Protein structure refinement algorithms

Protein structure prediction has remained a major challenge in structural biology for more than half a century. Accelerated and cost efficient sequencing technologies have allowed researchers to sequence new organisms and discover new protein sequences. Novel protein structure prediction technologies will allow researchers to study the structure of proteins and to determine their roles in the underlying biology processes and develop novel therapeutics.

Difficulty of the problem stems from two folds: (a) describing the energy landscape that corresponds to the protein structure, commonly referred to as force field problem; and (b) sampling of the energy landscape, trying to find the lowest energy configuration that is hypothesized to be the native state of the structure in solution. The two problems are interweaved and they have to be solved simultaneously. This thesis is composed of three major contributions. In the first chapter we describe a novel high-resolution protein structure refinement algorithm called GRID. In the second chapter we present REMCGRID, an algorithm for generation of low energy decoy sets. In the third chapter, we present a machine learning approach to ranking decoys by incorporating coarse-grain features of protein structures.

Russian wheat aphids (Diuraphis noxia) in China : native range expansion or recent introduction?

In this study, we explore the population genetics of the Russian wheat aphid (RWA) (Diuraphis noxia), one of the world’s most invasive agricultural pests, in north-western China. We have analysed the data of 10 microsatellite loci and mitochondrial sequences from 27 populations sampled over 2 years in China. The results confirm that the RWAs are holocyclic in China with high genetic diversity indicating widespread sexual reproduction. Distinct differences in microsatellite genetic diversity and distribution revealed clear geographic isolation between RWA populations in northern and southern Xinjiang, China, with gene flow interrupted across extensive desert regions. Despite frequent grain transportation from north to south in this region, little evidence for RWA translocation as a result of human agricultural activities was found. Consequently, frequent gene flow among northern populations most likely resulted from natural dispersal, potentially facilitated by wind currents. We also found evidence for the longterm existence and expansion of RWAs in China, despite local opinion that it is an exotic species only present in China since 1975. Our estimated date of RWA expansion throughout China coincides with the debut of wheat domestication and cultivation practices in western Asia in the Holocene. We conclude that western China represents the limit of the far eastern native range of this species. This study is the most comprehensive molecular genetic investigation of the RWA in its native range undertaken to date and provides valuable insights into the history of the association of this aphid with domesticated cereals and wild grasses.

High-resolution refinement of orthorhombic bovine pancreatic phospholipase A2

The X-ray structure of recombinant bovine pancreatic phospholipase A(2) (PLA2), which specifically catalyzes the cleavage of the sn-2 acylester bond of phospholipids, has been refined at 1.5 Angstrom resolution. The crystal belongs to the space group P2(1)2(1)2(1) with unit-cell parameters a = 47.12, b = 64.59 and c = 38.14 Angstrom similar to the native enzyme reported previously by Dijkstra et nl. [J. Mel. Biol. (1981), 147, 97-123]. The refinement converged to an R value of 18.4% (R-free = 22.8%) for 16 374 reflections between 10.0 and 1.5 Angstrom resolution. The surface-loop residues (60-70) art: ordered in the present orthorhombic recombinant enzyme, but disordered in the trigonal recombinant enzyme. The active-site residues, His48, Asp99, and the catalytic water superimpose well with the trigonal form. Besides the catalytic water which is hydrogen bonded to His48, it is often seen that there is a second water attached to the same N atom of His48 and simultaneously hydrogen bonded to the O atom of Asp49. It is thought that the second water facilitates the tautomerism of His48 for enzyme catalysis, The catalytic water is also hydrogen bonded to the equatorial water coordinated to the calcium ion, In addition to the equatorial water, there is also an axial calcium water and the additional structural water. These five common water molecules are hydrogen bonded to the additional 16 water molecules in the present orthorhombic structure which may further enhance the structural integrity of the active site. Besides the protein and one calcium ion, a total of 134 water molecules were located in the present high-resolution refinement.

Fate of potassium fertilisers applied to clay soils under rainfed grain cropping in south-east Queensland, Australia

Negative potassium (K) balances in all broadacre grain cropping systems in northern Australia are resulting in a decline in the plant-available reserves of K and necessitating a closer examination of strategies to detect and respond to developing K deficiency in clay soils. Grain growers on the Red Ferrosol soils have increasingly encountered K deficiency over the last 10 years due to lower available K reserves in these soils in their native condition. However, the problem is now increasingly evident on the medium-heavy clay soils (Black and Grey Vertosols) and is made more complicated by the widespread adoption of direct drill cropping systems and the resulting strong strati. cation of available K reserves in the top 0.05-0.1 m of the soil pro. le. This paper reports glasshouse studies examining the fate of applied K fertiliser in key cropping soils of the inland Burnett region of south-east Queensland, and uses the resultant understanding of K dynamics to interpret results of field trials assessing the effectiveness of K application strategies in terms of K availability to crop plants. At similar concentrations of exchangeable K (K-exch), soil solution K concentrations and activity of K in the soil solution (AR(K)) varied by 6-7-fold between soil types. When K-exch arising from different rates of fertiliser application was expressed as a percentage of the effective cation exchange capacity (i.e. K saturation), there was evidence of greater selective adsorption of K on the exchange complex of Red Ferrosols than Black and Grey Vertosols or Brown Dermosols. Both soil solution K and AR(K) were much less responsive to increasing K-exch in the Black Vertosols; this is indicative of these soils having a high K buffer capacity (KBC). These contrasting properties have implications for the rate of diffusive supply of K to plant roots and the likely impact of K application strategies (banding v. broadcast and incorporation) on plant K uptake. Field studies investigating K application strategies (banding v. broadcasting) and the interaction with the degree of soil disturbance/mixing of different soil types are discussed in relation to K dynamics derived from glasshouse studies. Greater propensity to accumulate luxury K in crop biomass was observed in a Brown Ferrosol with a KBC lower than that of a Black Vertosol, consistent with more efficient diffusive supply to plant roots in the Ferrosol. This luxury K uptake, when combined with crops exhibiting low proportional removal of K in the harvested product (i.e. low K harvest index coarse grains and winter cereals) and residue retention, can lead to rapid re-development of stratified K profiles. There was clear evidence that some incorporation of K fertiliser into soil was required to facilitate root access and crop uptake, although there was no evidence of a need to incorporate K fertiliser any deeper than achieved by conventional disc tillage (i.e. 0.1-0.15 m). Recovery of fertiliser K applied in deep (0.25-0.3 m) bands in combination with N and P to facilitate root proliferation was quite poor in Red Ferrosols and Grey or Black Vertosols with moderate effective cation exchange capacity (ECEC, 25-35 cmol(+)/kg), was reasonable but not enough to overcome K deficiency in a Brown Dermosol (ECEC 11 cmol(+)/kg), but was quite good on a Black Vertosol (ECEC 50-60 cmol(+)/kg). Collectively, results suggest that frequent small applications of K fertiliser, preferably with some soil mixing, is an effective fertiliser application strategy on lighter clay soils with low KBC and an effective diffusive supply mechanism. Alternately, concentrated K bands and enhanced root proliferation around them may be a more effective strategy in Vertosol soils with high KBC and limited diffusive supply. Further studies to assess this hypothesis are needed.

Approaching theoretical strengths by synergistic internal and external size refinement

Refinement of the internal grain size leads to strengthening by retarding dislocation motion. There have also been recent reports that a reduction in external diameter enhances the strength of single crystal pillars. Here we show, in a hitherto unexplored domain, a synergistic increase in strength by a combined reduction in internal (0.5 mu m) and external (20-50 mu m) dimensions, with strengths at failure approaching the theoretical value. (c) 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Structural refinement, optical and electrical properties of Ba1-x Sm-2x/3](Zr0.05Ti0.95)O-3 ceramics

Samarium doped barium zirconate titanate ceramics with general formula Ba1-x Sm-2x/3](Zr0.05Ti0.95)O-3 x = 0, 0.01, 0.02, and 0.03] were prepared by high energy ball milling method. X-ray diffraction patterns and micro-Raman spectroscopy confirmed that these ceramics have a single phase with a tetragonal structure. Rietveld refinement data were employed to model BaO12], SmO12], ZrO6], and TiO6] clusters in the lattice. Scanning electron microscopy shows a reduction in average grain size with the increase of Sm3+ ions into lattice. Temperature-dependent dielectric studies indicate a ferroelectric phase transition and the transition temperature decreases with an increase in Sm3+ ion content. The nature of the transition was investigated by the Curie-Weiss law and it is observed that the diffusivity increases with Sm3+ ion content. The ferroelectric hysteresis loop illustrates that the remnant polarization and coercive field increase with an increase in Sm3+ ions content. Optical properties of the ceramics were studied using ultraviolet-visible diffuse reflectance spectroscopy.

Investigation of native defects and property of bulk ZnO single crystal grown by a closed chemical vapor transport method

Hall effect, Raman scattering, photoluminescence spectroscopy (PL), optical absorption (OA), mass spectroscopy, and X-ray diffraction have been used to study bulk ZnO single crystal grown by a closed chemical vapor transport method. The results indicate that shallow donor impurities (Ga and Al) are the dominant native defects responsible for n-type conduction of the ZnO single crystal. PL and OA results suggest that the as-grown and annealed ZnO samples with poor lattice perfection exhibit strong deep level green photoluminescence and weak ultraviolet luminescence. The deep level defect in as-grown ZnO is identified to be oxygen vacancy. After high-temperature annealing, the deep level photoluminescence is suppressed in ZnO crystal with good lattice perfection. In contrast, the photoluminescence is nearly unchanged or even enhanced in ZnO crystal with grain boundary or mosaic structure. This result indicates that a trapping effect of the defect exists at the grain boundary in ZnO single crystal. (C) 2007 Elsevier B.V. All rights reserved.

Refining near-native protein-protein docking decoys by local resampling and energy minimization

How to refine a near-native structure to make it closer to its native conformation is an unsolved problem in protein-structure and protein-protein complex-structure prediction. In this article, we first test several scoring functions for selecting locally resampled near-native protein-protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance-scaled Ideal-gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein-InteRaction Energy) for optimization and re-ranking. Significant improvement of final top-1 ranked structures over initial near-native structures is observed in the ZDOCK 2.3 decoy set for Benchmark 1.0 (74% whose global rmsd reduced by 0.5 angstrom or more and only 7% increased by 0.5 angstrom or more). Less significant improvement is observed for Benchmark 2.0 (38% versus 33%). Possible reasons are discussed.

Rietveld refinement, microstructure, conductivity and impedance properties of Ba[Zr0.25Ti0.75]O-3 ceramic

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Structural refinement, optical and electrical properties of [Ba1-x Sm-2x/3](Zr0.05Ti0.95)O-3 ceramics

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Reducing competition in agroforestry by pruning native trees.

The degree to which pruning helps reestablish balance in agroforestry was assessed in a system established in São Carlos, São Paulo, Brazil, in 2008. Seven native tree species were planted at a density of 600 trees/ha in five strips of three rows each, and annual crops were cultivated in the 17-m crop strips between the tree strips. Competition was established after 35 months, decreasing the aboveground biomass production of corn planted close to the trees. An assessment of black oats in the dry season following tree pruning showed that the proximity of trees caused reductions in plant and panicle density, aboveground biomass production, number of grains per panicle and grain weight. Because pruning was not sufficient to maintain crop yields, tree thinning is recommended in order to minimize competition and restore conditions for adequate crop production.