Protein Folding: A Perspective from Theory and Experiment

The mechanism of protein folding (represented schematically below) is one of the most fascinating problems in the field of chemical reactions. This review presents the progess made recently in understanding key elements of this reaction and describes a solution to the often quoted Levinthal Paradox.     

Synthesis and properties of 4,5‐dihydrobenzo[e]imidazo[2,1‐c][1,4,2]diazaphosphinine derivatives

A number of 4,5‐dihydrobenzo[e]imidazo[2,1‐c][1,4,2]diazaphosphinine derivatives were prepared by the direct phosphorylation of 1‐(4‐Chlorophenylcarboxamido)‐2‐(1H‐1‐imidazolyl)‐5‐trifluoromethylbenzene in basic medium with phosphorus(III) bromide and dibromophenylphosphine. The tricyclic compounds 6a, 6b , and 9 having a trivalent phosphorus atom undergo the diazaphosphinine ring opening upon treatment with secondary amines in the presence of sulfur. © 2002 John Wiley & Sons, Inc. Heteroatom Chem 13:84–92, 2002; DOI 10.1002/hc.10000     

Is perturbation DFT approach applicable to purely repulsive fluids?

A recently proposed third order + second order perturbation density functional theory (DFT) approach is tested for the validity and applicability to purely repulsive model fluids subjected to various external fields. Hard core repulsive Yukawa potential, point particle Yukawa potential, and inverse power potential are employed as sample models. Theoretical DFT results are compared with the corresponding simulation data obtained by grand canonical ensemble Monte Carlo simulation. This comparison indicates that the third order + second order perturbation DFT approach is suitable for these purely repulsive fluids only on condition of high accuracy of the imported bulk second order direct correlation function (DCF). However, in this case the origin of the successful performance somewhat differs from that observed for the mean field approximation applied to van der Waals fluids. In the present case it originates from the observation that the bulk second order DCF is strongly dependent on the density argument for the hard-core part, while for the distances exceeding the core dimension this dependence is considerably weaker.     

Profiling of hydroxycinnamic acid amides in Arabidopsis thaliana pollen by tandem mass spectrometry

Phenylpropanoid polyamine conjugates are widespread in plant species. Their presence has been established in seeds, flower buds, and pollen grains. A biosynthetic pathway proposed for hydroxycinnamoyl spermidine conjugates has been suggested for the model plant Arabidopsis thaliana with a central acyl transfer reaction performed by a BAHD-like hydroxycinnamoyl transferase. A detailed liquid chromatography (LC)–electrospray ionization–mass spectrometry- and tandem-mass-spectrometry (MS/MS)-based survey of wild-type and spermidine hydroxycinnamoyl transferase (SHT) mutants identified more than 30 different bis- and tris-substituted spermidine conjugates, five of which were glycosylated, in the methanol-soluble fraction of the pollen exine. On the basis of characterized fragmentation patterns, a high-throughput LC–MS/MS method for highly sensitive HCAA relative quantification (targeted profiling) was developed. Only minor qualitative and quantitative differences in the pattern of bis-acyl spermidine conjugates in the SHT mutant compared to wild-type plants provide strong evidence for the presence of multiple BAHD-like acyl transferases and suggest a much more complex array of enzymatic steps in the biosynthesis of these conjugates than previously anticipated.     

Fragmentation behavior of Amadori‐peptides obtained by non‐enzymatic glycosylation of lysine residues with ADP‐ribose in tandem mass spectrometry

Mono‐ and poly‐adenosine diphosphate (ADP)‐ribosylation are common post‐translational modifications incorporated by sequence‐specific enzymes at, predominantly, arginine, asparagine, glutamic acid or aspartic acid residues, whereas non‐enzymatic ADP‐ribosylation (glycation) modifies lysine and cysteine residues. These glycated proteins and peptides (Amadori‐compounds) are commonly found in organisms, but have so far not been investigated to any great degree. In this study, we have analyzed their fragmentation characteristics using different mass spectrometry (MS) techniques. In matrix‐assisted laser desorption/ionization (MALDI)‐MS, the ADP‐ribosyl group was cleaved, almost completely, at the pyrophosphate bond by in‐source decay. In contrast, this cleavage was very weak in electrospray ionization (ESI)‐MS. The same fragmentation site also dominated the MALDI‐PSD (post‐source decay) and ESI‐CID (collision‐induced dissociation) mass spectra. The remaining phospho‐ribosyl group (formed by the loss of adenosine monophosphate) was stable, providing a direct and reliable identification of the modification site via the b‐ and y‐ion series. Cleavage of the ADP‐ribose pyrophosphate bond under CID conditions gives access to both neutral loss (347.10 u) and precursor‐ion scans (m/z 348.08), and thereby permits the identification of ADP‐ribosylated peptides in complex mixtures with high sensitivity and specificity. With electron transfer dissociation (ETD), the ADP‐ribosyl group was stable, providing ADP‐ribosylated c‐ and z‐ions, and thus allowing reliable sequence analyses. Copyright © 2010 John Wiley & Sons, Ltd.     

Electrochemical study of self-assembled monolayer adsorption

The electrochemical behaviour of self-assembled monolayer (SAM) of aliphatic hexadecanethiol was studied by cyclic voltammetry (CV), elimination voltammetry with linear scan (EVLS) and crystal quartz microbalance (QCM). SAMs were electrochemically created on gold-coated QCM crystal through the sulphur in 1-hexadecanethiol molecule head group. The effect of thiol concentration and potential scan rate on the SAM formation was studied. Formation of SAM was confirmed by CV and QCM. EVLS results revealed the kinetically controlled process followed with electrode reaction in adsorbed state characteristic for SAM formation at lower concentration. The electrode reaction of a totally adsorbed electroactive species was indicated by means of a peak-counter peak signal at higher thiol concentration.     

Molecular Structures of Dimeric and Trimeric Dineopentylaluminum Hydride and Trimeric Diphenylaluminum Hydride

The synthesis of dineopentylaluminum hydride, H‐Al(CH₂CMe₃)₂, is known in the literature since 1988. We determined the crystal structure of this important starting material and found different ring sizes with dimeric versus trimeric formula units. The molecular shape depends on the polarity of the solvent used for recrystallization (n‐pentane or 1,2‐difluorobenzene). The synthesis of diphenylaluminum hydride, which is also long known in the literature, was optimized. It has a trimeric structure in the solid state with an Al₃H₃ heterocycle.     

Oxidation of quinolones with peracids (an in situ EPR study)

4‐Oxoquinoline derivatives (quinolones) represent heterocyclic compounds with a variety of biological activities, along with interesting chemical reactivity. The quinolone derivatives possessing secondary amino hydrogen at the nitrogen of the enaminone system are oxidized with 3‐chloroperbenzoic acid to nitroxide radicals in the primary step while maintaining their 4‐pyridone ring. Otherwise, N‐methyl substituted quinolones also form nitroxide radicals coupled with the opening of the 4‐pyridone ring in a gradual oxidation of the methyl group via the nitrone–nitroxide spin‐adduct cycle. This was confirmed in an analogous oxidation using N,N‐dimethylaniline as a model compound. N‐Ethyl quinolones in contrast to its N‐methyl analog form only one nitroxide radical without a further degradation. Copyright © 2013 John Wiley & Sons, Ltd.     

129I levels in soils from Ukraine and Slovenia in the last decade

¹²⁹I is important as an environmental tracer of the biogeochemical cycling of iodine and of the dissemination of nuclear pollution, because anthropogenic ¹²⁹I has been released from only few point sources and with its short mixing time its distribution therefore reveals the movement of ¹²⁹I in the environment. A radiochemical neutron activation analysis method was developed to measure the concentration of ¹²⁹I in soil samples. A procedure to pre-concentrate iodine from up to 150?g of soil was developed and validated using IAEA standard reference material IAEA-375 (Chernobyl soil). The method was applied to determine ¹²⁹I/¹²⁷I isotopic ratios as well as ¹²⁹I and ¹²⁷I concentrations in soils from several locations in Ukraine collected in 2006, 1996, 1993 and 1989, and from Slovenia, collected at various places in 2009 and 2006. The ¹²⁷I concentrations in surface soils from Ukraine were in the range 2.3–23.1?µg?g^?1 and for ¹²⁹I (11.1–245.7)?·?10^?8?µg?g^?1 dry matter with the highest value of 1.47?·?10^?3?µg?g^?1 found in a soil sample collected in Yaniv, Ukraine in July 1993. In soil samples from Slovenia ¹²⁷I concentrations ranged 0.73–130?µg?g^?1 and ¹²⁹I (8.0–245.7)?·?10^?8?µg?g^?1. The ¹²⁹I/¹²⁷I isotopic ratios of surface soils from Ukraine were in the range of the order of 10^?9–10^?5 and of 10^?10–10^?8 for soils from Slovenia. The highest isotopic ratio 13.6?·?10^?5 was found in a soil sample collected in Yaniv, Ukraine in July 1993.