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Biomedical subjects

E D Atkins

Publications and source records attributed to E D Atkins.

At least 19 recordsLinked to original sources
PubMed1992

Elongational flow studies on DNA in aqueous solution and stress-induced scission of the double helix.

Elongational flow techniques are used to investigate the birefringent response and flow-induced molecular scission of monodisperse phage-DNA samples in aqueous solution. A 4-roll mill apparatus was used to characterize the solutions at low stain rates, epsilon less than or equal to 300 s-1, and the opposed jets apparatus used to study fracture of the DNA molecules at strain rates up to 15 x 10(3) s-1. The molecular weight values were measured before and after fracture in elongational flow using the high-resolution technique of pulsed field gel electrophoresis (PFGE). The birefringent response incorporates both rigid and flexible components. The birefringence is nonlocalized and rises gradually to a plateau value, similar to rigid-rod behavior. In addition a certain minimum value in the strain rate is necessary, an onset value epsilon 0, before the signal appears, indicating a flexible component. This behavior is consistent with a hinged-rod model and is similar to that observed for the protein collagen molecule at elevated temperature. We propose that this type of behavior is likely for multistrand rope-like macromolecules where localized separation or partial untwisting of the intertwined chains occurs, creating temporary hinges, in accordance with biochemical evidence for sequence-specific sites of flexibility. Results are presented on the entanglement effects at high concentrations. We have calculated rotational diffusion rates as a function of concentration and molecular weight. Using PFGE to measure the molecular weight profiles, our fracture studies at high strain rates demonstrate chain halving and quartering in accordance with the predictions of the thermally activated barrier to scission theory for single-chain polymers.

DNA, Viral↗
PubMed1992

Visualization of the algal polysaccharide carrageenan by scanning tunnelling microscopy.

Scanning tunnelling microscopy has been used to obtain images in the constant-current mode in air and moist conditions at molecular resolution for the kappa- and iota-carrageenan algal polysaccharides. The molecules were deposited from an aqueous solution onto a graphite substrate. The samples formed aligned nematic-like arrays and were also found as individual molecules. The molecular dimensions of width, height and repeat distance along the molecule were found to be close to the values previously determined by X-ray diffraction. The results support a molecular model based on a double-helix structure for carrageenan.

Carbohydrate Sequence↗
PubMed1991

Molecular transforms of kappa carrageenan and furcellaran from mixed gel systems.

X-ray fibre diffraction studies of furcellaran-carob, furcellaran-tara, and furcellaran-konjac mannan mixed gels have failed to reveal any evidence for the predicted intermolecular binding between the algal polysaccharide helix and the galactomannan or glucomannan (konjac) mannan). In the absence of such interactions, mixed gels of kappa carrageenan-konjac mannan and furcellaran-konjac mannan, have been used to obtain good quality molecular transforms of the kappa carrageenan and furcellaran molecules in an oriented nematic liquid crystalline form. Analyses of the pattern support double helix structures with threefold symmetry with helix pitch of 2.5 nm. The absence of a 0.83 nm meridional in kappa carrageenan necessitates zero axial translation from the exact half-stagger position, contrary to the model building prediction. An axial translation from half-stagger is necessary for furcellaran.

Alginates↗
PubMed1989

Molecular organization of type IV collagen: polymer liquid crystal-like aspects.

A new X-ray diffraction pattern from type IV collagen is described, which can be interpreted on the basis of crystalline and liquid crystalline origins of the reflections. Bovine anterior lens capsules extracted with 1 M NaCl and oriented by extension of 60% under constant load gave medium angle X-ray diffraction patterns showing many of the characteristics typical of liquid crystals. Prominent features, apart from those wide angle features attributable to the collagen triple helix, are (1) a four-point pattern of broad reflections at d-spacing 3.9 nm, and layer line spacing near 5 nm. (2) A broad intense equatorial peak centred at 1.24 nm, indicative of liquid-like lateral molecular associations. (3) A set of five sharp, streaked meridional reflections (previously obscured by the broad peak near 5 nm in unextracted capsules). (4) A further six higher angle reflections of a diffuse, arced and broad appearance on the meridian. The sharp streaked meridional reflections emanate from a long-range periodicity of units 8-9 nm in diameter. These features form a self-consistent system if interpreted on the basis of a staggered liquid crystal-like array of collagen molecules, in which case the first five meridionals and remaining broad reflections, sampled on the meridian, can all be indexed as orders of 21 nm.

Collagen↗
PubMed1983

Dermatan sulfate: molecular conformations and interactions in the condensed state.

The molecular conformations and manner of aggregation has been determined for three allomorphs of the connective tissue polysaccharide dermatan sulfate by analysis of X-ray diffraction from oriented, polycrystalline fibers of sodium salts. One allomorph is unique among glycosaminoglycans in having right-handed (8(3)) helical chains. Two such chains pack antiparallel in a tetragonal unit cell (a = b = 1.267 nm, c = 7.353 nm) with P4(3)2(1)2 space group symmetry. The 3(2) chains of the second allomorph are organized in a trigonal unit cell (a = b = 1.460 nm, c = 2.823 nm, space group symmetry P3(2)21) containing two left-handed antiparallel polysaccharide molecules. (The chirality of this allomorph has been assumed to be the same as in other 3-fold glycosaminoglycan helices, since discrimination between 3(1) and 3(2) symmetries was found not to be possible.) The archiral 2(1) helices of the third allomorph, pack probably in an orthorhombic unit cell (a = 1.151 nm, b = 1.065 nm, c = 1.878 nm, space group symmetry P2(1)2(1)2(1)) that contains again two antiparallel polymer molecules. Each dermatan sulfate chain is stabilized intramolecularly by O3-O5 hydrogen bonds across the beta (1 leads to 4) linkage. There are two intermolecular hydrogen bonds per tetrasaccharide repeat in the tetragonal structure and two per disaccharide in the trigonal structure. Fourier difference syntheses indicated equivalents of four sodium ions per tetrasaccharide and two sodium ions per disaccharide in the tetragonal and trigonal structures, respectively. The cations are either partially or fully hydrated and link dermatan sulfate chains either intra- or intermolecularly by involving besides other polyanion oxygen atoms, carboxylate and sulfate oxygen atoms. The probable mode of packing in the orthorhombic structure indicates a pair of hydrogen bonds between adjacent antiparallel polysaccharide chains and suggests plausible cationic sites in the unit cell.

Carbohydrate Conformation↗
PubMed1977

Molecular conformation of sodium heparan sulphate in the condensed phase.

By using the X-ray-diffraction results reported previously for sodium heparan sulphate, a twofold helical conformation with an axially projected disaccharide repeat (h) equal to 0.93 nm has been examined in detail. On the basis of a repeating sequence of 1,4-alpha-D-glucosamine and 1,4-beta-D-glucuronic acid, trial and stereochemically feasible molecular models were computer-generated. An optimum twofold helical conformation is proposed, incorporating stabilizing intra-chain hydrogen bonds across both glycosidic linkages.

Glycosaminoglycans↗
PubMed1974

X-ray fibre diffraction of cartilage proteoglycan aggregates containing hyaluronic acid.

Ordered conformations of proteoglycan-hyaluronic acid aggregates in the intercellular matrix in cartilage were observed by X-ray diffraction. The sodium salt form of three samples, (a) aggregated proteoglycan, (b) disaggregated proteoglycan and (c) reconstituted disaggregated proteoglycan, give essentially similar X-ray fibre-type diffraction photographs. The patterns correlate with the chondroitin 4-sulphate component and can be interpreted as twofold helical conformations, similar to that observed previously for the free acid form of chondroitin 4-sulphate (Isaac & Atkins, 1973). The information takes us one step nearer the situation found in cartilage in vivo.

Animals↗
PubMed1974

Crystallization of macromolecular heparin.

X-ray fibre-diffraction photographs were obtained from oriented films of the sodium salt of macromolecular heparin (molecular weight approx. 10(6)) prepared from rat skin. Two distinct molecular chain conformations corresponding to two different crystal lattices were observed as a function of relative humidity. The first conformation, obtained at 78% relative humidity, has a layer-line spacing of 1.73nm, which can be interpreted as an approximate twofold helix. On increasing the relative humidity to 84% a second phase with a layer-line repeat of 1.65nm is obtained with the reflexions indexing on a triclinic unit cell similar to that obtained previously (Nieduszynski & Atkins, 1973) for pig mucosal heparin.

Animals↗
PubMed1973

Hyaluronates: relation between molecular conformations.

The discovery that both potassium and sodium salts of hyaluronic acid can exist in a double-strand helical conformation that will convert to the already known single-strand helical structures illustrates the remarkable conformational versatility of this biopolymer. X-ray diffraction was used to monitor variations in molecular conformation as a function of several independent, controllable variables, such as relative humidity, temperature, and applied tension. A scheme is presented for the interrelation of a range of hyaluronate conformations.

Humidity↗