The Critical Role of N- and C-Terminal Contact in Protein Stability and Folding of a Family 10 Xylanase under Extreme Conditions

Background: Stabilization strategies adopted by proteins under extreme conditions are very complex and involve various kinds of interactions. Recent studies have shown that a large proportion of proteins have their N- and C-terminal elements in close contact and suggested they play a role in protein folding and stability. However, the biological significance of this contact remains elusive. Methodology: In the present study, we investigate the role of N- and C-terminal residue interaction using a family 10 xylanase (BSX) with a TIM-barrel structure that shows stability under high temperature,alkali pH, and protease and SDS treatment. Based on crystal structure,an aromatic cluster was identified that involves Phe4, Trp6 and Tyr343 holding the Nand C-terminus together; this is a unique and important feature of this protein that might be crucial for folding and stabilityunder poly-extreme conditions. Conclusion: A series of mutants was created to disrupt this aromatic cluster formation and study the loss of stability and function under given conditions. While the deletions of Phe4 resulted in loss of stability, removal of Trp6 and Tyr343 affected in vivo folding and activity. Alanine substitution with Phe4, Trp6 and Tyr343 drastically decreased stability under all parameters studied. Importantly,substitution of Phe4 with Trp increased stability in SDS treatment.Mass spectrometry results of limited proteolysis further demonstrated that the Arg344 residue is highly susceptible to trypsin digestion in sensitive mutants such as DF4, W6A and Y343A, suggesting again that disruption of the Phe4-Trp6-Tyr343 (F-W-Y) cluster destabilizes the N-and C-terminal interaction. Our results underscore the importance of N- and C-terminal contact through aromatic interactions in protein folding and stability under extreme conditions, and these results may be useful to improve the stability of other proteins under suboptimal conditions.

Invariant-preserving Petri net reduction and conditions for invariant-existence

The use of invariants is an important tool for analysis of distributed and concurrent systems modeled by Petri nets. For a large practical system, the computation of desired invariants by the existing techniques is a time-consuming task. This paper proposes a theoretical foundation for simplified computation of desired invariants. We provide invariant-preserving Petri net reduction rules followed by the conditions for the existence of invariants in various well-structured nets. If an invariant exists, it can be found directly from the net structure using the formulas derived, or by applying the existing techniques on the reduced net.

Foaming of slags under dynamic conditions

Slag foaming under dynamic conditions has been studied in laboratory scale to examine the influence of properties commonly used to describe the foaminess and foam stability of slags under steady-state conditions. Synthetically produced slags with compositions relevant to tool steel and stainless steel production were studied through X-ray equipment in measurements simulating the dynamic conditions found in real processes. It is found that the dynamic systems display a more complex behavior than systems Under steady state. Traditional theories for foaming do not seem to be valid for slag foaming under dynamic conditions. The foam displays a fluctuating behavior, which the presently available models are not able to take into account. The concept of a foaming index does not seem to be applicable, resulting in the need for alternative models.

The fluctuations in slag foam under dynamic conditions

In the present article, slag foaming phenomenon under dynamic conditions is critically analyzed on the basis of the results of high-temperature X-ray image analysis experiments. The results indicate that the mismatch between the gas generation rate and gas escape rate has a serious impact on the foam height. This mismatch is attributed to the chemical reaction rate, which has to be considered in modeling slag foaming under dynamic conditions. The results further imply that a critical ratio of bubble size/crucible size exists, where wall effects are likely to become prominent.

Drop formation in non-newtonian liquids under pulsed conditions

Drop formation from single nozzles under pulsed flow conditions in non-Newtonian fluids following the power law model has been studied. An existing model has been modified to explain the experimental data. The flow conditions employed correspond to the mixer—settler type of operation in pulsed sieve-plate extraction columns. The modified model predicts the drop sizes satisfactorily. It has been found that consideration of non-Newtonian behaviour is important at low pulse intensities and its significance decreases with increasing intensity of pulsation. Further, the proposed model for single orifices has been tested to predict the sizes of drops formed from a sieve-plate distributor having four holes, and has been found to predict the sizes fairly well in the absence of coalescence.

In situ surface modification of molybdenum-doped organic-inorganic hybrid TiO2 nanoparticles under hydrothermal conditions and treatment of pharmaceutical effluent

Molybdenum-doped TiO2 organic-inorganic hybrid nanoparticles were synthesized under mild hydrothermal conditions by in situ surface modification using n-butylamine. This was carried out at 150 degrees C at autogeneous pressure over 18 h. n-Butylamine was selected as a surfactant since it produced nanoparticles of the desired size and shape. The products were characterized using powder X-ray diffraction, Fourier transform infrared spectrometry, dynamic light-scattering spectroscopy, UV-Vis spectroscopy and transmission electron microscopy. Chemical oxygen demand was estimated in order to determine the photodegradation efficiency of the molybdenum-doped TiO2 hybrid nanoparticles in the treatment of pharmaceutical effluents. It was found that molybdenum-doped TiO2 hybrid nanoparticles showed higher photocatalytic efficiency than untreated TiO2 nanoparticles.

The Single Langmuir Probe under Orbital-Limited Conditions in a Low-Density Collisional Plasma

The cylindrical Langmuir probe under orbital-limited conditions was used to determine the charge density in a low-density collisional plasma. The Langmuir's theory was applied to both electron and ion saturation currents in their respective accelerating regions. Present study indicates that the length of the probe significantly affects the probe characteristics. A probe of suitable length under orbital-limited conditions may be useful under the experimental conditions where the radius of the probe is much smaller than the Debye lengt.

A Direct Approach to the Problem of Diffraction by a Half-Plane under Mixed Boundary Conditions

A general direct technique of solving a mixed boundary value problem in the theory of diffraction by a semi-infinite plane is presented. Taking account of the correct edge-conditions, the unique solution of the problem is derived, by means of Jones' method in the theory of Wiener-Hopf technique, in the case of incident plane wave. The solution of the half-plane problem is found out in exact form. (The far-field is derived by the method of steepest descent.) It is observed that it is not the Wiener-Hopf technique which really needs any modification but a new technique is certainly required to handle the peculiar type of coupled integral equations which the Wiener-Hopf technique leads to. Eine allgemeine direkte Technik zur Lösung eines gemischten Randwertproblems in der Theorie der Beugung an einer halbunendlichen Ebene wird vorgestellt. Unter Berücksichtigung der korrekten Eckbedingungen wird mit der Methode von Jones aus der Theorie der Wiener-Hopf-Technik die eindeutige Lösung für den Fall der einfallenden ebenen Welle hergeleitet. Die Lösung des Halbebenenproblems wird in exakter Form angegeben. (Das Fernfeld wurde mit der Methode des steilsten Abstiegs bestimmt.) Es wurde bemerkt, daß es nicht die Wiener-Hopf-Technik ist, die wirklich irgend welcher Modifikationen bedurfte. Gewiß aber wird eine neue Technik zur Behandlung des besonderen Typs gekoppelter Integralgleichungen benötigt, auf die die Wiener-Hopf-Technik führt.

Diffraction of a cylindrical pulse by a half plane under mixed boundary conditions

The general time dependent source problem has been solved by the method of transforms (Laplace, Lebedev–Kontorovich in succession) and the solution is obtained in the form of an infinite series involving Legendre functions. The solutions in the case of harmonic time dependence and the incident plane wave have been derived from the above solution and are presented in the form of an infinite series. In the case of an incident plane wave, the series has been summed and the final solution involves an improper integral which behaves like a complementary error function for large values of the argument. Finally, the far field evaluation has been shown. The results are compared with those of Sommerfeld's half-plane diffraction problem with unmixed boundary conditions.

Analysis of continuum using boundary compatibility conditions of integrated force method

Static and vibration problems of an indeterminate continuum are traditionally analyzed by the stiffness method. The force method is more or less non-existent for such problems. This situation is primarily due to the incomplete state of development of the compatibility conditions which are essential for the analysis of indeterminate structures by the flexibility method. The understanding of the Compatibility Conditions (CC) has been substantially augmented. Based on the understanding of CC, a novel formulation termed the Integrated Force Method (IFM) has been established. In this paper IFM has been extended for the static and vibration analyses of a continuum. The IFM analysis is illustrated taking three examples: 1. (1) rectangular plate in flexure 2. (2) analysis of a cantilevered dam 3. (3) free vibration analysis of a beam. From the examples solved it is observed that the force response of an indeterminate continuum with mixed boundary conditions can be generated by IFM without any reference to displacements in the field or on the boundary. Displacements if required can be calculated by back substitution.

Formation and preservation of pedogenic carbonates in South India, links with paleo-monsoon and pedological conditions: Clues from Sr isotopes, U-Th series and REEs

The influence of the pedogenic and climatic contexts on the formation and preservation of pedogenic carbonates in a climosequence in the Western Ghats (Karnataka Plateau, South West India) has been studied. Along the climosequence, the current mean annual rainfall (MAR) varies within a 80 km transect from 6000 mm at the edge of the Plateau to 500 mm inland. Pedogenic carbonates occur in the MAR range of 500-1200 mm. In the semi-arid zone (MAR: 500-900 mm), carbonates occur (i) as rhick hardpan calcretes on pediment slopes and (ii) as nodular horizons in polygenic black soils (i.e. vertisols). In the sub-humid zone (MAR: 900-1500 mm), pedogenic carbonates are disseminated in the black soil matrices either as loose, irregular and friable nodules of millimetric size or as indurated botryoidal nodules of centimetric to pluricentimetric size. They also occur at the top layers of the saprolite either as disseminated pluricentimetric indurated nodules or carbonate-cemented lumps of centimetric to decimetric size. Chemical and isotopic (Sr-87/Sr-86) compositions of the carbonate fraction were determined after leaching with 0.25 N HCl. The corresponding residual fractions containing both primary minerals and authigenic clays were digested separately and analyzed. The trend defined by the Sr-87/Sr-86 signatures of both labile carbonate fractions and corresponding residual fractions indicates that a part of the labile carbonate fraction is genetically linked to the local soil composition. Considering the residual fraction of each sample as the most likely lithogenic source of Ca in carbonates, it is estimated that from 24% to 82% (55% on average) of Ca is derived from local bedrock weathering, leading to a consumption of an equivalent proportion of atmospheric CO2. These values indicate that climatic conditions were humid enough to allow silicate weathering: MAR at the time of carbonate formation likely ranged from 400 to 700 mm, which is 2- to 3-fold less than the current MAR at these locations. The Sr, U and Mg contents and the (U-234/U-238) activity ratio in the labile carbonate fraction help to understand the conditions of carbonate formation. The relatively high concentrations of Sr, U and Mg in black soil carbonates may indicate fast growth and accumulation compared to carbonates in saprolite, possibly due to a better confinement of the pore waters which is supported by their high (U-234/U-238) signatures, and/or to higher content of dissolved carbonates in the pore waters. The occurrence of Ce, Mn and Fe oxides in the cracks of carbonate reflects the existence of relatively humid periods after carbonate formation. The carbonate ages determined by the U-Th method range from 1.33 +/- 0.84 kyr to 7.5 +/- 2.7 kyr and to a cluster of five ages around 20 kyr, i.e. the Last Glacial Maximum period. The young occurrences are only located in the black soils, which therefore constitute sensitive environments for trapping and retaining atmospheric CO2 even on short time scales. The maximum age of carbonates depends on their location in the climatic gradient: from about 20 kyr for centimetric nodules at Mule Hole (MAR = 1100 mm/yr) to 200 kyr for the calcrete at Gundlupet (MAR = 700 mm/yr, Durand et al., 2007). The intensity of rainfall during wet periods would indeed control the lifetime of pedogenic carbonates and thus the duration of inorganic carbon storage in soils. (C) 2010 Elsevier Ltd. All rights reserved.