Conformational study of poly(α,β-L-aspartic acid)

The conformation of several samples of poly(α,β-L -Asp) with a molar fraction of β-bonds ranging from 0.1 to 0.55 was investigated by means of ir and CD spectroscopy and potentiometric titration and compared with the results obtained previously with poly(α-L -Asp). All samples investigated underwent a conformational change induced by changes in their degree of ionization: unpronounced ir absorption of amide V at 650 cm^?1 was shifted to 620 cm^?1 and substantially increased on deionization; CD spectra changed with the degree of ionization, passing through an isosbestic point; and the pattern of the titration curves was more complex than that of a simple polyelectrolyte. The conformation developing with the decreasing degree of ionization may be considered to be α-helix, as deduced according to the analogous behavior of other polypeptides. The extent of the conformational change in the individual samples depends on the molar fraction of β-bonds: the higher it is, the lower is the helix-forming ability of the sample.     

Medicinal importance of fungal β-(1→3), (1→6)-glucans

Non-cellulosic β-glucans are now recognized as potent immunological activators, and some are used clinically in China and Japan. These β-glucans consist of a backbone of glucose residues linked by β-(1→3)-glycosidic bonds, often with attached side-chain glucose residues joined by β-(1→6) linkages. The frequency of branching varies. The literature suggests β-glucans are effective in treating diseases like cancer, a range of microbial infections, hypercholesterolaemia, and diabetes. Their mechanisms of action involve them being recognized as non-self molecules, so the immune system is stimulated by their presence. Several receptors have been identified, which include: dectin-1, located on macrophages, which mediates β-glucan activation of phagocytosis and production of cytokines, a response co-ordinated by the toll-like receptor-2. Activated complement receptors on natural killer cells, neutrophils, and lymphocytes, may also be associated with tumour cytotoxicity. Two other receptors, scavenger and lactosylceramide, bind β-glucans and mediate a series of signal pathways leading to immunological activation. Structurally different β-glucans appear to have different affinities toward these receptors and thus generate markedly different host responses. However, the published data are not always easy to interpret as many of the earlier studies used crude β-glucan preparations with, for the most part, unknown chemical structures. Careful choice of β-glucan products is essential if their benefits are to be optimized, and a better understanding of how β-glucans bind to receptors should enable more efficient use of their biological activities.     

Biosynthesis of β-glucans by cell-free extracts from saccharomyces cerevisiae

Cell-free extracts from Saccharomyces cerevisiae catalyzed the incorporation of glucosyl residues from UDP-[U-¹⁴C]glucose into β-1, 3-glucans which contained a significant proportion of β-1, 6-glycosidic linkages. When GDP-[U-¹⁴C]-glucose was used as substrate only trace amounts of glucose were incorporated. Activity of β-glucan synthetase was distributed among membrane and cell wall fractions, specific activity being higher in this latter. β-Glucan synthesized by membrane and cell wall fractions contained 0.6% and 2.5% of β-1, 6-glycosidic linkages respectively. A marked decrease in the activity of β-glucan synthetase occurred as the cells aged. Significant activity of glycogen synthetase was detected only in cells which had reached the stationary phase of growth.     

Conformational studies of -glucans

A study of the effect of linkage on the possible conformations of di-and polysaccharides of α-D -glucose and also the probable intramolecular hydrogen bonds has been made. The differences in the nature of linkage is shown to effect the energetically preferred conformations; (1 → 2) linkages lead only to righthanded helical conformations, (1 → 3) linkages lead to extended as well as both left and righthanded helical conformations; (1 → 4) linkages lead to both right-and lefthanded wide helical conformations. The possible hydrogen bonds between adjacent residues are also dependent on the nature of the linkage. A comparison of the conformational data of α-D -glucans with those of β-D -glucans has indicated that the favored conformations and hydrogen bonds between contiguous residues in the chain are influenced by the configuration at the anomeric carbon atom in all the three types of polysaccharides. From the energy calculations a probable conformation (?M = ?10°, ψM = ?30°, ?N = ?23°, ψN = ?19°) has also been proposed for crystalline mycodextran in conformity with x-ray data. This conformation contains two types of hydrogen bonds between contiguous residues one between 0–2 and 0–3 atoms at (1 → 4) linkage and the other between 0?2 and 0–4 atoms at (1 → 3) linkage in the chain. The conformation of maltose unit (?10°,?30°) that is likely to occur in the crystalline mycodextran coincides with the minimum energy conformation of maltose.     

Structural classification of αββ and ββα supersecondary structure units in proteins

We present a fully automatic structural classification of supersecondary structure units, consisting of two hydrogen-bonded β strands, preceded or followed by an α helix. The classification is performed on the spatial arrangement of the secondary structure elements, irrespective of the length and conformation of the intervening loops. The similarity of the arrangements is estimated by a structure alignment procedure that uses as similarity measure the root mean square deviation of superimposed backbone atoms. Applied to a set of 141 well-resolved nonhomologous protein structures, the classification yields 11 families of recurrent arrangements. In addition, fragments that are structurally intermediate between the families are found; they reveal the continuity of the classification. The analysis of the families shows that the α helix and β hairpin axes can adopt virtually all relative orientations, with, however, some preferable orientations; moreover, according to the orientation, preferences in the left/right handedness of the α–β connection are observed. These preferences can be explained by favorable side by side packing of the α helix and the β hairpin, local interactions in the region of the α–β connection or stabilizing environments in the parent protein. Furthermore, fold recognition procedures and structure prediction algorithms coupled to database-derived potentials suggest that the preferable nature of these arrangements does not imply their intrinsic stability. They usually accommodate a large number of sequences, of which only a subset is predicted to stabilize the motif. The motifs predicted as stable could correspond to nuclei formed at the very beginning of the folding process. Proteins 30:193–212, 1998. © 1998 Wiley-Liss, Inc.     

Conformational behavior of α,α-dialkylated peptides

The preferred conformations of N-acetyl-N′-methyl amides of some dialkylglycines have been determined by empirical conformational-energy calculations; minimum-energy conformations were located by minimizing the energy with respect to all the dihedral angles of the molecules. The conformational space of these compounds is sterically restricted, and low-energy conformations are found only in the regions of fully extended and helical structures. Increasing the bulkiness of the substituents on the C^α, the fully extended conformation becomes gradually more stable than the helical structure preferred in the cases of dimethylglycine. This trend is, however, strongly dependent on the bond angles between the substituents on the C^α atom: In particular, helical structures are favored by standard values (111°) of the N-C^α-C′ angle, while fully extended conformations are favored by smaller values of the same angle, as experimentally observed, for instance, in the case of α,α-di-n-propylglycine.     

Structure and physicochemical properties of barley non-starch polysaccharides — I. Water-extractable β-glucans and arabinoxylans

Water-soluble non-starch polysaccharides were extracted from a Canadian malting barley (cv. Harrington) by sequential treatment with water at 40 °C (WE40) and 65 °C (WE65). The yields were 1.4 and 1.3% (w/w), respectively, of the dry barley grist. The WE40 extract was composed of 82.5% glucose, 8.9% xylose, and 7.0% arabiose residues, whereas WE65 contained 93.3% Glc, 3.3% Xyl, and 2.5% Ara. Only minute amounts of mannose and galactose residues were found in either fraction. Both extracts were further fractionated by stepwise (NH₄)₂SO₄ precipitation into several polysaccharide populations. Subfractions from both extracts, obtained up to 45% saturation with (NH₄)₂SO₄, contained mostly β-glucans, whereas subfractions precipitated at increasing saturation levels of (NH₄)₂SO₄ (45–100%) contained progressively more arabinoxylans and less β-glucans. Compared to WE40, the WE65 extract was enriched in β-glucan populations with higher molecular size, higher limiting viscosity values, and higher content of β-(1 → 4) linkages. The ratio of tri-/ tetrasaccharide oligomers was also higher in β-glucans extracted at 65 °C than those extracted at 40 °C. Arabinoxylans in both extracts, WE40 and WE65, were highly substituted and contained large proportions of doubly substituted xylose residues.     

Studies on the 5α-androstane-3β, 17β-diol-6α-hydroxylase and on the 5α-androstane-3β, 17β-diol-7α-hydroxylase in anterior hypophysis of male rats.

In anterior pituitaries from male rats, it appeared that 5α-androstane-3β, 17β-diol was quickly metabolized into 5α-androstane-3β,6α-17β-triol and 5α-androstane-3β,7α, 17β-triol by action of 6α- and 7α-hydroxylases. Hydroxysteroid hydroxylases were located in endoplasmic reticulum and were dependent on NADPH⁺. Their optimum pH was 8.0, optima temperature, 37°C, and their apparent Km was 2.7 μM. Hydroxylative reactions were not reversible and not modified by gonadectomy. Hydroxylation seemed an efficient control of the pituitary level of 5α-andros-tane-3β, 17β-diol.     

Characteristics of films prepared from native and modified branched β-1,3- -glucans

The properties of films prepared from a high molecular weight (mol. wt: 7·5 × 10⁶ g/mol) branched β-1,3- -glucan (schizophyllan) and a polyalcohol (mol. wt: 7·3 × 10⁶ g/mol) derived from schizophyllan by periodate oxidation and subsequent borohydride reduction are described. The films can only be prepared by casting from aqueous solutions, because the polymers are not thermoplastic. They have a low permeability to oxygen, but a high permeability to water vapour. The tensile strength of the films is 45–58 N/mm⁻² for schizophyllan and 12–18 N/mm² for the polyalcohol, and both, but especially the polyalcohol films, have a low elongation at break. Films prepared from both polymers, under conditions where the triple helices are disrupted (>0·01 NaOH), show lower tensile strength and elongations at break as well as higher oxygen permeabilities. A relationship exists between the water content of the films and the tensile strength.     

Conformational studies of linear β-D-1,4′-mannan and galactan

The nonbonded interaction energy of disaccharides, mannobiose and galactobiose and polysaccharides mannan and galactan have been computed as a function of dihedral angles (?,ψ). The conformation (40°, ?20°) has been preferred for the mannan chain from nonbonded interaction energy considerations. The O₅…O₃′ type of intramolecular hydrogen bond has been found to be possible in the above conformation. Comparison of the allowed region of mannan with those of cellulose and xylan indicates that the monomer unit, in mannan chain has slightly higher freedom of rotation than that of cellulose and less than that of xylan. As in cellulose and mannan, the freedom of rotation of the monomer units in β-1,4′ galactan is highly restricted. Unlike mannan (which prefers an extended conformation) the β-1,4′ galactan prefers a helical conformation similar to amylose. Just as in amylose the O₂…O₃′ type hydrogen bond between contiguous residues is also possible in β-1,4′ galactan.     

Structure and physicochemical properties of barley non-starch polysaccharides—II. Alkaliextractable β-glucans and arabinoxylans

Three fractions containing hemicellulosic material were obtained by sequential extraction of barley residue (left after removal of water-extractable polysaccharides) with saturated barium hydroxide [Ba(OH)₂ fraction], distilled water [Ba(OH)₂/H₂O fraction], and 1 m sodium hydroxide [NaOH fraction]. The yields of the fractions were 1.6, 1.7, and 2.6% (w/w), respectively, of the dry barley grist. The Ba(OH)₂ fraction contained mainly arabinose and xylose, 35.8% and 60.9%, respectively. The Ba(OH)₂/H₂O fraction in addition to 26.7% Ara and 36.6% Xyl contained also 34.8% Glc. The NaOH fraction was composed of 14.2% Ara, 44.0% Xyl, and 40.9% Glc. The Ba(OH)₂/H₂O and NaOH extracts were further fractionated by stepwise (NH₄)₂SO₄ precipitation into several subfractions with varying amounts of β-glucans and arabinoxylans. β-Glucans in Ba(OH)₂/H₂O and NaOH fractions were characterized by high ratios of β-(1→4)/β-(1→3) linkages, large amounts of contiguously linked β-(1→4) segments, and high ratios of cellotriosyl/cellotetraosyl units. The alkali-extractable arabinoxylans, especially those NaOH-extractable, were characterized by a very low degree of substitution, high xylose/arabinose ratio, and a small content of doubly substituted xylose residues. Some populations of arabinoxylans displayed structural features that would enable them to self-associate or to interact with β-glucans.     

Conformational diversity in prion protein variants influences intermolecular β‐sheet formation

A conformational transition of normal cellular prion protein (PrP^C) to its pathogenic form (PrP^Sc) is believed to be a central event in the transmission of the devastating neurological diseases known as spongiform encephalopathies. The common methionine/valine polymorphism at residue 129 in the PrP influences disease susceptibility and phenotype. We report here seven crystal structures of human PrP variants: three of wild‐type (WT) PrP containing V129, and four of the familial variants D178N and F198S, containing either M129 or V129. Comparison of these structures with each other and with previously published WT PrP structures containing M129 revealed that only WT PrPs were found to crystallize as domain‐swapped dimers or closed monomers; the four mutant PrPs crystallized as non‐swapped dimers. Three of the four mutant PrPs aligned to form intermolecular β‐sheets. Several regions of structural variability were identified, and analysis of their conformations provides an explanation for the structural features, which can influence the formation and conformation of intermolecular β‐sheets involving the M/V129 polymorphic residue.     

Theoretical studies on β-lactam antibiotics. IV. Conformational analysis of novel β-lactam antibiotics and the binding specificities of crosslinking enzyme(s) and β-lactamases

Conformational-energy calculations were carried out on the new family of β-lactam antibiotics (viz., thienamycin, PS-5, 1-oxa- and 1-thiapenems, and their close analogs); these exhibit broad-spectrum antibacterial activity and stability towards β-lactamase-producing strains. The bicyclic ring system in all the compounds studied was found to be highly rigid and to favor only one conformation. This is in contrast to findings in penicillins, where the five-membered ring assumes two puckered conformations. The relative orientations of the bicyclic ring system and the nature and configuration of the substituent at C-5 position, besides nonplanarity of the lactam peptide bond, are shown to be important for biological activity. The present study, in agreement with x-ray studies, predicts that the lactam peptide bond in 1-carbapenem is more nonplanar than in 1-thiapenem. These studies also suggest that the conformational requirement of bicyclic ring system to bind to crosslinking enzyme(s) and β-lactamases is very similar.     

Conformational flexibility of peptides containing α,β-unsaturated amino acid residues. I. Conformational analysis of N-acetyl-N′-methylamides of dehydroalanine and N-methyldehydroalanine

Conformational energy calculations on the N-acetyl-N′-methylamides of dehydroalanine and N-methyldehydroalanine indicate that their conformational behavior is very different from that of the corresponding saturated compounds. The conformational data in the literature from x-ray and nmr investigations on peptides containing α,β-unsaturated residues are discussed on the basis of these theoretical results.     

Syntheses and anti‐tubercular activity of β‐substituted and α,β‐disubstituted peptidyl β‐aminoboronates and boronic acids

Tuberculosis is still affecting millions of people worldwide, and new resistant strains of Mycobacterium tuberculosis are being found. It is therefore necessary to find new compounds for treatment. In this paper, we report the synthesis and in vitro testing of peptidyl β‐aminoboronic acids and β‐aminoboronates with anti‐tubercular activity. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.