bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular configuration of amylose and its complexes in aqueous solutions. Part IV. Determination of DP of amylose by measuring the concentration of free iodine in solution of amylose–iodine complex
Authors: Szejtli J. , Richter M. , Augustat S. 
Published: December 2004

AbstractIn aqueous solutions of the amylase–iodine complex the concentration of free iodine [If]v after reaching equilibrium (or closely approximating it) is determined by the following factors: temperature, pH, concentration of iodide ions and amylose, and DP of amylose. In the present paper the role of temperature, amylose concentration, and DP has been investigated. At half‐saturation of amylose by iodine, the reciprocal value of free iodine defines the equilibrium constant: 1/[If]v = K. The relation between [If]v, in normality and temperature is the following: 5 + log [If]v = −(2.132/T) + 8.52, for DPn = 1290, 0.4 mg. amylose in 100 ml. 0.1N HCl. The value of the energy of activation Ea between 2 and 52°C. is 9.72 kcal./mole. The influence of amylose concentration [Am] on photometrically determined [If]v, at 20°C, in the range of 0.1–1.2 mg./100 ml. 0.1 N HCl for DPn = 1290 is: 5 + log [If]v = 0.209 − 0.047 log [Am]. At [Am] = 0.6 mg. amylose/ 100 ml. 0.1 N HCl and 20°C, the value of [If]v depends on DPn as follows: 5 + log [If]v = 0.085 = + 0.222 log (104/DPn). These above equations are summarized by the relation: [If]v = exp {16.865 − (Ea/RT)}[Am]0.047(104/DPn)0.222 ×10−5
Considering that the determination of [If]v by automatic photometric titration can be performed quickly and with appropriate reproducibility, this method is convenient for a rapid empirical and approximate determination of DP of amylose on a microscale. The iodine‐binding capacity [IBC] as well as the value of λmax, have been also investigated as functions of DPn, by photometric and by amperometric titration.
On the complex formation of acridine dyes with DNA. VII. Dependence of the binding on the dye structure
Authors: Löber G. , Achtert G. 
Published: December 2004

AbstractThe binding constants for the complex formation of more than twenty ring nitrogen‐and amino‐substituted acridine derivatives with calf thymas DNA were measured by a fluorescence method. DNA quenches the fluorescence of the aminoacridine dyes so long as both amino hydrogens are not substituted. These dyes show an enhancement of their fluorescence intensity in the presence of DNA. Typical representatives of both are proflavine and acridine orange derivatives, respectively. A discussion of steric and electronic influences of various substituents attached to the ring nitrogen and amino groups on the binding led to the concept of different conformations for intercalated acridines without amino groups and the aminoacridines. The electrostatic binding site of the former seems to be the positively charged ring nitrogen, while the binding sites in the aminoacridines are so located that the amino groups are directed towards the negatively charged DNA phosphates.
Dielectric properties of hemoglobin and myoglobin II. Dipole moment of sperm whale myoglobin
Authors: Schlecht Peter 
Published: December 2004

AbstractThis paper is concerned with the molecular origin of the dipole moment of sperm whale myoglobin as it can be calculated from the dielectric dispersion at 1 Mcps on the basis of a mechanism of orientational polarization. It was possible to compare the dielectric increment of native myoglobin and its change during the reaction with bromo acetate with dipole moments calculated according to the known coordinates of the charged groups of the molecule. The agreement between the two shows that in myoglobin only the permanent dipole moment due to these charged groups is important, and that contributions from other possible sources remain within the limits of experimental error.
Fluorescence polarization study of DNA–proflavine complexes
Authors: Ellerton Nerida F. , Isenberg Irvin 
Published: December 2004

AbstractThe binding of proflavine to DNA has been studied by measuring the polarization and intensity of emission of DNA–dye complexes. Such measurements also permit the determination of the fluorescence of the bound dye as a function of the degree of binding. Techniques of emission spectroscopy permit the study of complexing at high phosphate to dye ratios, and we have examined complexes formed at up to 12,300:1 phosphates to dye. At high phosphate to dye ratios, we find that equilibrium plots of the binding data show only one type of binding. Reports in the literature of multiple binding constants are shown to be due to the incorrect assumption that the fluorescence of the bound dye is independent of the amount bound. The emission properties can be qualitatively accounted for by assuming that nearest‐neighbor interaction between bound dyes quenches the fluorescence. We report that, within experimental error, the binding constant is insensitive to the base content of the DNA. The DNA‐dye complexes show a temperature dependent depolarization, the cause of which is, as yet, unknown. Heat denaturation of the DNA–dye complex may be followed on a Perrin plot.
Thermal conformational transformation of tropocollagen. I. Calorimetric study
Authors: Privalov P. L. , Tiktopulo E. I. 
Published: December 2004

AbstractEffects of heat in heated solution of tropocollagens of different origins were calorimetrically studied. It was found that denaturation enthalpy and entropy of different tropocollagens increase with increasing imino acid content and thermostability. It is shown that the value and dependence of denaturational enthalpy and entropy on the denaturation temperature for tropocollagens with different imino acid contents are inconsistent with the assumption that the native structure of tropocollagen is stabilized only by intramolecular hydrogen bonds. A supposition is made that the regular water structure near the macromolecule plays an essential role in stabilizing the structure. From the character of tropocollagen melting curves in salt‐free solution it is found that the tropocollagen macromolecule is linearly heterogeneous. It is shown that the complex pattern of thermal absorption observed in tropocollagen salt, solution is connected with pre‐denaturational conformational transformation when approaching conditions close to the physiological.
Polymerization of amino acid derivatives by polymer catalysts. V. Polymerization of DL‐β‐phenylalanine N‐carboxyanhydride by several poly(N‐alkylamino acid) diethylamides
Authors: Sisido Masahiko , Imanishi Yukio , Okamura Seizo 
Published: December 2004

AbstractThe polymerization of DL‐β‐phenylalanine N‐carboxyanhydride (NCA) initiated by poly(N‐benzylglycine)diethylamide (DEA) and poly(N‐methyl‐DL‐alanine)DEA has been investigated. As previously reported, polysarcosine DEA, poly‐N‐ethylglycine DEA, and poly‐N‐n‐propylglycine DEA showed marked accelerations in the polymerization of DL‐β‐phenylalanine NCA as compared with the polymerization initiated by low molecular weight, amines having similar base strength. However, this phenomenon (the chain effect) was not observed with the two polymer catalysts studied in the present investigation With poly‐N‐methyl‐DL‐alanine DEA, adsorption of DL‐β‐phenylalanine NCA onto the polymer chain takes place, though not so effectively as with other polypeptides, so the absence of chain effect was ascribed to a reduced flexibility of the polymer chain. With poly(N‐benzylglycine)DEA, the reactivity of terminal base group was found to be much lower than that of other polymer catalysts. However, the absence of the chain effect would be attributed to the rigidity of polymer chain of poly‐N‐benzylglycine DEA due to the bulkiness of the N‐benzyl group.
Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleolides
Authors: Cantor Charles R. , Warshaw Myron M. , Shapiro Herman 
Published: December 2004

AbstractThe circular dichroism (CD) spectra of the four usual deoxymononucleosides, all sixteen deoxydinucleotides, and a number of trinucleotides have been measured. The dimer spectra are quite different from the sum of the spectra of their constituent monomers. This indicates the presence of base‐stacked conformations analogous to those found for ribonucleoside diphosphates. The CD spectra of several deoxytrinucleotide diphosphates and single‐strand f 1 DNA can be calculated fairly well by using a semi‐empirical nearest‐neighbor approach. There is little or no effect of terminal phosphate or of salt concentration on the optical properties of most deoxy oligomers. The possibility of simultaneous analysis of mixtures of deoxypurine or deoxypyrimidine sequence isomers has been examined. This seems to be a viable approach for the analysis of purine runs but cannot promise much success for pyrimidine runs.
Electric and hydrodynamic properties of polypeptides in solution. II. Conformation of poly(L‐glutamic acid) in various organic solvents
Authors: Matsumoto Mitsuhiro , Watanabe Hiroshi , Yoshioka Koshiro 
Published: December 2004

AbstractThe electric birefringence of poly(L‐glutamic acid) (PLGA) in methanol, dimethyl sulfoxide, dimethylformamide, N‐methylacetamide, trifluoroacetic acid, dioxane–water mixtures (3:1 and 4:1 by volume), and dioxane–formamide mixture (1:1 by volume) has been measured by the use of the rectangular pulse technique at 30 °C. The intrinsic viscosity has also been measured at the same temperature. The magnitude of the specific Kerr constant and the intrinsic viscosity suggests that PLGA is helical and has a large dipole moment in methanol, dimethyl sulfoxide, dimelhylformamide, N‐methylacetamide, and dioxane–water mixtures. In this case we have obtained the length distribution curve and the mean length of PLGA molecules from the decay of the electric birefringence, by applying the method recently developed for helical polypeptides. Furthermore, we have proposed and applied a method of obtaining the mean dipole moment and the optical anisotropy factor from the field strength dependence of the electric birefringence for polydisperse systems on the basis of the knowledge on the length distribution. The results show that PLGA may have a different helical conformation in dimethyl sulfoxide. The specific Kerr constant of PLGA in trifluoroacetic acid is very small, which suggests that PLGA is a random coil in this solvent.
Sedimentation and viscosity of bacteriophage T7 DNA in presence of CH3HgOH
Authors: Gruenwedel Dieter W. , Brown Susan E. 
Published: December 2004

AbstractThe effects of increasing concentartions of methylmercuric hydroxide (CH3HgOH) on the rate of sedimentation, S0, and intrinsic viscosity, [η], of T7 DNA have been studied at 20°C in 0.005, 0.05, and 0.5M Na2SO4, respectively, whereby each salt solvent conatined, in addition, 0.005M sodium borate, pH 9.18, as a buffer. Both S0 and [η] are independent of organomercurial concentration as long as DNA remains native. Denaturation, brought about by the complexing of CH3HgOH with the polymer, produces large changes in S0 as wll as [η]. The sedimentation coefficient increases strongly with increasing oragnomercurial concentration once strand separation has occured. Experimental difficulties prevented measuring of [η] in the posttransition region. The data on S0 have been used, in combination with available information on the so‐called density increment (∂ρ/∂c2), to obtain information on the frictional properties of single‐stranded and methylmercurated T7 DNA. The frictional coefficient, defined as f′2 = M2(∂p/∂c2)/S0ηNA, where M2 is the molecular wieght of T7 DNA, c2 is the concentration of DNA in g/ml of solution, ηr the realtive viscosity of the salt solvents, and NA is Avogadro's number, was evaluated for all three salt media as a function of organomercurial concentration. f′2 of native T7 DNA was found not to be sensitive to changes in ionic strngth; but f′2 of single‐stranded and methylmercurated T7 DNA varied strongly with salt concentration. Since f′2 of single‐stranded T7 DNA was barely affected by organomercurial concentration at a given ionic strength, it is concluded that the dramatic variations of S0 with pM (pM ≡ ‐log[CH3HgOH]) observed in the posttransition zone reflect only changes in the thermodynamic interactions (“preferential interactions”) existing between DNA and the vatious other solution components, but not changes in the coil dimensions of the polymer.
Adsorption of molecular oxygen by polymer covalently bonded co(II) porhyrin complex in toluene
Authors: Hasegawa Etsuo , Kanayama Tatsuya , Tsuchida Eishun 
Published: December 2004

AbstractReaction betwenn molecular oxygen and polystyrene covalently bonded Co(II) protoporphyrin IX complex, which was prepaired by the incorporation of a cobaltous ion into the metal‐free porphyrin polymer, was studied in the presence of N‐ethylimidazole by measuring visible absorption and electron spin resonance spectra. It was found that the complex forms a monomeric oxygen adduct reversibly at low temperature dependent on oxygen pressure. In the presence of molecular oxygen, a new electron spin resonance signal due to the oxygen complex at giso=2.02 shows no superhyperfine splitting structure in fluid toluene solution even at −80 °C, but it was observed in frozen toulene glass solution at −120°C, The oxygen adducts of the complexes between C0(II) protoporphyrin IX dimethyl ester and N‐ethylimidazole and copoly(styrene‐N‐vinylimidazole) showed eight resolved superhyperfine splitting at −40 and −60°C, respectively. The polymer covalently bonded Co(II) complex with N‐ethylimidazole was oxidized at room temperature under oxygen atmosphere. It was suggested that a Co(II) porphyrin–oxygen adduct with an axial ligand may be oxidised monomolecularly at high temperature.
Protonated polynucleotide structures. IX. Disproportionation of poly (G)·poly (C) in acid medium
Authors: Thiele Danielle , Guschlbauer Wilhelm 
Published: December 2004

AbstractThe interaction between poly (G) and poly (C) was investigated in neutral and acid medium by optical methods. Three main points arise from this investigation. (1) The formation of poly (G)·poly (C) was complete only above an ionic strength of about 0.6M [Na+]. Lowering the ionic strength increased the amounts of free poly (G) and free poly (C) that could be detected. (2) When titrating towards acid pH values a transition took place which was characterized by potentiometry, mixing curves, and circular dichroism: a three‐stranded poly (G)·poly (C)·poly (C+) complex was formed analogous to the transition observed for the acid titration of poly (I)·poly (C). (3) Even when the poly (G)·poly (C) complex was incompletely formed (at low ionic strength) in neutral medium all poly (C) entered the triple‐stranded complex.
Acridine orange–poly (α‐L‐glutamic acid) complexes. I. Stoichiometry and stacking coefficients
Authors: Myhr Brian C. , Foss John G. 
Published: December 2004

AbstractBy means of fluorescence, absorption, and acid‐base titrations, it has been shows that there is a one‐to‐one correspondence between free carboxylates and bound acridine orange in the dye‐polyacid complex. Contrary to expections, stacking coefficients for the dye were found to be virtually the same on binding to the helical or coiled polyacid, indicating a strong similarity in the binding sites for both forms of the polyelectrolyte.
Statistical thermodynamics of nucleic acid melting transitions with coupled binding equilibria
Authors: Crothers Donald M. 
Published: December 2004

AbstractEquations are developed to describe the shift in the temperature of the helix–coil transition when small molecules bind to nucleic acids. Included are high polymers, oligonucleotides, and oligomer–polymer interactions. The equations prescribe simple ways of plotting experimental data to evaluate transition and binding parameters.
Volume and sound velocity changes accompanying the α‐helix to β‐form and coil to α‐helix transitions in aqueous solution
Authors: Noguchi Hajime , Yang Jen Tsi 
Published: December 2004

AbstractThe volume increment per amino acid residue for the α‐helix to β‐form transition of uncharged poly‐L‐lysine in aqueous solution was 3.8 ml in water and 4.3 ml in 0.2M and 1M NaBr solutions at 26°C, respectively. The sound velocity of the polymer solution was greater with the β‐helix than with the β‐form, but the difference was less in dilute salt solutions and disappeared in 1 or 2M NaBr solution. Thus, the β poly‐L‐lysine solution was slightly more compressible than the α‐polymer solution, but this difference was diminished with increasing salt concentration. Both the volume change and the change in adiabatic compressibility of the polymer solution suggest that hydrophobic interactions among the lysyl groups in the β‐form reduce the amount of “icebergs” surrounding the polymer molecules as compared with the amount originally present with the α‐helix. The coil‐to‐helix transition of poly‐L‐glutamic acid in aqueous solution was also accompanied by a decrease in sound velocity. This can be attributed to the reduction of the water of hydration which is less compressible than free water.
Normal mode spectrum of the parallel‐chain β‐sheet
Authors: Bandekar Jagdeesh , Krimm S. 
Published: December 2004

AbstractNormal mode calculations have been carried out for parallel‐chain β‐sheet structures. These include the parallel‐chain pleated sheet of poly(L‐alanine) and the parallel‐chain rippled sheet of polyglycine. Dipole derivative coupling has been included for amide I and II modes, and the effects of parallel‐sheet and antiparallel‐sheet arrangements of varying separation have been examined for the poly(L‐alanine) case. Some amide and nonamide modes are distinctly different from their antiparallel‐chain counterparts, thus providing a basis for distinguishing between such structures from their ir and Raman spectra. As in our previous studies, these results emphasize the need for both kinds of spectral data in order to draw definitive conclusions about conformation.
Thermodynamics of the various forms of the dodecamer d(ATTACCGGTAAT) and of its constituent hexamers from proton nmr chemical shifts and UV melting curves: Three‐state and four‐state thermodynamic models
Authors: Pieters Jane M. L. , Mellema Jan‐Remt , Van Den Elst Hans , Van Der Marel Gijs A. , Van Boom Jacques H. , Altona Cornelis 
Published: December 2004

AbstractChemical shifts of base and H1′ protons of the single‐stranded hexamers d(ATTACC) and d(GGTAAT), of the 1 : 1 mixtures of these complementary hexamers, and of the self‐complementary dodecamer d(ATTACCGGTAAT) were measured at various temperatures in aqueous solution. Four different sample concentrations were used in the case of the dodecamer and of the mixture of the complementary hexamers; the individual hexamers were measured at two different DNA concentrations. Absorbance temperature profiles at five different NaCl concentrations were measured for the dodecamer in order to quantify the effect of the ionic strength on the duplex formation.Under suitable conditions of nucleotide concentration, temperature, and ionic strength, the dodecamer adopts either a B‐DNA duplex or a hairpin‐loop structure. Chemical shift vs temperature profiles, constructed for all samples, were used to obtain thermodynamic parameters either for the various stacking interactions in the single strands or for the duplex or the hairpin‐loop formation. In the analysis of the duplex formation of the hexamers, a two‐state approach appeared too simple, because systematic deviations were revealed. Therefore, a new three‐state model (DUPSTAK) was developed. In order to investigate the magnitude of error arising from the use of the two‐state approach in cases where the DUPSTAK model appears more appropriate, a series of test calculations was made. The magnitude of error in the enthalpy and in the entropy of duplex melting is found to depend linearly upon the actual melting temperature and not upon the individual ΔHand ΔSvalues.Thermodynamic analysis of the chemical shift vs temperature profiles in D2O solution (no added salt) yields an averageTmdvalue of 341 K (1MDNA) and ΔHof −121 kJ · mol−1for the dimer/random‐coil transition of the hexamer duplex d(ATTACC) · d(GGTAAT). For the duplex ⇄ random‐coil transition of the 12‐mer d(ATTACCGGTAAT) an averageTmdvalue of 336 K (1MDNA) and ΔHof −372 kJ · mol−1are found. The hairpin/random‐coil transition of d(ATTACCGGTAAT) is characterized by a rather large ΔHvalue, −130 kJ · mol−1, and an averageTmhvalue of 304 K.
Elongational flow studies on type IV collagen: Comparison with type I
Authors: Barnard K. , Atkins E. D. T. , Taylor M. A. , Gathercole L. J. 
Published: December 2004

AbstractElongational 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, \documentclass{article}\pagestyle{empty}\begin{document}$\dot{\varepsilon}$\end{document} ⩾ 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. © 1993 John Wiley & Sons, Inc.
Crystal structures of two cyclic pseudopentapeptides containing ψ[CH2S] and ψ[CH2SO] backbone surrogates
Authors: Ma Sougen , Richardson John F. , Spatola Arno F. 
Published: December 2004

AbstractThe solid state conformations of cyclo[Gly–Proψ[CH2S]Gly–D–Phe–Pro] and cyclo[Gly–Proψ[CH2–(S)–SO]Gly–D–Phe–Pro] have been characterized by X‐ray diffraction analysis. Crystals of the sulfide trihydrate are orthorhombic, P212121, witha= 10.156(3) Å,b= 11.704(3) Å,c= 21.913(4) Å, andZ= 4. Crystals of the sulfoxide are monoclinic, P21, witha= 10.662(1) Å,b= 8.552(3) Å,c= 12.947(2) Å, β = 94.28(2), andZ= 2. Unlike their all‐amide parent, which adopts an all‐transbackbone conformation and a type II β‐turn encompassing Gly‐Pro‐Gly‐D‐Phe, both of these peptides contain acisGly1‐Pro2bond and form a novel turn structure, i.e., a type II′ β‐turn consisting of Gly–D–Phe–Pro–Gly. The turn structure in each of these peptides is stabilized by an intramolecular H bond between the carbonyl oxygen of Gly1and the amide proton ofD‐Phe4. In the cyclic sulfoxide, the sulfinyl group is not involved in H bonding despite its strong potential as a hydrogen‐bond acceptor. The crystal structure made it possible to establish the absolute configuration of the sulfinyl group in this peptide. The two crystal structures also helped identify a type II′ β‐turn in the DMSO‐d6solution conformers of these peptides. © 1993 John Wiley & Sons, Inc.