Protection of DNA against low-energy electrons by amino acids: A first-principles molecular dynamics study

Using first-principles molecular dynamics simulations, we have investigated the notion that amino acids can play a protective role when DNA is exposed to excess electrons produced by ionizing radiation. In this study we focus on the interaction of glycine with the DNA nucleobase thymine. We studied thymine-glycine dimers and a condensed phase model consisting of one thymine molecule solvated in amorphous glycine. Our results show that the amino acid acts as a protective agent for the nucleobase in two ways. If the excess electron is initially captured by the thymine, then a proton is transferred in a barrier-less way from a neighboring hydrogen-bonded glycine. This stabilizes the excess electron by reducing the net partial charge on the thymine. In the second mechanism the excess electron is captured by a glycine, which acts as a electron scavenger that prevents electron localization in DNA. Both these mechanisms introduce obstacles to further reactions of the excess electron within a DNA strand, e.g. by raising the free energy barrier associated with strand breaks.

Facile synthesis of methyl 2-amino-3-(2-methyl-3-quinolyl)propanoate

Methyl 4-acetyl-5-(2-nitrophenyl)pyrrolidine-2-carboxylate 5, readily available in one step by a 1,3-dipolar cycloaddition, undergoes reduction, cyclisation and fragmentation to the corresponding quinoline when treated with hydrogen and palladium.

ASYMMETRIC-SYNTHESIS OF S-(+)-4-AMINO-5-HEXYNOIC ACID

4-Amino-5-hexynoic acid is efficiently synthesised in eight steps (overall yield 10%) from commercially available (S)-glutamic acid. The key step was conversion of an aldehyde to an acetylene using diethylmethydiazophosphonate.

STEREOSELECTIVE ROUTE TO HIGHLY FUNCTIONALIZED AMINO-ALCOHOLS

Acyclic amino alcohols can be obtained in high stereoisomeric purity by Stevens [2,3] rearrangement of tetrahydropyridine salts followed by reduction of the ketones and ring opening of the disubstituted pyrrolidine.

Ultrafast charge dynamics in an amino acid induced by attosecond pulses

In the past few years, attosecond techniques have been implemented for the investigation of ultrafast dynamics in molecules. The generation of isolated attosecond pulses characterized by a relatively high photon flux has opened up new possibilities in the study of molecular dynamics. In this paper, we report on experimental and theoretical results of ultrafast charge dynamics in a biochemically relevant molecule, namely, the amino acid phenylalanine. The data represent the first experimental demonstration of the generation and observation of a charge migration process in a complexmolecule, where electron dynamics precede nuclear motion. The application of attosecond technology to the investigation of electron dynamics in biologically relevant molecules represents a multidisciplinary work, which can open new research frontiers: those in which few-femtosecond and even subfemtosecond electron processes determine the fate of biomolecules. It can also open new perspectives for the development of new technologies, for example, in molecular electronics, where electron processes on an ultrafast temporal scale are essential to trigger and control the electron current on the scale of the molecule.

Capturing Goodwillie's Derivative

Recent work of Biedermann and Roendigs has translated Goodwillie's calculus of functors into the language of model categories. Their work focuses on symmetric multilinear functors and the derivative appears only briefly. In this paper we focus on understanding the derivative as a right Quillen functor to a new model category. This is directly analogous to the behaviour of Weiss's derivative in orthogonal calculus. The immediate advantage of this new category is that we obtain a streamlined and more informative proof that the n-homogeneous functors are classified by spectra with an action of the symmetric group on n objects. In a later paper we will use this new model category to give a formal comparison between the orthogonal calculus and Goodwillie's calculus of functors.

Burkholderia cenocepacia and Salmonella enterica ArnT proteins that transfer 4-amino-4-deoxy-L-arabinose to lipopolysaccharide share membrane topology and functional amino acids

We recently demonstrated that incorporation of 4-amino-4-deoxy-l-arabinose (l-Ara4N) to the lipid A moiety of lipopolysaccharide (LPS) is required for transport of LPS to the outer membrane and viability of the Gram-negative bacterium Burkholderia cenocepacia. ArnT is a membrane protein catalyzing the transfer of l-Ara4N to the LPS molecule at the periplasmic face of the inner membrane, but its topology and mechanism of action are not well characterized. Here, we elucidate the topology of ArnT and identify key amino acids that likely contribute to its enzymatic function. PEGylation assays using a cysteineless version of ArnT support a model of 13 transmembrane helices and a large C-terminal region exposed to the periplasm. The same topological configuration is proposed for the Salmonella enterica serovar Typhimurium ArnT. Four highly conserved periplasmic residues in B. cenocepacia ArnT, tyrosine-43, lysine-69, arginine-254 and glutamic acid-493, were required for activity. Tyrosine-43 and lysine-69 span two highly conserved motifs, 42RYA44 and 66YFEKP70, that are found in ArnT homologues from other species. The same residues in S. enterica ArnT are also needed for function. We propose these aromatic and charged amino acids participate in either undecaprenyl phosphate-l-Ara4N substrate recognition or transfer of l-Ara4N to the LPS.

Fluorescent Signalling of the Brain Neurotransmitter Gamma Amino Butyric Acid and Related Amino Acid Zwitterions

Fluorescent PET (photoinduced electron transfer) sensor 1 with monoaza-18-crown-6 ether and guanidinium receptor units shows a significant fluorescence enhancement with y-aminobutyric acid (GABA) in mixed aqueous solution.

Calluna vulgaris root cells show increased capacity for amino acid uptake when colonized with the mycorrhizal fungus Hymenoscyphus ericae

Ericoid mycorrhizas are believed to improve N nutrition of many ericaceous plant species that typically occur in habitats with impoverished nutrient status, by releasing amino acids from organic N forms. Despite the ubiquity of mycorrhizal formation the mechanisms and regulation of nutrient transport in mycorrhizal associations are poorly understood. We used an electrophysiological approach to study how amino acid transport characteristics of Calluna vulgaris were affected by colonization with the ericoid mycorrhiza fungus Hymenoscyphus ericae. Both the V_max and K_m parameters of amino acid uptake were affected by fungal colonization in a manner consistent with an increased availability of amino acid to the plant. The ecophysiological significance of altered amino acid transport in colonized root cells of C. vulgaris is discussed. © New Phytologist (2002).

4-Amino-1,8-naphthalimide-based Tröger's bases as high affinity DNA targeting fluorescent supramolecular scaffolds

The synthesis and photophysical and biological investigation of fluorescent 1,8-naphthalimide conjugated Troger's bases 1-3 are described. These structures bind strongly to DNA in competitive media at pH 7.4, with concomitant modulation in their fluorescence emission. These structures also undergo rapid cellular uptake, being localized within the nucleus within a few hours, and are cytotoxic against HL60 and (chronic myeloid leukemia) K562 cell lines.

Mild temperature palladium-catalyzed ammoxidation of ethanol to acetonitrile

The ammoxidation of ethanol is investigated as a renewable process for the production of acetonitrile from a bio-feedstock. Palladium catalysts are shown to be active and very selective (>99%) to this reaction at moderate to low temperatures (150-240 °C), with acetonitrile yields considered a function of Pd morphology. Further investigations reveal that the stability of these catalysts is influenced by an unselective product, and that any deactivation observed is reversible. Interpretation of this deactivation allows operating conditions to be defined for the stable, high yielding production of acetonitrile from ethanol.