Structures of apo and GTP-bound molybdenum cofactor biosynthesis protein MoaC from Thermus thermophilus HB8

The first step in the molybdenum cofactor (Moco) biosynthesis pathway involves the conversion of guanosine triphosphate (GTP) to precursor Z by two proteins (MoaA and MoaC). MoaA belongs to the S-adenosylmethioninedependent radical enzyme superfamily and is believed to generate protein and/or substrate radicals by reductive cleavage of S-adenosylmethionine using an Fe-S cluster. MoaC has been suggested to catalyze the release of pyrophosphate and the formation of the cyclic phosphate of precursor Z. However, structural evidence showing the binding of a substrate-like molecule to MoaC is not available. Here, apo and GTP-bound crystal structures of MoaC from Thermus thermophilus HB8 are reported. Furthermore, isothermal titration calorimetry experiments have been carried out in order to obtain thermodynamic parameters for the protein-ligand interactions. In addition, molecular-dynamics (MD) simulations have been carried out on the protein-ligand complex of known structure and on models of relevant complexes for which X-ray structures are not available. The biophysical, structural and MD results reveal the residues that are involved in substrate binding and help in speculating upon a possible mechanism.

Excited-state structures of molecules with nearby electronic states

Vibronic coupling among the nearby excited electronic states via the in-plane and the out-of-plane nuclear motions is examined in benzene, pyrazine, formaldehyde and thioformaldehyde. Results reveal that in benzene the structure distorts via the most active nuclear bending (planar) motion while in the other molecules the structures distort through an out-of-plane bending motion in their respective lowest excited states.

Electronic structures of electron donor-acceptor complexes: results from ultraviolet photoelectron spectroscopy and molecular orbital calculations

HeI photoelectron spectra of 1:1 electron donor-acceptor complexes are discussed in the light of molecular orbital calculations. The complexes discussed include those formed by BH3, BF3 and SO2. Some systematics have been found in the ionization energy shifts of the complexes compared to the free components and these are related to the strength of the donor-acceptor bond. Hel spectra of hydrogen bonded complexes are discussed in comparison with results from MO calculations. Limitations of such studies as well as scope for further investigations are indicated.

HARMONY: a server for the assessment of protein structures

Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (phi, psi) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located at http://caps.ncbs.res.in/harmony/

Crystal structures and photocatalysis of the triclinic polymorphs of BiNbO4 and BiTaO4

The high-temperature polymorphs of two photocatalytic materials, BiNbO4 and BiTaO4 were synthesized by the ceramic method. The crystal structures of these materials were determined by single-crystal X-ray diffraction. BiNbO4 and BiTaO4 crystallize into the triclinic system P (1) over bar (No. 2), with a = 5.5376(4) angstrom, b = 7.6184(3) angstrom, c = 7.9324(36) angstrom, alpha = 102.565(3)degrees, beta = 90.143(2)degrees, gamma = 92.788 (4)degrees, V = 326.21 (5) angstrom(3). Z = 4 and a = 5.931(1) angstrom, b = 7.672(2) angstrom, c = 7.786(2) angstrom, alpha = 102.94 (3)degrees, beta = 90.04(3)degrees gamma = 93.53(3)degrees, V = 344.59(1) angstrom(3) and Z = 4, respectively. The structures along the c-axis, consist of layers of [Bi2O2] units separated by puckered sheets of (Nb/Ta)O-6 octahedra. Photocatalytic studies on the degradation of dyes indicate selectivity of BiNbO4 towards aromatics containing quinonic and azo functional groups

Topology design of three-dimensional structures using hybrid finite elements

Conventional three-dimensional isoparametric elements are susceptible to problems of locking when used to model plate/shell geometries or when the meshes are distorted etc. Hybrid elements that are based on a two-field variational formulation are immune to most of these problems, and hence can be used to efficiently model both "chunky" three-dimensional and plate/shell type structures. Thus, only one type of element can be used to model "all" types of structures, and also allows us to use a standard dual algorithm for carrying out the topology optimization of the structure. We also address the issue of manufacturability of the designs.

Am unexpected entry into the silver(I) chemistry of diphosphazane ligands: Crystal and molecular structures of [Ag{Ph2PN(Pr-i)PPh2}(CF3SO3)](2), [Ag{Ph2PN(Pr-i)PPh(OC6H3Me2-2,6)}(2)]PF6, and [Ag-3(mu-Cl)(2){Ph2PN(R)PPh2}(3)]PF6 (R = H, Pr-i)

Mononuclear, binuclear and trinuclear silver(l) complexes were obtained unexpectedly while probing the reactivity of diphosphazane ligands of the type X2PN(Pr-i)PXY towards the ruthenium-based precursor Ru(bipy)(2)Cl-2 center dot 2H(2)O, in the presence of a silver salt as a chloride scavenger. Subsequently, the reactions of AgX [X = Cl, NO3 or CF3SO3] with Ph2PN(R)PPh(Y) [R = H, Y = Ph; R = Pr-i, Y = Ph or OC6H3Me2-2,6] in a 1: 1 or 1:2 molar ratio have been investigated. Mononuclear or binuclear Ag(I) complexes containing either chelating or bridging diphosphazane ligands are obtained. Trinuclear silver(l) complexes are accessible by the treatment of diphosphazane ligands, Ph2PN(R)PPh2 [R = H, Pr-i] with AgCl using piperidine as the solvent. In the presence of a suitable chloride donor species, the mononuclear and binuclear complexes of Ph2PN(Pr-i)PPh2 are transformed slowly to the trinuclear complex [Ag-3(mu-Cl)(2){Ph2PN(Pr-i)PPh2}(3)]X, over a period 20 h. The structures of representative complexes have been confirmed by X-ray crystallography and the salient structural features are discussed

Study of the electronic structures of high Tc cuprate superconductors by electron energy loss and secondary electron emission spectroscopies

Energy loss spectra of superconducting YBa2Cu3O6.9' Bi1.5Pb0.5Ca2.5Sr1.5Cu3O10+δ and Tl2CaBa2Cu3O8 obtained at primary electron energies in the 170–310 eV range show features reflecting the commonalities in their electronic structures. The relative intensity of the plasmon peak shows a marked drop across the transition temperature. Secondary electron emission spectra of the cuprates also reveal some features of the electronic structure.

Novel organic porous solids with channel and layered structures from 1,3,5-triazine-2,4,6-triaminehexaacetic acid and its calcium salt

Single crystals of a symmetrically substituted molecule, 1,3,5-triazine-2,4,6-triaminehexaacetic acid, (TTHA) and its Ca2+ salt have been synthesized, the analysis of which reveals the existence of novel channel type cavities and helical packing organizations in the crystals.

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.

Evidence for two distinct orthorhombic structures associated with different Tc regimes in LnBa2Cu3O7 − δ (Ln = Nd, Eu, Gd and Dy): A study of the dependence of superconductivity on oxygen stoichiometry

Superconductivity in LnBa2Cu3O7 − δ with Ln = Nd, Eu, Gdand Dy has been investigated as a function of δ, closely following the accompanying changes in crystal structure. Orthorhombic GdBa2Cu3O7 − δ and DyBa2Cu3O7 − δ show a Tc of ≈ 90 K up to δ = 0.2 and a lower Tc plateau (40–50 K) in the δ range 02 to 0.4, similar to that found in YBa2Cu3O7 − δ. The orthorhombic structure II in the lower Tc regions is different from the structure I in the 90 K Tc (low δ) region. The unit cell parameters of the orthorhombic I structure in the high Tc region bear the relationship of a a ≠ b not, vert, similar c/3. This relationship is not seen in the low Tc plateau. The low Tc plateau region does not distinctly manifest itself in NdBa2Cu3O7 − δ just as in LaBa2Cu3O7 − δ.