bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intra‐ and intermolecular charge‐transfer interactions between terminal electron donor and acceptor attached to poly(γ‐benzyl‐L‐glutamate) in solution
Authors: Sisido Masahiko , Shimizu Toshimi , Imanishi Yukio , Higashimura Toshinobu 
Published: December 2004

AbstractPoly(γ‐benzyl‐L‐glutamate) having a terminal dimethylaminoanilide group as an electron donor (D) and a terminal 3,5‐dinitrobenzoyl group as an electron acceptor (A) (A‐[Glu(OBzl)]n‐D) was synthesized by the N‐carboxyanhydride method. Polymer samples were fractionated by gel chromatography and their number‐average degrees of polymerization n were determined by the absorbances of the terminal chromophores. These polymers in chloroform and dimethylformamide solutions showed a charge‐transfer (CT) absorption band around 455 nm, and the fraction of the polymer forming the CT complex was evaluated as a function of the chain length. CT absorption for short chains (n = 5 ∼ 20) was attributed to intramolecular CT complex in which the A‐[Glu(OBzl)]n‐D chain takes cyclic conformations. An optimum chain length for the intramolecular CT was found to be n ≅ 10, where the [Glu(OBzl)]n chain may most easily bend back to form cyclic conformations. Stronger CT absorption observed for longer chains than n = 20 was shown to be intermolecular, and an intermolecular head‐to‐tail aggregation was found to be a cause of the strong CT interaction. All helical A‐[Glu(OBzl)]n‐D chains were found to form the head‐to‐tail dimers in chloroform solution.
Fluorescence‐detected circular dichroism of dinucleoside phosphates. A study of solution conformations and the two‐state model
Authors: Reich Charles , Tinoco Ignacio 
Published: December 2004

AbstractThree fluorescent dinucleoside phosphates containing 1,N6‐ethenoadenosine (εA), εApεA, εApεC, and εApU were studied using fluorescence‐detected circular dichroism (FDCD), circular dichroism (CD), and absorption measurements. The FDCD data indicate that εApεC and εApU can be described as two‐state systems consisting of a fluorescent species and a stacked, nonfluorescent species. Thermodynamic stacking parameters are calculated for these molecules using the van't Hoff equation. εApεA is found to be a more complicated system with a fluorescent CD which is different in shape, but comparable in magnitude, to the conventional CD of the dimer. This molecule, unlike the other two dinucleoside phosphates, cannot be characterized as a two‐state system; it is described as consisting of at least three states at temperatures above 35°C. The CD data were subjected to a linear analysis in order to determine the minimum number of states present. In agreement with the FDCD data, εApεC and εApU are found to consist of a minimum of two states, while εApεA is indicated to have at least three. The more complicated behavior of the latter dimer is also indicated by the values of the unstacked CD obtained in the van't Hoff analysis.
Calorimetric determination of the enthalpy of ionization of oxidized and reduced horse heart cytochrome c
Authors: Marini M. A. , Martin C. J. , Berger R. L. 
Published: December 2004

AbstractThe heats of ionization of protons, ΔHi, of oxidized and reduced horse heart cytochrome c in 0.15M KCl at 20°C were determined using a titration calorimeter which simultaneously afforded the potentiometric titration curve. Reproducibility of the thermal titrations is within 2%, and evaluation of the heats observed after the heat loss corrections is estimated to be within 5%. A single titration of oxidized cytochrome c from pH 11 to 3 is in excellent agreement with the thermal titration of this protein obtained with flow calorimetry. The thermal titration, however, is not reversible, due in part to the loss of titratable group(s) in this pH region and to the heat contribution of the acid and alkaline conformational changes which occur. Although of lesser magnitude, the reduced form also indicates similar thermal transitions. These differences are due solely to conformational contributions to the thermal process, since the potentiometric curves are reversible. The nature of the irreversibility for oxidized cytochrome c appears to involve the loss of a group with pK′ 8.9 and the shift of two groups from pK′ 5.6 to 4.8. Thermal difference curves for this process indicate that heats of −7.8 and −24.1 kcal/mol are liberated which are centered at pH 9.3 and 3.9, respectively.
A quantitative test of Zimm's model for the rotor‐speed‐department sedimentation of linear DNA molecules
Authors: Clark Roger William , Lange Christopher S. 
Published: December 2004

AbstractIn 1974, Zimm described a theory which predicts that the sedimentation coefficient of high‐molecular‐weight DNA will decrease as the rotor speed of measurement increases. In 1979, this theory was revised, and the new formula predicts speed‐dependence effects that are substantially smaller than the predictions of the original version. This report describes the results of subjecting both the original and the revised versions of the theory to quantitative tests using a well‐defined sucrose‐gradient system and a DNA of known molecular weight (T4c DNA). T4c bacteriophage is a mutant, whose DNA contains the unmodified base cytosine, instead of the glucosylated hydroxymethylcytosine characteristic of the T‐even bacteriophages, and has a molecular weight of 115 ± 3 × 106. The DNA of the wild‐type phage (T4D+) was also used in some experiments.In addition to the quantitative tests, the experiments test for an effect first observed by Rubenstein and Leighton, which showed that the sedimentation coefficient measured for T2 DNA depended on the composition of the centrifuge tube used for the measurement (tube composition effect). It can be inferred from this observation that an interaction occurs between particle and tube wall during sedimentation, and this leads to a reduction in sedimentation velocity independent of the reduction in S described by Zimm's theory.The results show that in the range of 25,000–50,000 rpm, the original but theoretically incorrect form of the theory quite accurately describes the sedimentation behavior of both T4c and T4D+ DNA, although T4D+ was a special case in some respects. The revised (corrected) form of the theory predicts much less of a speed‐dependence effect than that actually observed. The discrepancy between corrected theory and observation suggests that other factors (perhaps arising from the use of the swinging bucket rotor geometry) are causing the additional observed reduction in S20,w. However, the experiments show that the tube composition effect does not seem to be one of these.
Unwinding of DNA induced by fluorescein mercuric acetate
Authors: Takeuchi Shintaro , Maeda Akio 
Published: December 2004

AbstractFluorescein mercuric acetate causes the unwinding of DNA and binds to the separated bases. This unwinding process can be followed by measuring absorption changes of this reagent. For untreated calf thymus DNA, the initial rate was very slow, and the shape of the kinetic curve was sigmoidal. When double‐strand breaks of DNA were produced by DNase II treatment or sonication, the initial rate increased and the sigmoidal character disappeared. The initial rate was shown to be proportional to the concentration of helix ends. From this relation the rate of unwinding was estimated to be 2.0 base pairs/sec at 1.0 × 10−5M fluorescein mercuric acetate and 25°C. DNase I treatment, which produces single‐strand breaks and a smaller number of double‐strand breaks, also increased the initial rate. However, this increase was due only to the double‐strand breaks, that is, single‐strand breaks had no significant effect on the initial rate. Also, uv irradiation increased the initial rate linearly with uv dose, at least up to 2 × 105 erg/mm2, suggesting that this increase is due to photoproducts other than usual pyrimidine dimers. We discuss the usefulness of this kinetic method in structural studies of DNA.
Fluorescent‐labeled collagen: Age‐related differences and fluorescence changes during the lag phase of fibril formation
Authors: Crabtree Donald V. , Fujimori Eiji 
Published: December 2004

AbstractAcid‐soluble collagens isolated from young and old rat tail tendon were fluorescent‐labeled with dansyl hydrazine, which is capable of reacting with aldehyde groups in collagen. The dansyl fluorescence of aged collagen exhibited a weak peak at 525 nm, whereas that of young collagen had a stronger broad peak at 500 nm. Fibril formation in vitro was partially inhibited in these dansylated collagens. During the turbidity lag phase, the dansyl fluorescence was found to increase (30–50%), also shifting to 485 nm. These changes reveal the telopeptide conformation changes occurring during this period. A new fluorescence peak at 420 nm also increased during fibril formation. When the dansylated collagen was irradiated in air with uv light (340 nm), a rapid decrease of the dansyl fluorescence with a concurrent shift to 490 nm occurred. Also, the formation of fibrils was further inhibited. With increasing temperature, the dansyl fluorescence of young collagen decreased, whereas that of old collagen substantially increased, particularly at the denaturation temperature around 38°C. After denaturation, both fluorescences became similar in their intensity and position (490 nm). These findings are discussed in connection with both age‐related structural changes of collagen and the mechanism of fibril formation.
Conformation of poly(L‐homoarginine)
Authors: Mita Kazuei , Ichimura Sachiko , Zama Mitsuo 
Published: December 2004

AbstractPoly(L‐arginine) assumes the α‐helix in the presence of the tetrahedral‐type anions or some polyanions by forming the “ringed‐structure bridge” between guanidinium groups and anions which is stabilized by a pair of hydrogen bonds and electrostatic interaction [Ichimura, S., Mita, K. & Zama, M. (1978) Biopolymers 17, 2769–2782; Mita, K., Ichimura, S. & Zama, M. (1978) Biopolymers 17, 2783–2798]. This paper describes the parallel CD studies on the conformational effects on poly (L‐homoarginine) of various mono‐, di‐, polyvalent anions and some polyanions, as well as alcohol and sodium dodecylsulfate. The random coil to α‐helix transition of poly(L‐homoarginine) occurred only in NaClO4 solution or in the presence of high content of ethanol or methanol. The divalent and polyvalent anions of the tetrahedral type (SO, HPO, and P2O), which are strong α‐helix‐forming agents for poly(L‐arginine), failed to induce the α‐helical conformation of poly(L‐homoarginine). By complexing with poly(L‐glutamic acid) or with polyacrylate, which is also a strong α‐helix‐forming agent for poly(L‐arginine), poly(L‐homoarginine) only partially formed the α‐helical conformation. Monovalent anions (OH−, Cl−, F−, and H2PO) did not change poly(L‐homoarginine) to the α‐helix, and in the range of pH 2–11, the polypeptide remained in an unordered conformation. In sodium dodecylsulfate, poly(L‐homoarginine) exhibited the remarkably enlarged CD spectrum of an extended conformation, while poly(L‐arginine) forms the α‐helix by interacting with the agent. Thus poly(L‐homoarginine), compared with poly(L‐arginine), has a much lower ability to form the α‐helical conformation by interacting with anions. The stronger hydrophobicity of homoarginine residue in comparison with the arginine residue would provide unfavorable conditions to maintain the α‐helical conformation.
Quasielastic light scattering by biopolymers. IV. Tertiary collapse of calf thymus DNA in 5.5M LiCl
Authors: Parthasarathy Nambi , Schmitz Kenneth S. , Cowman Mary K. 
Published: December 2004

AbstractCircular dichroism has been commonly employed to infer the conformation of DNA in solution. The basis of the conformational assignments is the work of Tunis‐Schneider and Maestre, wherein CD spectra of DNA were obtained under conditions comparable to those employed in the x‐ray diffraction studies of A‐, B‐, and C‐DNA. It has recently been suggested that the CD spectrum of DNA in chromatin, which is similar to the CD spectrum of the C‐form DNA, is a superposition of the normal B‐DNA spectrum and a single negative band, centered at 275 nm. This negative band is qualitatively identical to the spectrum for condensed Ψ‐form DNA. We have employed the hydrodynamic methods of quasielastic light scattering and sedimentation velocity to determine the extent of DNA tertiary structural alteration in 5.5M LiCl as a possible explanation of the C‐form CD spectrum. These studies suggest an eightfold contraction of the Stokes hydrodynamic volume for calf thymus DNA in going from 0.4M NH4Ac to 5.5M LiCl, with no change in molecular weight. The estimated maximum presistence length of DNA in 5.5M LiCl is estimated to be 20.0 nm compared to the “minimum” value of 44.7 nm in NaCl solutions. The value 20.0 nm corresponds to a maximum radius of 16.7 nm for a “continuously coiled” cylinder of DNA, which compares with the value 5.0 nm of DNA in the nucleosome unit of chromatin.
Local conformations of ends of α‐helical poly[Glu(OBzl)] studied by circular dichroism of terminal chromophores
Authors: Shimizu Toshimi , Sisido Masahiko , Imanishi Yukio , Higashimura Toshinobu 
Published: December 2004

AbstractConformations of terminal peptide units of α‐helical poly(γ‐benzyl‐L‐glutamate), poly‐[Glu(OBzl)], were examined by an induced circular dichroism (CD) of chromophores which were covalently attached to both ends of the chain. In chloroform, where the helical poly‐[Glu(OBzl)] exists as a head‐to‐tail‐type dimeric associate, the chromophores showed a strong CD induced by an asymmetric perturbation from the helical structure. The induced CD almost disappeared by an addition of a few percent of dichloroacetic acid, which has been reported as a powerful breaker of the associate. These results are explained by an incorporation of terminal peptide units into a helical conformation in the head‐to‐tail associate and a local unfolding of the terminal portions by the addition of acid. An induced CD of a charge‐transfer complex between the two terminal chromophores was also observed and the structure of the helix–helix junction of the head‐to‐tail dimer is discussed.
Proton NMR study of the interaction of cis‐dichloro‐diamine‐platinum(II) with poly(I) and poly(I)·poly(C)
Authors: Fazakerley G. Victor , Hermann Dominique , Guschlbauer Wilhelm 
Published: December 2004

AbstractThe fixation of cis (NH3)2Cl2Pt(II) to poly(I)·poly(C) leads to the formation of two complexed species. One involves coordination to a single base (accounting for about 70% of the total platinum bound over the rb range 0.07–0.25) and the other to two bases which are not adjacent to each other but may be on the same strand and separated by a loop. Reaction of the platinum compound with poly(I) gives in addition to the above two species a minor one (about 15%, independent of rb over the range 0.05–0.30) in which the platinum is bound to two adjacent bases. The availability of such coordination reduces the dominance of the 1:1 species, which, however, remains the major one (ca. 55%).
The nonplanar peptide unit. IV. Geometry and nonplanar distortions of the cis‐peptide unit
Authors: Kolaskar A. S. , Sarathy K. P. 
Published: December 2004

AbstractSemiempirical quantum chemical calculations were carried out using the CNDO/2 and the INDO methods on the model compound cis‐N‐methylacetamide in order to get an insight into the problem of possible nonplanar distortions of the cis‐peptide unit. In addition, the crystal structure data of cyclic peptides containing cis‐peptide units were analyzed. These studies have indicated that the dihedral angles θN and Δω are correlated approximately by the relation Δω = −θN, whereas θC is small and is uncorrelated with Δω, as was found in the case of the trans‐peptide unit. Both theory and crystal data suggest that out‐of‐plane distortions at the nitrogen atom of the peptide unit were quite likely to occur and should be included in the conformational calculations. The average geometry for the planar cis‐peptide unit has also been obtained from the observed examples.
Dynamics of tyrosine ring rotations in a globular protein
Authors: McCammon J. A. , Karplus M. 
Published: December 2004

AbstractThe dynamics of activated rotations of a tyrosine ring inside the bovine pancreatic trypsin inhibitor have been studied by computer simulation. The simulation method consists of two parts. In the first part, typical transition‐state configurations of the protein atoms are prepared. In the second part, the classical equations of motion for the protein atoms are solved to yield trajectories which pass through these transition‐state configurations. Analysis of the trajectories shows that the ring is driven over the rotational potential barrier by nearly impulsive collisions with atoms of the surrounding protein matrix. The collisions are similar to those that occur while the ring oscillates about its equilibrium orientation. The frequency and strength of the collisions are such that transition‐state theory is approximately valid for this simple reaction. The enthalpy of activation is substantially reduced by bond‐angle deformations which occur rapidly on the time scale of the barrier crossing. Small, transient packing defects in the protein appear to play a role in initiating the ring rotation.
The linear relationship between iodine staining and average chain length of the unbranched amyloglucans
Authors: Fales Frank W. 
Published: December 2004

AbstractA simple straight‐line relationship between iodine staining and the average chain length (CL) of the linear amyloglucans has been derived utilizing the published data of Baldwin et al. [J. Am. Chem. Soc. 66, 111 (1944)], Bailey and Whelan [J. Biol. Chem. 236, 939 (1961)], Szejtli et al. [Biopolymers 5, 5 (1976)], Pfannemüller et al. [Biopolymers 10, 243 (1971)], and Banks et al. [Carbohydr. Res. 17, 25 (1971)]. The iodine staining characteristics—the wavelength of maximal optical absorbance (λM); the maximal absorbance (AM); and the iodine binding capacity (Ib) per chain—are all linearly related to the chain length. As an example, Ib per chain is linearly related to the CL and in the formula of a straight line: Y = nX − c where Y equals Ib per chain (or Ib × CL); X equals the CL, n is the slope, and c is the intercept of the Y‐axis by the straight line. Thus, CL and Ib are related as follows: CL = c/(n − Ib) Using the data of Banks et al., it was found that the slope was not affected by changes in temperature, but the Y‐intercept became less negative with decreasing temperature. Thus, the number of glucose residues per iodine molecule in the helix did not change, but shorter chain length species could complex with the iodine, and a larger fraction of each chain could form the helical configuration with iodine as the temperature was reduced. These findings suggest that the CL and therefore the number‐average degree of polymerization and the number‐average molecular weight of the unbranched amyloglucans could be determined by AM, Ib or λM measurements after standardization under precise experimental conditions.
Influence of methanol on the rotational diffusion of poly(L‐lysine) in the helix–coil transition
Authors: Hanssum H. , Rüterjans H. 
Published: December 2004

Abstract13C spin‐lattice relaxation times of poly(L‐lysine) have been obtained at 67.9 MHz in aqueous solution and in a mixed solvent (40% methanol/60% water). A concomitant determination of the conformation by CD permits the correlation of conformation and rotational diffusion of the polymer. The dependence on pH of the spin‐lattice relaxation times of the 13Cα and the side‐chain carbon resonances reflects the diffusional motion in the random‐coil conformation, in the helix–coil transition, and in the conformation of the α‐helix. In the mixed solvent the reorientational correlation time of the Cα‐Hα vector increases from τ = 0.37 nsec (random coil) to τ = 12.0 nsec (α‐helix). In aqueous solution the correlation time of this vector increases from τ = 0.33 nsec (random coil) to τ ≫ 11 nsec. The reorientation rates of the side‐chain methylene groups in the two solvents are markedly different. The reorientation of all methylene groups is reduced in the mixed solvent.
Cation effects on the nonlinear electrical properties of DNA solutions
Authors: Marion C. , Hanss M. 
Published: December 2004

AbstractThe nonlinear electrical properties of DNA solutions were measured when different monovalent cations were added to DNA. The influence of different parameters has been examined: fundamental frequency, field strength, and concentration. A linear relationship between the harmonic current Ih and the DNA concentration is shown, even for higher concentration values (400 mg/l.). The frequency dispersion of Ih has the same shape for all the cations and the low‐frequency amplitude of Ih increases in the following order: Li+ < Na+ < K+ < NH < Cs+. The nonlinear polarizability values are compared with the linear ones determined using the very low field electric birefringence technique. Both linear and nonlinear values are of the same order of magnitude. It is thought that the nonlinear electrical property of high‐molecular‐weight DNA mainly results from the deformation of the DNA coils by the electric field.
Dependence of the internal relaxation time for DNA on salt type as inferred by quasielastic light scattering
Authors: Parthasarathy Nambi , Schmitz Kenneth S. 
Published: December 2004

AbstractQuasielastic light scattering methods were used to study calf thymus DNA in solutions of LiCl, NaCl, NH4Ac, and NH4Cl. Plots of the reciprocal relaxation time (1/τ) vs sin2(θ/2), where θ is the scattering angle, exhibit two linear regions, in accordance with theories for semiflexible polymers based on the t → 0 approximation. In these theories the slope of the linear region at low angles is associated with the translational diffusion coefficient (Dt), whereas the slope of the linear region at high angles is associated with the segmental diffusion coefficient (Ds = kT/ƒs). The midpoint of the “transition” between these two linear regions is associated with the mean displacement between segments (b). Data presented here indicate that the Rouse‐Zimm parameters b and ƒs are significantly different for DNA in 0.4M NH4Cl relative to the other salts at comparable ionic strengths. It is suggested that this difference reflects local solvent structure and that both b and Ds are sensitive to the local water structure.
Laser Raman spectroscopic studies of poly(r‐cytidylic acid) and poly(r‐adenylic acid) complexes with poly(L‐lysine) and poly(L‐arginine)
Authors: Hernández Luis A. , Vieta René S. , Jao Tze‐Chi 
Published: December 2004

AbstractComplexes of polyribocytidylic acid and polyriboadenylic acid with poly(L‐lysine) and poly(L‐arginine) were studied by Raman spectroscopy. The backbones of both polynucleotides are distorted by poly(L‐arginine). On the other hand, poly(L‐lysine) could distort the backbone of polyriboadenylic acid but not that of polyribocytidylic acid. In general, poly(L‐arginine) can increase the order of the base stacking, while poly(L‐lysine) causes disordering in the base stacking.
Sodium counterion activity of poly(S‐carboxymethyl‐L‐cysteine) and the beta–random‐coil transition
Authors: Ooi Kenta , Maeda Hiroshi , Ikeda Shoichi 
Published: December 2004

AbstractSodium ion activity was measured using a Na‐glass electrode in a solution of poly(S‐carboxymethyl‐L‐cysteine) with no added salt at various degrees of neutralization and various concentrations for samples of different molecular weights. The conformational change from random coil to the β‐structure was detected from the activity coefficient of counterions, as well as from CD. At a constant degree of neutralization, the activity coefficient is insensitive to a concentration change not only in the random‐coil state, but also in the range of conformational change if the concentration is below about 3 × 10−2 monomolal. At high concentrations of about 5 × 10−2 monomolal, however, the activity coefficient becomes low, probably due to the occurrence of the stacking of the pleated sheets.