bluuebunny/crossref_metadata_2025_split huggingface dataset:
Superhelix density heterogeneity in closed circular intracellular PM2 DNA
Authors: Ostrander Daryl A. , Gray Horace B. 
Published: December 2004

AbstractCovalently closed intracellular DNA obtained from Pseudomonas BAL 31 20 min after infection with PM2 phage has been shown to be heterogeneous in superhelix density. Analytical band sedimentation, in the presence of low concentrations of ethidium bromide, has been carried out on fractions centripetal and centrifugal to the mode of a single band of closed circular DNA in a preparative propidium iodide–CsCl buoyant density gradient. Different average sedimentation rates, as well as different band shapes, have been observed for upper and lower fractions centrifuged at a dye concentration near the minimum in s° versus ethidium bromide concentration titrations performed on DNA from proximate intermediate fractions. Similar differences, although not as pronounced, have been obtained at a dye concentration corresponding to a point in the steep region of the titrations. Differential band sedimentation experiments performed on the same fractions have confirmed these results.Differential band sedimentation experiments on similarly fractionated mature PM2 I DNA (closed circular form) have shown slight differences in the relative sedimentation rates of upper and lower fractions at dye concentrations corresponding to the steep regions in the titrations. The same experiments, when performed on nicked circular DNA obtained from heating both the mature and intracellular fractions, showed no evidence of differences in sedimentation coefficients. Such results may indicate slight heterogeneity in the superhelix density of viral PM2 I DNA; however, the degree of this heterogeneity would be somewhat less than that of the intracellular DNA.The possibility that superhelix density heterogeneity may arise from displacement loops, which have been found at low levels in intracellular PM2 DNA, has been subjected to experimental tests. Unless such structures are originally present and removed by the isolation procedure, this possibility may be rejected.
Synthesis and conformational study of poly(Nδ‐carbobenzoxy, Nδ‐benzyl‐L‐ornithine) and poly(Nδ‐benzyl‐L‐ornithine)
Authors: Yamamoto Hiroyuki , Hayakawa Tadao , Yang Jen Tsi 
Published: December 2004

AbstractPoly(Nδ‐carbobenzoxy, Nδ‐benzyl‐L‐ornithine) (PCBLO) was prepared by the standard NCA method. PCBLO was converted into poly(Nδ‐benzyl‐L‐ornithine) (PBLO) through decarbobenzoxylation with hydrogen bromide. The monomer Nδ‐benzyl‐L‐ornithine was synthesized by reacting L‐ornithine with benzaldehyde, followed by hydrogenation. The conformation of the two polypeptides was studied by optical rotatory dispersion and circular dichroism. PCBLO forms a right‐handed helix in helix‐promoting solvents. In mixed solvents of chloroform and dichloroacetic acid (DCA) it undergoes a sharp helix–coil transition at 12% (v/v) DCA at 25°C, as compared with 36% for poly(Nδ‐carbobenzoxy‐L‐ornithine) (PCLO). Like PCLO, the helix–coil transition is “inverse,” that is, high temperature favors the helical form. PBLO is soluble in water at pH below 7 and has a “coiled” conformation. In 88% (v/v) 1‐propanol above pH (apparent) 9.6 it is completely helical. In 50% 1‐propanol the transition pH (apparent) is about 7.4; this compares with a pHtr of about 10 for poly‐L‐ornithine in the same solvent.
Side‐chain effect on conformation of ionizable polypeptides in aqueous solution
Authors: Murai Norio , Sugai Shintaro 
Published: December 2004

AbstractIn order to study the effect of side‐chain length on the conformation of polypeptides, conformational changes of various ionic polypeptides with various lengths of side chain, poly‐Nε‐glutaryl‐L‐lysine (PGL), poly‐Nδ‐glutaryl‐L‐ornithine (PGO), poly‐Nε‐succinyl‐L‐lysine (PSL), and poly‐Nδ‐succinyl‐L‐ornithine (PGO), were investigated by ORD, potentiometric titration, and dilatometric measurements in aqueous solution. The results of optical rotation and potentiometric titration measurements indicate strongly that the α‐helix stability increases in the sequence PSO < PSL ∼ PGO < PGL, which corresponds to increased side‐chain length. The volume change associated with the helix–coil transition also increased in the above sequence. This series of polymers seems to be more hydrophobic compared with poly‐L‐glutamic acid or poly‐L‐lysine, as suggested from the values of enthalpy and entropy changes for coil–helix transitions.
Solvent effects on the orientaion of naphthalene rings in the side chain of poly‐γ‐1‐naphthylmethyl‐L‐glutamate
Authors: Ueno Akihiko , Toda Fujio , Iwakura Yoshio 
Published: December 2004

AbstractThe orientation of naphthalene rings in the side chain of poly‐γ‐1‐naphthylmethyl‐L‐glutamate (PNLG) in mixed solvents of dichoroethane (DCE) and hexafluoroisopropanol (HFIP) has been studied together with its conformation by infrared, circular dichroism, and fluorescence spectra. The CD pattern of PNLG varies with the solvent composition while it maintains the α‐helical conformation. The fluorescence spectra of PNLG in solution show excimer emission of the naphthalene chromophores. The ratio of intensity of the excimer emission to that of the normal fluorescence decreases as the HFIP component in the solvent increases. It is suggested that the naphthalene rings in the side chain of α‐helical PNLG are more rigidly orientated in the solvents of higher HFIP ratio.
Conformational stability in dinucleoside phosphate crystals. Semiempirical potential energy calculations for uridylyl‐3′‐5′‐adenosine monophosphate (UpA) and guanylyl‐3′,5′‐cytidine monophosphate (GpC)
Authors: Broyde S. B. , Stellman S. D. , Hingerty B. , Langridge R. 
Published: December 2004

AbstractClassical potential energy calculations were performed for the dinucleoside phosphates UpA and GpC. Two widely accessible low‐energy regions of conformation space were found for the ω′, ω pair. That of lowest energy contains conformations similar to helical RNA, with ω′ and ω in the vicinity of 300° and 280°, respectively. All five experimental observations of crystalline GpC, two of ApU, and the helical fragment of ApApA fall in this range. The second lowest region has ω′ and ω at about 20° and 80°, respectively, which is in the general region of one experimentally observed crystalline conformer of UpA, and the nonhelical region of ApApA.It is concluded that GpC and ApU, which were crystallized as either sodium or calcium salts, are shielded from each other in the crystal by the water of hydration and are therefore free to adopt their predicted in vacuo minimum energy helical conformations. By contrast, crystalline UpA had only 1/2 water per molecule, and was forced into higher energy conformations in order to maximize intermolecular hydrogen bonding.
Structure of aggregates and helix–coil transition of polypeptides by dielectric measurements. II. Poly‐D,L‐phenylalanine and poly‐β‐benzyl‐L‐aspartate in chloroform–dichloroacetic acid mixtures
Authors: Marchal E. 
Published: December 2004

AbstractThe dielectric absorption of poly‐DL‐phenylalanine and poly‐γ‐benzyl‐L‐aspartate (PLAB) was measured in very dilute solutions to determine the type of molecular association and to locate the helix–coil transition. Both polypeptides were present as associated helices in chloroform. The mode of aggregation, which was determined by measuring the dipole moment and the critical frequency, did not depend on the polarity of the side chain but rather on that of the solvent.In both polymers, the dissociation of the aggregates in chloroform was observed on addition of small amounts of dichloroacetic acid; further addition of the acid lead to the helix–coil transition.No second region of dielectric absorption that might be related to the kinetics of the transition was found during the helix–coil transition of PBLA.
Molecular conformation of polysaccharides in solution. Changes in the optical rotation and in the elution pattern of gel filtration
Authors: Hirano Shigehiro , Kondo‐Ikeda Sumiyo 
Published: December 2004

AbstractMolecular conformation of some polysaccharides in aqueous solution in evidenced by changes in the optical rotation and in the elution pattern of gel filtration. The changes in the specific rotation against that in water are expressed as a molar conformational value [K]: −495° for colominic acid in 1.0 N NaOH solution, and −180° for hyaluronate (HA), +85° for corneal keratin sulfate, and +234° for amylose in 8 M urea solution. The gel filtration of amylose and HA dissolved in 8 M urea solution shows elution patterns distinctly different from those dissolved in water. The phenomena are attributable to a molecular conformational transition of polysaccharide molecules in aqueous solution.
Calculations of the circular dichroism of double‐helical nucleic acids. I. Effects involving π → π* transitions
Authors: Studdert David S. , Davis Robert C. 
Published: December 2004

AbstractThe circular dichroism of double‐helical nucleic acids was calculated as a function of geometry using the theory of Tinoco and Johnson. This theory does not include contributions of near ultraviolet transitions that are not π → π* in nature. The calculated circular dichroism shows a strong dependence on the distance of base pairs from the helix axis and the tilt of the base pair. Smaller dependences are predicted for the propeller‐like twist of a base pair and for variation of the angular increment per base pair. Moderately good agreement between calculated and many experimentally observed spectra could be generated.
Calculation of the circular dichroism of double‐helical nucleic acids. III. Dependence of the results on the choice of wave functions for purines and pyrimidines
Authors: Studdert David S. , Davis Robert C. 
Published: December 2004

AbstractThe circular dichroism of double‐helical nucleic acids was calculated using three different sets of wave functions for the purine and pyrimidine chromophores. Different wave functions give qualitatively the same types of spectra. Quantitatively, the differences are very substantial. However, the dependence of calculated circular dichroism spectra on nucleic acid geometry and base composition is very similar for the three different sets of wave functions. Each set of wave functions could be used to reproduce some, but not all experimentally observed spectra. The geometries required to reproduce experimentally observed spectra consistently require double‐helical geometries similar to the B or C forms of DNA.
Collagenase induced changes in the circular dichroism spectrum of collagen
Authors: Chu F. H. , Lukton A. 
Published: December 2004

AbstractThe maximum at 220 nm in the circular dichroism spectrum of native collagen solution changed to a negative value after heat denaturation or collagenase hydrolysis. The enzyme induced rate of CD change at 220 nm was shown to be first order in collagen concentration. The specific rate constant k is actually a combined rate constant kfast and kslow in which the ratio kf/ks is 4.1. The initial rates were linear with respect to enzyme concentration, and the Km was found to be 5.5 × 10−7 M. The rate of ultraviolet hyperchromicity at 220 nm on collagen hydrolysis was determined. The kfast was the same as that obtained by CD. The kf/ks ratio was 4.6. Both methods may be readily used to assay for collagenase activity.
The effect of neutral salts on the conformational transition of poly‐α‐amino acids. I. Potentiometric titration and optical rotatory dispersion studies
Authors: Conio G. , Trefiletti V. , Bodria F. , Troglia C. , Patrone E. 
Published: December 2004

AbstractThe effect of salts on the coil‐to‐helix transition of poly‐α‐amino acids was investigated by optical rotatory dispersion and potentiometric titration techniques. Both charge‐dependent and charge‐independent contributions to the free energy were considered.The free energy of formation ΔF° of the uncharged α‐helix from the uncharged random coil for poly‐L‐glutamic acid (PGA) decreases very rapidly in the limit of zero added salt concentration. This effect probably depends on the uncertainty affecting the choice of the extrapolation of the apparent pK for the random coil at low ionic strength. Above 0.1 M salt, where the free energy determination becomes meaningful, the anions and cations investigated do not affect the value of ΔF°, with the exception of Li+. Our data support the point of view that this cation binds to the peptide group.A class of salts produces an increase of the helical content of poly‐L‐ornithine (PO) both at low and high degree of ionization. This effect appears to be anion dependent. It is shown that (1) no change of ΔF° is involved; (2) recent theories of polyelectrolyte solutions cannot account for our results. We suggest that a true site binding of the anions to the charged amino groups occurs. The role of electrostatic binding in determining the conformational stability of proteins in the presence of some anions is stressed, and a general treatment for the electrostatic binding equilibria is outlined.
Vibrational analysis and dispersion curves of poly‐L‐hydroxyproline chain
Authors: Srivastava R. B. , Gupta V. D. 
Published: December 2004

AbstractDispersion curves and frequency distribution for poly‐L‐hydroxyproline (PLHP) chain were obtained using Wilson's GF matrix method as modified by Higgs. These are compared with those of poly‐L‐proline II and polyglycine II, which also have three‐fold screw symmetry. Ring and skeletal modes characteristic of PLHP are identified and the assignments of observed infrared and Raman frequencies are reported. Urey‐Bradley force constants were evaluated.
A circular dichroism study of poly dG, poly dC, and poly dG:dC
Authors: Gray Donald M. , Bollum F. J. 
Published: December 2004

AbstractWe have measured the ultraviolet circular dichroism spectra of oligo d(pG)5, poly dN AcG, poly dI, poly dC, two samples of poly dG, and four samples containing double‐stranded poly dG:dC. We find that oligo d(pG)5 and poly dG exist in self‐complexed forms as well as in single‐stranded forms. Unlike the self‐complexed form of poly dG, the single‐stranded form of poly dG can hydrogen‐bond with single‐stranded poly dC. We present spectral data for double‐stranded poly dG:dC, which can be used to help characterize poly dG:dC preparations and which provide a basis for resolving discrepancies among other reported poly dG:dC spectra.
Reversible oxygenation of heme bound to polyvinylpyridine and polyvinylimidazole
Authors: Tsuchida Eishun , Honda Kenji , Sata Hiroshi 
Published: December 2004

AbstractThe interaction between heme bound to poly‐4‐vinylpyridine (PVP) or poly‐N‐vinyl‐2‐methylimidazole (PVMI) and molecular oxygen (O2) was studied. In this paper, the reactions of some types of heme with O2 in organic solvents, particularly in N,N‐dimethylformamide (DMF) were discussed. The free heme not bound to an axial base was easily oxidized irreversibly to hemin in DMF with bubbled O2. The hemochromogens complexed with pyridine, imidazole, or their polymeric derivatives such as PVP and PVMI bound O2 to one of the axial coordination sites. The characteristic absorption band assignable to the resulting oxygenated heme was observed at 402 nm. This absorption band could be changed back to the characteristic band of the reduced hemochromogen at 418 nm by removing O2 dissolved in the DMF solution by a vacuum or by a stream of nitrogen. Thus, the hemochromogens bound to the synthetic polymers were found to adsorb and desorb O2 reversible in DMF.When the polymeric ligands were used, the equilibrium constants in the complexation of heme with these polymers were about 102 times as large as those of the corresponding monomeric ligands. The oxygenation rates and the capacities of O2 of the polymeric hemochromogens were larger than those of the monomeric hemochromogens. In addition, the oxygenation rate of the polymer complex was changeable owing to the conformational change of the polymeric ligand; this rate increased about ten times under the optimal condition.
Proton and phosphorus magnetic relaxation studies on the dynamic structure of single‐stranded polyriboadenylic acid
Authors: Akasaka Kazuyuki 
Published: December 2004

AbstractProton and phosphorus‐31 nuclear spin‐lattice relaxation times (T1) have been measured with the Fourier‐transform method at 100 and 40.5 MHz, respectively, on single‐stranded polyriboadenylic acid (poly(A)) in a neutral D2O solution in the temperature range of 14–82°C. T1 minimum is observed around 35–45°C for H(8), H(1′), and phosphorus resonances. Rotational correlation times have been deduced from the T1 data, which indicate that the sugar–phosphate backbone as well as the base–sugar segment is undergoing rapid internal motion of 10−8–10−10 sec range. The molecular motion of the sugar–phosphate backbone as deduced from the phosphorus relaxation is well‐characterized by a single activation enthalpy of 8.1 kal/mole for the whole temperature range of 14–82°C. Activation enthalpies of similar magnitude have been obtained for the motion of the adenine–ribose moiety from H(8) and H(1′) relaxation. The relative magnitude of T1 for H(8) and H(1′) infers that the poly(A) nucleotide exists on the average as anti in the single‐stranded form. The phosphorus T1 value is consistent with a conformation such that both C(4′)–C(5′) and C(4′)–C(3′) bonds are nearly trans to their connected O–P bonds.
Statistical thermodynamics of oligomer–polymer interactions
Authors: Delisi Charles 
Published: December 2004

AbstractA new method for formulating partition functions for a system of particles interacting on a one‐dimensional lattice has recently been developed.3,4 In this paper the method is applied to oligomer–polymer systems. The details of the connection between this method and the matrix formulation are first established. The method is then used to find expressions for the partition function of an oligomer–polymer system when the oligomers have a distribution of lengths and an alternating sequence.
Conformational change of the triple‐helical structure. I. Synthesis of model peptides of collagen by the solid‐phase method
Authors: Sutoh Kazuo , Noda Haruhiko 
Published: December 2004

AbstractAs model peptides of collagen, (Pro‐Pro‐Gly)n (n = 10, 12, 14, and 15) and (Pro‐Pro‐Gly)n(Ala‐Pro‐Gly)m(Pro‐Pro‐Gly)n (2n + m = 15; m = 1, 3, and 5) were synthesized by the solid‐phase method. The final products were pure when checked by high‐voltage paper electrophoresis and by amino acid analysis. Elemental composition was also examined.
A statistical mechanical study of helix–coil transition in concentrated solutions of polypeptides and proteins
Authors: Maleev V. Ya. , Gasan A. I. 
Published: December 2004

AbstractThe helix–coil transition in polypeptides was studied by methods of statistical mechanics, taking account of interaction between “melted” amide groups through hydrogen bonds. The statistical sums are calculated in the explicit form for two limit cases: (1) the dilute solution when the main contribution is given by collisions of two particles; (2) “condensation” when contacting macromolecules form a united aggregate. In the first case the transition enthalpy was shown to decrease linearly when the concentration increases, while at the appropriate choice of theoretical parameters, melting temperature and range are almost independent of the concentration. In the second case the structural transition parameters were shown to be independent of the concentration (the saturation effect). These results agree with the experimental data on synthetic polypeptides reported by other authors and with data on some globular proteins (serum and egg albumin) reported in this paper.
Electrical properties of hydrated collagen. II. Semiconductor properties
Authors: Tomaselli Vincent P. , Shamos Morris H. 
Published: December 2004

AbstractThe dc conductivity of hydrated bovine Achilles' tendon collagen has been determined as a function of hydration over a limited temperature range. At ambient temperature the conductivity changes from 10−15 (Ω cm)−1 in the dry state to about 10−8 (Ω cm)−1 at ∼24% water content by weight. For all temperatures the conductivity increases exponentially with hydration obeying σ(h) = A exp (βh), where h is a measure of the hydration, A is independent of temperature, and the parameter β ∼ T−1. It is shown that the data may be described by an impurity‐type mechanism in which the effective activation energy for the process is dependent on temperature and hydration. Conduction is assumed to be electronic with the impurity (water) acting as a donor. In the solid state the effect of water on the conductivity is reversible indicating the absence of chemical alteration of the hydrated collagen.
Helix–coil transition in heterogeneous DNA
Authors: Fixman Marshall 
Published: December 2004

AbstractThe broadening of a helix–coil transition due to base pair heterogeneity is calculated on the basis of a cumulant perturbation expansion in the quasi‐grand ensemble. In this ensemble the fictitious, homogeneous chain, to which the perturbation is referred, automatically decreases its correlation length as the heterogeneity increases. This “renormalization” seems to stabilize the perturbation expansion, in view of the good agreement between the present results and the exact theory of a heterogeneous polypeptide helix–coil transition. For the DNA model in which ring entropy is included, the transitions is found to be extremely narrow for an infinite random chain with conventional parameters. A tentative reconciliation of this result with contradictory calculations of some other workers is offered on the basis of end effects, coarse graining, or approximation to the ring entropy. An application of the new method to DNA with a non‐random base pair distribution requires evaluation of the correlation function between molecular states (helix or coil), at different sites of the reference chain. The evaluation is reduced to quadrature, but numerical calculations have been made only for the random chain.
Physical properties of endonuclease S1 digestion products of DNA renaturation intermediates
Authors: Miller Stephen J. , Wetmur James G. 
Published: December 2004

AbstractThe growth of the weight‐average double‐strand length of renaturing sonicated DNA was investigated as a function of the degree of renaturation. Endonuclease S1 was used to digest single‐strand ends and gaps. The ratio of the average renatured length to the initial length was found to be 0.6 ± 0.1 early in the reaction and to approach 1.0 at infinite time, while the ratio of the average single‐strand length of native regions increased from 0.6 ± 0.1 to 0.8 ± 0.1 at infinite time. The ratio increases are nonlinear, with the greatest growth occuring around 50% renaturation. Relaxation times of double‐strand DNA were measured in low salt using alternating field electric birefringence and were found to increase to only 70% of the relaxation time of the initial DNA at infinite time. In the molecular‐weight range examined (150–320,000 daltons), relaxation times vary with the 2.3 ± 0.3 power of molecular weight.