ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures

ProBiS-Database is a searchable repository of precalculated local structural alignments in proteins detected by the ProBiS algorithm in the Protein Data Bank. Identification of functionally important binding regions of the protein is facilitated by structural similarity scores mapped to the query protein structure. PDB structures that have been aligned with a query protein may be rapidly retrieved from the ProBiS-Database, which is thus able to generate hypotheses concerning the roles of uncharacterized proteins. Presented with uncharacterized protein structure, ProBiS-Database can discern relationships between such a query protein and other better known proteins in the PDB. Fast access and a user-friendly graphical interface promote easy exploration of this database of over 420 million local structural alignments. The ProBiS-Database is updated weekly and is freely available online at http://probis.cmm.ki.si/database.     

Quantitative analysis of complex amino acids and RGD peptides by X‐ray photoelectron spectroscopy (XPS)

The C 1 s, N 1 s, and O 1 s core level binding energies (BEs) of the functional groups in amino acids (glycine, aspartic acid, glutamic acid, arginine, and histidine) with varied side‐chains and cell‐binding RGD‐based peptides have been determined and characterized by X‐ray photoelectron spectroscopy with a monochromatic Al K_α source. The zwitterionic nature of the amino acids in the solid state is unequivocally evident from the N 1 s signals of the protonated amine groups and the C 1 s signature of carboxylate groups. Significant adventitious carbon contamination is evident for all samples but can be quantitatively accounted for. No intrinsic differences in the XP spectra are evident between two polymorphs (α and γ) of glycine, indicating that the crystallographic differences have a minor influence on the core level BEs for this system. The two nitrogen centers in the imidazole group of histidine exhibit an N 1 s BE shift that is in line with previously reported data for theophylline and aqueous imidazole solutions, while the nitrogen and carbon chemical shifts reflect the unusual guanidinium chemical environment in arginine. It is shown that the complex envelopes of C 1 s and O 1 s photoemission spectra for short‐chain peptides can be analyzed quantitatively by reference to the less complex XP spectra of the constituent amino acids, provided the peptides are of high enough purity. The distinctive N 1 s photoemission from the amide linkages provides an indicator of peptide formation even in the presence of common impurities, and variations in the relative intensities of N 1 s were found to be diagnostic for each of the three peptides investigated (RGD, RGDS, and RGDSC). Copyright © 2013 John Wiley & Sons, Ltd.     

Ultraviolet Reflection Irradiances and Exposures in The Constructed Environment For Horizontal,Vertical and Inclined Surfaces

Ultraviolet (UV) reflection in the urban constructed environment is not well understood for topical issues such as measuring and modeling the received UV exposure due to that UV reflection for outdoor workers. Both predominantly specular and diffuse reflecting surface types have been identified and investigated for the erythemal UV reflection ratio variation due to solar zenith angle and orientation. This paper presents relationships between erythemal UV reflection ratios measured for non‐horizontal and horizontal surfaces, with predominantly specular surface types indicating stronger relationships with solar zenith angles than diffuse reflecting surfaces types. Erythemal UV exposures caused by the same reflecting surface types at three inclinations are also investigated. Non‐horizontal surfaces can increase erythemal UV exposures compared to erythemal UV exposures received from the same horizontal surface by factors of 1.07–1.46 for specific body sites and by 1.01–1.70 for averages of group body sites for zinc aluminium coated steel sheeting.     

The Mechanism of Reaction between Poly(vinyl Alcohol) and Phosphorous Acid

The reaction mechanism of phosphorous acid and poly(vinyl alcohol) is presented. It has been found that there during this reaction mono- and diesters are formed in which most of the acid radicals are in the phosphonic form. To confirm the presence of this form in the product obtained, reactions with diethyleneamine and chloral have been carried out as characteristic tests for phosphonic groups. The occurrence of C—P bonds resistant to hydrolysis has been also found in the reaction product.     

Application of Sulfinyl bis(2,4‐dihydroxythiobenzoyl) in the Synthesis of N‐Substituted 2‐Amino‐5‐(2,4‐dihydroxyphenyl)‐1,3,4‐thiadiazoles

One‐stage synthesis of N‐substituted 2‐amino‐5‐(2,4‐dihydroxyphenyl)‐1,3,4‐thiadiazoles is described. The compounds were prepared by the reaction of the sulfinyl bis(2,4‐dihydroxythiobenzoyl) (STB) with 4‐substituted 3‐thiosemicarbazides. STB was obtained from 2,4‐dihydroxybenzenecarbodithioic acid and thionyl dichloride. The structure of compounds was confirmed by IR, ¹H NMR, ¹³C NMR, and EI‐MS data.     

Evaluation of a purge-and-trap injection system for capillary gas chromatography-microwave induced plasma-atomic emission spectrometry for the determination of volatile selenium compounds in water

A method is presented for the selective determination of the volatile selenium species dimethylselenide and dimethyldiselenide, using a commercially available purge-and-trap injection system coupled to capillary gas chromatography-microwave induced plasma-atomic emission spectrometry. The efficiency of the purging step was evaluated and the parameters affecting the purge and trap processes were optimized. The method was applied to the determination of volatile selenium compounds in lake water. Relative detection limits of 2ng/l for dimethylselenide and dimethyldiselenide, corresponding to an absolute detection limit of 10 pg, were achieved.     

Pyracene‐Linked Bis‐Imidazolylidene Complexes of Palladium and Some Catalytic Benefits Produced by Bimetallic Catalysts

Two new palladium complexes with a pyracene‐linked bis‐imidazolylidene (pyrabim) group have been obtained and fully characterized. The related monometallic analogues were obtained from the coordination of an acetanaphthene‐supported N‐heterocyclic carbene (NHC). The catalytic properties of all complexes were studied in the acylation of aryl halides with hydrocinnamaldehyde, and in the Suzuki–Miyaura coupling of aryl halides and aryl boronic acids. The results show that the presence of a second metal in the dimetallic complexes induces some benefits in the catalytic behavior of the complexes. This effect is more pronounced in the Suzuki–Miyaura coupling, for which the dimetallic complexes exhibit significantly higher activity than their monometallic counterparts.     

Biparametric multicommutated flow analysis system for determination of human serum phosphoesterase activity

A multicommutated flow analysis (MCFA) system constructed of microsolenoid valves and pumps offering simultaneous determination of activity of acid phosphatase (ACP) and alkaline phosphatase (ALP) in human serum samples has been developed. The MCFA system is based on optoelectronic flow-through detector made of two light emitting diodes and operating according to paired emitter detector diode (PEDD) principle. This photometric PEDD device has been dedicated for detection of p-nitrophenol (NP) generated in the course of enzymatic hydrolysis of p-nitrophenyl phosphate and optimized for the determination of NP in human serum samples. The developed PEDD-based MCFA system allows independent optimization of conditions for reaction and detection steps of photometric ACP and ALP bioassays. Moreover, it allows elimination of photometric interferences from serum matrix components according to two-points kinetic mode of measurement. The single measurement cycle takes 12 min, consists of four measurements (two for each phosphoesterase) and enables determination of serum ACP and ALP activities at physiological and pathological levels. The real analytical utility of the developed MCFA system has been confirmed by analysis of control sera as well as real human serum samples from healthy persons and oncological patients.     

Efficient One‐Pot Synthesis of a Densely Functionalized Tetrahydropyridine in the Presence of [1,1′‐Binaphthalene]‐2,2′‐diol/Indium(III) Chloride (binol/InCl3) or Simple Brønsted Acids as Catalysts

The highly functionalized tetrahydropyridine 4 was obtained in an indium(III) chloride catalyzed multi‐component reaction from benzaldehyde, 4‐methoxyaniline, and ethyl acetoacetate (=ethyl 3‐oxobutanoate) in the presence of [1,1′‐binaphthalene]‐2,2′‐diol (binol). It was found that binol played a beneficial role in this reaction, allowing a substantial decrease of the amount of indium salt. Also, simple organic Brønsted acids may serve as effective organocatalysts in this process.