Competition between hydrogen bonds and halogen bonds in complexes of formamidine and hypohalous acids

Quantum chemical calculations have been per-formed for the complexes of formamidine (FA) and hypohalous acid (HOX, X = F, Cl, Br, I) to study their structures, properties, and competition of hydrogen bonds with halogen bonds. Two types of complexes are formed mainly through a hydrogen bond and a halogen bond, respectively, and the cyclic structure is more stable. For the F, Cl, and Br complexes, the hydrogen-bonded one is more stable than the halogen-bonded one, while the halogen-bonded structure is favorable for the I complexes. The associated H-O and X-O bonds are elongated and exhibit a red shift, whereas the distant ones are contracted and display a blue shift. The strength of hydrogen and halogen bonds is affected by F and Li substitutents and it was found that the latter tends to smooth differences in the strength of both types of interactions. The structures, properties, and interaction nature in these complexes have been understood with natural bond orbital (NBO) and atoms in molecules (AIM) theories.     

Unraveling tissue regeneration pathways using chemical genetics

Identifying the molecular pathways that are required for regeneration remains one of the great challenges of regenerative medicine. Although genetic mutations have been useful for identifying some molecular pathways, small molecule probes of regenerative pathways might offer some advantages, including the ability to disrupt pathway function with precise temporal control. However, a vertebrate regeneration model amenable to rapid throughput small molecule screening is not currently available. We report here the development of a zebrafish early life stage fin regeneration model and its use in screening for small molecules that modulate tissue regeneration. By screening 2000 biologically active small molecules, we identified 17 that specifically inhibited regeneration. These compounds include a cluster of glucocorticoids, and we demonstrate that transient activation of the glucocorticoid receptor is sufficient to block regeneration, but only if activation occurs during wound healing/blastema formation. In addition, knockdown of the glucocorticoid receptor restores regenerative capability to nonregenerative, glucocorticoid-exposed zebrafish. To test whether the classical anti-inflammatory action of glucocorticoids is responsible for blocking regeneration, we prevented acute inflammation following amputation by antisense repression of the Pu.1 gene. Although loss of Pu.1 prevents the inflammatory response, regeneration is not affected. Collectively, these results indicate that signaling from exogenous glucocorticoids impairs blastema formation and limits regenerative capacity through an acute inflammation-independent mechanism. These studies also demonstrate the feasibility of exploiting chemical genetics to define the pathways that govern vertebrate regeneration.     

Making carbon-nitrogen bonds in biological and chemical synthesis

The function of many biologically active molecules requires the presence of carbon-nitrogen bonds in strategic positions. The biosynthetic pathways leading to such bonds can be bypassed through chemical synthesis to synthesize natural products more efficiently and also to generate the molecular diversity unavailable in nature.     

A stand-alone adenylation domain forms amide bonds in streptothricin biosynthesis

The streptothricin (ST) antibiotics, produced by Streptomyces bacteria, contain L-β-lysine ((3S)-3,6-diaminohexanoic acid) oligopeptides as pendant chains. Here we describe three unusual nonribosomal peptide synthetases (NRPSs) involved in ST biosynthesis: ORF 5 (a stand-alone adenylation (A) domain), ORF 18 (containing thiolation (T) and condensation (C) domains) and ORF 19 (a stand-alone A domain). We demonstrate that ST biosynthesis begins with adenylation of L-β-lysine by ORF 5, followed by transfer to the T domain of ORF 18. In contrast, L-β-lysine molecules adenylated by ORF 19 are used to elongate an L-β-lysine peptide chain on ORF 18, a reaction unexpectedly catalyzed by ORF 19 itself. Finally, the C domain of ORF 18 catalyzes the condensation of L-β-lysine oligopeptides covalently bound to ORF 18 with a freely diffusible intermediate to release the ST products. These results highlight an unusual activity for an A domain and unique mechanisms of crosstalk within NRPS machinery.     

Effects of earthworm mucus and amino acids on cadmium subcellular distribution and chemical forms in tomato seedlings

In order to investigate the basic mechanism of earthworm activities enhancing plants growth and heavy metals accumulations. A hydroponic experiment was carried out to investigate the effects of earthworm mucus and mimic amino acids solution of earthworm mucus on cadmium (Cd) subcellular distributions and chemical forms in tomato seedlings. The result showed that earthworm mucus significantly increased the concentrations of Cd stored in soluble fraction in subcellular distribution and the concentrations of inorganic and soluble forms of Cd in tomato seedlings, which may explain the increase plants growth and Cd accumulation by earthworm mucus. Meanwhile, amino acids have same function as earthworm mucus, but the effect was much lower than of earthworm mucus. These results indicated that earthworm mucus could increase tomato seedlings growth and Cd accumulations through changing Cd subcellular distribution and chemical forms in plants.     

Rat lung decellularization using chemical detergents for lung tissue engineering

Although pulmonary diseases account for a large number of deaths in the world, most have no treatment other than transplantation. New therapeutic methods for lung treatment include lung tissue engineering and regenerative medicine. Lung decellularization has been used to produce an appropriate scaffold for recellularization and implantation. We investigated 3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate (CHAPS) with sodium dodecyl sulfate (SDS) and Triton X-100 detergents for effecting rat lung decellularization. We evaluated using conventional histology, immunofluorescence staining and SEM methods for removing nuclear material while leaving intact extracellular matrix proteins and three-dimensional architecture. We investigated different concentrations of CHAPS, SDS and Triton X-100 for different periods. We found that 2 mM CHAPS + 0/1% SDS for 48 h was the best among the treatments investigated. Our method can be used to produce an appropriate scaffold for recellularization by stem cells and for investigations ex vivo and in vivo.     

Transformation of chemical energy in biomolecular systems with hydrogen bonds

The mechanism underlying the excitation of the hydrogen bond with ATP hydrolysis was considered. Coulomb interactions of the proton of the hydrogen bond A-H...B with the electrical field of the covalent bond of ADP-P were calculated. It was shown that the electrical field of the covalent bond of ADP-P excites oscillations of the proton in the complex with the hydrogen bond A-H...B and displaces it from the equilibrium towards the covalent bond. The distortion of the potential curve depends on a change in the length of the covalent bond of ADP-P. Adiabatic potentials U0 and UN of the ADP-P system were calculated, which correspond to the ground and excited states of the H-bond proton. It was found that as the length of the bond of ADP-P (rho) increases, the branches of the adiabatic potential U0(rho) and UN(rho) intersect. At the intersection point, the system can transit to the branch UN(rho), which can lead to a reduction of the barrier and a break of the covalent bond of ADP-P. Presumably, this mechanism is universal for processes of transformation of the chemical energy of ATP to the energy of excited hydrogen bond, a mechanism for the maintenance of heat balance and reduction of entropy in a living organism.     

The chemical forms of mercury in human hair: a study using X-ray absorption spectroscopy

Abstract  

Human hair is frequently used as a bioindicator of mercury exposure. We have used X-ray absorption spectroscopy to examine the chemical forms of mercury in human hair samples taken from individuals with high fish consumption and concomitant exposure to methylmercury. The mercury is found to be predominantly methylmercury–cysteine or closely related species, comprising approximately 80% of the total mercury, with the remainder an inorganic thiolate-coordinated mercuric species. No appreciable role was found for selenium in coordinating mercury in hair.     

On available forms of chemical compounds in soils

Different methods are used to study available forms of chemical compounds in soils. The sequential extraction method is described in detail. Also, a comparative overview is given of the most frequently extracted fractions of chemical elements (water-soluble, exchangeable, specifically sorbed, carbonate, bonded to organics, Fe and Mn oxides/hydroxides, and aluminosilicates), as well as of relevant extractants. Advantages and disadvantages of various extractants are discussed, and ways to improve their selectivity are proposed. It is also shown that the content of available forms of chemical compounds in soil can be used for estimating the extent of industrial soil pollution.     

Essential fatty acids in adipose tissue

Among the numerous causes of lipomobilization of fatty acids from the adipose tissue it is also carbon tetrachloride (CCl4). The research shows that the saturated fatty acids decreased in this tissue of the rats injected with CCl4, even if the linolenic and alpha-linolenic acids are present in the diet.     

Alpha-lactalbumin forms a compact molten globule in the absence of disulfide bonds.

Human alpha-lactalbumin (alpha-LA) is a four disulfide-bonded protein that adopts partially structured conformations under a variety of mildly denaturing conditions. At low pH, the protein is denatured but compact, with a high degree of secondary structure and a native-like fold. This is commonly referred to as a molten globule. A variant of alpha-LA, in which all eight cysteines have been mutated to alanine (all-Ala alpha-LA), has been studied using NMR spectroscopy. At low pH all-Ala alpha-LA is nearly as compact as wild type alpha-LA. Urea-induced unfolding experiments reveal that the residues that remain compact in the absence of disulfide bonds are those that are most resistant to unfolding in the wild-type alpha-LA molten globule. This is particularly remarkable because this stable core is formed by segments of the polypeptide chain from both the N- and C-termini. These results show that the overall architecture of the protein fold of alpha-LA is determined by the polypeptide sequence itself, and not as the result of cross-linking by disulfide bonds, and provide insight into the way in which the sequence codes for the fold.     

The genesis of movement-related human brain potentials in different forms of motor pathology]

To study the role of subcortical structures and cerebellum nuclei in the genesis of the human brain potentials connected with motion patients were examined with parkinsonism and hyperkinetic form of children cerebral paralysis. In one group of patients the motor responses were recorded by means of long-term electrodes implanted with the medical purpose into the ventro-oral group of thalamus nuclei, subcortical nuclei and dentate cerebellum nuclei. In patients of the second group potentials, connected with motion were led from the scalp before and after one-moment destruction in the zone of the same structures. In ventro-oral and reticular thalamus nuclei lateral and medial segments of the pale globe and in the cerebellum dentate nucleus post-motor components were recorded which were considered as electrographic expression of motion realization and completion processes (P2 and N3) and also as slow negative oscillation (component N1), that pointed to participation of the studied structures not only in regulation of voluntary movement but also in the process of movement preparation. Absence of N2 component at recording motor responses from deep electrodes and its sufficient stability at scalp leads gave the reason to suggest that its genesis was connected with the cortex activity.     

Determination of double bond positions in fatty acids with conjugated double bonds

The positions of the double bonds in fatty acids with conjugated double bonds may be determined by mass spectrometry of the methyl esters of their trimethylsilyl ether derivatives obtained by hydroxylation of the double bonds followed by silylation of the resulting polyols. The method has been applied to trans-9,trans-11- and trans-10, trans-12-octadecadienoic acid.     

A new visualization scheme of chemical energy density and bonds in molecules

Covalent bond describes electron pairing in between a pair of atoms and molecules. The space is partitioned in mutually disjoint regions by using a new concept of the electronic drop region R_D, atmosphere region R_A, and the interface S (Tachibana in J Chem Phys 115:3497–3518, 2001). The covalent bond formation is then characterized by a new concept of the spindle structure. The spindle structure is a geometrical object of a region where principal electronic stress is positive along a line of principal axis of the electronic stress that connects a pair of the R_Ds of atoms and molecules. A new energy density partitioning scheme is obtained using the Rigged quantum electrodynamics (QED). The spindle structure of the stress tensor of chemical bond has been disclosed in the course of the covalent bond formation. The chemical energy density visualization scheme is applied to demonstrate the spindle structures of chemical bonds in H₂, C₂H₆, C₂H₄ and C₂H₂ systems.Figure Field theory of the energy density.     

Location of double bonds and cyclopropane rings in fatty acids by mass spectrometry

Electron-impact mass spectrometric procedures for locating the position of double bonds and cyclopropane rings in long-chain fatty acids are reviewed. Since unsaturation is not located directly by mass spectrometry, the properties of suitable derivatives are summarized. Epoxides are readily prepared from double bonds and on opening of the ring with various reagents useful derivatives are obtained, the most promising to date being hydroxymethoxy esters whose trimethylsilyl ethers give good mass spectra. Trimethylsilyl ethers of vicinal diols, prepared by direct hydroxylation, are recommended for the analysis of polyunsaturated fatty acid esters using combined gas chromatography-mass spectrometry. Oxymercuration-demercuration techniques are very convenient and one particular procedure can specifically locate unsaturation up to five carbons distant from the carboxyl group. An alternative approach enables the location of double bonds and cyclopropane rings in fatty acids by direct mass spectrometry of pyrrolidides. Cyclopropane rings can be positively located in fatty acid esters by mass spectrometry of isomeric ketones or methoxy derivatives prepared by chromium trioxide oxidation on poron trifluoride-catalysed methoxylation, respectively. A variety of other procedures are also considered and some guidelines are given for choosing a method to suit a particular unsaturated acid.