Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

用共振光散射技术研究蛋白质与丽春红2R的相互作用

在pH3．50的Britton-Robinson缓冲溶液中，丽春红2R与蛋白质发生结合反应，使最大波长为352．5nm的共振散射光谱得到加强。据此建立了利用丽春红2R作探针，用共振散射光谱技术测定蛋白质的新方法。散射光强度与牛血清白蛋白(BSA)、人血清白蛋白(HAS)和免疫球蛋白(IgG)的浓度在0．25～17．5μg／mL范围内成正比。方法的稳定性好，快速、简便，绝大多数氨基酸、金属离子均不产生干扰，用于人血清样品中蛋白质的测定，获得了满意的结果，加标回收率为93．4％～100．1％。     

On-line identification of tropane alkaloids from Erythroxylum vacciniifolium by liquid chromatography-UV detection-multiple mass spectrometry and liquid chromatography-nuclear magnetic resonance spectrometry

The bark of catuaba (Erythroxylum vacciniifolium Martius, Erythroxylaceae), a tree native to the northern part of Brazil, was investigated for its alkaloid content. With the aim of obtaining preliminary structure information on-line, the alkaloid extract was analysed by high-performance liquid chromatography coupled to diode array UV detection, to mass spectrometry and to nuclear magnetic resonance. Interpretation of on-line spectroscopic data obtained from this extract led to structural elucidation of six new alkaloids and partial identification of 18 potentially original alkaloids bearing the same tropane skeleton esterified in positions 3 and 6 by 1-methyl-1H-pyrrol-2-carboxylic acid and/or 4-hydroxy-3,5-dimethoxybenzoic acid.     

Observation of self-ion-molecule reactions during collisionally activated dissociation in an ion-trap mass spectrometer

This paper describes the formation of protonated molecules ([M + H]+) and adduct ions by self-ion-molecule reactions (SIMR) during collisionally activated decomposition (CAD) of methyne addition ions ([M + CH]+) produced from chemical ionization (CI) or SIMR in both an external and internal source ion-trap mass spectrometer (ITMS). The CAD results for the methyne addition ions of dopamine produced from both SIMR and dimethyl ether CI undertaken in the external and internal source ITMS were compared in order to prove the occurrence of SIMR during CAD processes. Compared with the external source ITMS, the internal source ITMS is much more easily applicable to this type of reaction owing to the large population of neutral analytes present in the trap.     

Resonance Rayleigh scattering determination of trace amounts of Al in natural waters and biological samples based on the formation of an Al(III)-morin-surfactant complex

A novel method for the determination of trace amounts of Al(III) based on resonance Rayleigh scattering (RRS) has been developed. In the presence of some surfactants, Al(III) can react with morin and form an Al(III)-morin-surfactant complex, which results in the enhancement of RRS intensity and the appearance of the corresponding RRS spectral characteristics. Their maximum scatter peaks are at 476 nm for the cetyltrimethylammonium bromide (CTAB) system, 489 nm for the cetylpyridinium chloride (CPC) system, 474 nm for the Triton X-100 system, and 473 nm for the Tween-20 system. The enhanced RRS intensity is directly proportional to the concentration of Al(III). The detection limits are in the range of (0.50-1.2)×10⁻⁷ mol l⁻¹ depending on the surfactant. The characteristics of RRS spectra of the complexes, the optimum conditions of these reactions and the influencing factors have been investigated. The method has high selectivity, and was successfully applied to the determination of Al(III) in natural and biological samples. Furthermore, according to different complexation capacity of Al(III)-morin-CTAB system under two pH conditions, speciation analysis of Al(III) in natural waters was explored. The labile monomeric Al fraction (mainly inorganic Al, Al_i) is determined at acidic pH and the total monomeric Al fraction (Al_a) is determined at alkaline pH. The results are in agreement with those obtained by Driscoll’s 8-hydroxyquinoline extraction-ion exchange method.     

Determining the chromophore in the amylopectin–iodine complex by theoretical and experimental studies

A partial hydrolysis of amylose followed by the addition of iodine provides a spectrum almost identical to that of the amylopectin–iodine (API) complex suggesting the involvement of smaller “amylose-like” units in the API complex. Our theoretical studies on different polyiodine and polyiodide species suggest that a nearly linear I₄ unit stabilized within the cavity of a small “amylose-like” helix is responsible for the characteristic API spectrum. Since there are 2.75 anhydroglucose residues (AGU) for every iodine atom in the amylose–iodine (AI) complex and a structural similarity exists between the API and the AI (amylose–iodine) complexes, we identify (C₆H₁₀O₅)₁₁I₄ to be the chromophore in the API complex. © 1994 John Wiley & Sons, Inc.     

Organoelement Compounds with Al?Al,Ga?Ga,and In?In Bonds

In the attempt to synthesize compounds with aluminum in a low oxidation state and an Al Al bond, by the reduction of alkylaluminum halides with alkali metals, analogous to a Wurtz coupling, in general the deposition of elemental aluminum and the formation of the corresponding trialkylaluminum compounds is observed. Thus, tetrasubstituted dialuminum compounds R₂Al AlR₂, apart from a few poorly characterized examples, were for a long time considered part of an unverified class of substances. Only with the sterically very highly shielded tetrakis[bis(trimethylsilyl)methyl]dialuminum did we achieve the synthesis of the first completely characterized organoelement compound with unlimited stability, which shows aluminum in the oxidation state + II and has an Al Al bond. In the meantime, corresponding compounds for the elements gallium and indium have been obtained. With the simple access to tetrasubstituted dimetal compounds, a fascinating new research area has opened for preparative chemistry, in which the particular interest will naturally lie in the reactive properties of the metal-metal bond.     

Probing in vitro digestion at oil–water interfaces

Interfacial layers have been widely applied to study the formation and stability of emulsion-based systems. However, the application of isolated interfaces to address digestibility of emulsions is often limited because of the complexity of experimental methods and results. This review summarizes the latest developments in analytical methods and literature data on effects of digestion on interfacial layers. Particular emphasis is given to understand the changes on interfacial magnitudes during oral, gastric, and duodenal digestion, either applied separately or sequentially. Limitations of interfacial aspects and key factors that influence emulsion microstructure in bulk and lipid digestion are identified. Understanding the behavior of interfacial layers upon gastrointestinal digestion promotes an accurate tracking of the physiological fate of emulsions.     

Fermentation characteristics and the dynamic trend of chemical components during fermentation of Massa Medicata Fermentata

As a representative of traditionally fermented Chinese medicine, Massa Medicata Fermentata (MMF) shows the functions of invigorating the spleen and stomach and promoting digestion, which plays an important role in the treatment of gastrointestinal diseases. The fermentation mechanism and the key factors that affect the quality of MMF have not been revealed yet, which has become an urgent issue that limits its clinical application. This article aims to systematically and comprehensively reveal the transformation of physical properties and the dynamic trend of chemical components including substrate components, volatile components, and lactic acid as anaerobic fermentation product during MMF fermentation. Along with obvious hyphae growth observed for MMF, the weight of MMF decreased, and the moisture and temperature increased. Through the quantified 14 components from substrate, ferulic acid increased from 45.53 ± 6.94 to 141.89 ± 78.40 μg/g, while glycosides and phenolic acids declined except caffeic acid. Also, within the 66 volatile components analyzed, alcohols and acids increased, while aldehydes and ketones decreased. Lactic acid was not detected in the fermentation substrate, but an apparent increase in lactic acid content was observed along with the increased fermentation days, resulting in 2.54 ± 0.15 mg/g on day 8. Based on the tested components, the fermentation process of MMF was discriminated into three distinct stages by principal component analysis, and an optimal fermentation time of four days was proposed. The results of this study will be of great significance to clarify the characteristics of fermentation and conduce to improving quality standards of MMF.     

On the Criteria of Instability for Electrochemical Systems

Both cyclic-voltammetry-based and impedance-based experimental criteria that have been developed recently for the oscillatory electrochemical systems are critically appraised with two typical categories of oscillators.Consistent conclusions can be drawn by the two criteria for the category of oscillators that involve the coupling of charge transfer mainly with surface steps(e.g.ad-and desorption)such as in the electrooxidation of C1 organic molecules.Whereas,impedance-based criterion is not applicable to the category of oscillators that involve the coupling of charge transfer mainly with mass transfer(e.g.diffusion and convection) such as in the Fe(CN)6^3- reduction accompanying periodic hydrogen evolution.The reason is that the negative impedance cannot include the feedback information of convection mass transfer induced by the hydrogen evolution.However,both positive and negative nonlinear feedbacks,i.e., the diffusion-limited depletion and convection-enhanced replenishment of the Fe(CN)6^3- surface concentration,that coexist between the bistability,i.e.,Fe(CN)6^3- reduction with and without hydrogen evolution at lower and higher potential sides respectively,are all reflected in the crossed cyclic voltammogram(CCV).It can be concluded that the voltammetry-based criterion(in time domain)is more intuitive,less time-consuming and has a wider range of applications than the impedancebased one (in frequency domain).