Investigations of Ramachandran disallowed conformations in protein domain families

In peptide and protein structures, occurrence of (phi,psi.) angles in the disallowed region of the Ramachandran map almost always suggests local regions of error or poor accuracy. However, very rarely genuine disallowed conformations occur as noted in the current study in proteins of known structure available at ultra-high resolution (<= 1.2 (A) over circle). In the current work, extent of conservation of genuine disallowed conformations in homologous proteins of known structures has been analyzed. From a dataset of 124 protein domain families, with structure of at least one constituent member in each family available at a resolution of 1.2 (A) over circle or better, we have analyzed the conservation of 221 disallowed conformations. It is observed that the disallowed conformation is only moderately conservedin protein domain families. In the gross dataset no particular residue type adopting disallowed conformation elicit high conservation of residue type though there are alignment positions in the dataset with complete conservation of both the residue type and the disallowed conformation. Conserved disallowed conformation in protein domain families play biologically significant role in roughly 50% of the cases. The residues with the disallowed conformation or its flanking residues are often located within or around the functional site of the protein. (C) 2013 Elsevier B.V. All rights reserved.

Heat transfer in plane Couette flow of a rarefied gas using Bhatnagar-Gross-Krook model

Using the linearized BGK model and the method of moments of half-range distribution functions the temperature jumps at two plates are determined, and it is found that the results are in fair agreement with those of Gross and Ziering, and Ziering.

Turbulence in the two-dimensional Fourier-truncated Gross-Pitaevskii equation

We undertake a systematic, direct numerical simulation of the twodimensional, Fourier-truncated, Gross-Pitaevskii equation to study the turbulent evolutions of its solutions for a variety of initial conditions and a wide range of parameters. We find that the time evolution of this system can be classified into four regimes with qualitatively different statistical properties. Firstly, there are transients that depend on the initial conditions. In the second regime, powerlaw scaling regions, in the energy and the occupation-number spectra, appear and start to develop; the exponents of these power laws and the extents of the scaling regions change with time and depend on the initial condition. In the third regime, the spectra drop rapidly for modes with wave numbers k > kc and partial thermalization takes place for modes with k < kc; the self-truncation wave number kc(t) depends on the initial conditions and it grows either as a power of t or as log t. Finally, in the fourth regime, complete thermalization is achieved and, if we account for finite-size effects carefully, correlation functions and spectra are consistent with their nontrivial Berezinskii-Kosterlitz-Thouless forms. Our work is a natural generalization of recent studies of thermalization in the Euler and other hydrodynamical equations; it combines ideas from fluid dynamics and turbulence, on the one hand, and equilibrium and nonequilibrium statistical mechanics on the other.

Structural and Sequence Characteristics of Long alpha Helices in Globular Proteins

Elucidation of the detailed structural features and sequence requirements for iv helices of various lengths could be very important in understanding secondary structure formation in proteins and, hence. in the protein folding mechanism. An algorithm to characterize the geometry of an alpha helix from its C-alpha coordinates has been developed and used to analyze the structures of long cu helices (number of residues greater than or equal to 25) found in globular proteins, the crystal structure coordinates of which are available from the Brookhaven Protein Data Bank, Ail long a helices can be unambiguously characterized as belonging to one of three classes: linear, curved, or kinked, with a majority being curved. Analysis of the sequences of these helices reveals that the long alpha helices have unique sequence characteristics that distinguish them from the short alpha helices in globular proteins, The distribution and statistical propensities of individual amino acids to occur in long alpha heices are different from those found in short alpha helices, with amino acids having longer side chains and/or having a greater number of functional groups occurring more frequently in these helices, The sequences of the long alpha helices can be correlated with their gross structural features, i.e., whether they are curved, linear, or kinked, and in case of the curved helices, with their curvature.

Coordination properties of vic-isonitrosoimines in their copper (II) and palladium (II) complexes

Preparation and structural characterization of palladium (II) complexes of ligands III-V and copper (II) complexes of III are reported. The elemental analyses of the complexes show that the metal: ligand ratio is 1 : 2. The electrical conductance in acetone shows the non-electrolytic nature of the complexes. The diamagnetic character suggests a gross square-planar geometry for the palladium (II) complexes. Copper (II) complexes are paramagnetic with/~eff.~l'90 B.M. Spectral data suggest that in all the complexes the ligand coordinates to the metal (II) symmetrically through isonitroso-nitrogen and imine-nitrogen, forming a ¡ membered chelate ring. Amine-exchange reactions of the complexes are discussed and compared on the basis of their structures.

Spatial variation of sequestered calcium in the multicellular stage of Dictyostelium discoideum as assayed by chlortetracycline fluorescence

Abstract. We have used chlortetracycline (CTC) as a fluorescent probe to detect the distribution of sequestered calcium in multicellular stages of Dictyostelium discoideum. Tips of late aggregates, slugs and early culminating masses fluoresce very strongly. Most of the fluorescence is intracellular in origin and emanates from a small number of intense punctate sources. The sources correspond in part to autophagic vacuoles viz. neutral-red staining, acidic digestive vesicles, and may also include intracellular organelles; cytoplasmic fluorescence is much weaker in comparison. The level of fluorescence drops in the middle portion of slugs and rises again in the posteriormost region, though not to as high a level as in the tip. This holds good irrespective of whether CTC is applied only in the neighbourhood of the aggregate centre, only in the aggregate periphery, or to the whole aggregate. We infer that there must be a good deal of mixing in the stages leading from aggregation to slug formation; thus the serial order in which cells enter an aggregate does not bear any relation to their ultimate fates. The other implication of our study is that calcium sequestration is much more extensive in prestalk and anterior-like cells than in prespore cells. These findings are discussed with regard to possible implications for pattern formation.

Role of histidine residues in EcoP15I DNA methyltransferase activity as probed by chemical modification and site-directed mutagenesis

Towards understanding the catalytic mechanism of M.EcoP15I [EcoP15I MTase (DNA methyltransferase); an adenine methyltransferase], we investigated the role of histidine residues in catalysis. M.EcoP15I, when incubated with DEPC (diethyl pyrocarbonate), a histidine-specific reagent, shows a time- and concentration-dependent inactivation of methylation of DNA containing its recognition sequence of 5'-CAGCAG-3'. The loss of enzyme activity was accompanied by an increase in absorbance at 240 nm. A difference spectrum of modified versus native enzyme shows the formation of N-carbethoxyhistidine that is diminished by hydroxylamine. This, along with other experiments, strongly suggests that the inactivation of the enzyme by DEPC was specific for histidine residues. Substrate protection experiments show that pre-incubating the methylase with DNA was able to protect the enzyme from DEPC inactivation. Site-directed mutagenesis experiments in which the 15 histidine residues in the enzyme were replaced individually with alanine corroborated the chemical modification studies and established the importance of His-335 in the methylase activity. No gross structural differences were detected between the native and H335A mutant MTases, as evident from CD spectra, native PAGE pattern or on gel filtration chromatography. Replacement of histidine with alanine residue at position 335 results in a mutant enzyme that is catalytically inactive and binds to DNA more tightly than the wild-type enzyme. Thus we have shown in the present study, through a combination of chemical modification and site-directed mutagenesis experiments, that His-335 plays an essential role in DNA methylation catalysed by M.EcoP15I.

Evolution of domain combinations in protein kinases and its implications for functional diversity

Protein kinases phosphorylating Ser/Thr/Tyr residues in several cellular proteins exert tight control over their biological functions. They constitute the largest protein family in most eukaryotic species. Protein kinases classified based on sequence similarity in their catalytic domains, cluster into subfamilies, which share gross functional properties. Many protein kinases are associated or tethered covalently to domains that serve as adapter or regulatory modules,naiding substrate recruitment, specificity, and also serve as scaffolds. Hence the modular organisation of the protein kinases serves as guidelines to their functional and molecular properties. Analysis of genomic repertoires of protein kinases in eukaryotes have revealed wide spectrum of domain organisation across various subfamilies of kinases. Occurrence of organism-specific novel domain combinations suggests functional diversity achieved by protein kinases in order to regulate variety of biological processes. In addition, domain architecture of protein kinases revealed existence of hybrid protein kinase subfamilies and their emerging roles in the signaling of eukaryotic organisms. In this review we discuss the repertoire of non-kinase domains tethered to multi-domain kinases in the metazoans. Similarities and differences in the domain architectures of protein kinases in these organisms indicate conserved and unique features that are critical to functional specialization. (C) 2009 Elsevier Ltd. All rights reserved.

Studies in sesquiterpenes—XXIX *1: Structure of himachalenes

α-and β-Himachalenes, the two major sesquiterpene components of the essential oil of Himalayan deodar (Cedrus deodara, Loud.) are shown to represent a new sequiterpenoid carbon framework. Evidence is presented which establishes their gross structures.

Reproductive behavior and health in consanguineous marriages

In many regions of Asia and Africa, consanguineous marriages currently account for approximately 20 to 50% of all unions, and preliminary observations indicate that migrants from these areas continue to contract marriages with close relatives when resident in North America and Western Europe. Consanguinity is associated with increased gross fertility, due at least in part to younger maternal age at first livebirth. Morbidity and mortality also may be elevated, resulting in comparable numbers of surviving offspring in consanguineous and nonconsanguineous families. With advances in medicine and public health, genetic disorders will account for an increased proportion of disease worldwide. Predictably, this burden will fall more heavily on countries and communities in which consanguinity is strongly favored, as the result of the expression of deleterious recessive genes. However, studies conducted in such populations indicate that the adverse effects associated with inbreeding are experienced by a minority of families.

A finite element analysis of dynamic fracture initiation by ductile failure mechanisms in a 4340 steel

In some recent dropweight impact experiments [5] with pre-notched bend specimens of 4340 steel, it was observed that considerable crack tunneling occurred in the interior of the specimen prior to gross fracture initiation on the free surfaces. The final failure of the side ligaments happened because of shear lip formation. The tunneled region is characterized by a flat, fibrous fracture surface. In this paper, the experiments of [5] (corresponding to 5 m/s impact speed) are analyzed using a plane strain, dynamic finite element procedure. The Gurson constitutive model that accounts for the ductile failure mechanisms of micro-void nucleation, growth and coalescence is employed. The time at which incipient failure was observed near the notch tip in this computation, and the value of the dynamic J-integral, J d, at this time, compare reasonably well with experiments. This investigation shows that J-controlled stress and deformation fields are established near the notch tip whenever J d , increases with time. Also, it is found that the evolution of micro-mechanical quantities near the notch root can be correlated with the time variation of J d .The strain rate and the adiabatic temperature rise experienced at the notch root are examined. Finally, spatial variations of stresses and deformations are analyzed in detail.

Nature's Swiss Army Knives: Ovipositor Structure Mirrors Ecology in a Multitrophic Fig Wasp Community

Background: Resource partitioning is facilitated by adaptations along niche dimensions that range from morphology to behaviour. The exploitation of hidden resources may require specially adapted morphological or sensory tools for resource location and utilisation. Differences in tool diversity and complexity can determine not only how many species can utilize these hidden resources but also how they do so. Methodology and Principal Findings: The sclerotisation, gross morphology and ultrastructure of the ovipositors of a seven-member community of parasitic wasps comprising of gallers and parasitoids developing within the globular syconia (closed inflorescences) of Ficus racemosa (Moraceae) was investigated. These wasps also differ in their parasitism mode (external versus internal oviposition) and their timing of oviposition into the expanding syconium during its development. The number and diversity of sensilla, as well as ovipositor teeth, increased from internally ovipositing to externally ovipositing species and from gallers to parasitoids. The extent of sclerotisation of the ovipositor tip matched the force required to penetrate the syconium at the time of oviposition of each species. The internally ovipositing pollinator had only one type of sensillum and a single notch on the ovipositor tip. Externally ovipositing species had multiple sensilla types and teeth on their ovipositors. Chemosensilla were most concentrated at ovipositor tips while mechanoreceptors were more widely distributed, facilitating the precise location of hidden hosts in these wasps which lack larval host-seeking behaviour. Ovipositor traits of one parasitoid differed from those of its syntopic galler congeners and clustered with those of parasitoids within a different wasp subfamily. Thus ovipositor tools can show lability based on adaptive necessity, and are not constrained by phylogeny. Conclusions/Significance: Ovipositor structure mirrored the increasingly complex trophic ecology and requirements for host accessibility in this parasite community. Ovipositor structure could be a useful surrogate for predicting the biology of parasites in other communities.

Costs and benefits of the presence of leopards to the sport-hunting industry and local communities in Niassa national reserve, mozambique

Sport hunting is often proposed as a tool to support the conservation of large carnivores. However, it is challenging to provide tangible economic benefits from this activity as an incentive for local people to conserve carnivores. We assessed economic gains from sport hunting and poaching of leopards (Panthera pardus), costs of leopard depredation of livestock, and attitudes of people toward leopards in Niassa National Reserve, Mozambique. We sent questionnaires to hunting concessionaires (n = 8) to investigate the economic value of and the relative importance of leopards relative to other key trophy-hunted species. We asked villagers (n = 158) the number of and prices for leopards poached in the reserve and the number of goats depredated by leopard. Leopards were the mainstay of the hunting industry; a single animal was worth approximately U.S.$24,000. Most safari revenues are retained at national and international levels, but poached leopard are illegally traded locally for small amounts ($83). Leopards depredated 11 goats over 2 years in 2 of 4 surveyed villages resulting in losses of $440 to 6 households. People in these households had negative attitudes toward leopards. Although leopard sport hunting generates larger gross revenues than poaching, illegal hunting provides higher economic benefits for households involved in the activity. Sport-hunting revenues did not compensate for the economic losses of livestock at the household level. On the basis of our results, we propose that poaching be reduced by increasing the costs of apprehension and that the economic benefits from leopard sport hunting be used to improve community livelihoods and provide incentives not to poach.

Finite-temperature dynamics of vortices in Bose-Einstein condensates

We study the dynamics of a single vortex and a pair of vortices in quasi two-dimensional Bose-Einstein condensates at finite temperatures. To this end, we use the stochastic Gross-Pitaevskii equation, which is the Langevin equation for the Bose-Einstein condensate. For a pair of vortices, we study the dynamics of both the vortex-vortex and vortex-antivortex pairs, which are generated by rotating the trap and moving the Gaussian obstacle potential, respectively. Due to thermal fluctuations, the constituent vortices are not symmetrically generated with respect to each other at finite temperatures. This initial asymmetry coupled with the presence of random thermal fluctuations in the system can lead to different decay rates for the component vortices of the pair, especially in the case of two corotating vortices.