Structural studies of decaying fluid turbulence: Effect of initial conditions

We present results from a systematic numerical study of structural properties of an unforced, incompressible, homogeneous, and isotropic three-dimensional turbulent fluid with an initial energy spectrum that develops a cascade of kinetic energy to large wave numbers. The results are compared with those from a recently studied set of power-law initial energy spectra [C. Kalelkar and R. Pandit, Phys. Rev. E 69, 046304 (2004)] which do not exhibit such a cascade. Differences are exhibited in plots of vorticity isosurfaces, the temporal evolution of the kinetic energy-dissipation rate, and the rates of production of the mean enstrophy along the principal axes of the strain-rate tensor. A crossover between "non-cascade-type" and "cascade-type" behavior is shown numerically for a specific set of initial energy spectra.

Structural Ordering of Disordered Ligand-Binding Loops of Biotin Protein Ligase into Active Conformations as a Consequence of Dehydration

Mycobacterium tuberculosis (Mtb), a dreaded pathogen, has a unique cell envelope composed of high fatty acid content that plays a crucial role in its pathogenesis. Acetyl Coenzyme A Carboxylase (ACC), an important enzyme that catalyzes the first reaction of fatty acid biosynthesis, is biotinylated by biotin acetyl-CoA carboxylase ligase (BirA). The ligand-binding loops in all known apo BirAs to date are disordered and attain an ordered structure only after undergoing a conformational change upon ligand-binding. Here, we report that dehydration of Mtb-BirA crystals traps both the apo and active conformations in its asymmetric unit, and for the first time provides structural evidence of such transformation. Recombinant Mtb-BirA was crystallized at room temperature, and diffraction data was collected at 295 K as well as at 120 K. Transfer of crystals to paraffin and paratone-N oil (cryoprotectants) prior to flash-freezing induced lattice shrinkage and enhancement in the resolution of the X-ray diffraction data. Intriguingly, the crystal lattice rearrangement due to shrinkage in the dehydrated Mtb-BirA crystals ensued structural order of otherwise flexible ligand-binding loops L4 and L8 in apo BirA. In addition, crystal dehydration resulted in a shift of similar to 3.5 angstrom in the flexible loop L6, a proline-rich loop unique to Mtb complex as well as around the L11 region. The shift in loop L11 in the C-terminal domain on dehydration emulates the action responsible for the complex formation with its protein ligand biotin carboxyl carrier protein (BCCP) domain of ACCA3. This is contrary to the involvement of loop L14 observed in Pyrococcus horikoshii BirA-BCCP complex. Another interesting feature that emerges from this dehydrated structure is that the two subunits A and B, though related by a noncrystallographic twofold symmetry, assemble into an asymmetric dimer representing the ligand-bound and ligand-free states of the protein, respectively. In-depth analyses of the sequence and the structure also provide answers to the reported lower affinities of Mtb-BirA toward ATP and biotin substrates. This dehydrated crystal structure not only provides key leads to the understanding of the structure/function relationships in the protein in the absence of any ligand-bound structure, but also demonstrates the merit of dehydration of crystals as an inimitable technique to have a glance at proteins in action.

Local structure in LaMnO3 and CaMnO3 perovskites: A quantitative structural refinement of mn K-edge XANES data

Hole-doped perovskites such as La1-xCaxMnO3 present special magnetic and magnetotransport properties, and it is commonly accepted that the local atomic structure around Mn ions plays a crucial role in determining these peculiar features. Therefore experimental techniques directly probing the local atomic structure, like x-ray absorption spectroscopy (XAS), have been widely exploited to deeply understand the physics of these compounds. Quantitative XAS analysis usually concerns the extended region [extended x-ray absorption fine structure (EXAFS)] of the absorption spectra. The near-edge region [x-ray absorption near-edge spectroscopy (XANES)] of XAS spectra can provide detailed complementary information on the electronic structure and local atomic topology around the absorber. However, the complexity of the XANES analysis usually prevents a quantitative understanding of the data. This work exploits the recently developed MXAN code to achieve a quantitative 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. The results derived from the EXAFS and XANES analyses are in good agreement, demonstrating that a quantitative picture of the local structure can be obtained from XANES in these crystalline compounds. Moreover, the quantitative XANES analysis provides topological information not directly achievable from EXAFS data analysis. This work demonstrates that combining the analysis of extended and near-edge regions of Mn K-edge XAS spectra could provide a complete and accurate description of Mn local atomic environment in these compounds.

Structural Studies Of Analgesics And Their Interactions .1. Crystal And Molecular-Structure Of Antipyrine

The complex crystallizes in the space group P21/c with four formula units in a unit cell of dimensionsa= 12.747, b= 7.416, c= 17.894 A and/3= 90.2 °. The structure has been solved by the symbolic addition procedure using three dimensional photographic data and refined to an R value of 0.079 for 2019 observed reflexions. The pyramidal nature of the two hetero nitrogen atoms in the antipyrine molecule is inter:nediate between that observed in free antipyrine and in some of its metal complexes. The molecule is more polar than that in crystals of free antipyrine but less so compared with that in metal complexes. In the salicylic acid molecule, the hydroxyl group forms an internal hydrogen bond with one of the oxygen atoms in the carboxyl group. The association between the salicylic acid and the antipyrine molecules is achieved through an intermolecular hydrogen bond with the other carboxyl oxygen atom in the salicylic acid molecule as the proton donor and the carboxyl oxygen atom of the antipyrine molecule as the acceptor

Structural stability of slender aerospace vehicles: Part I Mathematical modeling

A detailed mechanics based model is developed to analyze the problem of structural instability in slender aerospace vehicles. Coupling among the rigid-body modes, the longitudinal vibrational modes and the transverse vibrational modes due to asymmetric lifting-body cross-section are considered. The model also incorporates the effects of aerodynamic pressure and the propulsive thrust of the vehicle. The model is one-dimensional, and it can be employed to idealized slender vehicles with complex shapes. Condition under which a flexible body with internal stress waves behaves like a perfect rigid body is derived. Two methods are developed for finite element discretization of the system: (1) A time-frequency Fourier spectral finite element method and (2) h-p finite element method. Numerical results using the above methods are presented in Part II of this paper. (C) 2010 Elsevier Ltd. All rights reserved.

Primary Structural Documentation of the Major Urinary Protein of the Indian Commensal Rat (Rattus rattus) Using a Proteomics Platform

Purpose: A number of proteome studies have been performed recently to identify pheromone-related protein expression and their molecular function using genetically modified rodents' urine. However, no such studies have used Indian commensal rodents; interestingly, in a previous investigation, we confirmed the presence of volatile molecules in commensal rodents urine and these molecules seem to be actively involved in pheromonal communication. Therefore, the present study aims to identify the major urinary protein [MUP] present in commensal rat urine, which will help us to understand the protein's expression pattern and intrinsic properties among the rodents globally. Experimental Design: Initially, the total urinary proteins were separated by 1-D and 2-D electrophoresis and then subsequently analyzed by Matrix Assisted Laser Desorption Ionization-Time of Flight and Mass Spectrometer (MALDI-TOF/MS). Furthermore, they were then fragmented with the aid of a Tandem Mass Spectrometer (TOF/TOF) and the identified sequences aligned and confirmed using similarity with the deduced primary structures of members of the lipocalin superfamily.Results: The SDS-PAGE protein profiles showed distinct proteins with molecular masses of 15, 22.4, 25, 28, 42, 50, 55, 68, and 91 kDa. Of these proteins, the 22.4 kDa protein was considered to be target candidate. When 2D electrophoresis was carried out, about similar to 50 spots were detected with different masses and various pI ranges. The 22.4 kDa protein was found to have a pI of about 4.9. This 22.4 kDa protein spot was digested and subjected to mass spectrometry; it was identified as rat MUP. The fragmented peptides from the rat MUP at 935, 1026, 1192, and 1303 m/z were further fragmented with the aid of MS/MS and generated de novo sequence and this confirmed this protein to be the MUP present in the urine of commensal rats.Conclusion: The present investigation confirms the presence of MUP with a molecular mass of 22.4 kDa in the urine of commensal rats. This protein may be involved in the binding of volatile molecules and opens up a discussion about how volatile and non-volatile molecules in the commensal rats' urine may contribute chemo-communication.

Structural aspects of semantic-directed clusters

Knowledge-based clusters are studied from the structural point of view. Generalized descriptions for such clusters are stated and illustrated. Peculiarities of certain knowledge-based cluster configurations are highlighted. The adequacy of the connectives logical and (“and”) logical or (“exclusive-or”) in describing such clusters is justified. The definition of “concept” is elaborated from the clustering point of view and used to establish the equivalence between, descriptions of clusters and concepts. The order-independence of semantic-directed clustering approach is established formally based on axiomatic considerations.

Structural studies of model peptides containing beta-, gamma- and delta-amino acids

The crystal structures of five model peptides Piv-Pro-Gly-NHMe (1), Piv-Pro-beta Gly-NHMe (2), Piv-Pro-beta Gly-OMe (3), Piv-Pro-delta Ava-OMe (4) and Boc-Pro-gamma Abu-OH (5) are described (Piv:pivaloyl; NHMe: N-methylamide; beta Gly:beta-glycine; OMe:O-methyl ester; delta Ava:delta-aminovaleric acid; gamma Abu:gamma-aminobutyric acid). A comparison of the structures of peptides 1 and 2 illustrates the dramatic consequences upon backbone homologation in short sequences. 1 adopts a type II beta-turn conformation in the solid state, while in 2, the molecule adopts an open conformation with the beta-residue being fully extended. Piv-Pro-beta Gly-OMe (3), which differs from 2 by replacement of the C-terminal NH group by an O-atom, adopts an almost identical molecular conformation and packing arrangement in the solid state. In peptide 4, the observed conformation resembles that determined for 2 and 3, with the delta Ava residue being fully extended. In peptide 5, the molecule undergoes a chain reversal, revealing a beta-turn mimetic structure stabilized by a C-H center dot center dot center dot O hydrogen bond.

Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics

The hydrophobic effect is widely believed to be an important determinant of protein stability. However, it is difficult to obtain unambiguous experimental estimates of the contribution of the hydrophobic driving force to the overall free energy of folding. Thermodynamic and structural studies of large to small substitutions in proteins are the most direct method of measuring this contribution. We have substituted the buried residue Phe8 in RNase S with alanine, methionine, and norleucine, Binding thermodynamics and structures were characterized by titration calorimetry and crystallography, respectively. The crystal structures of the RNase S F8A, F8M, and F8Nle mutants indicate that the protein tolerates the changes without any main chain adjustments, The correlation of structural and thermodynamic parameters associated with large to small substitutions was analyzed for nine mutants of RNase S as well as 32 additional cavity-containing mutants of T4 lysozyme, human lysozyme, and barnase. Such substitutions were typically found to result in negligible changes in Delta C-p and positive values of both Delta Delta H degrees and aas of folding. Enthalpic effects were dominant, and the sign of Delta Delta S is the opposite of that expected from the hydrophobic effect. Values of Delta Delta G degrees and Delta Delta H degrees correlated better with changes in packing parameters such as residue depth or occluded surface than with the change in accessible surface area upon folding. These results suggest that the loss of packing interactions rather than the hydrophobic effect is a dominant contributor to the observed energetics for large to small substitutions. Hence, estimates of the magnitude of the hydrophobic driving force derived from earlier mutational studies are likely to be significantly in excess of the actual value.

Analysis of the beta-glucoside utilization (bgl) genes of Shigella sonnei: evolutionary implications for their maintenance in a cryptic state

The pattern of expression of the genes involved in the utilization of aryl beta-glucosides such as arbutin and salicin is different in the genus Shigella compared to Escherichia coli. The results presented here indicate that the homologue of the cryptic bgl operon of E. coli is conserved in Shigella sonnei and is the primary system involved in beta-glucoside utilization in the organism. The organization of the bgl genes in 5. sonnei is similar to that of E. coli; however there are three major differences in terms of their pattern of expression. (i) The bglB gene, encoding phospho-beta-glucosidase B, is insertionally inactivated in 5. sonnei. As a result, mutational activation of the silent bgl promoter confers an Arbutin-positive (Arb(+)) phenotype to the cells in a single step; however, acquiring a Salicin-positive (Sal(+)) phenotype requires the reversion or suppression of the bglB mutation in addition. (ii) Unlike in E. coli, a majority of the activating mutations (conferring the Arb(+) phenotype) map within the unlinked hns locus, whereas activation of the E. coli bgl operon under the same conditions is predominantly due to insertions within the bglR locus. (iii) Although the bgl promoter is silent in the wild-type strain of 5. sonnei (as in the case of E. coli), transcriptional and functional analyses indicated a higher basal level of transcription of the downstream genes. This was correlated with a 1 bp deletion within the putative Rho-independent terminator present in the leader sequence preceding the homologue of the bglG gene. The possible evolutionary implications of these differences for the maintenance of the genes in the cryptic state are discussed.

Synthesis and structural aspects of quasicrystals in Mg-Al-Ag system: Mg4Al6Ag

The existence of an icosahedral phase in Mg−Al−Ag is better understood on a crystallographic basis rather than on a quantum structural diagram basis. The quasicrystalline structure is delineated in terms of quasiperiodic arrangement of Pauling triacontahedra, which can be identified in the equilibrium structure. Subtle differences in the electron diffraction patterns have been recorded compared to the ideal quasicrystalline pattern. The misalignment of spots and distortions are better attributed to higher order rational approximate structure than anisotropic phason strain. Ares of diffuse intensity have been related to the ordering among the atoms in the clusters.

Structural aspects of high-temperature cuprate superconductors

High-temperature superconductivity constitutes the most sensational discovery of recent times. Since these new superconductors are complex metal oxides, chemistry has had a big role to play in the investigations. For the first time, stoichiometry, structure, bonding, and such chemical factors have formed central themes in superconductivity, an area traditionally dominated by physicists. These oxide superconductors have given a big boost to solid-state chemistry.

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.

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