +/- 3 degrees C at 40 mM serine and from 67 +/- 1 degrees C to 72 +/- 1 degrees C at 20 mM serine, respectively. Using stopped flow spectrophotometry k values of (49 +/- 5)(.)10(-3) s(-1) and (69 +/- 7).10(-3) s(-1) for sheep liver and E. coli enzymes were determined at 50 mM serine. The binding of serine monitored by intrinsic fluorescence and sedimentation velocity measurements indicated that there was no generalized change in the structure of both proteins. However, visible CD measurements indicated a change in the asymmetric environment of pyridoxal 5'-phosphate at the active site upon binding of serine to both the enzymes. The formation of an external aldimine was accompanied by a change in the secondary structure of the enzymes monitored by far UV-CD spectra. Titration microcalorimetric studies in the presence of serine (8 mM) also demonstrated a single class of binding and the conformational changes accompanying the binding of serine to the enzyme resulted in a more compact structure leading to increased thermal stability of the enzyme.

Phase relations in the system Cu─Ho─O and stability of Cu2Ho2O5

The phase relations in the system Cu-Ho-O have been determined at 1300 K using X-ray diffraction, optical microscopy, and electron microprobe analysis of samples equilibrated in evacuated quartz ampules and in pure oxygen. Only one ternary compound, Cu2Ho2O5, was found to be stable. The Gibbs free energy of formation of this compound has been measured using the solid-state cell Pt,Cu2O + Cu2Ho2O5 + Ho2O3/(Y2O3)ZrO2/CuO + Cu2O,Pt in the temperature range of 973 to 1350 K. For the formation of Cu2Ho2O5 from its binary component oxides, 2CuO(s) + Ho2O3(S) --> Cu2Ho2O5(s) DELTAG-degrees = 11190 - 13.8T(+/- 120) J-mol-1 Since the formation is endothermic, CU2Ho2O5 becomes thermodynamically unstable with respect to CuO and Ho2O3 below 810 K. When the oxygen partial pressure over Cu2Ho2O5 is lowered, it decomposes according to the reaction 2Cu2Ho2O5(s) --> 2Ho2O3(s) + 2Cu2O(S) + O2(g) for which the equilibrium oxygen potential is given by DELTAmu(O2) = - 238510 + 160.2T(+/- 450) J.mol-1 The decomposition temperature at an oxygen partial pressure of 1.52 x 10(4) Pa was measured using a combined DTA-TGA apparatus. Based on these results, an oxygen potential diagram for the system Cu-Ho-O at 1300 K is presented.

Stability of copper tolerance in Thiobacillus ferrooxidans

A strain of Thiobacillus ferrooxidans MAL-4-1 was adapted to grow at higher concentrations of copper by repeated subculturing in the presence of increasing levels of added cupric ions in 9K medium. The strains adapted to copper were found to be more efficient in bioleaching of copper from concentrates. When copper tolerant strains were back cultured repeatedly in 9K medium without cupric ions, the initially developed metal tolerance was observed to be lost. This indicates that the copper tolerance developed is stress-dependent and not a permanent trait of the adapted strain.