DIRECT OBSERVATION OF NATIVE AND UNFOLDED GLUCOSE-OXIDASE STRUCTURES BY SCANNING-TUNNELING-MICROSCOPY

Native and unfolded glucose oxidase (GOD) structures have been directly observed with scanning tunnelling microscopy (STM) for the first time. STM images show an opening butterfly-shaped pattern for the native GOD. When GOD molecules are extended on anodi

Consensus scoring for enriching near-native structures from protein-protein docking decoys

The identification of near native protein-protein complexes among a set of decoys remains highly challenging. A stategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu.

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.

Characterizing a monotopic membrane enzyme. Biochemical, enzymatic and crystallization studies on Aquifex aeolicus sulfide:quinone oxidoreductase

Monotopic membrane proteins are membrane proteins that interact with only one leaflet of the lipid bilayer and do not possess transmembrane spanning segments. They are endowed with important physiological functions but until now only few of them have been studied. Here we present a detailed biochemical, enzymatic and crystallographic characterization of the monotopic membrane protein sulfide:quinone oxidoreductase. Sulfide:quinone oxidoreductase is a ubiquitous enzyme involved in sulfide detoxification, in sulfide-dependent respiration and photosynthesis, and in heavy metal tolerance. It may also play a crucial role in mammals, including humans, because sulfide acts as a neurotransmitter in these organisms. We isolated and purified sulfide:quinone oxidoreductase from the native membranes of the hyperthermophilic bacterium Aquifex aeolicus. We studied the pure and solubilized enzyme by denaturing and non-denaturing polyacrylamide electrophoresis, size-exclusion chromatography, cross-linking, analytical ultracentrifugation, visible and ultraviolet spectroscopy, mass spectrometry and electron microscopy. Additionally, we report the characterization of its enzymatic activity before and after crystallization. Finally, we discuss the crystallization of sulfide:quinone oxidoreductase in respect to its membrane topology and we propose a classification of monotopic membrane protein crystal lattices. Our data support and complement an earlier description of the three-dimensional structure of A. aeolicus sulfide:quinone oxidoreductase (M. Marcia, U. Ermler, G. Peng, H. Michel, Proc Natl Acad Sci USA, 106 (2009) 9625-9630) and may serve as a reference for further studies on monotopic membrane proteins. (C) 2010 Elsevier B.V. All rights reserved.

Tide-influenced acidic hydrothermal system offshore NE Taiwan

Elemental sulfur and hydrogen sulfide emitted offshore of northeastern Taiwan known to local fishermen for generations, but never studied until recently, are found to have originated from a cluster of shallow (< 30 m depth) hydrothermal vents. Among the mounds is a massive 6 m high chimney with a diameter of 4 m at the base composed of almost pure sulfur and discharging hydrothermal fluid containing sulfur particles. The sulfur in the chimney has a delta(34)S= 1.1 parts per thousand that is isotopically lighter than seawater. A yellow smoker at shallow depths with such characteristics has never been reported on anywhere else in the world. Gas discharges from these vents are dominated by CO2 (> 92%) with small amounts of H2S. Helium isotopic ratios 7.5 times that of air indicate that these gases originate from the mantle. High temperature hydrothermal fluids have measured temperatures of 78-116 degrees C and pH (25 degrees C) values as low as 1.52, likely the lowest to be found in world records. Low temperature vents (30-65 degrees C) have higher pH values. Continuous temperature records from one vent show a close correlation with diumal tides, suggesting rapid circulation of the hydrothermal fluids. (c) 2005 Elsevier B.V. All rights reserved.

Authigenic sulfide minerals and their sulfur isotopes in sediments of the northern continental slope of the South China Sea and their implications for methane flux and gas hydrate formation

This is a report of the study of the authigenic sulfide minerals and their sulfur isotopes in a sediment core (NH-1) collected on the northern continental slope of the South China Sea, where other geophysical and geochemical evidence seems to suggest gas hydrate formation in the sediments. The study has led to the findings: (1) the pyrite content in sediments was relatively high and its grain size relatively large compared with that in normal pelagic or hemipelagic sediments; (2) the shallowest depth of the acid volatile sulfide (AVS) content maximum was at 437.5 cm (> 2 mu mol/g), which was deeper than that of the authigenic pyrite content maximum (at 141.5-380.5 cm); (3) delta S-34 of authigenic pyrite was positive (maximum: +15 parts per thousand) at depth interval of 250-380 cm; (4) the positive delta S-34 coincided with pyrite enrichment. Compared with the results obtained from the Black Sea sediments by Jorgensen and coworkers, these observations indicated that at the NH-1 site, the depth of the sulfate-methane interface (SMI) would be or once was at about 437.5-547.5 cm and the relatively shallow SMI depth suggested high upward methane fluxes. This was in good agreement with the results obtained from pore water sulfate gradients and core head-space methane concentrations in sediment cores collected in the area. All available evidence suggested that methane gas hydrate formation may exist or may have existed in the underlying sediments.

Suitability of extractants for predicting available sulfur in natural grassland in the Inner Mongolia steppe of China

It was the objective of this study to compare the suitability of different extractants for predicting the availability of sulfur (S) in natural grassland in a sulfur response trial on three different soil types in the Inner Mongolia steppe of China. For soil analysis, seven different extractants have been employed. The inorganic SO4-S concentration was determined by ion chromatography. Additionally, in the Ca(H-2-PO4)(2) extract the total soluble S was determined employing turbidimetry. Weak salt solutions (0.15% CaCl2, Ca(H2PO4)(2), and KH2PO4) extracted similar amounts Of SO4-S. Extraction with 0.025 M KCl provided the lowest SO4-S values. Deionized water dissolved significantly more SO4-S in the control plots than most weak salt extractants. The concentration of soluble organic S decreased in the control plots after 100 days of plant growth, indicating that the organic S pool contributed significantly to the S nutrition of the forage crops. Significant relationships among the SO4-S in the soil determined in different extracts and crop yield, sulfur content in the forage, and total sulfur uptake were only found for the Ca(H2PO4)(2) extract. In general, the correlation coefficients proved to be unsatisfactory for field experimentation.

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.

胶东蓬家夼式金矿床矿床成因模型与找矿模型研究

The dynamic environments of mineralization in Mesozoic Jiaodong gold mine concentrated area can be devided into two types, compressive environment which related to intracontinental collision and extensional environment which related to intracontinental volcanic rift. The altered rock type (Jiaojia type) and quartz vein type (Linglong type) which related to the former one, were discovered for several years, and became the main types of gold deposits in recent years. A new type gold deposit, syn-detachment altered tectonic breccia type gold deposit, such as Pengjiakuang gold deposit and Songjiagou gold deposit has been discovered on the northeastern margin of Jiaolai Basin. In this paper, the new type of gold deposit has been studied in detail. The study area is located at the northeastern boundaries of Jiaolai Basin, and between the Taocun-Jimo Fault and Wji-Haiyang Fault, in the eastern part of the Jiaodong Block. Pengjiakuang gold deposit and Songjiagou gold deposit occur in a arc-shape detachment fault zone between conglomerate of Lower Cretaceous Laiyang Formation and metamorphic complex of Lower Proterozoic Jingshan Group. Regional geological studies show that Kunyuanshan and Queshan granite intrusions and Qingshanian volcanism were formed in different period of lithospheric thinning of East China in Mesozoic. Granite intrusions were formed in compressive environment, while Qingshanian volcanism were formed in extensional environment. They are all related to the detachment of Sulu Orogenic Belt and the sinistral motion of Tanlu Fault. The Pengjiakuang detachment systems which were formed in the the sinistral motion of Tanlu Fault are the important ore-controlling and ore-containing structure. The Pengjiakuang type gold deposit, controlled by detachment structure, was formed before Yanshanian volcanic period concerning with mixture of meteoric water and magmatic water found in fluid inclusions of gold ores. The minerogenetic epoch has been proposed in 90～120Ma. the host rocks have been extensively subjected to pyritization, silicification, sericitization and carbonatization. Individual ore-body has maximum length of 800m, oblique extension of 500～700m and gold grade of 1～43 * 10~(-6). Native gold is disseminated in silicified, phyllic or carbonatized tectonic breccia. Sulfur, carbon and lead isotope studies on gold ores and wall rocks show that the sulfur come from the metamorphic complex of Lower Proterozoic Jingshan Group, carbon comes from the marble in Jingshan Group, while a part of lead comes from the mantle. The mineralizing fluid is rich in Na~+ and Cl~-, but relatively impoverished in K~+ and F~-. According to the date from hydrogen and oxygen isotopic compositions (δ~(18)OH_2O = 0.59%～4.03%, δDH_2O = -89.5%～97.9%), the conclusion can be reached that the mineralizing fluid of Pengjiakuang gold deposit was a kind of mixed hydrothermal solution which was mainly composed of meteoric water and magmatic water. A genetical model has been formulated. Some apparent anomaly features which show low in the central part and high in the both sides corresponding to the gold-bearing structure, were sum up after analying a vast amount of date by prospecting the orebodies using gamma-ray spectrometer, electrogeochemical parameter technique, controlled source audio magnetic telluric (CSAMT) and shallow surface thermometry in Pengjiakuang gold deposit. The location forecasting problem of buried orebodies has been solved according to these features, and the successful rate is very high in well-drilling. The structural geological-geophysical-geochemical prospecting model has been formulated on the base of the study of geological, geophysical and geochemical characteristics of Pengjiakuang type gold deposit, and the optimum combinational process of geophysical and geochemical prospecting techniques has been summed up. A comparative study shows that the Pengjiakuang type gold deposit, the syn-detachment altered tectonic breccia type gold deposit, is different from Jiaojia type gold deposits and Linglong type gold deposits, in Jiaodong Block. In general, if formed under an extensional tectonic condition and located at detachment fault zone along the margin of Mesozoic Jiaolai basin, and the gold mineralization has also close genetic relationship with alkaline magamtism. Being a new type of gold deposit in Jiaodong gold mine concentrated area, it could be potential to explore in the same regions which processed the same ore-forming geological conditions and mineralization informations.