Characterization of the sodium binding sites in microcrystalline ATP by Na-solid-state NMR and ab initio calculations

Stepwise conformational transition of disodium adenosine 5′-triphosphate (Na₂ATP) crystals as a function of relative humidity (r.H.), was examined by means of high resolution ²³Na, ³¹P solid state NMR spectroscopy and quantum mechanics calculations. ²³Na-MQMAS solid state NMR spectra of hydrated disodium salts of adenosine 5,5′-triphosphate were measured to characterize the individual sodium sites. Quadrupolar coupling constants (C_Q), and the asymmetry parameters of the electric field gradient tensors (η) of sodium-23 determined by quantum mechanical calculations (gaussian03) using larger clusters than in previous studies were compared to the experimental ²³Na-MQMAS spectra.     

The application of ab initio molecular orbital theory to structural moieties of carbohydrates

Ab initio molecular orbital calculations were made on methoxymethanol, a model for the hemiacetal and acetal moieties in aldopyranoses and methyl aldopyranosides, thereby improving on the previous calculations using methanediol. The new calculations confirmed the favored conformations already deduced, and gave, for the conformational-energy differences and CO bond-length variations, values more appropriate to the carbohydrate systems, as confirmed by a re-examination of the experimental data from crystal-structure determinations. From the results, it was predicted that the OCH₃ bond in methyl aldopyranosides is lengthened; this is supported by the experimental data. An examination of the angles and bond-lengths in the pyranoid ring and of the linkage bonds of oligosaccharides indicated that similar electronic effects involving the oxygen lone-pair electrons apply to oligo- and poly-saccharides.     

The dynamic role of distal side residues in heme hydroperoxidase catalysis. Interplay between X-ray crystallography and ab initio MD simulations

The enzymatic cycle of hydroperoxidases involves the resting Fe(III) state of the enzyme and the high-valent iron intermediates Compound I and Compound II. These states might be characterized by X-ray crystallography and the transition pathways between each state can be investigated using atomistic simulations. Here we review our recent work in the modeling of two key steps of the enzymatic reaction of hydroperoxidases: the formation of Cpd I in peroxidase and the reduction of Cpd I in catalase. It will be shown that small conformational motions of distal side residues (His in peroxidases and His/Asn in catalases), not,or only partially, revealed by the available X-ray structures, play an important role in the catalytic processes examined.     

Infrared and Raman spectroscopy of carbohydrates. Part VI: Normal coordinate analysis of V-amylose

A normal coordinate analysis of V-amylose has been performed for an isolated 6₁ helical chain. Negligible splitting from interactions of vibrations of successive residues is expected between A and E vibrational species due to the large size of the monomer unit. As a result, calculation of only the totally symmetric A modes represents an adequate approximation to the vibrational spectrum of helical polysaccharides. Using this method together with a valence force field we have obtained good agreement between the observed and calculated frequencies. In addition, the computed potential energy distribution and Cartesian displacement coordinates match previous experimental assignments, based on deuterium exchange. The analysis also supports the proposed mechanism for conversion of V-amylose to the more extended B-form. This conversion results in an observed frequency shift for the Raman line at 946 cm^?1 which is predicted by the calculations.     

Pisum sativum and vicia faba carbohydrates: Part IV — Granular structure of wrinkled pea starch

The granular structure of wrinkled pea starch, compared to two other B-type starches, potato and amylomaize, has been studied, using physical, chemical and enzymic methods both before and after lintnerisation (2·2n HCl, 35°C). Wrinkled pea starch, which was composed mainly (90%) of compound granules, had an apparent amylose content of 75·4% when measured at +2°C. Native granules showed weak B-type crystallinity. The fraction (27·4%) which was easily degraded during lintnerisation and which corresponded to the amorphous phase, was smaller than for other starches. The degradation rate of the more organised phase was low (6% in 17 days). The residue remaining after exposure to acid for 42 days presented a very high, B-type crystallinity but with the same sorption properties as native starch, which indicates that water is part of the crystallites. The crystalline phase is composed of linear chains of $\text{DP}$ 25, distributed asymmetrically. The native starch showed a single gelatinisation endotherm between 117 and 133°C and with a ΔH of 0·7 cal. g^?1 dry starch, which is somewhat lower than other B-type starches.     

Variability in structural carbohydrates and in vitro digestibility of forages. 4. Fenugreek (Trigonella foenum-graecum)

The chemical composition of ten genotypes of fenugreek, with and without a pretreatment with neutral detergent, has been determined together with dry matter digestibility in vitro. Preliminary extraction with neutral detergent lowered the percentage yield of acid detergent fibre and about 84% of this decrease was observed in the reduction of cellulose level.Dry matter digestibility in vitro was significantly correlated with acid detergent and cellulose when sequential extraction was done. It was considered necessary to use sequential analysis to determine the chemical composition of fenugreek forage.     

Longevity of seven species of cactophilic Drosophila and D. melanogaster on carbohydrates

Adults of 6 species of Drosophila that use decaying prickly pear cactus (Opuntia sp.) as breeding and feeding sites were compared to each other and to D. nigrospiracula, whose host is saguaro cactus, and to the cosmopolitan D. melanogaster, in their utilization of 21 sugars for longevity (time to 50% mortality). In general, the utilization of sugars by these flies for longevity followed the pattern observed with the other insects. None of the species were able to live very long on solutions of pentoses, uronic acids, inositol, rhamnose, sorbose or the β-linked disaccharides, lactose and cellobiose. Althogh all could use glucose, fructose, sucrose, maltose and melezitose well, their life spans on galactose, mannose, trehalose and raffinose were more variable. Two of the Opuntia feeders were also tested on a number of other carbohydrates. Ribitol, mannitol, sorbitol and xylitol significantly prolonged the life of D. arizonensis but not that of D. wheeleri. Neither species lived long on solutions of arabitol, galactitol, starch, inulin or on arabogalactan.     

Computational bioinorganic chemistry. Part III. The tools of the trade: from high-level ab initio calculations to structural bioinformatics

Having long focused on the electronic-structural aspects of metalloenzymes and their synthetic models, Abhik is currently exploring a number of synthetic problems related to self-assembly processes, dynamic combinatorial libraries, and fluorine chemistry.     

The role of lipopolysaccharide moieties in macrophage response to Escherichia coli

Lipopolysaccharide (LPS) is the main component of Gram-negative bacteria that - upon infection - activates the host immune system and is crucial in fighting pathogens as well as in the induction of sepsis. In the present study we addressed the question whether the key structural components of LPS equally take part in the activation of different macrophage immune responses. By genomic modifications of Escherichia coli MG1655, we constructed a series of strains harboring complete and truncated forms of LPS in their cell wall. These strains were exposed to RAW 264.7 macrophages, after which phagocytosis, fast release of pre-synthesized TNF and activation of NF-κB signal transduction pathway were quantified. According to our results the core and lipid A moieties are involved in immune recognition. The most ancient part, lipid A is crucial in evoking immediate TNF release and activation of NF-κB. The O-antigen inhibits phagocytosis, leading to immune evasion.     

Hydrodynamic calculations on the movements of cilia and flagella I. Paramecium

Calculations of the velocity profile, force, moment and bending moment using a theoretical model are carried out for the three-dimensional “conical-helical” beat of a cilium of Paramecium multimicro-nucleatum. The mean velocity profile obtained by numerical computation is found to be twisted in form: it is inclined at a slight angle to the effective stroke at the top of the cilia sublayer, but twists around with the recovery stroke in the lower part of the sublayer. The force and moment are larger during the fast effective stroke, but over a complete cycle their contributions are approximately zero. Calculations on the bending moments reveals that they are larger during the recovery stage of the beating cycle.     

Production of carbohydrates by the marine diatom Chaetoceros affinis var. willei (Gran) Hustedt. II. Preliminary investigation of the extracellular polysaccharide

The isolation of an extracellular polysaccharide from cultures of Chaetoceros affinis var. willei (Gran) Hustedt is described. The polysaccharide behaved as a homogeneous, polyanionic compound in free-boundary electrophoresis at both pH 2 and 7. It contained sulphur, presumably as sulphate half ester groups (8.7% of SO₂Na), and the following monosaccharides were tentatively identified: rhamnose, fucose, arabinose, and galactose, with the two former constituting 63% of the polysaccharide preparation. The main cellular polysaccharide was a glucan and could be extracted from the cells by dilute acid. The remaining material gave, after hydrolysis, a complex mixture of monosaccharides with rhamnose as the major component. It is concluded that the extracellular polysaccharide is probably excreted from healthy cells.     

Production of carbohydrates by the marine diatom Chaetoceros affinis var. willei (Gran) Hustedt. I. Effect of the concentration of nutrients in the culture medium

The chemical composition of cells of Chaetoceros affinis var. willei (Gran) Hustedt grown in batch culture was markedly influenced by the concentration of nutrients in the medium. In the logarithmic growth phase the content of cellular glucan was relatively low, but in the stationary phase the glucan content showed a rapid increase which seemed to coincide with the depletion of nitrate from the medium. This led to very pronounced variations in the ratio of protein to carbohydrate. This ratio can easily be determined and seems to be a sensitive and convenient parameter for characterizing the physiological state of the diatom cells.     

Application of CNDO2 theoretical calculations to interpretation of the chemical reactivity and biological activity of the syn and anti diolepoxides of benzo[a]pyrene

$\text{CNDO}\text{2}$ molecular orbital theoretical calculations performed on the anti and syn diolepoxides (1 and 2) of the potent carcinogen benzo[a]pyrene provide insight into the molecular structure and reactivity of these mutagenic and carcinogenic hydrocarbon metabolites. Hydrogen-bonded interaction between the 7-HO proton and the epoxide oxygen atom of 2 is shown to be absent in the normal semichair conformation of the tetrahydro ring, (H…O bond distance = 2.7 Å), but is energetically favored in a somewhat distorted puckered structure (H…O bond distance = 1.7 Å). Unexpectedly, internal H-bonding alters the relative electron density at C₉ and C₁₀, leading to prediction of the former as the more electrophilic center. Since all reactions of 2 take place exclusively at C₁₀, transannular H-bonding is concluded not to contribute significantly to the structure of 2. Diolepoxide reactions with both weak and strong nucleophiles and with DNA are discussed and the mechanisms interpreted in terms of molecular structure as determined by the theoretical calculations.