Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Background: Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability. Methods: In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues. Results: The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs. Conclusion: In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.

Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks

Background: Thermophilic proteins sustain themselves and function at higher temperatures. Despite their structural and functional similarities with their mesophilic homologues, they show enhanced stability. Various comparative studies at genomic, protein sequence and structure levels, and experimental works highlight the different factors and dominant interacting forces contributing to this increased stability. Methods: In this comparative structure based study, we have used interaction energies between amino acids, to generate structure networks called as Protein Energy Networks (PENs). These PENs are used to compute network, sub-graph, and node specific parameters. These parameters are then compared between the thermophile-mesophile homologues. Results: The results show an increased number of clusters and low energy cliques in thermophiles as the main contributing factors for their enhanced stability. Further more, we see an increase in the number of hubs in thermophiles. We also observe no community of electrostatic cliques forming in PENs. Conclusion: In this study we were able to take an energy based network approach, to identify the factors responsible for enhanced stability of thermophiles, by comparative analysis. We were able to point out that the sub-graph parameters are the prominent contributing factors. The thermophiles have a better-packed hydrophobic core. We have also discussed how thermophiles, although increasing stability through higher connectivity retains conformational flexibility, from a cliques and communities perspective.

Room-temperature equal channel angular extrusion of pure magnesium

In this paper, we demonstrate a way to impart severe plastic deformation to magnesium at room temperature to produce ultrafine grain size of similar to 250 nm through equal channel angular extrusion (ECAE). The strategy to deform magnesium at lower temperature or to achieve such grain sizes has been proposed as: (i) to obtain a suitable initial orientation with high Schmid factor for basal slip and low Schmid factor for pyramidal/prismatic slip; (ii) to take advantage of low stacking fault energy of basal and high stacking fault energies of prismatic/pyramidal planes in order to relatively work-harden the basal plane with respect to the pyramidal/prismatic plane; and (iii) to lower the temperature of deformation in steps, leading to continual refinement of grains, resulting in finer grain size. The experimental as well as simulated texture of ECAE-processed samples indicate that the deformation mechanism leading to ultrafine grain size is slip-dominated. The recrystallization mechanism during ECAE has been found to be orientation-dependent. (C) 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Asymtotic solution of the Frieman and Book equation for the pair-correlation function

Using Thomé's procedure, the asymptotic solutions of the Frieman and Book equation for the two-particle correlation in a plasma have been obtained in a complete form. The solution is interpreted in terms of the Lorentz distance. The exact expressions for the internal energy and pressure are evaluated and they are found to be a generalization of the result obtained earlier by others.

Direct stability evaluation of power systems with detailed generator models using structure-preserving energy functions

Energy-based direct methods for transient stability analysis are potentially useful both as offline tools for planning purposes as well as for online security assessment. In this paper, a novel structure-preserving energy function (SPEF) is developed using the philosophy of structure-preserving model for the system and detailed generator model including flux decay, transient saliency, automatic voltage regulator (AVR), exciter and damper winding. A simpler and yet general expression for the SPEF is also derived which can simplify the computation of the energy function. The system equations and the energy function are derived using the centre-of-inertia (COI) formulation and the system loads are modelled as arbitrary functions of the respective bus voltages. Application of the proposed SPEF to transient stability evaluation of power systems is illustrated with numerical examples.

Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis

Background: One of the major challenges in understanding enzyme catalysis is to identify the different conformations and their populations at detailed molecular level in response to ligand binding/environment. A detail description of the ligand induced conformational changes provides meaningful insights into the mechanism of action of enzymes and thus its function. Results: In this study, we have explored the ligand induced conformational changes in H. pylori LuxS and the associated mechanistic features. LuxS, a dimeric protein, produces the precursor (4,5-dihydroxy-2,3-pentanedione) for autoinducer-2 production which is a signalling molecule for bacterial quorum sensing. We have performed molecular dynamics simulations on H. pylori LuxS in its various ligand bound forms and analyzed the simulation trajectories using various techniques including the structure network analysis, free energy evaluation and water dynamics at the active site. The results bring out the mechanistic details such as co operativity and asymmetry between the two subunits, subtle changes in the conformation as a response to the binding of active and inactive forms of ligands and the population distribution of different conformations in equilibrium. These investigations have enabled us to probe the free energy landscape and identify the corresponding conformations in terms of network parameters. In addition, we have also elucidated the variations in the dynamics of water co-ordination to the Zn2+ ion in LuxS and its relation to the rigidity at the active sites. Conclusions: In this article, we provide details of a novel method for the identification of conformational changes in the different ligand bound states of the protein, evaluation of ligand-induced free energy changes and the biological relevance of our results in the context of LuxS structure-function. The methodology outlined here is highly generalized to illuminate the linkage between structure and function in any protein of known structure.

Dynamics of sheared inelastic dumbbells

We study the dynamical properties of the homogeneous shear flow of inelastic dumbbells in two dimensions as a first step towards examining the effect of shape on the properties of flowing granular materials. The dumbbells are modelled as smooth fused disks characterized by the ratio of the distance between centres (L) and the disk diameter (D), with an aspect ratio (L/D) varying between 0 and 1 in our simulations. Area fractions studied are in the range 0.1-0.7, while coefficients of normal restitution (e(n)) from 0.99 to 0.7 are considered. The simulations use a modified form of the event-driven methodology for circular disks. The average orientation is characterized by an order parameter S, which varies between 0 (for a perfectly disordered fluid) and 1 (for a fluid with the axes of all dumbbells in the same direction). We investigate power-law fits of S as a function of (L D) and (1 - e(n)(2)) There is a gradual increase in ordering as the area fraction is increased, as the aspect ratio is increased or as the coefficient of restitution is decreased. The order parameter has a maximum value of about 0.5 for the highest area fraction and lowest coefficient of restitution considered here. The mean energy of the velocity fluctuations in the flow direction is higher than that in the gradient direction and the rotational energy, though the difference decreases as the area fraction increases, due to the efficient collisional transfer of energy between the three directions. The distributions of the translational and rotational velocities are Gaussian to a very good approximation. The pressure is found to be remarkably independent of the coefficient of restitution. The pressure and dissipation rate show relatively little variation when scaled by the collision frequency for all the area fractions studied here, indicating that the collision frequency determines the momentum transport and energy dissipation, even at the lowest area fractions studied here. The mean angular velocity of the particles is equal to half the vorticity at low area fractions, but the magnitude systematically decreases to less than half the vorticity as the area fraction is increased, even though the stress tensor is symmetric.

Temperature and concentration dependence of adsorption properties of methane in NaY: a molecular dynamics study

Molecular dynamics calculations on methane sorbed in NaY (Si/Al = 3.0) employing realistic methane-methane and methane-zeolite intermolecular potential functions at different temperatures (50, 150, 220, and 300 K) and concentrations (2, 4, 6, and 8 molecules/cage) are reported. The thermodynamic results are in agreement with the available experimental data. Guest-guest and guest-host radial distribution functions (rdfs), energy distribution functions, distribution of cage occupancy, center-of-cage-center-of-mass (coc-com) rdfs, velocity autocorrelation functions for com and angular motion and the Fourier transformed power spectra, and diffusion coefficients are presented as a function of temperature and concentration. At 50 K, methane is localized near the adsorption site. Site-site migration and essentially free rotational motion are observed at 150 K. Molecules preferentially occupy the region near the inner surface of the alpha-cage. The vibrational frequencies for the com of methane shift toward higher values with decreasing temperature and increasing adsorbate concentration. The observed frequencies for com motion are 36, 53, and 85 cm-1 and for rotational motion at 50 K, 95 and 150 cm-1 in agreement with neutron scattering data. The diffusion coefficients show a type I behavior as a function of loading in agreement with NMR measurements. Cage-to-cage diffusion is found to be always mediated by the surface.

Nonaxisymmetric unsteady motion over a rotating disk in the presence of free convection and magnetic field

The nonaxisymmetric unsteady motion produced by a buoyancy-induced cross-flow of an electrically conducting fluid over an infinite rotating disk in a vertical plane and in the presence of an applied magnetic field normal to the disk has been studied. Both constant wall and constant heat flux conditions have been considered. It has been found that if the angular velocity of the disk and the applied magnetic field squared vary inversely as a linear function of time (i.e. as (1??t*)?1, the governing Navier-Stokes equation and the energy equation admit a locally self-similar solution. The resulting set of ordinary differential equations has been solved using a shooting method with a generalized Newton's correction procedure for guessed boundary conditions. It is observed that in a certain region near the disk the buoyancy induced cross-flow dominates the primary von Karman flow. The shear stresses induced by the cross-flow are found to be more than these of the primary flow and they increase with magnetic parameter or the parameter ? characterizing the unsteadiness. The velocity profiles in the x- and y-directions for the primary flow at any two values of the unsteady parameter ? cross each other towards the edge of the boundary layer. The heat transfer increases with the Prandtl number but reduces with the magnetic parameter.

Microstructure evolution and hardness variation during annealing of equal channel angular pressed ultra-fine grained nickel subjected to 12 passes

The microstructure, thermal stability and hardness of ultra-fine grained (UFG) Ni produced by 12 passes of equal channel angular pressing (ECAP) through the route Bc were studied. Comparing the microstructure and hardness of the as-ECAPed samples with the published data on UFG Ni obtained after 8 passes of ECAP through the route Bc reveals a smaller average grain size (230 nm in the present case compared with 270 nm in 8-pass Ni), significantly lower dislocation density (1.08 x 10(14) m(-2) compared with 9 x 10(14) m(-2) in 8-pass Ni) and lower hardness (2 GPa compared with 2.45 GPa for 8-pass Ni). Study of the thermal stability of the 12-pass UFG Ni revealed that recovery is dominant in the temperature range 150-250A degrees C and recrystallisation occurred at temperatures > 250 A degrees C. The UFG microstructure is relatively stable up to about 400 A degrees C. Due to the lower dislocation density and consequently a lower stored energy, the recrystallisation of 12-pass ECAP Ni occurred at a higher temperature (similar to 250 A degrees C) compared with the 8-pass Ni (similar to 200 A degrees C). In the 12-pass Nickel, hardness variation shows that its dependence on grain size is inversely linear rather than the common grain size(-0.5) dependence.

Gibbs energy of formation of orthorhombic CaZrO3

The Gibbs free energy of formation of the orthorhombic form of CaZrO3(o) from monoclinic ZrO2(m) and periclase CaO(p) has been determined as a function of temperature in the range 950-1225 K, using an electrochemical cell incorporating single-crystal CaF2 as the solid electrolyte. The results are corrected for the small solid solubility of CaO in ZrO2. For the reaction, ZrO2(m) + CaO(p) --> CaZrO3(o), DELTAG(phi) = -31590 -13.9T(+/- 180) J mol-1. The ''second-law'' enthalpy of formation of CaZrO3 obtained from the results of this study at a mean temperature of 1090 K is in excellent agreement with the high-temperature solution calorimetric measurements of Muromachi and Navrotsky at 1068 K (J. Solid State Chem., 72 (1988) 244), and the average value of the bomb and acid solution calorimetric studies of Lvova and Feodosev (Zh. Fiz. Khim., 38 (1964) 28), Korneev et al. (Izv. Akad. Nauk SSSR, Neorg. Mater., 7 (1971) 886) and Brown and Bennington (Thermochim. Acta, 106 (1986) 183). The standard entropy of CaZrO3(o) at 298.15 K from the free energy data is 96.4 (+/- 3.5) J K-1 mol-1. The results of this study are discussed in comparison with high-temperture e.m.f. measurements reported in the literature on cubic zirconia solid solutions.

Solvation dynamics, energy distribution and trapping of a light solute ion

In the theoretical treatments of the dynamics of solvation of a newly created ion in a dipolar solvent, the self-motion of the solute is usually ignored. Recently, it has been shown that for a light ion the translational motion of the ion can significantly enhance its own rate of solvation. Therefore, solvation itself may not be the rate determining step in the equilibration. Instead, the rate determining step is the search of the low energy configuration which serves to localize the light ion. In this article a microscopic calculation of the probability distribution of the interaction energy of the nascent charge with the dipolar solvent molecules is presented in order to address this problem of solute trapping. It is found that to a good approximation, this distribution is Gaussian and the second moment of this distribution is exactly equal to the half of its own solvation energy. It is shown that this is in excellent agreement with the simulation results that are available for the model Brownian dipolar lattice and for liquid acetonitrile. If the distortion of the solvent by the ion is negligible then the same relation gives the energy distribution for the solvated ion, with the average centered at the final equilibrium solvation energy. These results are expected to be useful in understanding various chemical processes in dipolar liquids. Another interesting outcome of the present study is a simple dynamic argument that supports Onsager's ''inverse snow-ball'' conjecture of solvation of a light ion. A simple derivation of the semi-phenomenological relation between the solvation time correlation function and the single particle orientation, reported recently by Maroncelli et al. (J. Phys. Chem. 97 (1993) 13), is also presented.

Effect of magnetic field on the binding energy of a hydrogenic donor in a vertical bar z vertical bar(2/3) quantum well

We have calculated the binding energy of a hydrogenic donor in a quantum well with potential shape proportional to \z\(2/3) as a function of the width of the quantum well and the barrier height under an applied uniform magnetic field along the a axis. As the well width decreases, the binding energy increases initially up to a critical well width (which is nearly the same for all magnetic fields) at which there is a turnover. The results are qualitatively similar to those of a hydrogenic donor in a rectangular well. We have also calculated [rho(2)](1/2) and [z(2)](1/2) for the donor electron. [rho(2)](1/2) is found to be strongly dependent on the magnetic field for a given well width and weakly dependent on the well width and the barrier height, for a given value of magnetic field [z(2)](1/2) is weakly dependent on the applied magnetic field. The probability of finding the donor electron inside the well shows a rapid decrease as the well width is reduced at nearly the well width at which the binding energy shows a maximum.

Performance of a mixed flow pump with varying tip clearance .1.

Measurements of the three-dimensional flow field entering and leaving a mixed flow pump of non-dimensional specific speed k = 1.89 [N-s = 100 r/min (metric)] are discussed as a function of flowrate. Flow reversal at inlet at reduced flows is seen to result in abnormally high total pressures in the casing region, but causes no noticeable discontinuities on the head-flow characteristics. Inlet prerotation is associated with the transport of angular momentum by the reversal eddy and begins with the initiation of flow reversal.

The structures of bacteriorhodopsin with different retinal-Schiff base orientations--computer modeling and energy minimization studies

Bacteriorhodopsin has been the subject of intense study in order to understand its photochemical function. The recent atomic model proposed by Henderson and coworkers based on electron cryo-microscopic studies has helped in understanding many of the structural and functional aspects of bacteriorhodopsin. However, the accuracy of the positions of the side chains is not very high since the model is based on low-resolution data. In this study, we have minimized the energy of this structure of bacteriorhodopsin and analyzed various types of interactions such as - intrahelical and interhelical hydrogen bonds and retinal environment. In order to understand the photochemical action, it is necessary to obtain information on the structures adopted at the intermediate states. In this direction, we have generated some intermediate structures taking into account certain experimental data, by computer modeling studies. Various isomers of retinal with 13-cis and/or 15-cis conformations and all possible staggered orientations of Lys-216 side chain were generated. The resultant structures were examined for the distance between Lys-216-schiff base nitrogen and the carboxylate oxygen atoms of Asp-96 - a residue which is known to reprotonate the schiff base at later stages of photocycle. Some of the structures were selected on the basis of suitable retinal orientation and the stability of these structures were tested by energy minimization studies. Further, the minimized structures are analyzed for the hydrogen bond interactions and retinal environment and the results are compared with those of the minimized rest state structure. The importance of functional groups in stabilizing the structure of bacteriorhodopsin and in participating dynamically during the photocycle have been discussed.