bluuebunny/crossref_metadata_2025_split huggingface dataset:
Salt effects on the conformation of α‐poly‐L‐glutamic acid
Authors: Jacobson A. L. 
Published: December 2004

AbstractThe optical rotatory dispersion in the range 630–340 mμ has been measured for aqueous solutions of the tetramethylammonium salt of α‐poly‐L‐glutamic acid to compare the effects produced by added tetramethylammonium chloride and magnesium chloride at equivalent ionic strengths. The addition of magnesium chloride significantly decreased the apparent pK of the α‐poly‐L‐glutamic acid. This large decrease in apparent pK makes the use of pH inadequate as a rough criterion of polymer conformation. Both the Moffitt b0 and the modified Drude constants λc have been calculated to compare helix content in presence and absence of divalent cation. Both estimations of helix content show the same trends with increased polymer ionization. At equivalent polymer ionization the divalent cation caused a significant increase in the helix content in the helix‐coil transition region.
Electrophoresis of the nucleic acids
Authors: Olivera Baldomero M. , Baine Peter , Davidson Norman 
Published: December 2004

AbstractA zone electrophoresis apparatus using ultraviolet, optics has been constructed to study nucleic acids at concentration less than 0.004%. Native DNA has a mobility about 15% higher than denatured DNA over a range of conditions of pH and ionic strength. DNA's from different sources have closely similar mobilities. A study of a molecular weight series of DNA indicates that the mobility is constant in the molecular weight range of 2.5 × 105 to 1.3 × 108. DNA mobilities change in the expected way with pH but the fractional change in mobility is less than the change in charge calculated by titration curves. A small decrease in mobility accompanies an increase in ionic strength. RNA's from various sources have mobilities slightly lower than denatured DNA except for s‐RNA which travels slightly faster.
Anomalous rotatory dispersion of metachromatic mucopolysaccharide‐dye complexes. I. Heparin
Authors: Stone Audrey Larack 
Published: December 2004

AbstractOptical rotatory dispersion measurements on metachromatic heparin:dye complexes have revealed Cotton effects in the absorption region of the hound dye which are dependent upon the “native” integrity of the heparin molecule and upon the dye to site ratio, that is, the dye array. According to the recent ideas concerning induced Cotton effects in external chromophores hound to helical polymers, heparin, a mucopolysaccharide, appears to exhibit helical secondary structure.
The adsorption of polyribonucleotides
Authors: Winsten Walter A. 
Published: December 2004

AbstractUsing a chromatographic technique, the adsorption of the polyribonucleotides s‐RNA and poly‐A provided with tri‐n‐butylammonium ions from an aqueous solution on to the surface of polymeric hydrocarbon granules has been demonstrated. The aqueous solution from which adsorption takes place is the aqueous phase which results on agitating together n‐butanol (100), water (130), tri‐n‐butylamine (10), n‐butyl ether (10), and glacial acetic acid (2.5) (parts by volume). Microporous polyethylene granules, microporous fluorinated polyethylene granules, and solid grains of polyethylene powder have been employed as adsorbents. The adsorbed polyribonucleotides could be eluted by aqueous solutions of sodium chloride, urea, or triethylammonium acetate. s‐RXA with tri‐n‐butylammonium counterions could also be adsorbed on polymethacrylic acid in tri‐n‐butylammonium form and eluted therefrom with aqueous urea solutions. It is considered that the adsorption from aqueous solution of polyribonucleotides with tri‐n‐butylammonium counterions on polymeric hydrocarbon surfaces is mediated by hydrophobic bond formation. Van der Waals forces may also contribute to the bonding. It is suggested that studies on the adsorption of polynucleotides provided with counterions: possessing nonpolar groups at an aqueous solution‐polymeric hydrocarbon interlace may permit the elaboration of experimental systems to serve as models for the evaluation of the role of hydrophobic and van der Waals bonding forces in the interaction of polynucleotides with cell membrane surfaces.
Bifunctional reagents and protein structure determination. The reaction of phenolic disulfonyl chlorides with lysozyme
Authors: Herzig David J. , Rees Allan W. , Day Richard A. 
Published: December 2004

AbstractIt was established that phenol‐2,4‐disulfonyl chloride and α‐naphthol‐2, 4‐disulfonyl chloride introduce new intramolecular or tertiary bonds into lysozyme. The phenolic hydroxyl group seems to make the cross linking reagents soluble in aqueous media; it was established that a sulfonylating; species does dissolve prior to hydrolysis but that the chlorosulfonyl groups are hydrolyzed within seconds of dissolution. New covalently linked residues were shown to be introduced by different, spectra. Peptide maps of the lysozyme treated with phenol‐2,4‐disulfonyl chloride. peroxidized, and digested with trypsin showed definite deletions and additions when compared with the control. Partial analysis of the peptides showed that cross linking between ε‐amino groups of lysine residues had occurred. A certain degree of stabilization of lysozyme to inactivation by certain inactivating conditions was noted after treatment with the two reagents. Ultra‐centrifugal analysis of the lysozyme treated with phenol‐2,4‐disulfonyl chloride showed that there was no detectable fraction having a higher molecular weight than native lysozyme. Tentative assignments of positions of cross linking were made.
Chain regularity and flow dichroism of deoxyribonucleic acids in solution
Authors: Wada Akiyoshi 
Published: December 2004

AbstractDeoxyribonucleic acids (DNA's) extracted from several biological sources have been studied by means of the flow dichroism method, using the transparent coaxial cylinder apparatus. This study has two purposes: (1) to make clear the hydrodynamic behavior of the DNA chain, and the regularity in the orientation of purine and phrimidine bases about the molecular axis; and (2) to develop this particular flow dichroism method as an established device for the study of chain regularity of DNA and other chain polymers. The velocity gradient dependence of dichroism agrees well, to a first approximation, with the behavior of a model of a hydrodynamically equivalent ellipsoid in revolution. Differences between theoretical and empirical curves have been tentatively ascribed to the flexibility of the chain under consideration. Two kinds of data, 1 lie rotary diffusion coefficient and internal dichroism, have been evaluated by a graphical device in which the double logarithmic plots of reduced dichroism and velocity gradient of flow are compared with the theoretical curve. The data obtained have shown good reproducibility for DNA samples prepared by the same method from the same biological source. However, a remarkable difference in internal dichroism and rotary diffusion constant has been observed between DNA groups of different biological origin. The difference may be caused by fragmentation of DNA during the deproteinization procedure, bill the possibility that some of these differences originate in the biological source of the DNA cannot be denied. Orientation of purine and phrimidine bases in aqueous solution is found to be quite regular in direction, as predicted by the Watson–Crick model. Dichroic spectra have shown that the direction of the oscillator dipole corresponding to the 260 mμ absorption band has a different angular relationship to the helical axis than the oscillator dipole for the 220 mμ band.
The renaturation of deoxyribonucleic acids. I. Rates of bimolecular reactions of complementary and noncomplementary Gaussian chains
Authors: Wada Akiyoshi , Yamagami Hiroko 
Published: December 2004

AbstractThe mechanism of the renaturation of DNA molecules is examined on the basis of the bimolecular interaction of Gaussian chain polymers. In the nucleus formation by hydrogen bonding in segment–segment interaction, two types of interchain interaction, that is, one between complementary chains and one between noncomplementary chains, and one noncomplementary intrachain interaction are considered to be, in competition. Several previously observed characteristics of the renaturation process are displayed by this simple model. In particular it accounts for the dependence of the extent of renaturation on the heterogeneity, molecular weight, and radius of gyration of DNA, and of the ratios of the reaction rates between complementary and noncomplementary segments. Among these variables the ratio of reaction rates has shown to have a quite specific value, as high as the order of 104, which favors the complementary‐strand interaction. This very great bias in favor of complementary strand interaction emphasizes that the renaturation phenomena displays the same character of biological specificity that is associated with enzyme–substrate interaction or antigen–antibody interaction. Moreover, since DNA is a good example of a one‐dimensional system, it seems to provide a suitable clue for pursuing the analysis of pattern recognition at the macromolecular level.
The role of the σ‐framework in the properties of the biological purines and pyrimidines: dipole moments and tautomeric equilibria
Authors: Berthod Hélène , Pullman Alberte 
Published: December 2004

AbstractDel Re's method for the study of saturated compounds has been adapted so as to deal with the σ‐framework of conjugated molecules. This modified procedure is used in evaluating the σ‐contribution to the dipole moments of the nucleic bases and of the A‐T and G‐C base pairs and also to the free energy change in the tautomeric, equilibria of the bases. Associated with an appropriate Hückel method for evaluating the π‐contribution, the results obtained predict a small resultant moment for A‐T versus a large moment for G‐C. The energy calculations predict the keto and amino forms of the bases to be the most stable forms and cytosine to be the most easily involved in tautomeric shift to the rare form.
Statistical mechanics of noncovalent bonds in polyamino acids. VII. Fluorescence as an indication of conformation
Authors: Poland Douglas C. , Scheraga Harold A. 
Published: December 2004

AbstractIt is shown how the technique of fluorescence may be used to assess conclusions about conformation which are based on a statistical mechanical treatment of simple protein models. Specifically, the state of bonding and distance between two chromophores in a molecule depend on the overall conformation, which can be computed for model systems. On the assumption that the intensity and polarization of fluorescence are affected by exciton transfer between the chromophores, it is possible to compute the effect of conformation on fluorescence. It is demonstrated that the conformational changes computed in the preceding paper will give rise to marked changes in the intensity and polarization of fluorescence.
Physical properties of periodate‐oxidized amylose: Aggregation of oxidized amylose in aqueous solutions
Authors: Erlander Stig R. , Griffin H. L. , Senti F. R. 
Published: December 2004

AbstractThe ability of periodate‐oxidized amylose to form aggregates in aqueous solution was studied by sedimentation, light scattering, and viscosity analyses. Ultracentrifuge schlieren patterns show that aggregation can be appreciable at pH 3.0 and 1.0. The hydroxyl ion‐catalyzed degradation of the oxidized amylose is faster at pH 3.0 than at pH 1.0. Viscosity and sedimentation analyses conducted at pH 3.0 show that a minimum in the degree of aggregation of the oxidized molecules is obtained at 15–25% oxidation. Solubulity studies and x‐ray diffraction patterns on retrograded amylose show that maximum solubility of the retrograded amylose is obtained by oxidizing to the extent of 25–35%. It was therefore concluded that in the general range of 20–30% periodate oxidation, the oxidized amylose has a minimum ability to form intermolecular hydrogen bonds. Outside of this range, oxidized amylose readily forms aggregates in aqueous solutions.
Optical rotatory dispersion of egg proteins. I. Ovalbumin, conalbumin, ovomucoid, and lysozyme
Authors: Tomimatsu Yoshio , Gaffield William 
Published: December 2004

AbstractOptical rotatory dispersions (ORD) of ovalbumin, conalbumin, ovomucoid, and lysozyme (muramidase) were measured in aqueous solution over a wavelength range of 195–600 mμ. The dispersion curves obeyed a one‐term Drude equation above 300 mμ. The strong Cotton effects in the ultraviolet showed peaks and troughs at about the same wavelength for all four proteins, but the crossover point for the 225 mμ Cotton effect for ovomucoid was appreciably lower than for the other proteins. Helical contents calculated by using the Moffitt equation, the trough value of the 225 mμ Cotton effect, and the expressions for helical content recently proposed by Schechter and Blout ranged from 5 to 34%. Except for ovomucoid, the trough value of the 225 mμ Cotton effect gave the lowest helical content.
Optical rotatory dispersion of poly‐L‐tyrosine in solution
Authors: Pao Yoh‐Han , Longworth Ruskin , Kornegay R. L. 
Published: December 2004

AbstractThis paper consists of a theoretical discussion of exciton band contributions to the optical rotatory dispersion of polypeptides in a specific context, namely that of poly‐L‐tyrosine in solution in α‐helix form. The calculated results when compared with existing data suggest that poly‐L‐tyrosine in aqueous solution at pH < 11.2 as studied by Fasman et al. and Beychok et al. is of right‐handed α‐helix conformation. Poly‐β‐L‐aspartate esters on the other hand are shown definitely to be of left‐handed conformation. Although there are undoubtedly interactions between neighboring side groups there is no evidence in optical rotatory dispersion data of existence of a stable helical arrangement of the side groups in poly‐L‐tyrosine. The NV1 exciton contributions below 1900 A. should provide reliable measures of the helix content and handed ness of the helix in polypeptides, and experimental techniques for the wavelengths below 1900 A. should be developed.
Molecular weight distribution of polymers of γ‐benzyl‐L‐glutamate
Authors: Scoffone Ernesto , Peggion Evaristo , Cosani Alessandro , Terbojevich Maria 
Published: December 2004

AbstractThe molecular weight distribution of poly‐γ‐benzyl‐L‐glutamate prepared by N‐carboxy anhydride (NCA) polymerization with the use of di‐n‐butylamine, diisopropylamine, and sodium methoxide as initiators was investigated. In every case, narrow distributions were found. Moreover the results allow us to conclude that the same polymerization mechanism is operative with each of the above initiators. The experimental distribution curves show fairly good agreement with the theoretical distributions expected for a polymerization process without termination.
Tritium–hydrogen exchange of poly‐L‐glutamic acid in aqueous solutions
Authors: Ikegami Akira , Yamamoto Sadaaki , Oosawa Fumio 
Published: December 2004

AbstractTo investigate the flexibility or motility of the secondary structure of poly‐L‐glutamic acid, a simple model molecule of proteins, the kinetics of the tritium–hydrogen exchange of this polymer in aqueous solutions was followed at various pH values by use of a freeze‐drying technique and a liquid scintillation counter. The most essential point of the experimental results is that all of the protons (or isotopes) attached to peptide nitrogens were exchanged according to a simple first‐order reaction and the rate was proportional to the fraction of random coil conformation determined by optical rotatory dispersion measurements. This means that the tritium attached to a peptide unit is exchangeable with a proton in water only when this unit is contained in the random coil structure and that the interchange of each unit between helical and random coil conformations takes place as a result of thermal fluctuation at very high frequency, although the average helical content of each molecule has a definite value.
X‐ray diffraction studies of the conformation of polymer molecules in solution. II. Poly‐3,5‐dibromotyrosine
Authors: Brady George W. , Salovey R. , Reddy J. M. 
Published: December 2004

AbstractX‐ray diffraction patterns from dilute solutions of poly‐3,5‐dibromo‐L‐tyrosine in dimethylformamide and equivalent concentrations of 2,6‐dibromophenol in the same solvent are compared. The intensity difference as a function of scattering angle is indicative of the arrangement of residues in the polymer. A novel averaging procedure is used to compute the intensity patterns arising from regular arrays of bromine atoms. Interbromine spacings measured on a Drieding model of a right‐handed α‐helix with side groups restricted to rigid positions of maximum stagger give moderate agreement with experiment. Very good agreement with observations is obtained by allowing for a small oscillation of phenyl rings which effectively cancels out the contribution of large distances to the intensity curve.
Kinetics of synthesis and/or conformational changes of biological macromolecules
Authors: Pipkin A. C. , Gibbs J. H. 
Published: December 2004

AbstractThe analogy, in both the thermodynamics and the kinetics, of reversible polymerizations on templates (in the case wherein these are catalyzed by exoenzymes) to helix–coil transitions (in the case where these proceed only from one end of each macromolecular chain) is presented. A suggestion, based on this analogy, is made concerning the possible nature of biological control of synthesis of macromolecules (enzyme induction and repression). The equations governing the kinetics of these one‐dimensional cooperative processes are presented and their solutions discussed.
Neighbor–neighbor interactions in single‐strand polynucleotides: Optical rotatory dispersion studies of the ribonucleotide ApApCp
Authors: Vournaki John N. , Scheraga Harold A. , Rushizky George W. , Sober Herbert A. 
Published: December 2004

AbstractThe neighbor–neighbor interactions in the small ribotrinucleotide ApApCp were investigated with the aid of optical rotatory dispersion measurements. This trinucleotide shows a Cotton effect between 220 and 325 mμ, in the region of its maximum ultraviolet absorption. The specific rotation of the trinucleotide is independent of concentration while the magnitude of the Cotton effect (levorotation) decreases markedly with increasing temperature. Such effects were not observed with the component nucleotides alone, in a simulated hydrolysis mixture, nor with the hydrolyzed trinucleotide. The Cotton effect is attributed to perturbation of the nucleotide base chromophores by neighbor–neighbor intramolecular interaction (stacking), without any hydrogen bonding being involved; this interaction decreases with increasing temperature because of increased internal rotational freedom about the single bonds of the backbone chain with an accompanying disruption of the neighbor–neighbor interaction between the bases. This explanation is supported by a statistical mechanical theory of neighbor‐neighbor interactions in polynucleotides, involving the forces between the bases. Application of this technique to further studies of polynucleotides and polypeptides is discussed.
Specific interactions in proteins due to proton fluctuations
Authors: Timasheff S. N. 
Published: December 2004

AbstractA theory of site–site interaction due to proton/charge fluctuations in protein molecules has been developed. It is shown that, with the proper geometric configuration of identical ionizable groups on matching sites, a specific attraction may be established. This attractive force has a bell‐shaped pH dependence and is maximal close to the pK of the groups involved. Various types of protein interactions are examined in the light of this theory.
Extrinsic cotton effects of aminoacridines bound to DNA
Authors: Blake A. , Peacocke A. R. 
Published: December 2004

AbstractThe optical rotatory dispersion curves of the proflavine cation were measured in the spectral range 400–500 mμ. No optical activity was observed for the free cation but a large positive Cotton effect appeared in the presence of DNA. The effect of ionic strength, denaturation of the DNA, and the DNA/proflavine ratio were studied. The dependence of the magnitude of the Cotton effect on the DNA/proflavine ratio suggests that a nearest‐neighbor interaction between bound proflavine molecules is necessary for optical activity. A simple statistical treatment was made which indicated that only a small number of proflavine molecules are required in close proximity for optical activity to occur. Denaturation of the DNA did not destroy the optical activity, which shows that long runs of DNA double helix are not necessary for optical activity of the ligand molecules. The optical rotatory dispersion curves of acridine orange which was bound to DNA were also measured. Two Cotton effects of opposite sense could be distinguished, the relative magnitudes of which depended on the DNA/acridine orange ratio and the state of denaturation of the DNA. The apparent differences from the proflavine‐DNA system can to a large extent be explained in terms of the tendency of acridine orange to form aggregates.
Studies of the helix–coil transition of poly‐L‐lysine in film and solution
Authors: Noguchi Hajime 
Published: December 2004

AbstractWater‐insoluble films of poly‐L‐lysine, crosslinked with formaldehyde, were suspended in aqueous media and their relative lengths measured as a function of pH. A sharp transition of the polymer was observed in the pH range which corresponded with that observed in polylysine solutions by optical rotation or dilatometry. In NaBr and NaCl solutions the coiled form of the polylysine film shrinks with increasing salt concentration, but in NaHCO3 solution the extent of the contraction is larger, and the coil–helix transition of polylysine occurs at lower pH when NaHCO3 is added to the medium. If one assumes the formation of amino carbamate in this case, this phenomenon can be well explained. Urea does break up the hydrogen bonds in helical polylysine film, but not completely. This result is interesting compared with that obtained for poly(L‐glutamic acid). After the coil–helix transition region was found by film experiments, the volume change associated with the coil‐to‐helix transition was measured and found to be about 1–l.5 ml. per amino residue after taking electrostatic interaction into consideration. This value is nearly same as that obtained for poly(L‐glutamic acid). By contrast, the value for poly‐γ‐benzyl‐L‐glutamate was reported to be −0.077 ml./mole of repeating unit. So it is still necessary to determine the magnitude and direction of the volume change for various kinds of polypeptides.