Molecular Basis of the Thermostability and Thermophilicity of Laminarinases: X-ray Structure of the Hyperthermostable Laminarinase from Rhodothermus marinus and Molecular Dynamics Simulations

Glycosyl hydrolases are enzymes capable of breaking the glycosidic linkage of polysaccharides and have considerable industrial and biotechnological applications. Driven by the later applications, it is frequently desirable that glycosyl hydrolases display stability and activity under extreme environment conditions, such as high temperatures and extreme pHs. Here, we present X-ray structure of the hyperthermophilic laminarinase from Rhodothermus marinus (RmLamR) determined at 1.95 angstrom resolution and molecular dynamics simulation studies aimed to comprehend the molecular basis, for the thermal stability of this class of enzymes. As most thermostable proteins, RmLamR contains a relatively large number of salt bridges, which are not randomly distributed on the structure. On the contrary, they form clusters interconnecting beta-sheets of the catalytic domain. Not all salt bridges, however, are beneficial for the protein thermostability: the existence of charge-charge interactions permeating the hydrophobic core of the enzymes actually contributes to destabilize the structure by facilitating water penetration into hydrophobic cavities, as can be seen in the case of mesophilic enzymes. Furthermore, we demonstrate that the mobility of the side-chains is perturbed differently in each class of enzymes. The side-chains of loop residues surrounding the catalytic cleft in the mesophilic laminarinase gain mobility and obstruct the active site at high temperature. By contrast, thermophilic laminarinases preserve their active site flexibility, and the active-site cleft remains accessible for recognition of polysaccharide substrates even at high temperatures. The present results provide structural insights into the role played by salt-bridges and active site flexibility on protein thermal stability and may be relevant for other classes of proteins, particularly glycosyl hydrolases.

The shoving model for the glass-former LiCl center dot 6H(2)O: A molecular dynamics simulation study

Molecular dynamics (MD) simulations of LiCl center dot 6H(2)O Showed that the diffusion coefficient D, and also I lie structural relaxation time , follow a power law at high temperatures, D(-1) proportional to (T - T(0))(-mu), with the same experimental parameters for viscosity (T(0) = 207 K, mu = 2.08). Decoupling between D and occurs at T(x) similar to 1.1 T(0). High frequency acoustic excitations for the LiCl center dot 6H(2)O model were obtained by the calculation of time correlation functions of mass current fluctuations. The temperature dependence of the instantaneous shear modulus, G,(T), was considered in the shoving model for supercooled liquids [J.C. Dyre, T. Christensen, N.B. Olsen, J. Non-Cryst. Solids 352 (2006) 4635] resulting in a linear relationship log (D(-1)) vs. G root T. (C) 2009 Elsevier B.V. All rights reserved.

Alkoxy Chain Effect on the Viscosity of a Quaternary Ammonium Ionic Liquid: Molecular Dynamics Simulations

The viscosity of ionic liquids based on quaternary ammonium cations is reduced when one of the alkyl chains is replaced by an alkoxy chain (Zhou et al. Chem. Eur. J. 2005, 11, 752.). A microscopic picture of the role played by the ether function in decreasing the viscosity of quaternary ammonium ionic liquids is provided here by molecular dynamics (MD) simulations. A model for the ionic liquid N-ethyl-N,N-dimethyl-N-(2-methoxyethyl)ammonium bis(trifluoromethanesulfonyl)imide, MOENM(2)E TFSI, is compared to the tetraalky-lammonium counterpart. The alkoxy derivative has lower viscosity, higher ionic diffusion coefficients, and higher conductivity than the tetraalkyl system at the same density and temperature. A clear signature of the ether function on the liquid structure is observed in cation-cation correlations, but not in anion-anion or anion-cation correlations. In both the alkyl and the alkoxy ionic liquids, there is aggregation of long chains of neighboring cations within micelle-like structures. The MD simulations indicate that the less effective assembly between the more flexible alkoxy chains, in comparison to alkyl chains, is the structural reason for higher ionic mobility in MOENM(2)E TFSI.

Structural studies of prephenate dehydratase from Mycobacterium tuberculosis H37Rv by SAXS, ultracentrifugation, and computational analysis

Tuberculosis (TB) is one of the most common infectious diseases known to man and responsible for millions of human deaths in the world. The increasing incidence of TB in developing countries, the proliferation of multidrug resistant strains, and the absence of resources for treatment have highlighted the need of developing new drugs against TB. The shikimate pathway leads to the biosynthesis of chorismate, a precursor of aromatic amino acids. This pathway is absent from mammals and shown to be essential for the survival of Mycobacterium tuberculosis, the causative agent of TB. Accordingly, enzymes of aromatic amino acid biosynthesis pathway represent promising targets for structure-based drug design. The first reaction in phenylalanine biosynthesis involves the conversion of chorismate to prephenate, catalyzed by chorismate mutase. The second reaction is catalyzed by prephenate dehydratase (PDT) and involves decarboxylation and dehydratation of prephenate to form phenylpyruvate, the precursor of phenylalanine. Here, we describe utilization of different techniques to infer the structure of M. tuberculosis PDT (MtbPDT) in solution. Small angle X-ray scattering and ultracentrifugation analysis showed that the protein oligomeric state is a tetramer and MtbPDT is a flat disk protein. Bioinformatics tools were used to infer the structure of MtbPDT A molecular model for MtbPDT is presented and molecular dynamics simulations indicate that MtbPDT i.s stable. Experimental and molecular modeling results were in agreement and provide evidence for a tetrameric state of MtbPDT in solution.

Microtubule dynamics in compatible and incompatible interactions of soybean hypocotyl cells with Phytophthora sojae

The arrangement of microtubules in soybean (Glycine max) cells was examined during compatible and incompatible interactions of hypocotyls of soybean cv. Harosoy (susceptible) and cv. Haro 1272 (resistant) with race 1 of the soybean-specific pathogen Phytophthora sojae. Both reaction types were similar during the first 3 h after zoospore inoculation in terms of the number of cells penetrated, and depth penetrated into the cortex. By 3 h postinoculation, clear differences had developed between the two interaction types: incompatible interactions were characterized by a hypersensitive response that was confined to single penetrated cells; while compatibly responding cells appeared unchanged. Both types of response were characterized by autofluorescence of cell walls or cytoplasm and, at 6 h after inoculation, complete disorganization of cell cytoplasm. Reorientation and loss of microtubules was seen in the early stages of the incompatible interaction in association with cellular hypersensitivity, but not in compatible responses. In cells adjacent to those that reacted hypersensitively, there was little evidence of change in microtubule orientation. Treatment of hypocotyls with the microtubule depolymerizer oryzalin prior to inoculation did not alter the compatible response, but led to breakdown of the incompatible response. Changes in microtubule orientation and state are thus among the first structural changes that are visible within cells during incompatibility in this system.

The credit spread dynamics of Latin American euro issues in international bond markets

This paper investigates two important relationships using the sovereign issues made by major Latin American economies in the international bond market: the determinants of credit spread changes using variables derived from structural and macroeconomic theory and the impact of a default episode on the underlying equilibrium dynamics. We find four significant determinants of credit spread changes: an asset and interest rate factor—consistent with structural models of credit spread pricing; the exchange rate—consistent with macroeconomic determinants and the slope of the yield curve—consistent with a business cycle effect. Also, an intra-regional analysis of sovereign yields reveals a shift in the long-run equilibrium dynamics around the Argentine default on the 23 December 2001.

Equilibration strategies in molecular dynamics simulation of polyethers

A comparison of the NVT and NVE ensemble simulations of tetraglyme showed that, in terms of energy, temperature and most of the structural features the results were very similar. However, major differences were observed in dynamic properties, ie in the mean square displacement and in the O--O distances. A fast equilibration method suitable for amorphous polymer systems is also detailed. This was accomplished by the reassignment of the velocity distribution to the particles, after the interruption of an NVE simulation.

Ion clustering in molecular dynamics simulations of sodium iodide solutions

Model systems of sodium iodide dissolved in dimethyl ether or 1,2-dimethoxyethane (glyme) were studied in order to investigate the structural and dynamic properties of ionic solutions in small and polymeric ethers. Full molecular dynamics simulations were performed at a range of different salt concentrations. An algorithm was designed which assigns ions to clusters and then calculates all the terms which contribute to ionic conductivity. In dilute solutions, free ions are the most common ionic species, followed by ion pairs. As the concentration increases, pairs become the most common species, with significant concentrations of clusters with 3 through 6 ions. Changing the solvent from dimethyl ether to glyme significantly decreases the ion clustering due to the chelate effect in which the two oxygens on a solvent stabilize an associated cation. The conductivity in stable systems is shown to be primarily the result of the movement of free ions and the relative movement of ions within neutral pairs. The Nernst-Einstein relation, commonly used in the discussion of polymer electrolytes, is shown to be inadequate to quantitatively describe conductivity in the model systems.

Investigation of proton dynamics and the proton transport pathway in choline dihydrogen phosphate using solid-state NMR

Choline dihydrogen phosphate has previously been shown to be a good ionic conductor as well as an excellent host for acid doping, leading to high proton conductivities required for e.g., electrochemical devices including proton membrane fuel cells and sensors. A combination of variable-temperature ¹H solid-state NMR and 2D NMR pulse sequences, including ³¹P and ¹³C CODEX and ¹H BaBa, show that the proton conduction mechanism primarily involves assisted transport via a restricted three-site motion of the phosphate unit around the P–O bond that is hydrogen bonded to the choline and exchange of protons between these anions. In other words, proton transport at ambient temperatures appears to occur most favorably along the crystallographic b axis, from phosphate dimer to dimer. At elevated temperatures exchange between the protons of the hydroxyl group on the choline cation and the hydrogen-bonded dihydrogen phosphate groups also contributes to the structural diffusion of the protons in this solid state conductor.

Integrated fluid-thermal-structural numerical analysis for the quenching of metallic components

The quenching of a metal component with a channel section in a water tank is numerically simulated. Computational fluid dynamics (CFD) is used to model the multiphase flow and the heat transfer in film boiling, nucleate boiling and convective cooling processes to calculate the difference in heat transfer rate around the component and then combining with the thermal simulation and structure analysis of the component to study the effect of heat transfer rate on the distortion of the U-channel component. A model is also established to calculate the residual stress produced by quenching. The coupling fluid-thermal-structural simulation provides an insight into the deformation of the component and can be used to perform parameter analysis to reduce the distortion of the component. © 2011 Shanghai Jiaotong University and Springer-Verlag Berlin Heidelberg.

Molecular dynamics study of response of liquid N,N-dimethylformamide to externally applied electric field using a polarizable force field

The behavior of Liquid N,N-dimethylformamide subjected to a wide range of externally applied electric fields (from 0.001 V/nm to 1 V/nm) has been investigated through molecular dynamics simulation. To approach the objective the AMOEBA polarizable force field was extended to include the interaction of the external electric field with atomic partial charges and the contribution to the atomic polarization. The simulation results were evaluated with quantum mechanical calculations. The results from the present force field for the liquid at normal conditions were compared with the experimental and molecular dynamics results with non-polarizable and other polarizable force fields. The uniform external electric fields of higher than 0.01 V/nm have a significant effect on the structure of the liquid, which exhibits a variation in numerous properties, including molecular polarization, local cluster structure, rotation, alignment, energetics, and bulk thermodynamic and structural properties.

Effects of micro-structural parameters on mechanical properties of carbon nanotube polymer nanocomposites

A comparison between the elastic modulus of carbon nanotube (CNT) polymer nano composites predicted by classical micromechanics theories, based on continuum mechanics and experimental data, was made and the results revealed a great difference. To improve the accuracy of these models, a new two-step semi-analytical method was developed, which allowed consideration of the effect of the interphase, in addition to CNT and matrix, in the modeling of nanocomposites. Based on this developed method, the inuence of microstructural parameters, such as CNT volume fraction, CNT aspect ratio, partial and complete agglomerations of CNTs, and overlap and exfoliation of CNTs, on the overall elastic modulus of nanocomposites was investigated. ©2014 Sharif University of Technology. All rights reserved.

The Influence of water and metal salt on the transport and structural properties of 1-Octyl-3-methylimidazolium Chloride

The addition of diluents to ionic liquids (ILs) has recently been shown to enhance the transport properties of ILs. In the context of electrolyte design, this enhancement allows the realisation of IL-based electrolytes for metal-air batteries and other storage devices. It is likely that diluent addition not only impacts the viscosity of the IL, but also the ion-ion interactions and structure. Here, we investigate the nano-structured 1-methyl-3-octylimidazolium chloride (OMImCl) with varying water concentrations in the presence of two metal salts, zinc chloride and magnesium chloride. We find that the choice of metal salt has a significant impact on the structure and transport properties of the system; this is explained by the water structuring and destructing properties of the metal salt.

The effect of fibrous structural difference on thermal insulation properties of biological composites: silkworm cocoons

As a biological fibrous structure, silkworm cocoon provides multiple protective functionalities to safeguard the silk moth pupa’s metabolic activity. The mechanism of this protection could be adopted in clothing manufacture to provide more comfortable apparel. In this study, the thermal insulation properties of both domestic Bombyx mori (B. mori) and wild Antheraea pernyi (A. pernyi) cocoons were investigated under both warm and cold environmental conditions. Computational fluid dynamics models have been developed to simulate the heat transfer process through both types of cocoon wall structures. The simulation results show that the wild A. pernyi cocoon reduces the intensity of convection and heat flux between the environment and the cocoon interior and has higher wind resistance than its domestic counterpart. Compared with A. pernyi cocoon, the B. mori cocoon facilitates easy air transfer and decreases the temperature lag when the surrounding conditions are changed. The new knowledge has significant implications for developing biomimetic thermal functional materials.