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.

The contribution of trace elements from seawater to chimneys: a case study of the native sulfur chimneys in the sea area off Kueishantao, northeast of Taiwan Island

Hydrothermal fluid containing abundant matter erupts from seafloor, meets ambient cold seawater and forms chimneys. So the main matter origins of chimneys are seawater and matter which are taken by hydrothermal fluid from deep reservoir. However, because of seawater's little contribution to the forming of chimneys, it is usually covered by the abundant matter which is taken by hydrothermal fluid. Therefore, chimneys formed in ordinary deep seawater hydrothermal activity, containing complex elements, cannot be used to study the seawater's contribution to their formation. While the native sulfur chimneys, formed by hydrothermal activity near the sea area off Kueishantao, are single sulfur composition (over 99%), and within chimneys distinct layers are seen. Different layers were sampled for trace element determination, with Inductively Coupled Plasma Mass Spectrometry (ICP-MS). By analyzing the data, we consider C-layer (secondary inner-layer) as the framework layer of the chimney which formed early (Fig. 4), and its trace elements derive from hydrothermal fluid. While the trace elements within A, B, D layers have undergone later alteration. A, B layers are affected by seawater and D layer by hydrothermal fluid. The increase of trace elements of A and B layers was calculated using C layer as background. Based on the known typical volume of chimneys of the near sea area off Kueishantao, we calculated the volume of seawater that contributed trace element to chimneys formation to be about 6.37 x 10(4) L. This simple quantified estimate may help us better understand the seafloor hydrothermal activity and chimneys.

Simultaneous determination of four phases of copper in geological samples

According to the specific property of respective phases in copper ore, optimal extracting condition for, tour phases of copper with five infusion was examined. After a series of experiments, for example, different weight Of sample, artificial mixed single phases sample and repeated experiment, the extracting ratio constants foil all phases in different infusions were obtained. The mathematical model which is on the basis of the stable extracting constant is established. Based on the purpose-control genetic algorithms, we only need to determine the total copper in the sample in different infusions under the selected condition, then the value of respective phase could be calculated. The-relative standard deviation are (%) free oxidized copper phase:1.5, conjunction oxidized copper phase: 17.6,, secondary copper sulfide phase: 1.9, primary copper sulfide phase : 2.7,total copper: 0.8.

Origin of a native sulfur chimney in the Kueishantao hydrothermal field, offshore northeast Taiwan

Analyses of rare earth and trace element concentrations of native sulfur samples from the Kueishantao hydrothermal field were performed at the Seafloor Hydrothermal Activity Laboratory of the Key Laboratory of Marine Geology and Environment, Institute of Oceanology, Chinese Academy of Sciences. Using an Elan DRC II ICP-MS, and combining the sulfur isotopic compositions of native sulfur samples, we studied the sources and formation of a native sulfur chimney. The results show, when comparing them with native sulfur from crater lakes and other volcanic areas, that the native sulfur content of this chimney is very high (99.96%), the rare earth element (REE) and trace element constituents of the chimney are very low (Sigma REE < 21x10(-9)), and the chondrite-normalized REE patterns of the native sulfur samples are similar to those of the Kueishantao andesite, implying that the interaction of subseafloor fluid-andesite at the Kueishantao hydrothermal field was of short duration. The sulfur isotopic compositions of the native sulfur samples reveal that the sulfur of the chimney, from H2S and SO2, originated by magmatic degassing and that the REEs and trace elements are mostly from the Kueishantao andesite and partly from seawater. Combining these results with an analysis of the thermodynamics, it is clear that from the relatively low temperature (< 116 degrees C), the oxygenated and acidic environment is favorable for formation of this native sulfur chimney in the Kueishantao hydrothermal field.

Distribution and mobility of metals in agricultural soils near a copper smelter in South China

The distribution and mobility of heavy metals in the paddy soils surrounding a copper smelting plant in south China was investigated. We assessed the degree of metal contamination using an index of geoaccumulation. The metals were divided into two groups: (1) Cu, Zn, Pb and Cd, whose concentrations were heavily affected by anthropogenic inputs, and (2) Ni, Co and Cr, which were mainly of geochemical origin. Concentrations of Cu, Cd, Zn, and Pb in the polluted soils were higher than the Chinese soil quality criteria. The chemical partitioning patterns of Pb, Zn and Cu indicated that Pb was largely associated with the residual and NH2OH HCl extractable fractions. In contrast, Cd was predominantly associated with the MgCl2 extractable fraction. A large proportion of Cu was bound to the acidic H2O2 extractable fractions, while Zn was predominantly found in the residual phase. The fraction of mobile species, which potentially is the most harmful to the environment, was found to be elevated compared to unpolluted soils in which heavy metals are more strongly bound to the matrix. The mobility of the metals was studied by water extraction using a modification of Tessier's procedure, and the order of mobility was Zn > Cd > Cu > Ce > Pb.

Cloning, characterization, and expression analysis of extracellular copper/zinc superoxide dismutase gene from bay scallop Argopecten irradians

Extracellular superoxide dismutase (ECSOD) is a major extracellular antioxidant enzyme that protects organs from damage by reactive oxygen species (ROS). We cloned a novel ECSOD from the bay scallop Argopecten irradians (AiECSOD) by 3' and 5' RACE. The full-length cDNA of AiECSOD was 893 bp with a 657 bp open reading frame encoding 218 amino acids. The deduced amino acid sequence contained a putative signal peptide of 20 amino acids, and sequence comparison showed that AiECSOD had low degree of homology to ECSODs of other organisms. The genomic length of the AiECSOD gene was about 5276 bp containing five exons and six introns. The promoter region contained many putative transcription factor binding sites such as c-Myb, Oct-1, Sp1, Kruppel-like, c-ETS, NF kappa B, GATA-1, AP-1, and Ubx binding sites. Furthermore, tissue-specific expressions of AiECSOD and temporal expressions of AiECSOD in haemocytes of bay scallops challenged with bacteria Vibrio anguillarum were quantified using qRT-PCR. High levels of expression were detected in haemocytes, but not in gonad and mantle. The expression of AiECSOD reached the highest level at 12 h post-injection with V. anguillarum and then returned to normal between 24 h and 48 h post-injection. These results indicated that AiECSOD was an inducible protein and that it may play an important role in the immune responses against V anguillarum. Crown Copyright (C) 2008 Published by Elsevier Ltd. All rights reserved.

Intracellular copper/zinc superoxide dismutase from bay scallop Argopecten irradians: Its gene structure, mRNA expression and recombinant protein

Superoxide dismutases are an ubiquitous family of enzymes that function to efficiently catalyze the dismutation of superoxide anions. Two unique and highly compartmentalized bay scallop Argopecten irradians superoxide dismutases: MnSOD and ecCuZnSOD, have been molecularly characterized in our previous study. To complete characterize the SOD family in A. irradians, a novel intracellular copper/zinc SOD from the A. irradians (Ai-icCuZnSOD) was obtained and characterized. The full-length cDNA of Ai-icCuZnSOD was 1047 bp with a 459 bp open reading frame encoding 152 amino acids. The genomic length of the Ai-icCuZnSOD gene was about 4279 bp containing 4 exons and 3 introns. The promoter region containing many putative transcription factor binding sites were analyzed. Furthermore, quantitative reverse transcriptase real-time PCR (qRT-PCR) analysis indicated that the highest expression of the Ai-icCuZnSOD was detected in gill and the expression profiles in hemocytes of bay scallops challenged with bacteria Vibrio anguillarum and lipopolysaccharide (LPS) were different. The result presented an increased expression after injection with LPS whereas no significant changes were observed after V. anguillarum injection. A fusion protein containing Ai-icCuZnSOD was produced in vitro. The rAi-icCuZnSOD is a stable enzyme, retaining more than 80% of its activity between 10 and 60 degrees C and keeping above 88% of its activity at pH values between 5.8 and 9. Ai-icCuZnSOD is more stable under alkaline than acidic conditions. Crown Copyright (C) 2009 Published by Elsevier Ltd. All rights reserved.

Biosorption of copper(II) from aqueous solutions by green alga Cladophora fascicularis

Biosorption is an effective means of removal of heavy metals from wastewater. In this work the biosorption behavior of Cladophora fascicularis was investigated as a function of pH, amount of biosorbent, initial Cu2+ concentration, temperature, and co-existing ions. Adsorption equilibria were well described by Langmuir isotherm models. The enthalpy change for the biosorption process was found to be 6.86 kJ mol(-1) by use of the Langmuir constant b. The biosorption process was found to be rapid in the first 30 min. The presence of co-existing cations such as Na+, K+, Mg2+, and Ca2+ and anions such as chloride, nitrate, sulfate, and acetate did not significantly affect uptake of Cu2+ whereas EDTA substantially affected adsorption of the metal. When experiments were performed with different desorbents the results indicated that EDTA was an efficient desorbent for the recovery of Cu2+ from biomass. IR spectral analysis suggested amido or hydroxy, C=O, and C-O could combine strongly with Cu2+.

Biosorption of copper (II) and lead (II) from aqueous solutions by nonliving green algae Cladophora fascicularis: Equilibrium, kinetics and environmental effects

Biosorption of Cu2+ and Pb2+ by Cladophora fascicularis was investigated as a function of initial pH, initial heavy metal concentrations, temperature and other co-existing ions. Adsorption equilibriums were well described by Langmuir and Freundlich isotherm models. The maximum adsorption capacities were 1.61 mmol/ g for Cu2+ and 0.96 mmol/ g for Pb2+ at 298K and pH 5.0. The adsorption processes were endothermic and biosorption heats calculated by the Langmuir constant b were 39.0 and 29.6 kJ/ mol for Cu2+ and Pb2+, respectively. The biosorption kinetics followed the pseudo- second order model. No significant effect on the uptake of Cu2+ and Pb2+ by co-existing cations and anions was observed, except EDTA. Desorption experiments indicated that Na(2)EDTA was an efficient desorbent for the recovery of Cu2+ and Pb2+ from biomass. The results showed that Cladophora fascicularis was an effective and economical biosorbent material for the removal and recovery of heavy metal ions from wastewater.

Preparation of Dendritic Copper Nanostructures and Their Characterization for Electroreduction

Dendritic copper nanostructures of different morphologies were synthesized by a surfactant-free electrochemical method. Single crystal nature of the nanostructures was revealed from their X-ray diffraction and electron diffraction patterns. Mechanism of dendrite formation was discussed from thermodynamic aspects using the concept of supersaturation. Supersaturation of the copper metal reduced on the surface of the electrode was the crucial factor for the generation of different morphologies. Effects of applied potential, temperature, and the solution concentration on the supersaturation were studied. The NO3- and H2O2 electroreduction ability of the dendritic materials was tested. Use of copper dendrite-modified electrode as NO3- sensor was demonstrated.

Copper complexation by fulvic acid affects copper toxicity to the larvae of the polychaete Hydroides elegans

Copper toxicity is influenced by a variety of environmental factors including dissolved organic matter (DOM). We examined the complexation of copper by fulvic acid (FA), one of the major components of DOM, by measuring the decline in labile copper by anodic stripping voltammetrically (ASV). The data were described using a one-site ligand binding model, with a ligand concentration of 0.19 mu mol site mg(-1) C, and a logK' of 6.2. The model was used to predict labile copper concentration in a bioassay designed to quantify the extent to which Cu-FA complexation affected copper toxicity to the larvae of marine polychaete Hydroides elegans. The toxicity data, when expressed as labile copper concentration causing abnormal development, were independent of FA concentration and could be modeled as a logistic function, with a 48-h EC50 of 58.9 mu g 1(-1). However, when the data were expressed as a function of total copper concentration, the toxicity was dependent on FA concentration, with a 48-h EC50 ranging from 55.6 mu g 1(-1) in the no-FA control to 137.4 mu g 1(-1) in the 20 mg 1(-1) FA treatment. Thus, FA was protective against copper toxicity to the larvae, and such an effect was caused by the reduction in labile copper due to Cu-FA complexation. Our results demonstrate the potential of ASV as a useful tool for predicting metal toxicity to the larvae in coastal environment where DOM plays an important role in complexing metal ions. (c) 2007 Elsevier Ltd. All rights reserved.

Electrochemical and thermodynamic investigation of diniconazole and triadimefon as corrosion inhibitors for copper in synthetic seawater

This paper presents the investigation of diniconzole and triadimefon as chemical corrosion inhibitors for freshly polished copper in synthetic seawater (3.5% NaCl solution). Determination of weight loss, polarization curves, electrochemical impedance spectroscopy (EIS), and SEM, were performed to analyze the inhibiting performance of these compounds. Polarization curves show that they act as mixed-type inhibitors. EIS indicates that an adsorption film of the inhibitors is formed on copper surface. The highest values of inhibition efficiency are respectively, 99.2% and 97.3% at 100 mg/L concentration. Thermodynamic calculation suggests that chemisorptions between the compounds and copper are accordance with Langmuir adsorption isotherm. (C) 2010 Elsevier Ltd. All rights reserved.

Diisothiocyanatobis(1-vinyl-1H-imidazole-kappa N-3)-copper(II)

In the title compound, [Cu(NCS)(2)(C5H6N2)(2)], each Cu atom is coordinated by two N atoms from two Eim (Eim = 1-vinyl-1H-imidazole) ligands and two N atoms from two isothiocyanate groups. The Cu atom adopts a square-planar geometry. The mean Cu-N(Eim) and Cu-N(NCS) distances are 1.960 (6) and 1.993 (6) angstrom, respectively.

Genetic variation within and among populations of Rhodiola alsia (Crassulaceae) native to the Tibetan Plateau as detected by ISSR markers

Genetic variation of 10 Rhodiola alsia ( Crassulaceae) populations from the Qinghai - Tibet Plateau of China was investigated using intersimple sequence repeat (ISSR) markers. R. alsia is an endemic species of the Qinghai - Tibet Plateau. Of the 100 primers screened, 13 were highly polymorphic. Using these primers, 140 discernible DNA fragments were generated with 112 (80%) being polymorphic, indicating pronounced genetic variation at the species level. Also there were high levels of polymorphism at the population level with the percentage of polymorphic bands (PPB) ranging from 63.4 to 88.6%. Analysis of molecular variance (AMOVA) showed that the genetic variation was mainly found among populations (70.3%) and variance within populations was 29.7%. The main factors responsible for the high level of differentiation among populations are probably the isolation from other populations and clonal propagation of this species. Occasional sexual reproduction might occur in order to maintain high levels of variation within populations. Environmental conditions could also influence population genetic structure as they occur in severe habitats. The strong genetic differentiation among populations in our study indicates that the conservation of genetic variability in R. alsia requires maintenance of as many populations as possible.

东天山红山高硫型浅成低温铜-金矿床氧化带的形成机理和硫酸盐矿物的系列发现及意义

Located in the Paleozoic uplift along the southern margin of Tu-Ha basin in eastern Xinjiang, the newly discovered Hongshan Cu-Au deposit occurs in the superimposed Mesozoic volcanic basin upon the north section of later Paleozoic Dananhu-Tousuquan accretionary arc. Kalatage Cu-Au orebelt is controlled by NWW-trend faults, and includes Hongshan and Meiling Cu-Au deposits. The host rocks of Hongshan ore district are mainly rhyolitic-dacitic ignimbrites, whereas Cu-Au mineralization is closely related to quartz porphyry, rhyolitic porphyry and granitic porphyry. Mineralization styles are dominantly veinlet-disseminated and veinlet, occasionally stockwork. The mineral association is chalcopyrite, pyrite, bornite, chalcocite and sphalerite. The hydrothermal alteration consists of silicfication, sericitization, alunitization, pyrophylitization, illitization, hydromuscovitization, and chloritization. Hongshan Cu-Au deposit, on the edge of the desert, is one of the driest areas in eastrn Tianshan. Moreover， the highest temperature has been up to 60℃, and the average rainfall receives only 34.1mm/y. The light rainfall and rapid evaporation in the vicinity of this deposit have allowed the formation of a great variety of water-soluble sulfates. Oxidization zone of this deposit lies on the upper part of primary sulfide orebodies appearing with a depth of 50-60m, which is dominant in sulfate minerals. 1. Based on the field observation, the volcanic and sub-volcanic rock composition, hydrothermal alteration, ore structure and mineralization characteristics, this paper proposed that the Hongshan Cu-Au deposit belongs to a transitional type from high-sulfide epithermal to porphyry Cu-Au deposit, which corresponds with the typical HS-epithermal deposit such as Zijinshan Au-Cu deposit in Fujian Province, SE-China. 2. The Hongshan copper-gold deposit was controlled by the tectonic, stratum, magma activity and volcanic apparatus, whereas Au mineralization is closely related to quartz porphyry, rhyolitic porphyry and fine grained pyritization in hydrothermal activity, and Cu mineralization is closely related to quartz porphyry and hydrothermal explosive breccia. 3. Oxidation zone of Hongshan Cu-Au deposit lies on the upper part of primary sulfide orebodies deposit. 23 sulfate minerals were identified in this work. The results of samples XRD and chemical analysis were furthermore confirmed through thermal, infrared spectrum and mössbauer spectrum analysis. Among those, nine minerals as Ferricopiapite, Cuprocopiapite, Rhomboclase, Parabutlerite, Krausite, Yavapaiite, Metasideronatrite Kroehnkite and Paracoquimbite were founded in China for the first time. And Paracoquimbite was secondly reported in the world (first case reported at 1938 in Chile). 4. EPMA analysis shows that Al impurity in crystal lattice is important to polytype formation of paracoquimbite and coquimbite besides stack fault. 5. Compared with Meiling Cu-Au deposit in the same Kalatage ore belt from the characteristics of δ34S of barite, lithofacies, hydrothermal alteration and homogeneous temperature, Hongshan Cu-Au deposit belongs to the same metallogenic system of HS-epithermal type as Meiling Cu-Au deposit. But Hongshan Cu-Au deposit has less extensive alteration and shallower denudation. 6. Sulfur isotope analyses show that δ34S values of pyrites vary in the range of +1.86‰~+5.69‰, with an average of 3.70‰, mostly in the range of +1.86‰~+3.20‰, and δ34Scp<δ34Spy. Therefore ore-forming fluid of porphyry comes from mantle and was contaminated by the earth’s crust. Sulfur isotope has reached balance in ore-forming process. 7. Sulfur isotope analyses show that δ34S values of sulfates vary in the range of +2.15‰~+6.73‰, with an average of +3.74‰, mostly equals as δ34S values of primary sulfides in Hongshan Cu-Au deposit. So supergene sulfates inherit sulfur of primary sulfide. δ34S values are mostly same in different sulfates. As well as pyrite and chalcopyrite, volcanic hot spring and associated native sulfur underground also provide water medium and sulfur during the formation process of sulfate. 8. According to the EPMA of sample chalcopyrite and pyrite in Hongshan Cu-Au, the value of Cu/Ni is 0.98-34.72, mostly close to the value of 5, which shows that Hongshan deposit is a typical volcanogenic magmaic hypothermal deposit. Au and Ag, Zn, Te and Bi are positive correlation, Cu and Hg, Se, Sb are positive correlation, indicates Au and Cu don’t locate in the factor of mineralization of same mineralization groups. The reasons of gold concentration in the oxidation zone are: 1). Change of redox potential (Eh) makes gold to deposit from the liquid of mineralization zone; 2). PH is one of the most factors of gold’s deposition; 3). Soluble complex and colloid of gold can be adsorbed easily. 9. The biotite and hornblende K-Ar isotopic ages from the wall rock－quartz diorite, biotite granite and monzonite granite are 231.99±3.45Ma, 237.97±2.36Ma and 296.53±6.69Ma respectively. The ore-bearing rhyolitic breccia lava contains breccia of the biotite granite which indicates the volcanism and related Cu-Au mineralization occurred later than the granite, possibly in Mesozoic. K-Ar ages of granitoids in Sanya, Baishiquan and Hongliugou area and Molybdenite Re-Os age of Baishan Mo deposit all are in Triassic. Besides late Paleozoic magmatism, igneous magmatic event of Mesozoic was widespread in eastern Tianshan. 10. The K-Ar age dating indicates that the K-Ar age of Voltaite occurred below surface 1m is 56.02±3.98Ma, K-Ar age of Ferricopiapite occurred below surface 1.5m is 8.62±1.12Ma, K-Ar age of Yavapaiite occurred below surface 14 m is 4.07±0.39Ma, and K-Ar age of Voltaite occurred below surface 10 m is 14.73±1.73Ma. So the age interval of oxidation zone of Hongshan copper-golden bed is between 60 -3.38Ma. Oxidization occurred at Caenozoic era (from 65Ma), which can be identified through comparing with different deposits oxidation zone in other countries. The coupling between global tectonic event and climatic change event which occur from Caenozoic era has some effect on epigeosphere system, which can act on the surface of bed oxidation zone similarly. It induces that the age mentioned above coincide with collision of India-Asia and multistage uplifting of Qinhai-Tibet Plateau happened subsequently. Bed oxidation zone is the effect and record of collision and uplifting of Tibet Plateau. The strong chemical weathering of surface accumulation to which was leaded by PETM event occurred Paleocene and Eocene is the reason of Voltaite sharply rises. On the contrary, Ferricopiapite formed due to the global cold weather. The predecessor did much research through biota, isotopes, susceptibility, but this paper try to use different sulfate mineral instead of climatic change. So the research of sulfate minerals not only indicates a great deal of oxidized zone feature, but also the intergrowth of sulfate minerals may be used to trace paleoenviroment and paleoclimate of oxidation zone. 11. Analysis of the information of alteration and mineralization features of four bore cores, induced activity polarization well logging and Eh-4 geophysical section, deep mineralization anomaly objects of Hongshan ore districts shows low resistance, middle and high polarization, measurements of Eh-4 consecutive conductance section show the existing of concealed porphyry ore body deeper than 450m, on the top of and around rock body there are low resistance body ranged from 100-300Ω•m, this area may be the ore-bearing part. In a word, Hongshan Cu-Au deposit deposit is a combine of upper HS-style epithermal Au deposit and deeper porphyry mineralization system. It has great potential to find large HS-style epithermal-porphyry Au-Cu deposits. This paper consists of seven chapters and twenty seven sections. The geological character of deposit is basic condition in this work. Constitute of oxidation zone, research of sulfate mineral, relation between oxidation and primary zone, K-Ar ages of potassic sulfate are key parts of thesis. Genesis of ore deposit is the further expansion of this research. Analysis of ore-controlling factors is the penetration above basic. Analysis of potential is application of exploration.