The interaction of superoxide radicals with active dicarbonyl compounds

The interaction of superoxide radical anion (O₂ ^??) with active dicarbonyls (methylglyoxal, glyoxal, and malonic dialdehyde) was studied. It was demonstrated that glyoxal and methylglyoxal inhibited superoxide-dependent accumulation of formazan; however, malonic dialdehyde stimulated this process. The formation of O₂ ^?? in these experiments occurred during the decomposition of the SOTS-1 azo initiator. On the other hand, all of the studied dicarbonyls in this system of O₂ ^?? generation competed for superoxide with the TIR ON spin trap. These compounds also inhibited luminal-dependent chemiluminescence during the AIBN azo initiator-induced peroxidation of liposomes from the egg phosphatidylcholine. A mechanism for the antiradical and antioxidant effects of the studied dicarbonyls, assuming the production of free radical intermediates in their reactions with O₂ ^?? or its protonated form, is proposed.     

Superoxide formation as a result of interaction of L-lysine with dicarbonyl compounds and its possible mechanism

The EPR signal recorded in reaction medium containing L-lysine and methylglyoxal is supposed to come from the anion radical (semidione) of methylglyoxal and cation radical of methylglyoxal dialkylimine. These free radical inter-mediates might be formed as a result of electron transfer from dialkylimine to methylglyoxal. The EPR signal was observed in a nitrogen atmosphere, whereas only trace amounts of free radicals were registered under aerobic conditions. It has been established that the decay of methylglyoxal anion radical on aeration of the medium is inhibited by superoxide dismutase. Using the methods of EPR spectroscopy and lucigenin-dependent chemiluminescence, it has been shown that nonenzymatic generation of free radicals including superoxide anion radical takes place during the interaction of L-lysine with methylglyoxal — an intermediate of carbonyl stress — at different (including physiological) pH values. In the course of analogous reaction of L-lysine with malondialdehyde (the secondary product of the free radical derived oxidation of lipids), the formation of organic free radicals or superoxide radical was not observed.     

Thiol peroxyl radical formation from the reaction of cysteine thiyl radical with molecular oxygen: an ESR investigation

Using Electron Spin Resonance (ESR) spectroscopy, we have identified the cysteine thiol peroxyl radical (CysSOO.) at low temperatures in two aqueous glasses. This radical shows a typical peroxyl radical ESR spectrum, but unlike carbon-based peroxyl radicals has a violet color (lambda max = 540 nm) and forms a new radical showing a singlet ESR spectrum when photobleached with visible light. The cysteine peroxyl radical reacts to form the cysteine sulfinyl radical (CysSO.) in the glass which allows warming to 165K. 17O isotopic substitution studies indicate dissolved molecular oxygen is the source of oxygen in CysSOO.. Anisotropic g-values and the parallel anisotropic 17O hyperfine couplings for this radical are reported.     

Theoretical studies on the heats of formation, densities, and detonation properties of substituted s-tetrazine compounds

Substituted s-tetrazine compounds were designed and investigated in order to find comprehensive relationships between the structures and performances of high-nitrogen energetic compounds. Density functional theory (DFT) was used to predict the optimized geometries, electronic structures, heats of formation and densities, and the detonation properties were evaluated by using the VLW equation of state (EOS). Calculation results show that there are good linear relationships between heats of formation, densities, detonation properties and the number of N atom in all designed high-nitrogen compounds. Furthermore, several designed high-nitrogen compounds show good detonation velocities and pressures compared with octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX), making them potential candidates for high-energy-density materials (HEDM).     

Sulfinyl radical formation from the reaction of cysteine and glutathione thiyl radicals with molecular oxygen

Using Electron Spin Resonance spectroscopy at low temperatures, we find that thiyl radicals resulting from irradiation of frozen aqueous solutions of a variety of thiols, including cysteine, glutathione, and penicillamine react with oxygen to form sulfinyl (RSO.) radicals. The identity of the cysteine sulfinyl radical has been confirmed by the use of molecular oxygen isotopically labeled with 17O. Previous workers have suggested the reaction of thiyl radicals and molecular oxygen resulted in the formation of the potentially damaging thiol peroxyl radical, RSOO.; our work shows no evidence for this species. The sulfinyl radicals are suggested to result from a direct reaction between thiyl radicals and molecular oxygen. This reaction results in the cleavage of the dioxygen bond.     

From pull-down data to protein interaction networks and complexes with biological relevance

Motivation: Recent improvements in high-throughput Mass Spectrometry(MS) technology have expedited genome-wide discovery of protein–proteininteractions by providing a capability of detecting proteincomplexes in a physiological setting. Computational inferenceof protein interaction networks and protein complexes from MSdata are challenging. Advances are required in developing robustand seamlessly integrated procedures for assessment of protein–proteininteraction affinities, mathematical representation of proteininteraction networks, discovery of protein complexes and evaluationof their biological relevance. Results: A multi-step but easy-to-follow framework for identifyingprotein complexes from MS pull-down data is introduced. It assessesinteraction affinity between two proteins based on similarityof their co-purification patterns derived from MS data. It constructsa protein interaction network by adopting a knowledge-guidedthreshold selection method. Based on the network, it identifiesprotein complexes and infers their core components using a graph-theoreticalapproach. It deploys a statistical evaluation procedure to assessbiological relevance of each found complex. On Saccharomycescerevisiae pull-down data, the framework outperformed othermore complicated schemes by at least 10% in F₁-measure and identified610 protein complexes with high-functional homogeneity basedon the enrichment in Gene Ontology (GO) annotation. Manual examinationof the complexes brought forward the hypotheses on cause offalse identifications. Namely, co-purification of differentprotein complexes as mediated by a common non-protein molecule,such as DNA, might be a source of false positives. Protein identificationbias in pull-down technology, such as the hydrophilic bias couldresult in false negatives. Contact: samatovan{at}ornl.gov Supplementary information: Supplementary data are availableat Bioinformatics online. Associate Editor: Jonathan Wren Present address: Department of Biomedical Informatics, VanderbiltUniversity, Nashville, TN 37232. The authors wish it to be known that, in their opinion, thefirst two authors should be regarded as joint First Authors.     

捕食者-猎物关系的理论和应用研究

捕食者和猎物相互关系的研究,长期以来一直是动物生态学研究的中心课题之一。这种研究可区分为3种类型:第一是理论研究,即组建各种数学模型以便模拟捕食者和猎物间的相互关系;第二是实验种群研究,通常是在实验室内选用原生动物和节肢动物实验种群对捕食一猎物间的动态关系进行观察,并将观察结果与理论模型进行比较;第三是在田间对自然种群中的捕食者-猎物关系进行研究,并利用从理论研究和实验种群研究中所总结出来的各种基本原理对观察资料进行分析。在应用生态学领域中,常常靠引进新的更加有效的天敌来控制各种害虫。这些实际工作有些已获得成功,也有不少未取得预期效果,不管成功与否,它们都可被看作是对捕食者-猎物关系所进行的田间实验.     

Spin trapping the cysteine thiyl radical with phenyl-N-t-butylnitrone

The cysteine thiyl radical has been detected in a variety of biological systems by means of the ESR spectrum of the adduct between the radical and nitrone spin traps. 5,5-Dimethyl-1-pyroline N-oxide (DMPO) is the spin trap of choice in these studies for several reasons. However, we show here that the adduct between the cysteine thiyl radical and phenyl-N-t-butylnitrone (PBN) spin trap can be observed under certain oxidizing conditions where the adduct with DMPO is not detected. This suggests the use of PBN in searching for the thiyl radical under such conditions.     

Theoretical studies on the interaction of guanine riboswitch with guanine and its closest analogues

Experimental studies (M. Mandal, B. Boese, J.E. Barrick, W.C. Winkler and R.R. Breaker, Riboswitches control fundamental biochemical pathways in bacillus subtilis and other bacteria, Cell 113 (2003), pp. 577–586) demonstrated that, besides recognising guanine with high specificity, guanine riboswitch could also bind guanine analogues, but the alteration of every functionalised position on the guanine heterocycle could cause a substantial loss of binding affinity. To investigate the nature of guanine riboswitch recognising metabolites, molecular docking and molecular dynamics simulation were carried out on diverse guanine analogues. The calculation results reveal that (1) most guanine analogues could bind to guanine riboswitch at the same binding pocket, with identical orientations and dissimilar binding energies, which is related to the positions of the functional groups; (2) the two tautomers of xanthine adopt different binding modes, and the enol-tautomer shows similar binding mode and affinity of hypoxanthine, which agrees well with the experimental results and (3) the riboswitch could form stable complexes with guanine analogues by hydrogen bonding contacts with U51 and C74. Particularly, U51 plays an important role in stabilising the complexes.     

Theoretical studies of the interaction between enflurane and water

Increase of the atmospheric concentration of halogenated organic compounds is partially responsible for a change of the global climate. In this work we have investigated the interaction between halogenated ether and water, which is one of the most important constituent of the atmosphere. The structures of the complexes formed by the two most stable conformers of enflurane (a volatile anaesthetic) with one and two water molecules were calculated by means of the counterpoise CP-corrected gradient optimization at the MP2/6–311++G(d,p) level. In these complexes the CH…O_w hydrogen bonds are formed, with the H…O_w distances varying between 2.23 and 2.32 Å. A small contraction of the CH bonds and the blue shifts of the ν(CH) stretching vibrations are predicted. There is also a weak interaction between one of the F atoms and the H atom of water, with the H_w…F distances between 2.41 and 2.87 Å. The CCSD(T)/CBS calculated stabilization energies in these complexes are between ?5.89 and ?4.66 kcal?mol^?1, while the enthalpies of formation are between ?4.35 and ?3.22 kcal?mol^?1. The Cl halogen bonding between enflurane and water has been found in two complexes. The intermolecular (Cl···O) distance is smaller than the sum of the corresponding van der Waals radii. The CCSD(T)/CBS stabilization energies for these complexes are about ?2 kcal?mol^?1.

Theoretical studies on the interaction of biphenyl inhibitors with Mycobacterium tuberculosis protein tyrosine phosphatase MptpB

MptpB is an essential secreted virulence factor for M. tuberculosis. Inhibition of MptpB impairs mycobacterial survival in host macrophages and thus helps reduce tuberculosis infections. However, the binding mode of the biphenyl inhibitors, which are known as some of the most potent MptpB inhibitors, remains unclear. In this study, to understand the interactions between biphenyl inhibitors and MptpB, docking and molecular dynamics simulations were carried out using AutoDock and GROMACS softwares. Calculation results show that all the biphenyl inhibitors can be docked to the binding site of MptpB, with the acid warheads forming a hydrogen bond network at the active site. But the binding modes of other terminals of these inhibitors are different. The cyclohexyl and trifluoromethyl substituents at R1 and R2 sites are necessary for the inhibitors to adopt their double-site binding mechanism. The estimated binding affinities are basically consistent with the experimental results. MD simulations show that these binding complexes display different stability.     

Theoretical studies of binding modes of two covalent inhibitors of cysteine proteases

Physiological and pathological roles of cysteine proteases make them important targets for inhibitor development. Although highly potent inhibitors of this group of enzymes are known, their major drawback is a lack of sufficient specificity. Two cysteine protease covalent inhibitors, viz. (i) Z-RL-deoxo-V-peptide-epoxysuccinyl hybrid, and (ii) Z-RLVG-methyl-, have been developed and modeled in the catalytic pocket of papain, an archetypal thiol protease. A number of configurations have been generated and relaxed for each system using the AMBER force field. The catalytic pockets S3 and S4 appear rather elusive in view of the observed inhibitors' flexibility. This suggest rather limited chances for the development of selective structure-based inhibitors of thiol proteases, designed to exploit differences in the structure of catalytic pockets of various members of this family.     

Fluorescence and ESR spectroscopy studies on the interaction of isoflavone genistein with biological and model membranes

Genistein (5,7,4′-trihydroxyisoflavone) the common soy beans isoflavone has attracted scientific interest due to its antioxidant, estrogenic, antiangiogenic and aniticancer activities. The aim of the present study was to investigate the interaction of genistein with biological (erythrocyte) and model membranes (dimyristoyl- and dipalmitoylphosphatidylcholine). Using Laurdan and Prodan as fluorescent probes, we demonstrated phase behavior and membrane fluidity changes induced by genistein. ESR spectroscopy revealed alterations caused by genistein in membrane domains structure and mobility of spin probes with free radicals located at different depths of membrane. The method of ESR spectra decomposition and computer simulation of the recorded spectra were used in order to visualize domain coexistence by GHOST condensation method. Fluorescence and ESR spectroscopy experiments performed at different temperatures enabled us to observe the effect of isoflavone on phospholipid bilayers in either gel or liquid crystalline phase. It was concluded that genistein preferentially intercalated into lipid headgroup region, to some extent into polar–apolar interface and only in minimal degree into hydrophobic core of the membrane. According to our best knowledge this is the first study on modification of domain structure of membranes by genistein.     

应用化学基因组信息预测小分子化合物的潜在生物靶标的理论方法

在后基因组时代,化学基因组技术在药物作用靶点的确认、小分子化合物对通路的作用,以及小分子先导化合物的识别等方面都有着广泛的应用,为新药研发提供了新的技术方法。本文主要介绍了当前几种基于化学基因组信息来预测小分子化合物潜在生物靶标的理论方法（包括化学相似性搜索方法、反向分子对接方法、数据挖掘方法以及生物活性谱图分析方法）,并分析了这些方法的优缺点以及应用前景。     

ESR spin-trapping studies on the formation of thiosulfate and sulfide radical anions in aqueous solutions

The first spin-trapping evidence for the formation of thiosulfate (S2O3-.) and sulfide (S-.) radical anions from the reactions of hydrogen peroxide with thiosulphate and sulphide ions, respectively, was presented by electron spin resonance (ESR) spectroscopy using 3,5-dibromo-4-nitrosobenzenesulfonate (DBNBS, 1a) as a spin-trap in aqueous solutions. From the facts that the short-lived radical anions, S2O3-. and S-., could be detected during the oxidation with H2O2, it is suggested that these radical anions may become one of the candidates for the toxicity of sulfide ion in the living body.