bluuebunny/crossref_metadata_2025_split huggingface dataset:
The distant shielding effect in trinucleoside diposphates
Authors: Kan Lou S. , Barrett J. C. , Ts'O P. O. P. 
Published: May 2005

AbstractA comparative study on the proton magnetic resonance of the dinucleoside monophosphates TpT, dApT, TpdA, the trinucleoside diphosphates dApTpT, TpTpdA, and poly T has been made. The purpose of this investigation was to establish whether in a trimer the proton chemical shifts of one terminal residue are influenced by the magnetic anistropy of the other terminal residue. The conformation of the trimers was first studied and shown to the similar to that of the corresponding dimer, except that of the percentage of the lefthanded conformers in the population of the trimers is probably lower than in the population of the dimers. The methylprotons, H‐6, and H‐1′ of the 3′‐terminal T residue in TpTpdA (or the 5′‐terminal T residue in dApTpT) are found to be more upfield than the same protons on the dimer TpT up to a magnitude of about 0.1 ppm. The shielding of these protons of the terminal T(s) in these trimers is even larger than those corresponding protons in the poly(T) at the same condition. From these results, it is concluded that a distant shielding effect is exerted by the 5′‐terminal. A residue (or by the 3′‐terminal A residue) on the other terminal residue in the trimers studied.
Destabilization of secondary structure in polyadenylic acid by formaldehyde
Authors: Stevens Charles L. 
Published: May 2005

AbstractResults of circular dichroism and ultraviolet absorption measurements of poly A in neutral aqueous formaldehyde solution are presented, which show that the hydroxymethylated residues retain the ability to stack, but the stacking tendency is diminished. The midpoint of the thermal denaturation profile falls from about 38°C to about 18°C on complete hydroxymethylation. Hydroxymethylation, however, appears to have only a small effect on the apparent standard enthalpy and entropy of stacking, both of which become slightly more negative. When present at concentrations greater than about 2 g/100 ml, formaldehyde has a further and somewhat more dramatic denaturing effect on poly A. This ability is probably related to the chemical similarity of aqueous formaldehyde (methylene glycol) and ethylene glycol, which is known to be an effective denaturant for nucleic acids. In the presence of 20 g/100 ml formaldehyde, a very broad thermally induced transition of poly A is observed through the loss of ultraviolet hypochromism. Only the low‐temperature part of the transition is observed; it appears to be completed only at temperatures well over 100°C where the hypochromism with respect to adenosine has largely disappeared. The transition cannot be identified with the unstacking reaction usually observed through thermal denaturation experiments in the absence of formaldehyde, although the associated structure may be related in some way. The molecular nature of the structure associated with the transition is not known.
Study of the self‐diffusion coefficients of cations in the presence of an acidic polysaccharide
Authors: Magdelenat Henri , Turq Pierre , Chemla Marius 
Published: May 2005

AbstractSelf‐diffusion coefficient measurements have been applied to the study of Na+, Ca++, and Sr++ in the presence of a linear acidic polysaccharide extracted from cartilage, i.e., chondroitin sulfate. A series of experimental determinations was made with and without supporting electrolytes, and an analysis of experiments involving the separation of the electrostatic interaction terms by an extension of Manning's theory produced results showing the preponderant nature of these electrostatic terms. The specificity of each type of ion or the influence of the pH can be considered merely as higher order corrections with respect to the preceding interactions. Counterion concentration ranges and pH ranges were determined, where either the alkaline‐earth counterions become free and hence move with their normal diffusion rate, or these cations are associated with the polyelectrolyte molecule, thus giving a diffusion coefficient similar to that of the macromolecule, or the apparent diffusion coefficients vary between these two extreme diffusion rates as a function of the association equilibria. This variation can be expressed as a function of the linear charge density parameter ξ related to the structure of the polyelectrolyte, the value of which was determined and found in good agreement with published values.
Synthesis and properties of alternating poly(Lys‐Phe) and comparison with the random copolymer poly(Lys51, Phe49)
Authors: Seipke Gerhard , Arfmann Hans‐Adolf , Wagner Karl G. 
Published: May 2005

AbstractThe alternating copolypeptide poly(Lys‐Phe) was obtained by synthesis and polymerization of the respective tetrapeptide. Conformation and conformational transitions in aqueous solutions and in water–organic solvent mixtures were determined and compared with those of the random copolymer poly(Lys51,Phe49) by circular dichroism measurements. The alternating copolymer reveals a very strong tendency to adopt the β structure, which is accomplished by raising the pH or by adding sodium perchlorate or methanol. Partial α‐helical conformation, however, is obtained in the presence of 10–20% of the strong helix‐forming solvent hexafluoroisopropanol. The random copolymer reveals a much weaker preference for the β structure. It assumes the α helix in mixtures of water with hexafluoroisopropanol and also in those with methanol. As was already reported by Peggion et al. and confirmed by the present work, the addition of sodium perchlorate also leads to the helix conformation [(1972) Biopolymers 11, 633], whereas β structure is obtained by raising the pH [(1970) Macromolecules 3, 194]. These studies reveal the significance of affinities determined by near neighbor interactions in polypeptides.
Infrared studies of stereoregularity of copoly(γ‐benzyl‐D,L‐glutamate) by the polymerization of the N‐carboxylic anhydride
Authors: Akaike Toshihiro , Inoue Shohei , Itoh Koichi 
Published: May 2005

AbstractThe D and L copolymerizations of γ‐benzyl glutamate N‐carboxylic anhydride (NCA) were carried out by two different initiators, n‐butylamine and sodium methoxide. The stereoregularity of the polymer was examined by infrared spectroscopy in the region 700–200 cm−1. A remarkable difference was found between the polymers obtained by these initiators in the region 450–400 cm−1. In the polymer obtained with sodium methoxide as initiator, the 409‐cm−1 peak assigned to local α‐helical conformation was not greatly affected by the amount of the L‐form, but in the polymer obtained by n‐butylamine this peak was much affected by the variation of L‐content. This indicates that the stereo‐selectivity of the polymerization in the sodium methoxide initiated system is higher than that in the n‐butylamine initiated system.
Hydrodynamic properties of a new plasma expander: Polyhydroxyethylaspartamide
Authors: Antoni G. , Neri P. , Pedersen T. G. , Ottesen M. 
Published: May 2005

AbstractThe intrinsic viscosity and molecular weight of several samples of polyhydroxyethylaspartamide with differing degrees of polymerization were determined and related, according to the Mark‐Howink equation. The a exponent is consistent with a random‐coil structure. The average unperturbed dimensions of the polymer, the dimensions in water, and the water–polymer interaction parameter were calculated according to Flory and Fox. The interaction of the polymer with water may explain its good efficacy as a plasma expander, as has previously been demonstrated in biological experiments. The behavior of the molecule in 6 M guanidine hydrochloride solution was also studied: this solvent has a very slight effect on the configuration of the polymer, in contrast with its normal effect on proteins.
Critical chain length for helix formation in L‐methionine oligopeptides
Authors: Becker Jeffrey M. , Naider Fred 
Published: May 2005

AbstractThe circular dichroism of a series of L‐methionine oligopeptides [BOC‐(Met)n‐OMe] was examined in trifluoroethanol and hexafluoroacetone sesquihydrate. The results indicate that the trimer through the hexamer exists predominantly in disordered conformations in these solvents. An abrupt change in the CD pattern at the heptamer in trifluoroethanol suggests that L‐methionine oligopeptides begin forming helices at this chain length.
Microcalorimetric investigation of dilute and concentrated solutions and films of the polydeoxynucleotide poly[d(A‐T)·d(A‐T)]
Authors: Andronikashvili E. L. , Mgeladze G. N. , Monaselidze J. R. , Lezius A. G. 
Published: May 2005

AbstractMicrocalorimetric heat capacity measurements on dilute and concentrated solutions and films of poly[d(A‐T)·d(A‐T)] in 2 M sodium chloride have been carried out. Values for enthalpy, entropy, and temperature of the helix–coil transition have been found to depend on the polymer concentration, and to have maxima near 20% (w/w) of polymer. The results are discussed in terms of polynucleotide hydration as one of the structure stabilizing factors.
Effects of microscopic and macroscopic viscosity on the rate of renaturation of DNA
Authors: Chang Chiang‐Tung , Hain Timothy C. , Hutton James R. , Wetmur James G. 
Published: May 2005

AbstractThe effect of solvent viscosity on DNA renaturation rates has been investigated as a function of temperature for a number of solvent systems. The results are all consistent with a microscopic viscosity limitation of the rate determining step. Rates of renaturation in perchlorate and quaternary ammonium salt solutions are also discussed. Increasing the macroscopic viscosity with dissolved neutral or anionic polymers increases, rather than decreases, renaturation rates due to the excluded volume of the dissolved polymers.
Probability of internal unwinding in the triple helix of collagen
Authors: Schwarz Martin , Poland Douglas 
Published: May 2005

AbstractHelix probability profiles are calculated for collagen models that take into account specific sequence and unwinding from the ends, by internal loops and by chain dissociation, using parameters from a previous study and the technique of the previous paper.2 An analysis is made of the occurrence of imino acids in known collagen sequences and no significant difference is found from random occurrence. Studies of model sequences generated by random placement of the imino acids show no tendency for collagen to unwind via internal loops even when one end is covalently linked and a loop is permanently nucleated at that end.
Studies on poly(L‐lysine50, L‐tyrosine50)–DNA interaction
Authors: Santella Regina M. , Li Hsueh Jei 
Published: May 2005

AbstractInteraction between poly(Lys50, Tyr50) and DNA has been studied by absorption, circular dichroism (CD), and fluorescence spectroscopy and thermal denaturation in 0.001M Tris, pH 6.8. The binding of this copolypeptide to DNA results in an absorbance enhancement and fluorescence quenching on tyrosine. There is also an increase in the tyrosine CD at 230 nm. The CD of DNA above 250 nm is slightly shifted to the longer wavelength which is qualitatively similar to, but quantitatively much smaller than, that induced by polylysine binding. At physiological pH the poly(Lys50, Tyr50)–DNA complex is soluble until there is one lysine and one tyrosine per nucleotide in the complex. The same ratio of amino acid residues to nucleotide has also been observed in copolypeptide‐bound regions of the complex. The addition of more poly(Lys50, Tyr50) to DNA yields a constant melting temperature, Tm′, for bound base pairs at 90°C which is close to that of polylysine‐bound DNA under the same condition. The melting temperature, Tm, of free base pairs at about 60°C on the other hand, is increased by 10°C as more copolypeptide is bound to DNA. As the temperature is raised, both absorption and CD spectra of the complexes with high coverage are changed, suggesting structural alteration, perhaps deprotonation, on bound tyrosine. The results in this report also suggest that intercalation of tyrosine in DNA is unlikely to be the mode of binding.
Synthesis and conformational properties of polypeptides containing long aliphatic side chains. Poly(Nε‐stearyl‐L‐lysine) and poly(Nε‐pelargonyl‐L‐lysine)
Authors: Shibaev Valery , Palumbo Manlio , Peggion Evaristo 
Published: May 2005

AbstractPoly(Nε‐stearyl‐L‐lysine) and poly(Nε‐pelargonyl‐L‐lysine) were synthesized both by polymerization of Nε‐pelargonyl and Nε‐stearyl‐L‐lysine NCA and by acylation of poly(L‐lysine) with pelargonyl and stearyl chloride. This second route has proven to be very useful, since completely acylated polymers are obtained in almost quantitative yield, whereas the usual scheme of preparation of ε protected poly(L‐lysine) cannot easily be applied due to solubility problems.Poly(Nεpelargonyl and stearyl‐L‐lysine) are soluble in alcohols containing linear aliphatic chains such as n‐butanol and n‐octanol and in mixtures of these alcohols with hydrocarbons such as n‐hexane and n‐heptane. Both polymers show an α‐helical conformation in the above solvents, which can be disrupted upon addition of sulfuric acid. Also in the solid state, poly(Nε‐stearyl‐L‐lysine) and poly(Nε‐pelargonyl‐L‐lysine) show X‐ray diffraction patterns typical of order structure.
Histone‐induced conformational changes in DNA as probed by quasi‐elastic light scattering
Authors: Wun K. L. , Prins W. 
Published: May 2005

AbstractQuasi‐elastic light scattering as measured by intensity fluctuation (self‐beat) spectroscopy in the time domain can be profitably used to follow both the translational diffusion D and the dominant internal flexing mode τint of DNA and its complexes with various histones in aqueous salt solutions. Without histones, DNA is found to have D = 1.6 × 10−8 cm2/sec and τint ≅ 5 × 10−4 sec in 0.8 M NaCl, 2 M urea at 20°C. Total histone as well as fraction F2A induce supercoiling (D = 2.6 × 10−8 cm2/sec, τint ≅ 2.8 × 10−4 sec) whereas fraction F1 induces uncoiling (D = 1.0 × 10−8 cm2/sec, τint ≅ 9.4 × 10−4 sec). Upon increasing the salt concentration to 1.5 M the DNA–histone complex dissociates (D = 1.8 × 10−8 cm2/sec). Upon decreasing the salt concentration to far below 0.8 M, the DNA–histone complex eventually precipitates as a chromatin gel.
Structure of guanylyl‐3′,5′‐cytidine monophosphate. II. Description of the molecular and crystal structure of the calcium derivative in space group P21
Authors: Hingerty B. , Subramanian E. , Stellman S. D. , Broyde S. B. , Sato T. , Langridge R. 
Published: May 2005

AbstractThe structural features of calcium guanosine‐3′,5′‐cytidine monophosphate (GpC) have been elucidated by X‐ray diffraction analysis. The molecule was crystallized in space group P21 with cell constants of a = 21.224 Å, b = 34.207 Å, c = 9.327 Å, and β = 90.527°, Z = 8. The hydration of the crystal is 21% by weight with 72 water molecules in the unit cell. The four GpC molecules in the asymmetric unit occur as two Watson‐Crick hydrogen‐bonded dimers related by a pseudo‐C face centering. Each dimer consists of two independent GpC molecules whose bases are hydrogen bonded to each other in the traditional Watson‐Crick fashion. Each dimer possesses a pseudo twofold axis broken by a calcium ion and associated solvent.The four molecules are conformationally similar to helical RNA, but are not identical to it or to each other. Instead, values of conformational angles reflect the intrinsic flexibility of the molecule within the range of basic helical conformations. All eight bases are anti, sugars are all C3′‐endo, and the C4′‐C5′ bond rotations are gauche‐gauche. The R factor is 12.6% for 2918 observed reflections at 1.2‐Å resolution.
Interpretation of hypochromic and hyperchromic intensity changes in the Raman spectra of polypeptides and polynucleotides undergoing transition
Authors: Painter P. C. , Koenig J. L. 
Published: May 2005

AbstractThe hyperchromic and hypochromic changes in the intensity of the amide‐I and amide‐III lines of polypeptides and certain ring vibrations of the bases of polynucleotides are shown to be related to similar changes in the lower energy uv absorption bands. The selection rules strictly limit the pairs of excited electronic states that can contribute to the elements of the polarizability matrix. An energy‐dependent term in this equation weights the contribution of the pairs of electronic transitions in favor of those involving the lower energy transitions. For both polypeptides and polynucleotides, there is a large hypochromic inensity change in the first π → π* exciton band upon the coil‐to‐helix transition. Through the selection rules, certain conformationally sensitive Raman lines are shown to derive their intensity predominantly from this band and hence also display hypochromism. Again, through an application of the selection rules, certain Raman lines can be demonstrated to depend predominantly for their intensity upon the n → π* transition, and consequently have the opposite hyperchromic intensity change upon the same conformational transition.
Racemization in the synthesis of polytripeptide models of collagen
Authors: Rapaka Rao S. , Bhatnagar R. S. , Nitecki D. E. 
Published: May 2005

AbstractRacemization in the synthesis of tripeptide intermediates and their polymers was investigated, using L‐amino acid oxidase. Stepwise investigation of peptide intermediates showed no racemization during peptide coupling steps or deprotection of benzyl esters by hydrogenolysis. Saponification of one of the methyl esters produced some racemization. Preparation of active esters from N‐protected tripeptide acids containing optically active C‐terminal amino acid, with one exception, produced racemization. The fractionated polymers were found to contain less racemized amino acids than the crude products or starting monomeric tripeptides, indicating that the racemized sequences gave rise to lower molecular‐weight oligomers. The sequences investigated were ‐Pro‐Pro‐Ala‐, ‐Ala‐Pro‐Pro‐, ‐Val‐Pro‐Pro‐, ‐Pro‐Pro‐Leu‐, ‐Pro‐Gly‐Leu‐, ‐Pro‐Gly‐Phe‐, ‐Pro‐Gly‐Val‐, ‐Gly‐Val‐Pro‐, ‐Phe‐Pro‐Gly‐, ‐Leu‐Pro‐Gly‐, and Ile‐Pro‐Gly‐.
Nonlinear electric properties of DNA solutions
Authors: Marion C. , Bernengo J. C. , Hanss M. 
Published: May 2005

AbstractDNA solutions are shown to present a nonlinear electric behavior. This property is measured through the third harmonic current intensity, which appears when the solution is placed in a sinusoidal electric field of moderately high strength (about 100 V·cm−1).The influence of different parameters has been examined: fundamental frequency, field strength, concentration, molecular weight, and conformation. By progressive sonication, it is shown that the harmonic current is linearly proportional to the DNA molecular weight, but under an Mr of approximately 106, the nonlinear electrical property decreases sharply and its spectrum shows a drastic change.It is thought that the harmonic current is not related to an orientational phenomenon; an explanation based on the electrical deformation of the molecule is suggested.
Nuclear spin‐relaxation studies of hydrated elastin
Authors: Ellis G. E. , Packer K. J. 
Published: May 2005

AbstractThe nuclear magnetic spin‐lattice and transverse relaxation processes for the 1H and 2D nuclei in purified elastin (ligamentum nuchae), exchanged and hydrated with excess D2O, have been studied in the temperature range 276°–340°K. The 2D relaxation results clearly show the presence of D2O (1) external to the bulk elastin sample, (2) in spaces within the bulk elastin, and (3) as an integral part of the protein on a molecular level. It is shown from these measurements that the protein on a molecular level. It is shown from these measurements that the water content of the protein itself changes from ∼0.8 g D2O/g dry elastin at ∼280°K to ∼0.2 g D2O/g dry elastin at ∼335°K, a decrease of 400%. The D2O content of the interfiber spaces decreases by less than 20% over the same temperature range. This fact throws considerable doubt on the validity of the values of β, the thermal expansion coefficient of elastin, used by other workers in discussion of the elastic mechanism in elastin. The elastin proton transverse relaxation shows the presence of three regions in elastin having different degrees of molecular mobility. These are assigned to protons associated with the crosslinks, a fairly mobile, hydrophobic, and low‐water‐content region, and a more mobile higher water‐content region. The temperature variation of the relative proportions of these three regions is explained in terms of a hypothetical temperature‐composition phase diagram in which the two mobile regions are represented as two partially miscible phases with different negative temperature coefficients of ‘solubility’ in water. The implications of these observations for current views of the nature of elastin are assessed. It is concluded that the spin‐relaxation results are consistent with a multiphase structural model for elastin.An approximate sorption isotherm for the water/elastin system is reported and shows the relatively weak nature of the water/elastin interaction.
Konformationsuntersuchungen an oligoalanin, substanz P und der myoglobinsequenz (66–73) der zirkulardichroismus von polyäthylenglykolgebundenen peptiden
Authors: Mutter M. , Mutter H. , Uhmann R. , Bayer E. 
Published: May 2005

AbstractThe conformation of polyethylene glycol‐bound peptides, synthesized by the liquid‐phase method, was investigated. This marcromolecular C‐terminal protecting group is transparent in the visible and the ultraviolet range to 190 nm and solubilizes peptides in many different solvents. The CD spectra of the polymer‐bound myoglobin sequence 66–73 and of the biologically active undecapeptide “substance P” were measured in each step of the synthesis. In both examples the formation of a secondary structure during the growth of the peptide chain was found.In the hydrophobic octapeptide containing the myoglobin sequence 66–73, the influence of either the blocked or the free N‐terminal amino group on the conformation was observed. The blocked octapeptide in trifluoroethanol showed a higher degree of α‐helix contribution than in its free state.The conformation of the polyethylene glycol‐bound nona‐ and decaalanine in trifluoroethanol and water was determined. The peptide with a free amino end group has β‐conformation in trifluoroethanol as well as in water. The corresponding N‐Boc‐protected derivatives show helical structure. The amino end group has a decisive influence on the formation of β‐structure.The method of CD investigation of polymer‐bound peptide sequences during the peptide synthesis in solution enables one to determine the influence of protecting groups and the chain end of a peptide on its conformation. It is also possible to study the relationship between the secondary structure, the chain length, and the kinetic of the coupling reaction in different solvents. Since the crystallization method for the liquid‐phase peptide synthesis allows one to synthesize peptides in very short time, a new method of studying peptide conformations is opened.