Amyloid-like fibril-forming supramolecular beta-sheets from a beta-turn forming tripeptide containing non-coded amino acids: the crystallographic signature

The crystal structure of a terminally protected tripeptide Boc-Leu-Aib-beta-Ala-OMe 1 containing non-coded amino acids reveals that it adopts a beta-turn structure, which sell-assembles to form a supramolecular beta-sheet via non-covalent interactions. The SEM image of peptide 1 exhibits amyloid-like fibrillar morphology in the solid state. (C) 2002 Elsevier Science Ltd. All rights reserved.

Low molecular weight organogelators from self-assembling synthetic tripeptides with coded amino acids: morphological, structural, thermodynamic and spectroscopic investigations

A series of self-assembling terminally blocked tripeptides (containing coded amino acids) form gels in various aromatic solvents including benzene, toluene, xylenes at low concentrations. However these tripeptides do not form gels in aliphatic hydrocarbons like n-hexane, cyclohexane, n-decane etc. Morphological studies of the dried gel indicate the presence of an entangled fibrous network, which is responsible for gelation. Differential scanning calorimetric (DSC) studies of the gels produced by peptide 1 clearly demonstrates thermoreversible nature of the gel and tripeptide-solvent complex may be produced during gel formation. FT-IR and H-1 NMR studies of the gels demonstrate that an intermolecular hydrogen-bonding network is formed during gelation. Single crystal X-ray diffraction studies for peptides 1, 2 and 3 have been performed to investigate the molecular arrangement that might be responsible for forming the fibrous network of these self-assembling peptide gelators. It has been found that the morph responsible for gelation of peptides 1, 2 and 3 in benzene is somewhat different from that of its xerogel.

Stabilization of two smallest possible diastereomeric beta-hairpins in a water soluble tetrapeptide containing non-coded alpha-amino isobutyric acid (Aib) and m-amino benzoic acid

Single crystal X-ray diffraction study reveals that the water soluble tetrapeptide H2N-Ile-Aib-Leu-m-ABA-CO2H, containing non-coded Aib (alpha-amino isobutyric acid) and m-ABA (meta-amino benzoic acid), crystallizes with two smallest possible diastereomeric beta-hairpin molecules in the asymmetric unit. Although in both of the molecules the chiralities at Ile(1) and Leu(3) are S, a conformational reversal in the back bone chain is observed to produce the beta-hairpins with beta-turn conformations of type II and II'. Interestingly Aib which is known to adopt helical conformation, adopts unusual semi-extended conformation with phi: -49.5(5)degrees, psi: 135.2(5)degrees in type II and phi: 50.6(6)degrees. psi: -137.0(4)degrees in type II' for occupying the i + 1 position of the beta-turns. The two hairpin molecules are further interlocked through intermolecular hydrogen bonds and electrostatic interactions between CO2- and -+NH3 groups to form dimeric supramolecular beta-hairpin aggregate in the crystal state. The CD measurement and 2D NMR study of the peptide in aqueous medium support the existence of beta-hairpin structure in water. (C) 2009 Elsevier B.V. All rights reserved.

X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)(2) molecules by a bis(9-aminoacridine-4-carboxamide) derivative

Acridine-4-carboxamides form a class of known DNA mono-intercalating agents that exhibit cytotoxic activity against tumour cell lines due to their ability to inhibit topoisomerases. Previous studies of bis-acridine derivatives have yielded equivocal results regarding the minimum length of linker necessary between the two acridine chromophores to allow bis-intercalation of duplex DNA. We report here the 1.7 angstrom resolution X-ray crystal structure of a six-carbon-linked bis(acridine-4-carboxamide) ligand bound to d(CGTACG)(2) molecules by non-covalent duplex cross-linking. The asymmetric unit consists of one DNA duplex containing an intercalated acridine-4-carboxamide chromophore at each of the two CG steps. The other half of each ligand is bound to another DNA molecule in a symmetry-related manner, with the alkyl linker threading through the minor grooves. The two crystallographically independent ligand molecules adopt distinct side chain interactions, forming hydrogen bonds to either O6 or N7 on the major groove face of guanine, in contrast to the semi-disordered state of mono-intercalators bound to the same DNA molecule. The complex described here provides the first structural evidence for the non-covalent cross-linking of DNA by a small molecule ligand and suggests a possible explanation for the inconsistent behaviour of six-carbon linked bis-acridines in previous assays of DNA bis-intercalation.

Overlapping double turn conformations adopted by tetrapeptides containing non-coded alpha-Amino Isobutyric Acid (AIB) and formation of tape-like structures through supramolecular helix mediated self-assembly

Single crystal X-ray diffraction studies and solvent dependent H-1 NMR titrations reveal that a set of four tetrapeptides with general formula Boc-Xx(1)-Aib(2)-Yy(3)-Zz(4)-OMe, where Xx, Yy and Zz are coded L- amino acids, adopt equivalent conformations that can be described as overlapping double turn conformations stabilized by two 4 -> 1 intramolecular hydrogen bonds between Yy(3)-NH and Boc C=O and Zz(4)-NH and Xx(1)C=O. In the crystalline state, the double turn structures are packed in head-to-tail fashion through intermolecular hydrogen bonds to create supramolecular helical structures. Field emission scanning electron microscopic (FE-SEM) images of the tetrapeptides in the solid state reveal that they can form flat tape-like structures. The results establish that synthetic Aib containing supramolecular helices can form highly ordered self-aggregated amyloid plaque like human amylin.

Design of supramolecular beta-sheet forming beta-turns containing aromatic rings and non-coded alpha-aminoisobutyric acid and the formation of flat fibrillar structures through self-assembly

Single crystal X-ray diffraction studies show that the three designed tripeptides Boc-Leu-Aib-m-NA-NO2 (I), Boc-Phe-Aib-m-NA-NO2 (II) and Boc-Pro-Aib-m-ABA-OMe (III) (Aib, -aminoisobutyric acid; m-NA, m-nitroaniline; m-ABA, m-aminobenzoic acid; Boc, t-butyloxycarbonyl) containing aromatic rings in the backbones adopt -turn structures that are self-assembled through intermolecular hydrogen bonds and van der Waals interactions to create layers of -sheets. Solvent-dependent NMR titration and CD studies show that the -turn structures of the peptides also exist in the solution phase. The field emission scanning electron microscopic and transmission electron microscopic images of the peptides in the solid state reveal fibrillar structures of flat morphology that are formed through -sheet mediated self-assembly of the preorganised -turn building blocks.

Composition, color, and texture of Thai indigenous and broiler chicken muscles

Chemical compositions and physical properties of mixed-sex Thai indigenous (Gallus domesticus) and broiler (commercial breed, CP707) chicken biceps femoris and pectoralis muscles were determined. Indigenous chicken muscles contained higher protein contents but lower fat and ash contents compared to broiler muscles (P < 0.001). The amino acid profile of the indigenous chicken muscles was similar to that of the broiler muscles except they were slightly richer in glutamic acid (P < 0.05). The indigenous chicken muscles contained more saturated and less polyunsaturated fatty acids than the broiler muscles. There were no differences in the monounsaturated fatty acid contents between the breeds. The total collagen contents of indigenous pectoralis and biceps femoris muscles were 5.09 and 12.85 mg/g, respectively, which were higher than those found in broiler pectoralis (3.86 mg/g) and biceps femoris muscles (8.70 mg/g) (P < 0.001). Soluble collagen contents were lower for indigenous pectoralis and biceps femoris muscles, 22.16 vs. 31.38% and 26.06 vs. 33.87%, respectively. The CIE system values of lightness (L*), redness (a*), and yellowness (b*) of indigenous chicken muscles were higher than those of broiler muscles. The shear values of indigenous chicken muscles either raw or cooked were higher than those of broiler muscles (P < 0.05). After cooking, the shear values decreased for broiler biceps femoris and pectoralis muscles (P < 0.05), whereas no change was observed for indigenous chicken biceps femoris muscle (P > 0.05). Shear values increased for indigenous chicken pectoralis muscle (P < 0.05).

Effect of heat treatment on the antioxidant activity, color, and free phenolic acid profile of malt

Green malt was kilned at 95 degrees C following two regimens: a standard regimen (SKR) and a rapid regimen (RKR). Both resulting malts were treated further in a tray dryer heated to 120 degrees C, as was green malt previously dried to 65 degrees C (TDR). Each regimen was monitored by determining the color, antioxidant activity (by both ABTS(center dot+) and FRAP methods), and polyphenolic profile. SKR and RKR malts exhibited decreased L* and increased b* values above approximately 80 degrees C. TDR malts changed significantly less, and color did not develop until 110 degrees C, implying that different chemical reactions lead to color in those malts. Antioxidant activity increased progressively with each regimen, although with TDR malts this became significant only at 110-120 degrees C. The RKR malt ABTS(center dot+) values were higher than those of the SKR malt. The main phenolics, that is, ferulic, p-coumaric, and vanillic acids, were monitored throughout heating. Ferulic acid levels increased upon heating to 80 degrees C for SKR and to 70 degrees C for RKR, with subsequent decreases. However, the levels for TDR malts did not increase significantly. The increase in free phenolics early in kilning could be due to enzymatic release of bound phenolics and/or easier extractability due to changes in the matrix. The differences between the kilning regimens used suggest that further modification of the regimens could lead to greater release of bound phenolics with consequent beneficial effects on flavor stability in beer and, more generally, on human health.

Amyloid-like fibrillogenesis through supramolecular helix-mediated self-assembly of tetrapeptides containing non-coded alpha-aminoisobutyric acid (Aib) and 3-aminobenzoic acid (m-ABA)

Single-crystal X-ray diffraction studies of two terminally protected tetrapeptides Boc-Ile-Aib-Val-m-ABA-OMe (I) and Boc-Ile-Aib-Phe-m-ABA-OMe (II) (Aib = alpha-aminoisobutyric acid; m-ABA = meta-aminobenzoic acid) reveal that they form continuous H-bonded helices through the association of double-bend (type III and I) building blocks. NMR Studies support the existence of the double-bend (type Ill and I) structures of the peptides in solution also. Field emission scanning electron-microscopic (FE-SEM) and high-resolution transmission electron-microscopic (HR-TEM) images of the peptides exhibit amyloid-like fibrils in the solid state. The Congo red-stained fibrils of peptide I and II, observed between crossed polarizers, show green-gold birefringence, a characteristic of amyloid fibrils.

Determination by MAD-DM of the structure of the DNA duplex d[ACGTACG(5-BrU)]2 at 1.46 Å and 100 K

A four-wavelength MAD experiment on a new brominated octanucleotide is reported here. d[ACGTACG(5-BrU)], C77H81BrN30O32P7, (DNA) = 2235, tetragonal, P43212 (No. 96), a = 43.597, c = 26.268 Å, V = 49927.5 Å3, Z = 8, T = 100 K, R = 10.91% for 4312 reflections between 15.0 and 1.46 Å resolution. The self-complementary brominated octanucleotide d[ACGTACG(5-BrU)]2 has been crystallized and data measured to 1.45 Å at both 293 K and a second crystal flash frozen at 100 K. The latter data collection was carried out to the same resolution at the four wavelengths 0.9344, 0.9216, 0.9208 and 0.9003 Å, around the Br K edge at 0.92 Å and the structure determined from a map derived from a MAD data analysis using pseudo-MIR methodology, as implemented in the program MLPHARE. This is one of the first successful MAD phasing experiments carried out at Sincrotrone Elettra in Trieste, Italy. The structure was refined using the data measured at 0.9003 Å, anisotropic temperature factors and the restrained least-squares refinement implemented in the program SHELX96, and the helical parameters are compared with those previously determined for the isomorphous d(ACGTACGT)2 analogue. The asymmetric unit consists of a single strand of octamer with 96 water molecules. No countercations were located. The A-DNA helix geometry obtained has been analysed using the CURVES program.

Computer vision and color measurement techniques for inline monitoring of cheese curd syneresis

Optical characteristics of stirred curd were simultaneously monitored during syneresis in a 10-L cheese vat using computer vision and colorimetric measurements. Curd syneresis kinetic conditions were varied using 2 levels of milk pH (6.0 and 6.5) and 2 agitation speeds (12.1 and 27.2 rpm). Measured optical parameters were compared with gravimetric measurements of syneresis, taken simultaneously. The results showed that computer vision and colorimeter measurements have potential for monitoring syneresis. The 2 different phases, curd and whey, were distinguished by means of color differences. As syneresis progressed, the backscattered light became increasingly yellow in hue for circa 20 min for the higher stirring speed and circa 30 min for the lower stirring speed. Syneresis-related gravimetric measurements of importance to cheese making (e.g., curd moisture content, total solids in whey, and yield of whey) correlated significantly with computer vision and colorimetric measurements..

Duplex stability of DNA.DNA and DNA.RNA duplexes containing 3 '-S-phosphorothiolate linkages

3′-S-Phosphorothiolate (3′-SP) linkages have been incorporated into the DNA strand of both a DNA·RNA duplex and a DNA·DNA duplex. Thermal melting (Tm) studies established that this modification significantly stabilises the DNA·RNA duplex with an average increase in Tm of about 1.4 °C per modification. For two or three modifications, the increase in Tm was larger for an alternating, as compared to the contiguous, arrangement. For more than three modifications their arrangement had no effect on Tm. In contrast to the DNA·RNA duplex, the 3′-S-phosphorothiolate linkage destabilised the DNA·DNA duplex, irrespective of the arrangement of the 3′-SP linkages. The effect of ionic strength on duplex stability was similar for both the phosphorothiolate-substituted and the unmodified RNA·DNA duplexes. The results are discussed in terms of the influence that the sulfur atom has on the conformation of the furanose ring and comparisons are also drawn between the current study and those previously conducted with other modifications that have a similar conformational effect.