bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous binding of adenosine and guanosine by polyuridylic acid: A further analysis
Authors: Schmitz Kenneth S. , Michael Schurr J. 
Published: May 2005

AbstractThe dialysis data of Pitha, Huang, and Ts'o for the simultaneous binding of adenosine and guanosine to polyuridylic acid are analyzed here using a grand‐partition function method described previously. The conclusion that the predominant mode of guanosine‐binding cannot be a competition with adenosine for the primary hydrogen‐bonding sites on the 2‐polyuridylic acid complex emerges from this analysis. By setting a reasonable upper limit to the amount of competitive binding that might occur, it is found that the difference in standard free energies for the binding of guanosine and adenosine must be at least FG − FA = 2400 cal/mole, provided the stacking energies for A − A, A − G, G − G interactions are all equal. This difference in binding free energies implies a specificity of at least 80: 1 in favor of A on the primary sites at 5°C. Since this is a lower limit, the actual binding specificity may well be much greater. The desirability of achieving specificity through repulsion of incorrect bases, rather than via attraction of correct bases, is discussed.
Conformations of cyclic peptides V. A proton magnetic resonance study of evolidine, cyclo‐Ser‐Phe‐Leu‐Pro‐Val‐Asn‐Leu
Authors: Kopple Kenneth D. 
Published: May 2005

AbstractThe 220 MHz proton magnetic resonance spectrum of the cyclic heptapeptide evoli‐dine, cyclo‐Ser‐Phe‐Leu‐Pro‐Val‐Asn‐Leu, has been analyzed. From the temperature dependence of chemical shift of the peptide protons in dimethyl sulfoxide, it is concluded that the peptide protons of the Asn and Phe residues are shielded from the solvent. This observation and H‐Cα‐N‐H dihedral angles, estimated from the corresponding coupling constants, are combined in a proposed conformation of the peptide backbone. The consistency of this conformation with other proton magnetic resonance observations is discussed.
Flow‐dichroic spectra of double‐stranded RNA
Authors: Wada Akiyoshi , Kawata Ikoi , Miura Kin‐Ichiro 
Published: May 2005

AbstractDouble stranded RNA from CPV and RDV have been studied by the flow‐dichroism technique. The flow orientation and dichroic spectra have shown that the molecular chain is flexible and has bases tilted slightly against the helix axis. It has been shown also that the wavelength dependency is similar to that of DNA, which strongly suggests the existence of an n − π* transition of bases around the 230 nm region.
Volume and sound velocity changes associated with coil‐β transition of poly (S‐carboxymethyl L‐cysteine) in aqueous solution
Authors: Makino Shio , Noguchi Hajime 
Published: May 2005

AbstractThe measurements were made for the volume and the sound velocity changes (ΔV and ΔU) on titrating the sodium salt of poly (S‐carboxymethyl L‐cysteine) with dilute HCl. For the reaction, COO− + H+ → COOH, ΔV per mole of H+ bound was + 12. 7 ml and +11. 4 ml in salt‐free and 0. 2 M NaCl solutions, respectively. Corresponding ΔU was about −13 cm/sec in salt‐free polymer solution where 11.5 mM carboxylate ion reacts with equimolar hydrogen ion. ΔV associated with the coil‐to‐β transition was found to be +2. 35 ml in H2O and +1. 90 ml in 0. 2 M NaCl per mole of amino acid residue, respectively. These values are larger than those obtained for the coil‐to‐helix transition of poly (L‐glutamic acid). ΔU for the transition was about −30 cm/sec in salt‐free solution of polymer concentration 0.0115 mole/liter. Possible sources of ΔV and ΔU for reaction; coil → β, are (1) the formation of void volume and (2) the changes in the extent of solvation in amide linkage and in side chain.
Base pairing equilibria between polynucleotides and complementary monomers
Authors: Davies R. J. H. , Davidson N. 
Published: May 2005

AbstractEquilibrium dialysis measurements and optical melting curve data have been used to study the formation and stability of a number of complexes between polynucleotides and complementary monomers. The cooperativity parameter, (dθ/d ln c)θ = 0.5, where θ is the fraction of U or C residues complexed, and c is the concentration of free monomer has been measured as 1.4 for the 2:1 poly U:d‐adenosine‐complex, and 2.05 for the 2:1 poly C:d‐guanosiue complex at pH 7. The variation of Tm with c for several complexes has been used to calculate their partial molar enthalpies of formation at the midpoint of the transition: in 1.0 MNa + at pH 7, for the 2:1 complex of poly‐U with 2‐amino‐adenine, this is − 18.7 kcal/mole of 2‐amino‐adenine, for poly‐U with adenosine it is − 18.7 kcal/ mole; for poly‐C with dG, it is − 16.8 kcal/mole. These results do not agree very well with calorimetric integral heats of reaction reported in the literature.33 Complexes with random copolymers were also studied. The random copolymer, poly‐UC, can form a mixed complex with dG and either dA or 2‐amino‐adenosine; the binding of dG is enhanced by an adenine derivative and vice versa.Similarly, poly AC can form a mixed complex with dG and 3‐methyl‐xanthine. In each case, it appears that the ideal composition is a 2:1 hydrogen‐bonded complex, but the actual stoichiometry is such that each base on the random polynucleotide binds less than one‐half of a molecule of its complementary monomer. Poly UG can bind dG and dA, but in a less cooperative and specific way.
Circular dichroism of native and reconstituted nucleohistones
Authors: Frič I. , Šponar J. 
Published: May 2005

AbstractCircular dichroism (CD) spectra of histone, DNA and native, partial and reconstituted nucleohistone complexes in 0.01 M Tris buffer in which nucleohistone complexes appear to be intact and in 2 M NaCl, in which complexes are mostly dissociated, have been compared. The CD spectra in the longwave region, where the protein contribution is negigible, reveal differences in the spectra for DNA in nucleohistone complexes as compared with that of free DNA, the difference being roughly proportional to the protein DNA ratio. An analysis of the shape of the first positive CD maximum suggests that we are probably dealing here with slight conformational changes on DNA. Minor differences between the behavior of native and reconstituted complexes may be due to the effect of different conformational states of the protein component.
Rotatory properties of molecules containing two peptide groups: experimental and theoretical results
Authors: Nielsen Eigil B. , Schellman John A. 
Published: May 2005

AbstractOptical rotation studies were performed on five compounds containing two peptide groups. Four of the molecules were confined to restricted regions of conformational space by the presence of closed rings. Solvent and temperature were varied, and theoretical calculations were done for each compound covering the appropriate conformational space. The interpretation which results is qualitatively successful over the conformational regions covered by the compounds. Quantitative correlation between theory and experiment will require compounds of high rigidity.
Block sequential polypeptides of L‐alanine and glycine with D, L‐glutamic acid
Authors: Iio Takayoshi I 
Published: May 2005

AbstractSequential polypeptides of L‐alanine(A) and glycine(G), which were incorporated between two blocks of poly(D,L‐glutamic acid) (DL), were synthesized by applying Merri‐field's solid‐phase method. On the basis of optical rotatory dispersion criteria, DL(A)38‐DL was found to assume the α‐helix in the whole range of the water‐methanol system; whereas other block sequential polypeptides were found to assume the random‐coiled conformation in water and partly the α‐helix at the high methanol content. The stability of the α‐helix decreased in the order: DL(A)38DL, DL(A2G)10DL, DL(A2G)6DL, and DL(A3G)7DL. This phenomenon may be explained in terms of the dependence of hydrophobic bonding between the C3H group of the ith L‐alanine regularly arranged on the surface of the α‐helix and the C2H group of the (i + 3)th residue on whether the residue is alanine or glycine. The role which the methanol plays in stabilizing the α‐helix is also discussed.
The infrared spectrum and water binding of collagen as a function of relative humidity
Authors: Susi H. , Ard J. S. , Carroll R. J. 
Published: May 2005

AbstractThe infrared spectra of undenatured bovine tendon collagen were investigated at 25°C and relative humidities from 0 to 95%. Suitable samples were prepared by forcing frozen suspensions of the material in distilled water through a stainless steel capillary. The samples were investigated by electron microscopy before and after the spectra were obtained to ascertain that no denaturation had taken place while the sample was exposed to infrared radiation. Temperature controlled absorption cells were constructed which permitted the passing of air with a known water content over the sample film. Gradual changes were observed in the frequencies and intensities of characteristic amide bands over the relative humidity range of 0 to 75%. These changes are particularly pronounced for the amide II band, associated with bending motions of peptide NH bonds. They lead to the conclusion that water molecules are gradually attached to peptide NH bonds within the triple helix over a wide range of relative humidity. Changes in CH deformation bands suggest that CH to O hydrogen bonding does occur and that it is more pronounced in collagen exposed to high relative humidity.
Conformation of poly‐S‐carboxyethyl‐L‐cysteine in aqueous solutions
Authors: Makda Hiroshi , Ikeda Rhoichi 
Published: May 2005

AbstractPoly‐S‐carboxyethyl‐L‐cysteine, a higher side‐chain homolog of poly‐S‐carboxymethyl‐L‐cysteine, has been prepared from poly‐S‐carbobenzoxyethyl‐L‐cysteine with hydrogen bromide in chloroform or acetic acid. The polymer is found to be in the β‐conformation of an antiparallel arrangement of polypeptide chains in solid films, both in acid and salt forms, when examined by infrared spectra. Aqueous solutions of t he polymer have been investigated by measurements of rotatory dispersion and circular dichroism as well as by infrared spectra in D2O. These properties show sharp changes around pH 5.5, as the pH of solution is varied. At higher ionization the polymer is randomly coiled, but at lower ionization it is in the β‐conformation. Dependence of the rotatory properties upon polymer concentration as well as on ionic strength has been observed even at the lowest degree of ionization attained, and this has been attributed to the formation of intermolecular β‐conformation in solutions. The β‐structure is characterized by a negative circular dichroic band at 223 mμ and a positive dichroic band at a wavelength lower than 200 mμ, and furt her by a negative bo value, −140°. The pH‐induced coil‐β transition of the polymer is compared with that of poly‐S‐carboxymethl‐L‐cysteine.
Molecular orbital calculations on the conformation of polypeptides and proteins. VIII. The conformational energy maps and stereochemical rotational slates of the asparaginyl, glutaminyl aspartyl and glutamyl residues
Authors: Maigret Bernard , Perahia David , Pullman Bernard 
Published: May 2005

AbstractQuantum‐mechanical calculations on the conformational energy map and stereo‐chemical rotational states of aminoacid residues by the PCILO method are extended to the asparaginyl, glutaminyl, aspartyl and glutamyl residues in their neutral form. One of the most outstanding features of the results is the occurrence of the global minimum (or of one of a few equivalent global minima) in the region of the left handed α‐helix for the first three of the above mentioned residues. The results of the calculations are compared with experimental data from eight, globular proteins which confirm that these residues may exist, in fact, in this conformation. They also enable to understand the experimentally observed possibility of helix reversal in esters of poly‐L‐aspartic acid as a function of substitutions in the side chain.
Calorimetry of rat tail tendon collagen before and after denaturation: the heat of fusion of its absorbed water
Authors: Haly A. R. , Snaith J. W. 
Published: May 2005

AbstractThe specific heat, of rat tail tendon at various water contents was measured as a function of temperature. The resulting graphs showed peaks arising from the melting, near 50°C, of helical material in the collagen, and from the melting of absorbed water in the range ‐40°C to 0°C. The heat of melting of helical material was 11.7 cal per gram of dry tendon. Determination of the heat and temperature of fusion of the absorbed water allowed resolution of the water into four states in the case of tendon before denaturation, and three states after denaturation. The four states are (1) water not freezable on cooling to ‐ 70°C, (2) freezable water with‐both heat and temperature of fusion different from the values for ordinary water, (3) freezable water with the heat of fusion of ordinary water, but a different temperature of fusion, and (4) water not distinguished from ordinary water. The fourth state was absent in denatured tendon. The results are discussed in terms of increasing size of clusters of absorbed water molecules.
Charge effects in the sedimentation of polyelectrolytes
Authors: Ziccardi Robert , Schumaker Verne 
Published: May 2005

AbstractThe theory for sedimentation of macromolecular polyelectrolytes in solutions of low‐ionic strength has been modified for the case of a supporting low molecular weight electrolyte possessing a partial specific volume close to unity. The final equations simplify greatly, allowing sedimentation data to be plotted in a linear fashion. These data then may be readily extrapolated to infinite dilution, yielding a value, So, simply related to size and shape. From the initial slope of such plots, the net charge on the macro‐molecular polyelectrolyte may be determined. It is suggested that tetramethyl‐ammonium chloride may prove to be a satisfactory supporting electrolyte for such studies.
Synthesis and optical studies of isoleucine oligopeptides in solution
Authors: Toniolo Claudio 
Published: May 2005

AbstractIn this paper we have successfully applied the dicyclohexylcarbodiimide and the acylazide coupling methods to the synthesis of a series of L‐isoleucine peptides from dimer to octamer. In the course of our synthetic, approach we employed t‐butyloxycarbonyl as the N‐protecting and methyl ester as the C‐protecting end groups. Peptide coupling reactions known to give products of high optical purity in good yields were used in these researches. Finally, we described preliminary stereochemical investigations on these homo‐oligopeptides using polarimetric and ultraviolet, absorption techniques. The con‐formational properties of high molecular weight poly‐α‐amino acids have attracted considerable attention as protein model compounds. In addition, investigations performed on oligopeptides have yielded important information concerning the dependence of secondary structure on chain length. Goodman and co‐workers2–5 have conducted extensive studies on the critical size for helix formation in L‐alanine, L‐aspartate and L‐glutamate oligomers and cooligomers. By a variety of techniques, they demonstrated that the onset of secondary structure is dependent both on the solvent and the nature of the side chain. In this and in the accompanying6 paper we report the extension of this approach to homo‐oligopeptides derived from L‐isoleucine, which is considered to be disruptive of α‐helices for steric reasons7 in proteins and polypeptides. In particular this manuscript will describe the synthesis of the homologous series of BOC‐L‐(Ileu)n‐OMe* (n = 2–8) and preliminary stereochemical investigations by means of polarimetry and ultraviolet (UV) spectroscopy. In the accompanying paper a much more detailed analysis of the stereochemistry of these oligopeptides will be reported.
Polyelectrolyte complexes of glycol chitosan with some polysaccharides. I. Mixing ratio and dielectric properties
Authors: Srinivasan R. , Kamalam R. 
Published: May 2005

AbstractThe formation of polyelectrolyte complexes of glycol chitosan (GlChi) with sodium salts of dextran sulfate (DS), carboxymethyl cellulose (CMC), polygalacturonic acid (GalUA)n, and alginic acid (AlgA) has been studied. The number of ionizable groups per pyranose ring and the degree of dissociation as a function of pH in the polycation and polyanions have been determined using conductometric and potentiometric titrations. The formation of the complexes at different pH values has been followed by turbidity measurements. It is found that stoichiometric complexes of the polycation with CMC, (GalUA)n, and AlgA are formed at a mixing ratio of 0.5, indicating that the conformation may correspond to chains of equal lengths. In the case of the complex of GlChi with DS, the stoichiometric composition corresponds to a mixing ratio of 0.62. Thin transparent films of the complexes have been obtained by dehydration under reduced pressure on a layer of mercury. The dielectric constant ε′ and loss ε″ of thin films of these complexes have been measured in the range of frequencies of 1–100 kHz at different temperatures above and below room temperature. The GlChi–DS complex shows very little change in the values of ε′ and ε″ with frequency or temperature. On the other hand, films of GlChi–CMC and GlChi–(GalUA)n complexes show a significant increase in ε′ and ε″ as the temperature is increased above room temperature. The increase is more prominent at low frequencies. This behavior is attributed to the Maxwell‐Wagner interfacial polarization. In the case of GlChi–AlgA film, the values of ε′ and ε″ increase enormously as the temperature increases. This behavior is similar to the increase in ε′ and ε″ observed by Michels et al. [(1965) J. Phys. Chem. 69, 1456–1465] as the salt concentration increases in another polyelectrolyte complex studied by them. The electric double‐layer mechanism proposed by Schwarz [(1962) J. Phys. Chem. 66, 2636–2642] to account for the dielectric properties of biocolloids is shown to account quantitatively for the observations on the GlChi–AlgA film.
Comparative microcalorimetric and dilatometric analysis of the interactions of quinacrine, chloroquine, and ethidium bromide with DNA
Authors: Delben Franco , Quadrifoglio Franco , Giancotti Vincenzo , Crescenzi Vittorio 
Published: May 2005

AbstractThe enthalpies of binding of chloroquine and quinacrine to DNA at different molar ratios of drug to DNA and at different ionic strengths have been measured. The limiting values obtained with quinacrine fall in the range found for typical intercalating agents (e.g., ethidium, proflavin, adriamycin), whereas the value obtained with chloroquine is always zero, independent of the ratio of drug to DNA and ionic strength. The dilatometric measurements performed on the same systems and on the ethidium–DNA system show that when ethidium and quinacrine bind to DNA at low drug/DNA ratios, a volume decrease of about 16 mL/mol of bound drug occurs. No change in volume is observed when the two drugs bind to DNA through external, electrostatic forces. The volume change can be attributed to the loss of structured water around hydrophobic moieties of the drug molecules, following intercalation. In contrast, chloroquine binding to DNA at low drug/DNA ratios is characterized by a volume change distinctly smaller than that shown by quinacrine. The low ΔVB and ΔHB values shown by chloroquine are discussed in terms of the mechanism of interaction with DNA.
Chromatin structure studied by linear dichroism at different salt concentrations
Authors: Tjerneld Folke , Nordén Bengt , Wallin Håkan 
Published: May 2005

AbstractWe have studied the linear dichroism (LD) of rat liver chromatin oriented by flow. Soluble chromatin, prepared by brief nuclease digestion, is found to exhibit a positive LD at low ionic strength (1 mM NaCl), with a constant LD/A over the absorption band centered at 260 nm (A, isotropic absorbance). Several previous dichroism studies on soluble chromatin have been performed on sonicated materials and have given negative LD, probably due to the presence of uncoiled DNA. The positive dichroism can be interpreted in terms of a supercoil of DNA in chromatin with a pitch angle larger than 55°, and is, for example, consistent with a model where the cylindrical nucleosome core particles are stacked face to face in the chromatin filament. In contrast to the nuclease‐digested chromatin, sonicated chromatin was confirmed to exhibit negative LD. This difference can be attributed to a partial uncoiling of the linker regions between the nucleosomes due to the shearing. The structural transition of chromatin to a compact form can be observed as a reduction of the positive LD of the nuclease‐digested chromatin to almost zero in 0.1 M NaCl or in 0.1 mM MgCl2. This transition is due to a decreased electrostatic repulsion between negative phosphate groups on the DNA chain. In the case of Na+, this can be explained as a screening effect due to the bulk concentration of Na+. With Mg2+ a considerably stronger effect may indicate a more localized binding to the phosphates. At ionic strengths higher than 0.5M NaCl, the dissociation of the histones from DNA leads to uncoiling of chromatin. The change in LD during this process shows that histone H1 contributes only to a small degree to the coiling of the DNA chain, whereas histones H3 and H4 play the major role in the coiling.
Thermodynamic functions of biopolymer hydration. I. Their determination by vapor pressure studies, discussed in an analysis of the primary hydration process
Authors: Lüscher‐mattli Madeleine , Rüegg Max 
Published: May 2005

AbstractThe primary hydration process of native biopolymers is analyzed in a brief review of the literature, pertaining to various aspects of biopolymer–water systems. Based on this analysis, a hydration model is proposed that implies that the solution conformation of native biopolymers is stable at and above a critical degree of hydration (hp′ = 0.06–0.1 g H2O/g polymer). This water content corresponds to the fraction of strongly bound water, and amounts to ∼20% of the primary hydration sphere. In order to test this model, detailed sorption–desorption scanning experiments were performed on a globular protein (α‐chymotrypsin). The results obtained are consistent with the proposed hydration model. They show that under certain experimental conditions, sorption isotherms can be obtained that do not exhibit hysteresis. These data represent equilibrium conditions and are thus accessible to thermodynamic treatment. Valid thermodynamic functions, pertinent to the interaction of water with biopolymers in their solution state, can be obtained from these sorption experiments.