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.

Structure of Ce1-xSnxO2 and its relation to oxygen storage property from first-principles analysis

CeO2-SnO2 solid solution has been reported to possess high oxygen storage/release property which possibly originates from local structural distortion. We have performed first-principles based density functional calculations of Ce1-xSnxO2 structure (x=0, 0.25, 0.5, 1) to understand its structural stability in fluorite in comparison to rutile structure of the other end-member SnO2, and studied the local structural distortion induced by the dopant Sn ion. Analysis of relative energies of fluorite and rutile phases of CeO2, SnO2, and Ce1-xSnxO2 indicates that fluorite structure is the most stable for Ce1-xSnxO2 solid solution. An analysis of local structural distortions reflected in phonon dispersion show that SnO2 in fluorite structure is highly unstable while CeO2 in rutile structure is only weakly unstable. Thus, Sn in Ce1-xSnxO2-fluorite structure is associated with high local structural distortion whereas Ce in Ce1-xSnxO2-rutile structure, if formed, will show only marginal local distortion. Determination of M-O (M=Ce or Sn) bond lengths and analysis of Born effective charges for the optimized structure of Ce1-xSnxO2 show that local coordination of these cations changes from ideal eightfold coordination expected of fluorite lattice to 4+4 coordination, leading to generation of long and short Ce-O and Sn-O bonds in the doped structure. Bond valence analyses for all ions show the presence of oxygen with bond valence similar to 1.84. These weakly bonded oxygen ions are relevant for enhanced oxygen storage/release properties observed in Ce1-xSnxO2 solid solution. (C) 2010 American Institute of Physics.

Limit Analysis of Slabs with Free Edge

The general method earlier developed by the writers for obtaining valid lower bound solutions to slabs under uniformly distributed load and supported along all edges is extended to the slabs with a free edge. Lower bound solutions with normal moment criterion are presented for six cases of orthotropically reinforced slabs, with one of the short edges being free and the other three edges being any combination of fixed and simply supported conditions. The expressions for moment field and collapse load are given for each slab. The lower bounds have been compared with the corresponding upper bound values obtained from the yield line theory with simple straight yield line modes of failure. They are also compared with Nielsen’s solutions available for two cases with isotropic reinforcement.

Reliability models for existing structures based on dynamic state estimation and data based asymptotic extreme value analysis

The problem of time variant reliability analysis of existing structures subjected to stationary random dynamic excitations is considered. The study assumes that samples of dynamic response of the structure, under the action of external excitations, have been measured at a set of sparse points on the structure. The utilization of these measurements m in updating reliability models, postulated prior to making any measurements, is considered. This is achieved by using dynamic state estimation methods which combine results from Markov process theory and Bayes' theorem. The uncertainties present in measurements as well as in the postulated model for the structural behaviour are accounted for. The samples of external excitations are taken to emanate from known stochastic models and allowance is made for ability (or lack of it) to measure the applied excitations. The future reliability of the structure is modeled using expected structural response conditioned on all the measurements made. This expected response is shown to have a time varying mean and a random component that can be treated as being weakly stationary. For linear systems, an approximate analytical solution for the problem of reliability model updating is obtained by combining theories of discrete Kalman filter and level crossing statistics. For the case of nonlinear systems, the problem is tackled by combining particle filtering strategies with data based extreme value analysis. In all these studies, the governing stochastic differential equations are discretized using the strong forms of Ito-Taylor's discretization schemes. The possibility of using conditional simulation strategies, when applied external actions are measured, is also considered. The proposed procedures are exemplifiedmby considering the reliability analysis of a few low-dimensional dynamical systems based on synthetically generated measurement data. The performance of the procedures developed is also assessed based on a limited amount of pertinent Monte Carlo simulations. (C) 2010 Elsevier Ltd. All rights reserved.

Charge Density Analysis of Crystals of Nicotinamide with Salicylic Acid and Oxalic Acid: An Insight into the Salt to Cocrystal Continuum

Charge density analysis from both experimental and theoretical points of view on two molecular complexes: one is formed between nicotinamide and salicylic acid, and the other formed between nicotinamide and oxalic acid brings out the quantitative topological features to distinguish a cocrystal from a salt.

Probabilistic Analysis of Cracking Moment of Reinforced Concrete Beams

Probabilistic analysis of cracking moment from 22 simply supported reinforced concrete beams is performed. When the basic variables follow the distribution considered in this study, the cracking moment of a beam is found to follow a normal distribution. An expression is derived, for characteristic cracking moment, which will be useful in examining reinforced concrete beams for a limit state of cracking.

An ab-initio study of the proton affinity of conjugated schiff-base and related nitrogen compounds: an analysis of the triggering site of bacteriorhodopsin

The chemical groups which take part in the proton transfer reaction in bacteriorhodopsin have been studied by ab initio quantum chemical methods. The various factors such as conjugation with a linear system, electron delocalization of the guanidine type, cis-trans isomerism, geometry distortion and hydrogen bonding with charged groups can influence the properties of a given chemical group. Several systems are studied at 4-31G and STO-3G levels. Some of the Schiff-base analogues and guanidine type molecules are characterized by their molecular orbital diagrams, energy levels and the nature of charge distribution. Also, the effects of the above-mentioned factors on proton affinity are studied. It is hoped that the values thus obtained can be helpful in evaluating various structural models for proton transfer.

Quantitative structural refinement of mn K edge XANES in LaMnO3 and CaMnO3 perovskites

The special magnetotransport properties of hole doped manganese perovskites originate from a complex interplay among structural, magnetic and electronic degree of freedom. In this picture the local atomic structure around Mn ions plays a special role and this is the reason why short range order techniques like X-ray absorption spectroscopy (XAS) have been deeply exploited for studying these compounds. The analysis of near edge region features (XANES) of XAS spectra can provide very fine details of the local structure around Mn, complementary to the EXAFS, so contributing to the full understanding of the peculiar physical properties of these materials. Nevertheless the XANES analysis is complicated by the large amount of structural and electronic details involved making difficult the quantitative interpretation.This work exploits the recently developed MXAN code to achieve a full structural refinement of the Mn K edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3, in which the Mn ions are present only in one charge state as Mn3+ and Mn4+ respectively. The good agreement between the results derived from the analysis of near edge and extended region of the XAS spectra demonstrates that a quantitative picture of the local structure call be obtained from structural refinement of Mn K edge XANES data in these crystalline compounds. The XANES analysis offers, in addition.. the possibility to directly achieve information on the topology of local atomic structure around the absorber not directly achievable from EXAFS.

Topological analysis off charge density distribution in concomitant polymorphs of 3-acetylcoumarin, a case off packing polymorphism

Detailed investigation of the charge density distribution in concomitant polymorphs of 3-acetylcoumarin in terms of experimental and theoretical densities shows significant differences in the intermolecular features when analyzed based on the topological properties via the quantum theory of atoms in molecules. The two forms, triclinic and monoclinic (Form A and Form B), pack in the crystal lattice via weak C-H---O and C-H---pi interactions. Form A results in a head-to-head molecular stack, while Form B generates a head-to-tail stack. Form A crystallizes in PI (Z' = 2) and Form B crystallizes in P2(1)/n (Z = 1). The electron density maps of the polymorphs demonstrate the differences in the nature of the charge density distribution in general. The charges derived from experimental and theoretical analysis show significant differences with respect to the polymorphic forms. The molecular dipole moments differ significantly for the two forms. The lattice energies evaluated at the HF and DFT (B3LYP) methods with 6-31G** basis set for the two forms clearly suggest that Form A is the thermodynamically stable form as compared to Form B. Mapping of electrostatic potential over the molecular surface shows dominant variations in the electronegative region, which bring out the differences between the two forms.

Crystallization and preliminary X-ray crystallographic analysis of a galactose-specific lectin from Dolichos lablab

The galactose-specific lectin from the seeds of Dolichos lablab has been crystallized using the hanging-drop vapour-diffusion technique. The crystals belong to space group P1, with unit-cell parameters a = 73.99, b = 84.13, c = 93.15 angstrom, alpha = 89.92, beta = 76.01, gamma = 76.99 degrees. X-ray diffraction data to a resolution of 3.0 angstrom have been collected under cryoconditions ( 100 K) using a MAR imaging-plate detector system mounted on a rotating-anode X-ray generator. Molecular-replacement calculations carried out using the available structures of legume lectins as search models revealed that the galactose-specific lectin from D. lablab forms a tetramer similar to soybean agglutinin; two such tetramers are present in the asymmetric unit.

Structural, dielectric and ferroelectric properties of four-layer Aurivillius phase Na0.5La0.5Bi4Ti4O15

Monophasic Na0.5La0.5Bi4Ti4O15 powders were synthesized via the conventional solid-state reaction route. The X-ray powder diffraction (XRD), selected area electron diffraction (SAED) and high resolution transmission electron microscopy (HRTEM) studies carried out on the as synthesized powdered samples confirmed the phase to be a four-layer Aurivillius that crystallizes in an orthorhombic A2(1)am space group. The microstructure and the chemical composition of the sintered sample were examined by scanning electron microscope (SEM) equipped with an energy dispersive X-ray analyzer (EDX). The dielectric properties of the ceramics have been studied in the 27-700 degrees C temperature range at various frequencies (100 Hz to 1 MHz). A sharp dielectric anomaly was observed at 580 degrees C for all the frequencies corresponding to the ferroelectric to paraelectric phase transition. Saturated ferroelectric hysteresis loops were observed at 200 degrees C and the associated remnant polarization (P-r) and coercive field (E-c) were found to be 7.4 mu C/cm(2) and 34.8 kV/cm, respectively. AC conductivity analysis confirmed the existence of two different conduction mechanisms in the ferroelectric region. Activation energies calculated from the Arrhenius plots were similar to 0.24 eV and similar to 0.84 eV in the 300-450 degrees C and 450-580 degrees C temperature ranges, respectively. (C) 2010 Elsevier B.V. All rights reserved.

Lectin Microarrays for Glycomic Analysis

Glycomics is the study of comprehensive structural elucidation and characterization of all glycoforms found in nature and their dynamic spatiotemporal changes that are associated with biological processes. Glycocalyx of mammalian cells actively participate in cell-cell, cell-matrix, and cell-pathogen interactions, which impact embryogenesis, growth and development, homeostasis, infection and immunity, signaling, malignancy, and metabolic disorders. Relative to genomics and proteomics, glycomics is just growing out of infancy with great potential in biomedicine for biomarker discovery, diagnosis, and treatment. However, the immense diversity and complexity of glycan structures and their multiple modes of interactions with proteins pose great challenges for development of analytical tools for delineating structure function relationships and understanding glycocode. Several tools are being developed for glycan profiling based on chromatography,m mass spectrometry, glycan microarrays, and glyco-informatics. Lectins, which have long been used in glyco-immunology, printed on a microarray provide a versatile platform for rapid high throughput analysis of glycoforms of biological samples. Herein, we summarize technological advances in lectin microarrays and critically review their impact on glycomics analysis. Challenges remain in terms of expansion to include nonplant derived lectins, standardization for routine clinical use, development of recombinant lectins, and exploration of plant kingdom for discovery of novel lectins.

Elasto-plastic Cracking Analysis of Reinforced Concrete

A new elasto-plastic cracking constitutive model for reinforced concrete is presented. The nonlinear effects considered cover almost all the nonlinearities exhibited by reinforced concrete under short term monotonic loading. They include concrete cracking in tension, plasticity in compression, aggregate interlock, tension softening, elasto-plastic behavior of steel, bond-slip between concrete, and steel reinforcement and tension stiffening. A new procedure for incorporating bondslip in smeared steel elements is described. A modified Huber-Hencky-Mises failure criterion for plastic deformation of concrete, which fits the experimental results under biaxial stresses better, is proposed. Multiple cracking at Gauss points and their opening and closing are considered. Matrix expressions are developed and are incorporated in a nonlinear finite element program. After the objectivity of the model is demonstrated, the model is used to analyze two different types of problems: one, a set of four shear panels, and the other, a reinforced concrete beam without shear reinforcement. The results of the analysis agree favorably with the experimental results.

High-yield bacterial expression and structural characterization of recombinant human insulin-like growth factor binding protein-2

The diverse biological activities of the insulin-like growth factors (IGF-1 and IGF-2) are mediated by the IGF-1 receptor (IGF-1R). These actions are modulated by a family of six IGF-binding proteins (ICFBP-1-6; 22-31 kDa) that via high affinity binding to the IGFs (K-D similar to 300-700 pM) both protect the IGFs in the circulation and attenuate IGF action by blocking their receptor access In recent years, IGFBPs have been implicated in a variety of cancers However, the structural basis of their interaction with IGFs and/or other proteins is not completely understood A critical challenge in the structural characterization of full-length IGFBPs has been the difficulty in expressing these proteins at levels suitable for NMR/X-ray crystallography analysis Here we describe the high-yield expression of full-length recombinant human IGFBP-2 (rhIGFBP-2) in Eschericha coli Using a single step purification protocol, rhIGFBP-2 was obtained with >95% purity and structurally characterized using NMR spectroscopy. The protein was found to exist as a monomer at the high concentrations required for structural studies and to exist in a single conformation exhibiting a unique intra-molecular disulfide-bonding pattern The protein retained full biologic activity. This study represents the first high-yield expression of wild-type recombinant human IGFBP-2 in E coli and first structural characterization of a full-length IGFBP (C) 2010 Elsevier Inc. All rights reserved