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E D Atkins

Publications and source records attributed to E D Atkins.

At least 19 recordsLinked to original sources
PubMed1998

Effect of local sequence inversions on the crystalline antiparallel beta-sheet lamellar structures of periodic polypeptides: implications for chain-folding.

The crystal structure and texture of the monodisperse periodic polypeptide [(AG)3EG(GA)3EG]10 (poly(+/-AG)3EG: A=alanine, G=glycine, E=glutamic acid) were analyzed by X-ray diffraction, Fourier transform infrared spectroscopy, and electron microscopy. Structure determination was aided by comparison with the recently described structure for the related periodic polypeptide [(AG)3EG]36 by Krejchi et al. (Macromolecules 1997;30:5012). Texture-oriented samples of poly(+/-AG)3EG were obtained by crystallization of the polymer from aqueous formic acid solution. The evidence supports an antiparallel (ap) beta-sheet protein structure and the X-ray diffraction signals index on an orthorhombic unit cell with parameters: a=0.950 nm (hydrogen-bond direction), b=1.052 nm (apbeta-sheet stacking direction), c=6.95 nm (chain direction). The absence of the (010) diffraction signal, a prominent signal in the poly(AG)3EG diffraction pattern, implies that the apbeta-sheets are 'apolar', i.e. both surfaces are equally populated with alanyl methyl groups. Selective line broadening of wide-angle diffraction signals with l not equal to 0 gives an estimated crystal size of approximately/= 4 nm in the chain direction. This observation, coupled with the appearance of low-angle particle interference peaks, indicates a crystal thickness considerably less than the chain length and suggests an adjacent-re-entry chain-folded lamellar structure incorporating the apbeta-sheet architecture. The polypeptide folds through gamma-turns, in-phase with the pseudo-octapeptide repeat; the glutamic acid residues occur on the lamellar surfaces. These results and those from the crystalline lamellae of poly(AG)3EG suggest that beta-turns are not compatible with these repetitively stacked apbeta-sheet structures. This implies that intersheet interactions of alanyl methyl groups and glycyl alpha-protons are not sufficiently strong to dictate the folding geometry in these structures.

Crystallization↗
PubMed1998

Investigation of glass-ionomer cements using differential scanning calorimetry.

Six commercial glass-ionomer cements commonly used for various dental applications have been investigated using differential scanning calorimetry (DSC). The heat-flow behaviour and heat capacity of the cements were measured during isothermal (at 37 degrees C) setting reactions. The DSC results show that all materials undergo an exothermic setting process, but with different enthalpies of reactions and different heat capacities; there are no remaining endo- or exothermic reactions after the setting of the cement. All materials examined were found to be effective thermal insulators.

Journal Article↗
PubMed1997

Effects of amino acid side-chain volume on chain packing in genetically engineered periodic polypeptides.

The fidelity of bacterial protein synthesis allows the production of architecturally well-defined polymeric materials through precise control of chain length, sequence, stereochemistry, and interchain interactions. In the present paper, we examine the relation between amino acid residue volume and crystalline unit cell dimensions, in a set of periodic protein polymers of repeating unit sequence -(AlaGly)3-X-Gly-, where X is Asn, Phe, Ser, Val, or Tyr. The proteins were overexpressed in Escherichia coli, purified by simple procedures based on acid/ethanol precipitation or insolubility in aqueous sodium dodecyl sulfate, and processed to form oriented crystalline mats by precipitation from formic acid under mechanical shear. X-ray diffraction analyses revealed that the basic structures of the -(AlaGly)3-X-Gly- polymers are identical to that previously reported for [(AlaGly)3-GluGly]36, [Krejchi, M.T., Atkins, E.D.T., Waddon, A.J., Fournier, M.J., Mason, T.L., and Tirrell, D.A. (1994) Science 265, 1427-1432], with the oligoalanylglycine segments forming antiparallel beta-sheets and the substituted amino acids occurring within three-residue folds at the lamellar surfaces. The X-ray diffraction signals for each member of the family index on an orthorhombic unit cell; the a-axis (hydrogen bond direction) and c-axis (chain direction) spacings remain invariant but the b-axis (sheet stacking direction) spacing increases with increasing volume of the substituted amino acid. The results obtained from a variant with alternating Glu and Lys substitution at the X position, together with the results previously reported for poly(L-alanylglycine) [Panitch, A., Matsuki, K., Cantor, E.J., Cooper, S.J., Atkins, E.D.T., Fournier, M.J., Mason, T.L., and Tirrell, D.A. (1997) Macromolecules 30, 42-49] are included for comparison. The average intersheet stacking distance (b/2) increases linearly with the volume of the amino acid inserted at position X. Because the chain-folded lamellar architecture adopted by these periodic polypeptides accommodates a wide range of residues differing in charge, steric bulk, and hydrophobicity, these results illustrate a new approach to the engineering of intermolecular interactions in polymeric solids.

Amino Acids↗
PubMed1994

Chemical sequence control of beta-sheet assembly in macromolecular crystals of periodic polypeptides.

A family of uniform periodic polypeptides has been prepared by bacterial expression of the corresponding artificial genes, with the objective of exploring the potential for control of supramolecular organization in genetically engineered protein-based polymeric materials. The repeating units of the polypeptides consist of oligomeric alanyl-glycine sequences interspersed with glutamic acid residues inserted at intervals of 8 to 14 amino acids. Crystallization of such materials from formic acid produces beta-sheet structures in the solid state, as shown by vibrational spectroscopy, nuclear magnetic resonance spectroscopy, and wide-angle x-ray diffraction. The diffraction results, together with observations from electron microscopy, are consistent with the formation of needle-shaped lamellar crystals whose thickness is controlled by the periodicity of the primary sequence. These results can be used to control solid-state structure in macromolecular materials.

Amino Acid Sequence↗
PubMed1993

Elongational flow studies on type IV collagen: comparison with type I.

Elongation flow techniques have been used to investigate the birefringent response of monodisperse type IV collagen in dilute solution and the results compared with type I collagen. A four-roll mill apparatus was used to characterize the solutions at low strain rates, epsilon < or = 300 s-1. The birefringence is nonlocalized and rises gradually to a plateau value, in accordance with rigid-rod behavior. The gradients of the tangent to the curves at zero strain rate are estimated for types IV and I collagen. The concentrations of the solutions used were in the dilute to semidilute regimes. Using a value of 300 nm for the length of type I collagen, values of 364-408 nm were calculated for the length of the type IV collagen molecule, depending on the concentration regime chosen, which is consistent with biochemical predictions based on a rigid molecule. The results imply that the behavior of type IV collagen molecules in solution is similar to type I collagen, despite the presence of several sequence interruptions in the type IV helix.

Chemistry, Physical↗
PubMed1993

Molecular bending and networks in a basement membrane-like collagen: packing in dogfish egg capsule collagen.

Low-angle X-ray diffraction data have been obtained from three mutually perpendicular axes through sheets of the collagenous egg capsule of the dogfish Scyliorhinus caniculus, a collagen that resembles type IV collagen. The data are interpreted in the light of the body of knowledge of the structure derived from transmission electron microscopy by Knight and Hunt. A model to account for the X-ray data is proposed incorporating the main dimensions of the Knight and Hunt model which are confirmed by the diffraction data. Several features of the diffraction patterns are not explained by the existing model however, and a new model is proposed to account for these features. This consists of antiparallel packed pairs of two mutually parallel molecules, each kinked and rotated so as to produce a four-fold helix resembling a crankshaft. This has the advantage of conferring intermolecular linkage in three dimensions throughout the structure with tetragonal symmetry and unit dimensions a = b = 22.6 nm, c (fibre axis direction) = 39.3 nm. The result is a fairly rigid open polygonal network or sponge-like architecture that is capable of accommodating large quantities of water and other molecules.

Animals↗
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↗
PubMed1980

Chemical cross-linking restrictions on models for the molecular organization of the collagen fibre.

The nature of the precise packing of collagen molecules into a collagen fibril, producing the characteristic regular banding, is still debatable. The problem has been approached using electron microscopy and X-ray diffraction techniques, and several models have been proposed, including hexagonal packing, an octafibril structure, a two-strand rope and a five-strand rope (for review, see ref. 1). For the past decade the pentafibrillar model, originally proposed by Smith, has been widely accepted as the fundamental building unit. This model, based on the quarter-stagger end-overlap hypothesis of Hodge and Petruska, was supported by the X-ray diffraction data of Miller and Wray. These X-ray data have now been reinterpreted by Hulmes and Miller in terms of a quasi-hexagonal packing of collagen molecules. We argue here that until other characteristic parameters are taken into account, in particular the chemical cross-linking evidence, the packing problem is still unresolved.

Collagen↗
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↗