Quaternary association in beta-prism I fold plant lectins: Insights from X-ray crystallography, modelling and molecular dynamics

Dimeric banana lectin and calsepa, tetrameric artocarpin and octameric heltuba are mannose-specific beta-prism I fold lectins of nearly the same tertiary structure. MD simulations on individual subunits and the oligomers provide insights into the changes in the structure brought about in the protomers on oligomerization, including swapping of the N-terminal stretch in one instance. The regions that undergo changes also tend to exhibit dynamic flexibility during MD simulations. The internal symmetries of individual oligomers are substantially retained during the calculations. Energy minimization and simulations were also carried out on models using all possible oligomers by employing the four different protomers. The unique dimerization pattern observed in calsepa could be traced to unique substitutions in a peptide stretch involved in dimerization. The impossibility of a specific mode of oligomerization involving a particular protomer is often expressed in terms of unacceptable steric contacts or dissociation of the oligomer during simulations. The calculations also led to a rationale for the observation of a heltuba tetramer in solution although the lectin exists as an octamer in the crystal, in addition to providing insights into relations among evolution, oligomerization and ligand binding.

Temperature-pressure-induced solid-solid < 100 > to < 110 > reorientation in FCC metallic nanowire: a molecular dynamic study

Atomistic simulation of initial < 100 > oriented FCC Cu nanowires shows a novel coupled temperature-pressure dependent reorientation from < 100 > to < 110 > phase. A temperature-pressure-induced solid-solid < 100 > to < 110 > reorientation diagram is generated for Cu nanowire with varying cross-sectional sizes. A critical pressure is reported for Cu nanowires with varying cross-sectional sizes, above which an initial < 100 > oriented nanowire shows temperature independent reorientation into the < 110 > phase. The effect of surface stresses on the < 100 > to < 110 > reorientation is also studied. The results indicate that above a critical cross-sectional size for a given temperature-pressure, < 100 > to < 110 > reorientation is not possible. It is also reported here that for a given applied pressure, an increase in temperature is required for the < 100 > to < 110 > reorientation with increasing cross-sectional size of the nanowire. The temperature-pressure-induced solid-solid < 100 > to < 110 > reorientation diagram reported in the present paper could further be used as guidelines for controlling the reorientations/shape memory in nano-scale applications of FCC metallic nanowires.

A new pentameric structure of rotavirus NSP4 revealed by molecular replacement

The region spanning residues 95-146 of the rotavirus nonstructural protein NSP4 from the asymptomatic human strain ST3 has been purified and crystallized and diffraction data have been collected to a resolution of 2.6 angstrom. Several attempts to solve the structure by the molecular-replacement method using the available tetrameric structures of this domain were unsuccessful despite a sequence identity of 73% to the already known structures. A more systematic approach with a dimer as the search model led to an unexpected pentameric structure using the program Phaser. The various steps involved in arriving at this molecular-replacement solution, which unravelled a case of subtle variation between different oligomeric states unknown at the time of solving the structure, are presented in this paper.

Molecular Dynamics of Thermotropic Liquid Crystals: Anomalous relaxation dynamics of calamitic and discotic liquid crystals

Recent optical kerr effect (OKE) studies have demonstrated that orientational relaxation of rod-like nematogens exhibits temporal power law decay at intermediate times not only near the isotropic–nematic (I–N) phase boundary but also in the nematic phase. Such behaviour has drawn an intriguing analogy with supercooled liquids. We have investigated both collective and single-particle orientational dynamics of a family of model system of thermotropic liquid crystals using extensive computer simulations. Several remarkable features of glassy dynamics are on display including non-exponential relaxation, dynamical heterogeneity, and non-Arrhenius temperature dependence of the orientational relaxation time. Over a temperature range near the I–N phase boundary, the system behaves remarkably like a fragile glass-forming liquid. Using proper scaling, we construct the usual relaxation time versus inverse temperature plot and explicitly demonstrate that one can successfully define a density dependent fragility of liquid crystals. The fragility of liquid crystals shows a temperature and density dependence which is remarkably similar to the fragility of glass forming supercooled liquids. Energy landscape analysis of inherent structures shows that the breakdown of the Arrhenius temperature dependence of relaxation rate occurs at a temperature that marks the onset of the growth of the depth of the potential energy minima explored by the system. A model liquid crystal, consisting of disk-like molecules, has also been investigated in molecular dynamics simulations for orientational relaxation along two isobars starting from the high temperature isotropic phase. The isobars have been so chosen that the phase sequence isotropic (I)–nematic (N)–columnar (C) appears upon cooling along one of them and the sequence isotropic (I)–columnar(C) along the other. While the orientational relaxation in the isotropic phase near the I–N phase transition shows a power law decay at short to intermediate times, such power law relaxation is not observed in the isotropic phase near the I–C phase boundary. The origin of the power law decay in the single-particle second-rank orientational time correlation function (OTCF) is traced to the growth of the orientational pair distribution functions near the I–N phase boundary. As the system settles into the nematic phase, the decay of the single-particle second-rank orientational OTCF follows a pattern that is similar to what is observed with calamitic liquid crystals and supercooled molecular liquids.

Molecular Identification and Phylogeny of Bactrocera Species (Diptera: Tephritidae)

Fruit flies that belong to the genus Bactrocera (Diptera: Tephritidae) are major invasive pests of agricultural crops in Asia and Australia. Increased transboundary movement of agricultural produce has resulted in the chance introduction of many invasive species that include Bactrocera mainly as immature stages. Therefore quick and accurate species diagnosis is important at the port of entry, where morphological identification has a limited role, as it requires the presence of adult specimens and the availability of a specialist. Unfortunately when only immature stages are present, a lacunae in their taxonomy impedes accurate species diagnosis. At this juncture, molecular species diagnostics based on COX-I have become handy, because diagnosis is not limited by developmental stages. Yet another method of quick and accurate species diagnosis for Bactrocera spp. is based on the development of species-specific markers. This study evaluated the utility of COX-I for the quick and accurate species diagnosis of eggs, larvae, pupae and adults of B. zonata Saunders, B. tau Walker, and B. dorsalis Hendel. Furthermore the utility of species-specific markers in differentiating B. zonata (500bp) and B. tau (220bp) was shown. Phylogenetic relationships among five subgenera, viz., Austrodacus, Bactrocera, Daculus, Notodacus and Zeugodacus have been resolved employing the 5' region of COX-I (1490-2198); where COX-I sequences for B. dorsalis Hendel, B. tau Walker, B. correcta Bezzi and B. zonata Saunders from India were compared with other NCBI-GenBank accessions. Phylogenetic analysis employing Maximum Parsimony (MP) and Bayesian phylogenetic approach (BP) showed that the subgenus Bactrocera is monophyletic.

Testing concordance in species boundaries using acoustic, morphological, and molecular data in the field cricket genus Itaropsis (Orthoptera: Grylloidea, Gryllidae: Gryllinae)

In most taxa, species boundaries are inferred based on differences in morphology or DNA sequences revealed by taxonomic or phylogenetic analyses. In crickets, acoustic mating signals or calling songs have species-specific structures and provide a third data set to infer species boundaries. We examined the concordance in species boundaries obtained using acoustic, morphological, and molecular data sets in the field cricket genus Itaropsis. This genus is currently described by only one valid species, Itaropsis tenella, with a broad distribution in western peninsular India and Sri Lanka. Calling songs of males sampled from four sites in peninsular India exhibited significant differences in a number of call features, suggesting the existence of multiple species. Cluster analysis of the acoustic data, molecular phylogenetic analyses, and phylogenetic analyses combining all data sets suggested the existence of three clades. Whatever the differences in calling signals, no full congruence was obtained between all the data sets, even though the resultant lineages were largely concordant with the acoustic clusters. The genus Itaropsis could thus be represented by three morphologically cryptic incipient species in peninsular India; their distributions are congruent with usual patterns of endemism in the Western Ghats, India. Song evolution is analysed through the divergence in syllable period, syllable and call duration, and dominant frequency.

Pillar height dependent formation of unprecedented Pd-8 molecular swing and Pd-6 molecular boat via multicomponent self-assembly

Three-component self-assembly of a cis-blocked 90 degrees Pd(II) acceptor with a mixture of a tetraimidazole and a linear dipyridyl donor self-discriminated into unusual Pd-8 molecular swing (1) and Pd-6 molecular boat (2), which are characterized by single-crystal X-ray diffraction analysis; their ability to bind C-60 in solution is established by fluorescence titration.

Self assembly of bivalent glycolipids on single walled carbon nanotubes and their specific molecular recognition properties

Solubilization of single walled carbon nanotubes (SWNTs) in aqueous milieu by self assembly of bivalent glycolipids is described. Thorough analysis of the resulting composites involving Vis/near-IR spectroscopy, surface plasmon resonance, confocal Raman and atomic force microscopy reveals that glycolipid-coated SWNTs possess specific molecular recognition properties towards lectins.

Insights into the Substrate Specificity of a Thioesterase Rv0098 of Mycobacterium Tuberculosis through X-ray Crystallographic and Molecular Dynamics Studies

The crystal structure of Rv0098, a long-chain fatty acyl-CoA thioesterase from Mycobacterium tuberculosis with bound dodecanoic acid at the active site provided insights into the mode of substrate binding but did not reveal the structural basis of substrate specificities of varying chain length. Molecular dynamics studies demonstrated that certain residues of the substrate binding tunnel are flexible and thus modulate the length of the tunnel. The flexibility of the loop at the base of the tunnel was also found to be important for determining the length of the tunnel for accommodating appropriate substrates. A combination of crystallographic and molecular dynamics studies thus explained the structural basis of accommodating long chain substrates by Rv0098 of M. tuberculosis.

Removal of Nitrogen Oxides in Diesel Engine Exhaust by Plasma Assisted Molecular Sieves

This paper reports the studies conducted on removal of oxides of nitrogen (NOx) from diesel engine exhaust using electrical discharge plasma combined with adsorbing materials such as molecular sieves. This study is being reported for the first time. The exhaust is taken from a diesel engine of 6 kW under no load conditions. The characteristic behavior of a pulse energized dielectric barrier discharge reactor in the diesel exhaust treatment is reported. The NOx removal was not significant (36%) when the reactor without any packing was used. However, when the reactor was packed with molecular sieves (MS -3A, -4A & -13X), the NOx removal efficiency was increased to 78% particularly at a temperature of 200 °C. The studies were conducted at different temperatures and the results were discussed.

Molecular charge-transfer interaction with single-layer graphene

While the effect of electrochemical doping on single-layer graphene (SG) with holes and electrons has been investigated, the effect of charge-transfer doping on SG has not been examined hitherto. Effects of varying the concentration of electron donor and acceptor molecules such as tetrathiafulvalene (TTF) and tetracyanoethylene (TCNE) on SG produced by mechanical exfoliation as well as by the reduction of single-layer graphene oxide have been investigated. TTF softens the G-band in the Raman spectrum, whereas TCNE stiffens the G-band. The full-width-at-half-maximum of the G-band increases on interaction with both TTF and TCNE. These effects are similar to those found with few-layer graphene, but in contrast to those found with electrochemical doping. A common feature between the two types of doping is found in the case of the 2-D band, which shows softening and stiffening on electron and hole doping, respectively. The experimental results are explained on the basis of the frequency shifts, electron-phonon coupling and structural inhomogeneities that are relevant to molecule-graphene interaction.

Intra-molecular hydrogen bonding with organic fluorine in the solution state: Deriving evidence by a two dimensional NMR experiment

The direct evidence for the existence of intra-molecular C-F center dot center dot center dot H-N hydrogen bond in organofluorine molecules, in the liquid state, is derived using NMR spectroscopy by the detection of long range interactions among fluorine, nitrogen and hydrogen atoms. The present study reports the determination of the relative signs and magnitudes of through space and through bond couplings to draw unambiguous evidence on the existence of weak molecular interactions involving organic fluorine. It is a simple, easy to implement, N-15 natural abundant two dimensional heteronuclear N-15-H-1 double quantum-single quantum correlation experiment. The existence of intra-molecular hydrogen bond is conclusively established in the investigated molecules. (C) 2011 Elsevier B.V. All rights reserved.

Self-Assembly of Manganese(I)-Based Molecular Squares: Synthesis and Spectroscopic and Structural Characterization

Syntheses of manganese(I)-based molecular squares have been accomplished in facile one-pot reaction conditions at room temperature. Self-assembly of eight components has resulted in the formation of M4L4-type metallacyclophanes [Mn(CO)(3)Br(mu-L)(4) (1-3) using pentacarbonylbromomanganese as metal precursor and rigid azine ligands such as pyrazine, 4,4'-bipyridine, and trans-1,2-bis(4pyridyl)ethylene, respectively, as bridging ligands. The metallacyclophanes have been characterized on the basis of IR, NMR, and UV-vis spectroscopic techniques and single-crystal X-ray diffraction methods.