bluuebunny/crossref_metadata_2025_split huggingface dataset:
A V7 conformation of dimethyl sulfoxide‐amylose complex
Authors: Simpson T. D. , Dintzis F. R. , Taylor N. W. 
Published: December 2004

AbstractX‐ray investigation of a crystalline complex between dimethyl sulfoxide (DMSO) and amylose indicates a sevenfold helical structure having an orthogonal unit cell: a = 30.23 Å, b = 28.18 Å, and C = 7.91 Å (helix axis). This helical amylose results from precipitation of amylose in DMSO solutions under suitably dry conditions using toluene as a precipitating agent. Analyses show a molar ratio of 0.95:2:0.4:0.08 for DMSO, amylose glucose units, water, and toluene, respectively. DMSO and amylose combine in at least two crystalline conformations, sixfold and sevenfold helices. The amount of water present influences the resulting conformation. The existence of the sevenfold helical solid indicates that the amylose sevenfold helix has greater stability than previously recognized by conformational energy calculations. In general, potential energy calculations cannot be correct that ignore the influence of guest molecules and their effects upon the maltose residue conformation and that lead to a sixfold helix as the most probable structure.
Fine structure of DNA melting curves
Authors: Lyubchenko Yu. L. , Frank–Kamenetskii M. D. , Volgodskii A. V. , Lazurkin Yu. S. , Gause G. G. 
Published: December 2004

AbstractTheoretical calculations predict that the differential melting curves for random polynucleotide sequences having lengths up to several tens of thousands of base pairs have a clear‐cut fine structure. This structure appears in the form of multiple narrow peaks 0.3–0.4°C wide on the bell shaped main curve. The differential melting curves have different shapes for different specific sequences. The theory also predicts the disappearance of the fine structure when the length of the sequence increases and when circular, covalently closed DNA is considered instead of the open structure. The predictions of the theory were confirmed by the measurements of differential melting curves for open and covalently closed circular forms of DNA for PM2 phage (N = 104 base pairs) and also for other phage DNA's of different length: T7 (N = 3.8 × 104); SD (N = 9.2 × 104); T2 (N = 17 × 104). It was shown that the effect of fine structure results mainly from the cooperative melting out of DNA regions 300–500 base pairs long.
Conformation of the cyclic tetrapeptide dihydrochlamydocin. Iabu‐L‐Phe‐D‐Pro‐LX, and experimental values for 3 → 1 intramolecular hydrogen bonds by X‐ray diffraction
Authors: Flippen Judith L. , Karle Isabella L. 
Published: December 2004

AbstractChlamydocin, Iabu‐L‐Phe‐D‐Pro‐LX, is a naturally occurring cyclic tetrapeptide that exhibits high cytostatic activity. The conformation of the peptide ring, as well as the stereo configuration in the vicinity of the epoxide ring, have been established by a single‐crystal X‐ray study of dihydrochlamydocin: C28H40N4O6·H2O. It crystallizes in the monoclinic space group P21 with a = 12.616(6) Å, b = 12.355(6) Å, c = 9.442(5) Å, and β = 99.5(1)°. The structure was solved by the symbolic addition procedure for phase determination followed by the tangent formula method of phase refinement. This structure represents the first cyclic tetrapeptide in which all four peptide units have been found in the trans conformation; however, each peptide unit is significantly nonplanar with ω angles deviating by 14–24° from the ideal value of 180°. This molecule contains two intramolecular 3 → 1 hydrogen bonds and experimentally determined parameters for these seven‐membered turns are presented.
Fluctuations of an α‐helix
Authors: Gō Mitiko , Gō Nobuhiro 
Published: December 2004

AbstractFluctuations in backbone dihedral angles in the α‐helical conformation of homopolypeptides are studied based on an assumption that the conformational energy function of a polypeptide consisting of n amino‐acid residues can be approximated by a 2n‐dimensional parabola around the minimum point in the range of fluctuations. A formula is derived that relates 〈ΔθiΔθj〉, the mean value of the product of deviations of dihedral angles ϕi and ψi (collectively designated by θi) from their energy minimum values, with a matrix inverse to the second derivative matrix F,n of the conformational energy function at the minimum point. A method of calculating the inverse matrix Fn−1 explicitly is given. The method is applied to calculating 〈ΔθiΔθj〉 for the α‐helices of poly(L‐alanine) and polyglycine. The autocorrelations 〈(Δϕi)2〉 and 〈(Δψi)2〉 at 300°K are found to be about 66 deg2 and 49 deg2, respectively, for poly(L‐alanine), and 84 deg2 and 116 deg2, respectively, for polyglycine. The length of correlations of fluctuations along the chain is found for both polypeptides to be about eight residues long.
Coenzyme models. IV. Effect of polymer micelles on rate and equilibrium of addition of cyanide ion to N‐substituted 3‐carboxamidopyridinium ions
Authors: Shinkai Seiji , Kunitake Toyoki 
Published: December 2004

AbstractThe water‐soluble poly(1‐vinyl‐2‐ethylimidazole) quaternized with ethyl bromide and lauryl bromide was prepared; lauryl group content, 8.8 mol% (L‐9), 28.9 mol% (L‐29), and 40.9 mol% (L‐41). The λmax value of methyl orange near 460 nm shifted to shorter wavelengths (417–433 nm) in the aqueous solution of L‐29 and L‐41, and the intrinsic viscosity of L‐29 was more than ten times smaller than that of L‐9. The rate and equilibrium constants (kƒ and K) for addition of cyanide ion to the N‐substituted 3‐carboxamidopyridinium ions were studied at 30°C, where N‐substituents employed were n‐propyl, n‐hexyl, benzyl, 2,6‐dichlorobenzyl, and n‐lauryl. The kinetic parameters for n‐lauryl‐3‐carboxamidopyridinium were markedly increased in the presence of L‐29 and L‐41 and with increasing polymer concentrations (84‐fold for kƒ and 7800‐fold for K), especially at low ionic strength, whereas L‐9 decelerated the addition reaction. These distinct behaviors mean that L‐29 and L‐41 are classified as micellelike polymers and L‐9 as a polyelectrolytelike polymer. However, L‐29 depressed the rate of the forward reaction for benzyl‐3‐carboxamidopyridinium, acting like a simple polyelectrolyte. Therefore, the polymer micelle can provide both the microenvironments characteristic of polyelectrolytes and micelles, depending on the hydrophobicity of substrates.
Interaction of water with poly‐α‐amino acids. I. Relationships between conformation and relaxation processes
Authors: Shiraishi H. , Hiltner A. , Baer E. 
Published: December 2004

AbstractThe relaxation behaviour of the sodium salt of poly (L‐glutamic acid) in the solid state has been examined by means of dynamic mechanical spectroscopy. Bound water was found to exert a profound influence on the relaxation behaviour and on a bulk property, the rigidity. Certain features of the loss spectrum have been identified with the hydration‐dependent β‐to‐α conformational transition. Thus two side‐chain relaxations are observed below ambient temperature, one associated with the β from (β1β) and a second at a lower temperature associated with the α form (β1α). The greater rigidity of the α form below the relaxation temperature and the larger rigidity drop accompanying the β1α can be explained in terms of the structural differences of the two conformations.
Heats of binding protons to globular proteins
Authors: Shiao D. D. F. , Sturtevant J. M. 
Published: December 2004

AbstractThe heats of binding of protons ΔHb to three globular proteins, lysozyme, chymotrysinogen A, and oxidized cytochrome c, from pH 11‐2 or lower at 25°C were determined by flow microcalorimetry. In addition, the acid–base titrations of chymotrypsinogen A and oxidized cytochrome c were investigated under conditions similar to those used in the calorimetric experiments. The results of the calorimetric experiments and the acid–base titrations for lysozyme and chymotrypsinogen A in the neutral and alkaline pH regions are in accord with the Linderström‐Lang model with a pH‐independent electrostatic factor. However, in order to interpret the results on oxidized cytochrome c in the same pH region, it is necessary to assume the protonation of two unidentified groups; one of these groups, with ΔHb = −18 kcal/mol and pKa = 9.4 was detected in previous work [Watt, G. D. & Sturtevant, J. M. (1969) Biochemistry 8, 4567]. The normal heats of protonation for carboxyl, ϵ‐amino, phenolic, α‐amino, and imidazole groups on globular proteins as deduced from the study are 0, −10.5, −6.3, −10.0, and −6.3 kcal/mol, respectively. ΔHb of chymotrypsinogen A between pH 4.5 and 1.3 is +30 kcal/mol. This value, which is undoubtedly too large to be accounted for by the protonation of normal carboxyl groups, leads to the conclusion that this protein undergoes a pH‐induced conformational change in this pH region. The same idea can be applied to explain the abnormal ΔHb observed for oxidized cytochrome c in the alkaline pH region.
Ultracentrifugal compression of gels
Authors: Bloomfield Victor A. 
Published: December 2004

AbstractIt has been observed that the amount of water associated with casein micelles is markedly higher when measured by intrinsic viscosity than by water content of the pelleted casein. A possible explanation of this discrepancy is that water is squeezed out of the pellet by the ultracentrifugal field. We have calculated the potential magnitude of this effect by considering a simple model system: an elastic gel swollen by solvent and compressed by the centrifugal field. Equilibrium is reached when the sum of the ultracentrifugal, elastic, and mixing free energies is a minimum. The equilibrium degree of swelling is calculated as a function of rotor speed, thickness of the unsolvated gel material, and enthalpy of mixing of solvent and solute. Sizable compressions can occur for highly swollen gels, if the enthalpy of mixing is moderately positive. Casein micelles from intrinsic viscosity measurements have a “hydration” of about 3.7 g water/g protein, corresponding to a swelling ratio of 6.3 relative to the dry protein. The observed pellet hydration is 1.9 g/g. Under the conditions of the experiment, pelleting at 25,000 rpm is predicted to decrease the swelling ratio to 4.9, and the hydration to 2.7 g/g, about half the observed decrease, if the enthalpy of mixing is 0.5 RT/mol segment. These calculations may be relevent to the deterination by pelleting of the solvent content of other biopolymer gels.
Spectroscopic properties of complexes of acridine orange with glycosaminoglycans. II. Aggregated complexes—evidence for long‐range order
Authors: Salter Mary K. , Abrahamson E. William , Rippon W. Barton 
Published: December 2004

AbstractAggregated complexes of acridine orange with dermatan and chondroitin sulfates have been studied in aqueous solution by absorption and circular dichroism spectroscopy. Aggregation was found to be favored at high‐dye and glycosaminoglycan concentrations, and in solutions where anionic sites of the glycosaminoglycan are effectively complexed with dye. The aggregates can be removed from solution by centrifugation at 27,000 × g for 1 hr or by filtration through a membrane containing pores of 0.1 μm diameter.The aggregated complexes exhibit large‐magnitude‐ellipticity circular dichroism bands. In addition, the circular dichroism spectrum observed for a solution containing aggregated acridine orange/chondroitin 4‐sulfate complexes is nearly a mirror image of that obtained for aggregated acridine orange/dermatan sulfate complexes.Cooperative alterations (sharp transitions) in the circular dichroism ellipticities of the aggregates occur at elevated temperatures, and result in spectroscopically distinct aggregates upon cooling. The circular dichroism properties and temperature effects are attributed to a supramolecular ordering of acridine orange/glycosaminoglycan complexes within the aggregates, which can be reorganized to a more stable form at high temperatures.Mixed aggregates, containing two different glycosaminoglycans, can be formed. The circular dichroism properties of the mixed aggregates also indicate the existence of long‐range order in the arrangement of the complexes. Mixed aggregates containing dermatan sulfate and either chondroitin 4‐sulfate or chondroitin 6‐sulfate resemble pure dermatan sulfate aggregates in circular dichroism characteristics.
Rapid characterization of protein molecular weights and hydrodynamic structures by quasielastic laser‐light scattering
Authors: McDonnell Milton Eddy , Jamieson A. M. 
Published: December 2004

AbstractTwo methods for the characterization of protein molecular weights from their diffusion coefficients are discussed. These measurements can be made quickly and reliably at low concentrations using quasielastic light‐scattering techniques. First, an empirical calibration of the diffusion coefficient at infinite dilution of denatured random coils against molecular weight is reported. The second method combines the measurement of D0 with the intrinsic viscosity [η]. This D0–[η] relationship proves to be very insensitive to polymers structure or solvent type. The data indicate that the ratio of the hydrodynamic radius measured by viscosity to the hydrodynamic radius measured by diffusion is about 15% smaller than that predicted by theoretical models. The nature of the molecular‐weight average obtained for polydisperse systems is defined for a Schulz distribution. These hydrodynamic methods have also been used to demonstrate the presence of chain branching in the glycoprotein ovomucoid. In addition, a method is proposed by which the effective segment length and an excluded volume parameter for random coils may be evaluated for diffusion measurements.
Interpretation of energy‐transfer experiments by theoretical studies of model compounds using semiempirical potential functions. I. Three‐linked aromatic peptide units
Authors: Guillard R. , Englert A. 
Published: December 2004

AbstractIt is shown that theoretical conformational analysis, based on the evaluation of semiempirical potential functions, can be used to compute the quantities relevant to the interpretation of energy‐transfer experiments. The relevant properties are computed for a segment of a polypeptide chain with the sequence Tyr‐Tyr. In particular, the average value of the orientation factor 〈κ2〉 and its distribution ƒ(κ2) are examined. It appears that the degrees of freedom for rotation of the side chains are not sufficient to randomize completely the orientation factor of the transition dipoles. Two additional degrees of freedom, namely the torsion angles around the valence bonds of the backbone, ψ1 and ϕ2, bring 〈κ2〉 close to the value that corresponds to randomly oriented transition dipoles.
Proton and phosphorus‐31 magnetic relaxation studies on the interaction of polyriboadenylic acid with Mn2+
Authors: Yamada Atsuko , Akasaka Kazuyuki , Hatano Hiroyuki 
Published: December 2004

AbstractProton and phosphorus‐31 nuclear spin–lattice relaxation times T1 and spin–spin relaxation times T2 have been measured on the single‐stranded polyriboadenylic acid [poly(A)]–Mn2+ system in a neutral D2O solution in the temperature range 10°–90°C at 100 and 40.5 MHz, respectively, with the Fourier transform nmr method. Minimum values of T1 have been found for all these nuclei, which have enabled the exact estimation of apparent distances from Mn2+ to H2, H8, H1′, and the phosphorus nucleus to be 4.7, 4.1, 5.2, and 3.0 Å, respectively. The electron spin of Mn2+ penetrates into the phosphorus nucleus, giving 31P hyperfine coupling of more than 106 Hz. Evidence of penetration of the electron spin into H8 and H2 is also obtained, suggesting direct coordination of nitrogen atoms of the adenine ring to the Mn2+ Ion. Combined with the result from proton relaxation enhancement of water, it is concluded that every Mn2+ ion added is bound directly to two phosphate groups with a Mn2+–phosphorus distance of 3.3 Å, while a part of the Mn2+ ions are simultaneouly bound to the adenine ring. It is estimated that 39 ± 13% and 13 ± 5% of Mn2+ are coordinated by N7 and N3 (or N1), respectively. The motional freedom of poly(A) in the environment of the Mn2+ binding site has been found to be quenched to the extent that the rotational motion becomes several times slower than that of the corresponding Mn2+–free poly(A). The activation energies for the molecular motion are, however, practically unchanged from those for Mn2+–free poly(A), and are found to be 8.3, 8.5, 6.1, and 8.7 kcal/mol for H8, H2, H1′, and phosphorus, respectively. T2 of phosphorus is determined by the dissociation rate (k−1) of Mn2+ from the phosphate group for the whole temperature range studied with activation enthalpy of 6.5 kcal/mol. The dissociation rates of Mn2+ from the adenine ring are also estimated from proton T2 values below 50°C.
The β association of (DLLys)10–(LVal)20–(DLLys)10: An nmr study
Authors: Schwartz Arnold M. , Fasman Gerald D. 
Published: December 2004

Abstract(DLLys)10–(LVal)20–(DLLys)10, a copolymer of a valine block in the β conformation with randomly coiled flanking blocks of lysine [Kubota, S. & Fasman, G. D. (1975) Biopolymers 14, 605–631], was studied by nuclear magnetic resonance. The peak areas of the NH and CH resonances of valine and lysine are concentration‐dependent with little chemical shift change. A model is presented describing the aggregation of the copolymer. Additional evidence, obtained by monitoring the spin‐lattice relaxation times of amino, amide, γ‐methyl‐valine, and ϵ‐methylene‐lysine, is consistent with the aggregation model. Hydrodynamic studies are presented which show monomer → oligomer aggregation of four or five subunits.
Viscosity at low shear and circular dichroism studies of heparin
Authors: Chung M. Ching Ming , Ellerton Nerida F. 
Published: December 2004

AbstractThe viscosity of heparin solution was investigated under conditions of low shear stress between 0.0193 and 0.222 dyne cm−2, in water, in the presence of various cations (Na+, K+, Cs+, Mg2+, Ba2+, Cu2+) and at several pH's. The viscosity was found to decrease with in creasing shear stress. Shear dependence was greatest in the absence of added salts, and decreased as the ionic strength increased.Differences in viscosity in the presence of various cations appear to be related to the binding affinity of these cations to heparin. Viscosity studies of the periodate oxidation of heparin confirmed that heparin contains vicinal hydroxyl groups in its primary structure.Circular dichroism spectra of the same heparin solutions were also studied. The binding process between Cu2+ and heparin appears to be different from that of other divalent ions. A reduction in the pitch of the helix would qualitatively explain the conformational changes that occur on binding Cu2+ to heparin. These changes are reversible on removal of Cu2+ and replacement with Na+. The circular dichroism spectrum was virtually lost for periodateoxidized heparin.
An electrostatic model for collagen fibrils. The interaction of reconstituted collagen with Ca++, Na+, and Cl−
Authors: Li Shu‐Tung , Katz Elton P. 
Published: December 2004

AbstractA model for the electrostatic properties of hydrated collagen fibrils, based on the concept of a “penetrable” protein, has been evaluated through studies of collagen fibrils that had been chemically modified to change their electrostatic properties,. A value of 0.28 ± 0.07 ml/g was found for the intrafibrillar space sterically inaccessible to a molecule that had an equivalent spherical radius of 4.5 Å.The net intrinsic charge on reconstituted collagen is +14 mol/mol under physiological conditions, but decreases, at constant pH, with ionic strength. A value of 7.1 for the pK of the histidine and α‐amino groups in reconstituted collagen was obtained through the application of the electrostatic model to this effect.The values obtained for calcium binding parameters for collagen fibrils, under solution conditions in which the nonspecific electrostatic properties of collagen fibrils were eliminated (3–5 M tetramethyl ammonium chloride), were in agreement with values obtained in 0.16 M NaCl solutions calculated through the use of the electrostatic theory. These are 0.73 ± 0.23 and 56.2 ± 12.3 sites per molecule with intrinsic association constants of 1101 ± 386 and 21.4 ± 5.2 M−1, respectively.The model also predicts that an average 4‐mV potential difference exists between the reconstituted collagen fibrils and physiological solutions, and that collagen fibrils under such conditions have piezoelectriclike properties.The pattern of interaction of ions with collagen fibrils is such that an allosteric mechanism for the catalytic step in the mineralization of collagen is a possibility.
Geometry of DNA–dye intercalation complexes from the study of linear dichroic spectra of stretched films
Authors: Kelly Gregory R. , Kurucsev Tomas 
Published: December 2004

AbstractFilms of DNA–dye complexes were combined with films of pure DNA deposited on poly(vinyl alcohol) support and stretched. Reproducible dichroic spectra were obtained after equilibration of the stretched films at 93% relative humidity. Dye diffusion into the supporting poly(vinl alcohol) matrix was eliminated. The long axis of intercalated acriflavine is perpendicular to the DNA helix; proflavine deviates slightly and 9‐aminoacridine significantly from such an intercalation geometry. The dichroism of two mutually perpendicularly polarized transitions of 9‐aminoacridine enabled us to determine both the angles of tilt and twist of the plane of the dye relative to the DNA helix in the complex.
Effect of europium(III) on the thermal denaturation and cleavage of transfer ribonucleic acids
Authors: Rordorf B. F. , Kearns D. R. 
Published: December 2004

AbstractThe interaction of tRNA with Eu(III) has been studied by optical and gel electrophoretic tecfhniques. At low levels (less than six metals per tRNA), Eu(III) stabilizes yeast tRNAPhe against thermal denaturation; however, at higher levels (about eight to ten Eu/tRNA) the tRNA is destabilized by Eu(III). This may have important implications regarding recent attempts to grow crystals of tRNA from solutions containing europium. Comparative studies of the effects of Mg(II) and Eu(III) on tRNA structure confirm that the first four Eu(III) ions are more strongly bound than Mg(II). At slightly elevated temperatures (50°C, pH 7) the binding of Eu(III) catalyzes the hydrolysis of the tRNA backbone. From an analysis of the fragments produced by the hydrolysis and of the variation in the rate of cleavage as a function of the metal per tRNA ratio, we conclude that (i) the addition of Eu(III) to the tRNA is sequential, (ii) the first Eu(III) is bound in close proximity to the two dihydrouridine residues, and (iii) the rate of hydrolysis depends on the number of Eu(III) free in solution. Metals bound at sites 2–4 are relatively much less active in promoting the cleavage but the metal bound at site 5 is again active. The initial cleavage products are shown to be identical with those obtained using magnesium, zinc, or lead.