Structural insights into the effect of isonucleosides on B-DNA duplexes using molecular-dynamics simulations

Some structural insights into the conformations of the isonucleosides containing duplexes have been provided. Unrestrained molecular-dynamics simulations on 18-mer duplexes with isonucleosides incorporated at the 3'-end or in the center of one strand have been carried out with explicit solvent under periodic boundary conditions using the AMBER force field and the particle mesh Ewald method. The Watson–Crick hydrogen-bonding patterns of the duplexes studied remained intact throughout the simulation. For the modified duplexes, the changes observed in the inter-base pair parameters and backbone torsional angles were primarily localized at the isonucleoside-inserted area. All five structures studied remained in the B-form family. The decreased stacking abilities indicated by the large changes in inter-base pair parameters and the large changes in backbones made the modified duplexes show a minor thermal destabilization in comparison with native DNA. The MM_PBSA method for estimating binding free energies on two complementary strands was used. The results showed that the binding free energies of isonucleoside-incorporated DNA duplexes were lower than the native DNA duplex, which is in good agreement with experimental observations.      

Mononuclear copper(II) nitrato complexes with methyl-substituted 4-nitropyridine N-oxide. Physicochemical and cytotoxic characteristics

Three new complexes, products of the interaction of Cu(NO₃)₂ and methyl-substituted 4-nitropyridine N-oxides were synthesized and characterized by elemental analysis, magnetic, spectroscopic (IR, FIR and EPR), thermal and X-ray methods. The complexes (magnetic moments 1.70-1.81 BM at 300 K) of general formula [Cu(H₂O)(NO₃)₂L₂], L = 2-methyl-4-nitropyridine N-oxide and [Cu(NO₃)₂ L′₂], where L′ = 2,6-dimethyl- and 2,3,6-trimethyl-4-nitropyridine N-oxide were obtained. The compounds were unstable upon dissolution. The X-ray single crystal structure of Cu(II) complex with 2,6-dimethyl-4-nitropyridine N-oxide was determined and analysed. The compounds and free ligands were tested in vitro on the cytotoxic activity against MCF-7 and SW-707 human cancer cell lines. The complexes with 4-nitropyridine N-oxide (a reference) and 2-methyl-4-nitropyridine N-oxide show a significant anti-proliferative activity against studied cell lines. A reciprocal relationship between the activity and the number of methyl groups was observed. Both ligands and complexes are cytotoxic active but to the different cell lines.     

Role of a disulphide bond in Helicobacter pylori arginase

Arginase is a binuclear Mn²⁺-metalloenzyme of urea cycle that hydrolyses arginine to ornithine and urea. Unlike other arginases, the Helicobacter pylori enzyme is selective for Co²⁺. Previous study reported that DTT strongly inhibits the H. pylori enzyme activity suggesting that a disulphide bond is critical for the catalysis. In this study, we have undertaken steady-state kinetics, circular dichroism and mutational analysis to examine the role of a disulphide bond in this protein. By mutational analysis, we show that the disulphide bond is not important for catalytic activity; rather it plays an important role for the stability of the protein as observed from thermal denaturation studies. The loss of catalytic activity in the wild-type protein with DTT is due to the interaction with Co²⁺. This is verified with the Mn²⁺-reconstituted proteins which showed a marginal loss in the activity with DTT.     

Conservation and divergence on plant seed 11S globulins based on crystal structures

The crystal structures of two pro-11S globulins namely: rapeseed procruciferin and pea prolegumin are presented here. We have extensively compared them with the other known structures of plant seed 11S and 7S globulins. In general, the disordered regions in the crystal structures among the 11S globulins correspond to their five variable regions. Variable region III of procruciferin is relatively short and is in a loop conformation. This region is highly disordered in other pro-11S globulin crystals. Local helical and strand variations also occur across the group despite general structure conservation. We showed how these variations may alter specific physicochemical, functional and physiological properties. Aliphatic hydrophobic residues on the molecular surface correlate well with T_m values of the globulins. We also considered other structural features that were reported to influence thermal stability but no definite conclusion was drawn since each factor has additive or subtractive effect. Comparison between proA3B4 and mature A3B4 revealed an increase in r.m.s.d. values near variable regions II and IV. Both regions are on the IE face. Secondary structure based alignment of 11S and 7S globulins revealed 16 identical residues. Based on proA3B4 sequence, Pro60, Gly128, Phe163, Phe208, Leu213, Leu227, Ile237, Pro382, Val404, Pro425 and Val 466 are involved in trimer formation and stabilization. Gly28, Gly74, Asp135, Gly349 and Gly397 are involved in correct globular folding.     

Proteolysis approach without chemical modification for a simple and rapid analysis of disulfide bonds using thermostable protease‐immobilized microreactors

Disulfide bonds in proteins are important not only for the conformational stability of the protein but also for the regulation of oxidation–reduction in signal transduction. The conventional method for the assignment of disulfide bond by chemical cleavage and/or proteolysis is a time‐consuming multi‐step procedure. In this study, we report a simple and rapid analysis of disulfide bond from protein digests that were prepared by the thermostable protease‐immobilized microreactors. The feasibility and performance of this approach were evaluated by digesting lysozyme and BSA at several temperatures. The proteins which stabilize their conformations by disulfide bonds were thermally denatured during proteolysis and were efficiently digested by the immobilized protease but not by free protease. The digests were directly analyzed by ESI‐TOF MS without any purification or concentration step. All four disulfide bonds on lysozyme and 10 of 17 on BSA were assigned from the digests by the trypsin‐immobilized microreactor at 50°C. The procedure for proteolysis and the assignment were achieved within 2 h without any reduction and alkylation procedure. From the present results, the proteolysis approach by the thermostable protease‐immobilized microreactor provides a strategy for the high‐throughput analysis of disulfide bond in proteomics.     

Seasonal variations and inherent variability of selenium in marine biota of a tropical wetland ecosystem: implications for bioindicator species

The present study was designed to study the seasonal variations of selenium in marine biota of different trophic levels collected from Sunderban deltaic complex, northeast India. The primary objective of this work is to provide baseline data for a future environmental quality programme. In general, the sequence of Se accumulation observed in biota is as follows: Bivalve>Zooplankton>Macroalgae>Pisces>Seagrass. An elevated level of Se was recorded during monsoon season. The Se level in zooplankton (4 μg/g) was three to four times higher than seagrass. The content of various soft tissues and shell in bivalves molluscs showed an organ-specific pattern in the following order: gill > visceral MASS = mantle > adductor muscle > podium > shell. Fish contain less Se in comparison with macroalgae, zooplankton and bivalves revealing poor or insignificant trophic transfer of Se in the marine food chain. Pelecyora trigona (Bivalve) seems to be reliable indicator of Se contamination because of its high accumulation capacity. An in-depth monitoring program is recommended in order to clarify the present trend and to establish the studied biota as indicator species.     

API法在马鞍山市空气质量评价中的应用

大气环境质量综合评价,就是将监测点的监测数据与国家规定的大气质量标准等级相比较,进行综合评价,为环保及相关职能部门提供科学管理与污染防治决策依据,并为社会公众对大气环境质量认识提供一种尺度。评价大气环境质量的方法较多,如人工神经元网络法、模糊聚类法、主成分分析法和空气污染指数ＡＰＩ法等。其中以空气污染指数ＡＰＩ法(ＡｉｒＰｏｌｌｕｔｉｏｎＩｎｄｅｘ,简称ＡＰＩ)应用较为普遍,它是将空气污染物浓度简化为指数形式来表征空气污染程度和空气质量的方法[1]。目前我国以ＳＯ2、ＮＯＸ和ＴＳＰ(总悬浮颗粒物)为大气环…     

Physical and chemical perturbations induce the formation of protein aggregates with different structural features

The in vitro aggregation of the model GST–GFP fusion protein was induced by several effectors, including those mimicking variations occurring under cell stress conditions. In particular, we examined the effects of thermal treatments, redox state and pH variations, salt addition, and freezing and thawing cycles. The resulting aggregates displayed different morphologies as seen by electron microscopy, and different secondary and tertiary structures, as indicated by Fourier transform infrared spectroscopy and fluorescence. Therefore, proteins can be forced to undergo multiple aggregation pathways that lead to assemblies with different molecular structures and, possibly, specific physiological and pathological roles.In conclusion, great caution should be taken in inferring conclusions on protein aggregation and disaggregation in vivo from results obtained using aggregates produced under non-physiological perturbations.