Stereoelectronic Properties of N-acetyl-α,β-dehydroamino acid N′-methylamides

Summary α,β-Dehydroamino acids are useful peptide modifiers. However, their stereoelectronic properties still remain insufficiently recognized. Based on FTIR experiments in the range ofv _s(N-H), AI, AII andv _s(C^α=C^β) and ab initio calculations with B3LYP/6–31G*, we studied the solution conformational preferences and the amide electron density perturbation of Ac-ΔXaa-NHMe, where ΔXaa=ΔAla, (E)-ΔAbu, (Z)-ΔAbu, (Z)-ΔLeu, (Z)-ΔPhe and ΔVal. Each of these dehydroamides adopts a C₅ structure, which in Ac-ΔAla-NHMe is fully extended and accompanied by the strong C₅ hydrogen bond. Interaction with bond C^α=C^β lessens the amidic resonance within the flanking amide groups. TheN-terminal C=O bond is noticeably shorter, both amide bonds are longer than the corresponding bonds in the saturated entities and the N-terminal amide system is distorted. Ac-ΔAla-NHMe constitutes an exception. ItsC-terminal amide bond is shorter than the standard one and both amide systems are ideally planar. Ac-(E)-ΔAbu-NHMe shares stereoelectronic features with both Ac-ΔAla-NHMe and (Z)-dehydroamides.     

Si60 fullerene-like cage passivated by F and Cl

It is generally considered that a bare Si₆₀ fullerene-like cage is geometrically unstable. In this paper, a Si₆₀ fullerene-like cage passivated by F or Cl atoms is investigated by the use of ab initio calculations based on density functional theory. The results show that passivated Si₆₀ cage can be stabilised in a perfect fullerene structure. The geometry, stability and electronic properties for the passivated Si₆₀ cage are discussed.     

Ozone mediators effect on “in vitro” scratch wound closure

The beneficial effect of low doses of ozone on wound healing has been well documented and attributed mainly to its bactericidal and pro-oxidant properties. Because ozone itself does not penetrate the cells but immediately reacts with polyunsaturated fatty acids, its effects are the results of oxidative mediators. Among the molecule produces by the interaction of ozone with biological systems, there are HNE and H₂O₂. At today, the cellular mechanisms accounting for the positive effects of mild ozonization on wound closure are still largely unexplored. The aim of the present study was to evaluate the effect of different non-toxic doses of ozonated saline ranging from 2 to 300?μM, in an in vitro wound scratch model by the use of human keratinocytes. The results showed that ozonated saline is able to improve in vitro wound healing by stimulating cell proliferation as measured by BrdU assay and PCNA protein levels. In order to better elucidate the molecules that play the main role in the beneficial effect of ozonated saline in wound healing, HNE and H₂O₂ were used alone or in combination to mimic ozonated saline effect. Surprisingly, keratinocytes treated with different doses of HNE and H₂O₂ did not significantly improve the wound closure, while the combination of the two compounds was able to improve wound closure. In addition, Nrf2 pathways were also activated as determined by its translocation to the nucleus and the increased HO1 gene expression. The present work suggests that ozonated saline effect on wound closure is the results of the combination of more molecules among which HNE and H₂O₂ play a key role.     

Construction and assessment of reaction models between F1F0-synthase and organotin compounds: molecular docking and quantum calculations

Organotin compounds are the active components of some fungicides, which are potential inhibitors of the F₁F₀-ATP synthase. The studies about the reaction mechanism might indicate a pathway to understand how these compounds work in biological systems, however, has not been clarified so far. In this line, molecular modeling studies and density functional theory calculations were performed in order to understand the molecular behavior of those compounds when they interact with the active site of the enzyme. Our findings indicate that a strong interaction with His132 can favor a chemical reaction with organotin compounds due to π–π stacking interactions with aromatic rings of organotin compounds. Furthermore, dependence on molecule size is related to possibility of reaction with the amino acid residue His132. Thus, it can also be noticed, for organotin compounds, that substituents with four carbons work by blocking the subunit a, in view of the high energy transition found characterized by steric hindrance.     

Theoretical study on the interactions between methanol and imidazolium-based ionic liquids

To better understand the property of the binary systems composing of imidazolium salt, [emim]⁺Aˉ (A=Clˉ, Brˉ, BF₄ˉ, and PF₆ˉ) and methanol, we have investigated in detail the interactions of methanol molecule with anions Aˉ, cation [emim]⁺, and ion pair [emim]⁺Aˉ of several ionic liquids (ILs) based on 1-ethyl-3-methylimidazolium cation by performing density functional theory calculations. It is found that H-bonds are universally involved in these systems, which may play an important role for the miscibility of methanol with imidazolium-based ILs. The interaction mechanisms of methanol molecule with anion and cation are found to be different in nature: the former mainly involves LP_X-s_{O - H}^* \sigma_{{O - H}}^{*} interaction, while the latter relates with the decisive orbital overlap of the type of LP_O-s_{C - H}^* \sigma_{{C - H}}^{*} . Based on the present calculations, we have provided some reasonable interpretations for properties of the binary mixtures of ILs and alcohol and revealed valuable information for the interaction details between ILs and alcohols, which is expected to be useful for the design of more efficient ILs to form superior solvent system with alcohol.     

Improving nitrogen-fixing systems and integrating them into sustainable rice farming

This paper summarizes recent achievements in exploiting new biological nitrogen fixation (BNF) systems in rice fields, improving their management, and integrating them into rice farming systems. The inoculation of cyanobacteria has been long recommended, but its effect is erratic and unpredictable. Azolla has a long history of use as a green manure, but a number of biological constraints limited its use in tropical Asia. To overcome these constraints, the Azolla-Anabaena system as well as the growing methods were improved. Hybrids between A. microphylla and A. filiculoides (male) produced higher annual biomass than either parent. When Anabaena from high temperature-tolerant A. microphylla was transferred to Anabaena-free A. filiculoides, A. filiculoides became tolerant of high temperature. Azolla can have multiple purposes in addition to being a N source. An integrated Azolla-fish-rice system developed in Fujian, China, could increase farmers' income, reduce expenses, and increase ecological stability. A study using Azolla labeled with ¹⁵N showed the reduction of N losses by fish uptake of N. The Azolla mat could also reduce losses of urea N by lowering floodwater-pH and storing a part of applied N in Azolla. Agronomically useful aquatic legumes have been explored within Sesbania and Aeschynomene. S. rostrata can accumulate more than 100kg N ha^-1 in 45 d. Its N₂ fixation by stem nodules is more tolerant of mineral N than that by root nodules, but the flowering of S. rostrata is sensitive to photoperiod. Aquatic legumes can be used in rainfed rice fields as N scavengers and N₂ fixers. The general principle of integrated uses of BNF in rice-farming systems is shown.     

MD Simulations of Liquids with Td,Oh Molecular Symmetry

Abstract

A new method is proposed for the calculation of intermolecular interactions in Molecular Dynamics simulations of liquids with T_d, O_h molecular symmetry. The new algorithm is based on the separation of the pair potential into a short-range and a long-range contribution described by a site-site and a spherical centre-centre potential model respectively using an additional cutoff distance. Test calculations for the Lennard-Jones fluids CCl₄ and SF₆ show significant savings in CPU time. We compare thermodynamic properties, pair correlation functions and a few dynamic autocorrelation functions obtained with the novel strategy with results of the commonly used algorithm for systems containing 864 molecules. Since no significant differences appear the new algorithm may be suggested as a useful contribution to the area of Molecular Dynamics simulation of liquids with these rather high molecular symmetries.     

Pollen morphological studies in subfamily Suaedoideae (Chenopodiaceae)

The pollen morphology of two Bienertia species and 28 Suaeda species from the Old World has been studied with light and scanning electron microscopy. Pollen morphological characters used in this study include pollen diameter, pore number, pore diameter, operculum diameter, chord distance, exine thickness, plus number and characteristics of exine spinules and operculum spinules. Using these characters, the pollen of Bienertia is clearly distinguished from that of Suaeda. In addition, pollen data support recent molecular studies which merge the genus Borszczowia into Suaeda. The pollen grains of Suaeda show notable variation; in some cases this allows morphological distinctions to be made between species. Taxonomically, pore number is observed to be a more useful character than pollen diameter. Principal components analysis (PCA) shows only a weak correlation between pollen characters and habit (life form), habitat, mode of photosynthesis or phylogenetic relationships. Interestingly, however, the annual C₃ and C₄ species of section Schoberia are usually characterised by a higher pore number than the perennial C₄ species.     

Intracellularly Truncated Human α2B-Adrenoceptors: Stable and Functional GPCRs for Structural Studies

All three α₂-adrenoceptor subtypes have a long third intracellular loop (3i), which is conserved by overall size and charge-hydrophobic properties but not by amino acid sequence similarity. These properties must be relevant for function and structure, because they have been preserved during hundreds of millions of years of evolution. The contribution of different loop portions to agonist/antagonist binding properties and G protein coupling of the human α_2B-adrenoceptor (α_2B-AR) was investigated with a series of 3i truncated constructs (Δ 3i). We used a variety of agonists/antagonists in competition binding assays. We stimulated α_2B-AR Δ3i with various agonists and measured [³⁵S]GTPγS binding in isolated cell membranes with or without antagonist inhibition. We also evaluated the ability of oligopeptides, analogous to the amino and carboxyl terminal parts of 3i, to promote G protein activation, monitored with the [³⁵S]GTPγS assay. Our results reveal that the carboxyl end residues of 3i, R360(6.24) to V372(6.36), are important for G_i/G_o protein activation. Deletions in regions from G206(5.72) to R245(5.110) altered the binding of some α_2B-AR agonists, indicating that agonist binding is dependent on the conformation of the 3i domain, possibly through the involvement of G protein interactions. The truncated receptor constructs may be more stable on purification and thus be useful for structural characterization of α_2B-AR.     

Effects of polyploidy on photosynthesis

In polyploid plants the photosynthetic rate per cell is correlated with the amount of DNA per cell. The photosynthetic rate per unit leaf area is the product of the rate per cell times the number of photosynthetic cells per unit area. Therefore, the photosynthetic rate per unit leaf area will increase if there is a less than proportional increase in cell volume at higher ploidal levels, or if cell packing is altered to allow more cells per unit leaf area. In autopolyploids (Medicago sativa, C₃ species, and Pennisetum americanum, C₄ species) there is a doubling of photosynthesis per cell and of cell volume in the tetraploid compared to the diploid. However, there is a proportional decrease in number of cells per unit leaf area with this increase in ploidy such that the rate of photosynthesis per leaf area does not change. There is more diversity in the relationship between ploidal level (gene dosage) and photosynthetic rates per unit leaf area in allopolyploids. This is likely to reflect the effects of natural selection on leaf anatomy, and novel genetic interactions from contributed genomes which can occur with allopolyploidy. In allopolyploid wheat (C₃ species) a higher cell volume per unit DNA at the higher ploidal level is negatively correlated with photosynthesis rate per unit leaf area. Although photosynthesis per cell increases with ploidy, photosynthesis per leaf area decreases, being lowest in the allohexaploid, cultivated bread wheat (Triticum aestivum). Alternatively, doubling of photosynthetic rate per cell with doubling of DNA, with apparent natural selection for decreased cell volume per unit DNA, results in higher rates of photosynthesis per leaf area in octaploid compared to tetraploid Panicum virgatum (C₄) which may be a case of allopolyploidy. Similar responses probably occur in Festuca arundinacea. Therefore, in some systems anatomical factors affecting photosynthesis are also affected by ploidal level. It is important to evaluate that component as well as determining the effect on biochemical processes. Current information on polyploidy and photosynthesis in several species is discussed with respect to anatomy, biochemistry and bases for expressing photosynthetic rates.Abbreviations Chl chlorophyll - RuBPC ribulose-1,5-bisphosphate carboxylase     

Biosynthesis of nitrogen-containing natural products,C7N aminocyclitols and bis-indoles,from actinomycetes

Actinomycetes are a major source of bioactive natural products with important pharmaceutical properties. Understanding the natural enzymatic assembly of complex small molecules is important for rational metabolic pathway design to produce “artificial” natural products in bacterial cells. This review will highlight current research on the biosynthetic mechanisms of two classes of nitrogen-containing natural products, C₇N aminocyclitols and bis-indoles. Validamycin A is a member of C₇N aminocyclitol natural products from Streptomyces hygroscopicus. Here, two important biosynthetic steps, pseudoglycosyltranferase-catalyzed C–N bond formation, and C₇-sugar phosphate cyclase-catalyzed divergent carbasugar formation, will be reviewed. In addition, the bis-indolic natural products indolocarbazole, staurosporine from Streptomyces sp. TP-A0274, and rearranged bis-indole violacein from Chromobacterium violaceum are reviewed including the oxidative course of the assembly pathway for the bis-indolic scaffold. The identified biosynthesis mechanisms will be useful to generating new biocatalytic tools and bioactive compounds.     

A structural model for the adduct between cytochrome c and cytochrome c oxidase

An ensemble of structural models of the adduct between cytochrome c and cytochrome c oxidase from Paracoccus denitrificans has been calculated based on the experimental data from site-directed mutagenesis and NMR experiments that have accumulated over the last years of research on this system. The residues from each protein that are at the protein–protein interface have been identified by the above experimental work, and this information has been converted in a series of restraints explicitly used in calculations. It is found that a single static structural model cannot satisfy all experimental data simultaneously. Therefore, it is proposed that the adduct exists as a dynamic ensemble of different orientations in equilibrium, and may be represented by a combination or average of the various limiting conformations calculated here. The equilibrium involves both conformations that are competent for electron transfer and conformations that are not. Long-range recognition of the partners is driven by non-specific electrostatic interactions, while at shorter distances hydrophobic contacts tune the reciprocal orientation. Electron transfer from cytochrome bc ₁ to cytochrome c oxidase is mediated through cytochrome c experiencing multiple encounters with both of its partners, only part of which are productive. The number of encounters, and thus the electron transfer rate, may be increased by the formation of a cytochrome bc ₁–cytochrome c oxidase supercomplex and/or (in human) by increasing the concentration of the two enzymes in the membrane space. Protein Data Bank Accession numbers The coordinates of the five best structural models for each of the four clusters have been deposited in the Protein Data Bank (PDB ID 1ZYY).     

Physicochemical characteristics of anaerobic H2-producing granular sludge

Granule-based biological H₂ production processes are gaining great popularity in recent years. An efficient and stable operating of such systems relies heavily on the performance of the H₂-producing granules (HPGs), which possess many unique properties compared with floc sludge and methanogenic granules. Hence, a full understanding of the sludge characteristics is essential. Especially, the physicochemical properties of HPGs may provide useful information for effective evaluation of system status. This review offers a systematical introduction of the physicochemical properties of HPGs, including size, morphology, settling velocity, permeability, rheology, surface charge, hydrophobicity and extracellular polymeric substances (EPS). We also analyze the relationships between these physicochemical factors and the system performance, and discuss the remaining challenges and future implications for sludge characterization and process monitoring. This work may facilitate a better understanding of granule-based biological H₂ production processes and offer a basis for timely process monitoring and manipulation.     

A quick solution structure determination of the fully oxidized double mutant K9-10A cytochrome c7 from Desulfuromonas acetoxidans and mechanistic implications

Lysines 9 and 10 in Desulfuromonas acetoxidans cytochrome c₇, which could be involved in the interaction mechanism with the redox partners, have been replaced by alanine residues using site-directed mutagenesis. The solution structure of the fully oxidized form of K9-10A cytochrome c₇, which is paramagnetic with three paramagnetic centers, has been determined via ¹H NMR. The assignment of the spectra has been performed through an automatic program whose algorithm and strategy are here described. The assignment of the NOESY spectra has been further extended by back calculating the NOESY maps. The final number of meaningful NOE-based upper distance limits was 1186. In the Restrained Energy Minimization calculations, 147 pseudocontact shift constraints were also included, which showed consistency with NOE-based constraints and therefore further contribute to validate the structure quality. A final family of 35 conformers was calculated with RMSD values with respect to the mean structure of 0.69 ± 0.17 Å and 1.05 ± 0.14 Å for the backbone and heavy atoms, respectively. The overall fold of the molecule is maintained with respect to the native protein. The loop present between heme III and heme IV results to be highly disordered also in the present structure although its overall shape mainly resembles that of the oxidized native protein, and the two strands which give rise to the short -sheet present at the N-terminus and connected by a turn containing the mutated residues, are less clearly defined. If this loop is neglected, the RMSD values are 0.52 ± 0.07 Å and 0.92 ± 0.06 Å for the backbone and heavy atoms, respectively, which represent a reasonable resolution. The relative distances and orientations of the three hemes are maintained, as well as the orientation of the imidazole rings of the axial histidine ligands, with the only exception of heme IV. Such difference probably reflects minor conformational changes due to the substitution of the vicinal Lys10 with an Ala. The replacement of the two lysines does not affect the reduction potentials of the three hemes, consistently with the expectations on the basis of the structure and electrostatic calculations. However, the replacement of the two lysines affects the reactivity of the mutant cytochrome c₇ with [Fe] hydrogenase, inducing a change in K _m. This finding is in agreement with the identification of the protein area around heme IV as the interacting site.     

Correlated ab initio molecular dynamics simulations of the acetone–carbon dioxide complex: implications for solubility in supercritical CO2

Ab initio molecular dynamics simulations of the acetone–CO₂ complex (MP2/6-31G(d) level) were performed to investigate the effect of dynamics at finite temperature on the weak electron donor–acceptor intermolecular interactions. In addition, we carried out a study of the free energy of formation of the complex by means of umbrella sampling technique at the MP2 level with a perturbative CCSD(T) correction. The potential of mean force was obtained along a reaction coordinate describing the acetone–CO₂ interaction. The results obtained here support some hypothesis that we already explored in past works using static electronic calculations. In particular, when interacting with a molecule having a carbonyl function, carbon dioxide displays both Lewis acid and Lewis base behaviour. This property can be exploited to design molecular systems that are easily solubilised in supercritical CO₂.     

The effects of soluble-Al on root growth and radicle elongation

Summary In order to determine the effects of concentration on plant growth, aluminium (Al) was extracted (10^–3 M CaCl₂) from 4 acid brown hill soils which had been treated with superphosphate at rates equivalent to 0 to 300 kg P ha^–1. The soils ranged in pH (CaCl₂) from 3.5 to 4.9, and Al concentration from 0 to 0.6 mM. The effects of Al on ryegrass growth in the 4 soils in a glasshouse was compared with its effect on radicle elongation of seeds germinated in contact with CaCl₂ extracts from the same soils.Ryegrass root growth in the glasshouse, and radicle elongation in the bioassay test were both unaffected by Al concentrations below 0.1 mM. Root growth was substantially reduced when Al concentration exceeded 0.1 mM and above 0.2 mM growth was almost completely inhibited. Radicle elongation rate was also reduced when the concentration of Al was greater than 0.2 mM agreeing well with the observation from the pot experiment.It is concluded that because of its speed and convenience the bioassay method offers a useful method of establishing critical levels of Al for crop plants.     

Evaluation of a novel aminopeptidase N inhibitor,in vitro,using two assay systems

The activities of the novel aminopeptidase N inhibitor (APNI), β-Amino-α-Hydroxyl-Phenyl butanic acid-Valine (AHPA-Val), were compared with APNI (amastatin). AHPA-Val and amastatin produced competitive inhibition of the hydrolysis of Tyr-Gly in the guinea-pig striatal membrane preparation, with K_i equal to 14.06 μM and 12.48 μM respectively. Met-enkephalin-induced twitch inhibition of the guinea-pig ileum preparation was enhanced by AHPA-Val and amastatin with pA_1/2 values (the negative logarithm concentration of APNI that decreased the IC₅₀ of Met-enkephalin by half), of 7.08 and 7.79 respectively. These results suggest that AHPA-Val has good activity as an APNI and that these two assay systems are useful for evaluating the potency of novel APNIs.     

Chloroquine inhibits autophagic flux by decreasing autophagosome-lysosome fusion

Macroautophagy/autophagy is a conserved transport pathway where targeted structures are sequestered by phagophores, which mature into autophagosomes, and then delivered into lysosomes for degradation. Autophagy is involved in the pathophysiology of numerous diseases and its modulation is beneficial for the outcome of numerous specific diseases. Several lysosomal inhibitors such as bafilomycin A₁ (BafA₁), protease inhibitors and chloroquine (CQ), have been used interchangeably to block autophagy in in vitro experiments assuming that they all primarily block lysosomal degradation. Among them, only CQ and its derivate hydroxychloroquine (HCQ) are FDA-approved drugs and are thus currently the principal compounds used in clinical trials aimed to treat tumors through autophagy inhibition. However, the precise mechanism of how CQ blocks autophagy remains to be firmly demonstrated. In this study, we focus on how CQ inhibits autophagy and directly compare its effects to those of BafA₁. We show that CQ mainly inhibits autophagy by impairing autophagosome fusion with lysosomes rather than by affecting the acidity and/or degradative activity of this organelle. Furthermore, CQ induces an autophagy-independent severe disorganization of the Golgi and endo-lysosomal systems, which might contribute to the fusion impairment. Strikingly, HCQ-treated mice also show a Golgi disorganization in kidney and intestinal tissues. Altogether, our data reveal that CQ and HCQ are not bona fide surrogates for other types of late stage lysosomal inhibitors for in vivo experiments. Moreover, the multiple cellular alterations caused by CQ and HCQ call for caution when interpreting results obtained by blocking autophagy with this drug.     

生物炭及其老化对农田NH3挥发及N2O排放的影响

生物炭具有减缓农田NH₃挥发和N₂O排放的重要潜力,但在施入环境后常常存在“老化”现象,这为其缓解全球变暖的长期有效性带来了不确定性。为了探明生物炭的长期效应,人工加速模拟了自然界中水分、温度、氧气、土壤矿物质及微生物多种老化因素,结合多元表征手段对比不同老化方式对生物炭性质的影响,利用主成分分析法建立新的生物炭性质综合指标来反映老化强度。再通过大田控制试验,采用原位通气法和静态箱—气相色谱法监测夏玉米生长周期内老化前后生物炭施用对农田NH₃挥发和N₂O排放的影响,为生物炭的可持续应用提供科学依据。结果表明,老化过程增加了原生物炭(BC)的氧含量、比表面积(S_BET)、总孔容(V_t)及含氧官能团数量,降低了灰分、碱性、碳含量、平均孔径及其芳香性,各老化作用强度排序为：氧化老化生物炭(OBC)>矿化老化生物炭(KBC)>微生物老化生物炭(MBC)>干湿循环老化生物炭(WBC)>冻融循环老化生物炭(FBC)>BC。生物炭的添加减少...     

Biochemical characterization of the δ-carbonic anhydrase from the marine diatom Thalassiosira weissflogii,TweCA

Abstract

Diatom genome sequences clearly reveal the presence of different systems for HCO₃^? uptake. Carbon-concentrating mechanisms (CCM) based on HCO₃^? transport and a plastid-localized carbonic anhydrase (CA, EC 4.2.1.1) appear to be more probable than the others because CAs have been identified in the genome of many diatoms. CAs are key enzymes involved in the acquisition of inorganic carbon for photosynthesis in phytoplankton, as they catalyze efficiently the interconversion between carbon dioxide and bicarbonate. Five genetically distinct classes of CAs exist, α-, β-, γ-, δ- and ζ and all of them are metalloenzymes. Recently we investigated for the first time the catalytic activity and inhibition of the δ-class CA from the marine diatom Thalassiosira weissflogii, named TweCA. This enzyme is an efficient catalyst for the CO₂ hydration and its inhibition profile with sulfonamide/sulfamate and anions have also been investigated. Here, we report the detailed biochemical characterization and chemico-physical properties of the δ-CA of T. weissflogii. The δ-CA encoding gene was cloned and expressed in Artic Express cells and the recombinant protein purified to homogeneity. Interesting to note that TweCA has no intrinsic esterase activity with 4-nitrophenyl acetate (pNpA) as substrate although the phylogenetic analysis showed that δ-CAs are closer to the α-CAs than to the other classes of such enzymes.