bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anti‐cooperative interactions in single‐strand oligomers of deoxyriboadenylic acid
Authors: Vournakis John N. , Poland Douglas , Scheraga Harold A. 
Published: December 2004

AbstractOptical rotatory dispersion measurements were made on the deoxyribo nucleotides d(pA)2, d(pA)4, d(pA)6 and poly(deoxyriboadenylic acid) at neutral pH over the temperature range 5–80°C. and were compared to similar data for the analogous oligoriboadenylic acids. The data were interpreted in terms of a temperature‐dependent stacking of the bases in the single‐strand deoxyribo oligomers. The thermal transition curves show an inverted chain‐length dependence compared to the ribo oligomer curves. These results are explained by a theory of anti‐cooperative interaction, where the nucleation parameter σ is >1. The theory, based on a one‐dimensional Ising model involving both attractive nearest‐neighbor and repulsive next‐nearest‐neighbor interactions, predicts the inverse chain length dependence and agrees rather well with the experimental data. At and above the transition temperature, the deoxyribo polymer is seen to consist of isolated stacked base pairs separated by at least one unit of random coil, there being only a very small probability for the existence of sequences of stacked residues longer than one. The partition function is seen to undergo an irregular behavior as a function of chain length because of the anti‐cooperative phenomenon. It is necessary to use an enthalpy of stacking of −5.0 kcal./mole in order to fit the experimental data with the theory. This value, 1.5 kcal./mole more positive than the ΔH found for the ribo oligomers, is reasonable, since the 2′ hydroxyl group would be expected to stabilize the stacking interaction in the ribo oligomers. Various kinds of distribution functions are calculated and plotted graphically for this theoretical model. A physical rationale is presented for the use of a repulsive next‐nearest‐neighbor term in this theory for the deoxyribo oligomers.
Stability of the α‐helix in poly(γ‐benzyl L‐glutamate) and related polymers
Authors: Fraser R. D. B. , Harrap B. S. , Ledger R. , Macrae T. P. , Stewart F. H. C. , Suzuki E. 
Published: December 2004

AbstractA series of poly(L‐glutamic acid) esters have been synthesized and studied by optical rotatory dispersion, x‐ray diffraction, and infrared spectrometry. The results obtained emphasize the importance of the outer portions of the side chains in determining both the stability and precise conformation of the α‐helix.
Conformational aspects of polypeptides. XXIV. Conformational energies of poly‐N‐methyl‐L‐alanine chains
Authors: Mark J. E. , Goodman Murray 
Published: December 2004

AbstractConformational energies of the poly‐N‐methyl‐L‐alanine chain have been calculated as a function of the rotational angles of its skeletal bonds, taking into account torsional potentials, van der Waals repulsions, and London attractions. Four pronounced minima in the energy were found; the relative magnitudes of the energies at these minima suggest that the preferred conformation of this chain is either a right‐handed, approximately threefold helix, or a slightly distorted, left‐handed α‐helix. Inclusion of an estimate of the dipolar contribution to the total conformational energy does not significantly affect this conclusion.
Viscolastic relaxations in solutions of poly(glutamic acid) and gelatin at ultrasonic frequencies
Authors: Wada Yasaku , Sasabe Hiroyuki , Tomono Makoto 
Published: December 2004

AbstractComplex shear viscosity η* = η′ –iη″ of poly (L‐glutarmic acid) solution was measured by the torsional crystal method at 50 kc./sec. as a function of pH. A sharp peak was found at the midpoint of the helix‐coil transition region in both η′ and η″. The relaxation time is calculated from η′ and η″ assuming a single relaxation process and the peak value at the midpoint of transition is estimated at 10−6sec. Such behavior agrees well with the prediction from the theory of Schwarz. The attenuation of longitudinal sound waves at,3 Me./sec. was measured as a function of pH for solutions of poly(glutamic acid), glutamic acid, and gelatin. A small attenuation peak was observed for the three solutions, the peak height being almost, the same for them. The peak is interpreted in terms of the dissociation reaction of side chains.
Effect of ions on the dielectric relaxation of DNA
Authors: Takashima Shiro 
Published: December 2004

AbstractThe dielectric relaxation of DNA solutions has been investigated with and without extraneous ions covering a wide frequency range. The effect of monovalent ions such as Na, K, and Li as well as divalent ions such as Mg, Ca, and Hg have been included in the study. These ions are found to have a profound effect on the dielectric increment and the relaxation time without affecting the molecular dimension drastically. This dielectric effect is interpreted as indicating the importance of counterion fluctuation on the low frequency dielectric constant of DNA in solution. The effect of an organic ion, tetra‐methylammoniun bromide, has also been studied. This ion has no noticeable effect. A simple theory is derived on the basis of a microscopic model to account for the effect of external ions on the dielectric behavior of solutions of DNA.
Synthesis of poly‐O‐tert‐butyl‐L‐serine and poly‐L‐serine
Authors: Tooney Nancy M. , Fasman Gerald D. 
Published: December 2004

AbstractThe synthesis of polymers containing O‐tert‐butyl‐L‐serine, O‐tert‐butyl‐DL‐serine, L‐serine, and DL‐serine is reported. The N‐benzyloxycarbonyl‐(L or DL)‐serine benzyl ester was used to synthesize the corresponding N‐benzyloxycarbonyl‐O‐tert‐butyl‐(Lor DL)‐serine benzyl ester. Catalytic hydrogenation of this material gave O‐tert‐butyl‐(Lor DL)‐serine. The reaction of O‐tert‐butyl‐(Lor DL)‐serine with phosgene produced the corresponding N‐carboxyanhydrides. The kinetics of polymerization of N‐carboxyanhydrides were investigated to facilitate, the preparation of block copolymers. The O‐tert‐butyl blocking group was removed from polymers by treatment with HCl and HBr in benzene. Both high molecular weight (water‐insoluble) and low molecular weight (water‐soluble) homopolymers have been prepared, as well as water‐soluble block copolymers of the type (DL‐serine)x (L‐serine)y, (DL‐serine)z.
Comments on the one‐dimensional ising model and its application to the cis–trans equilibrium in poly‐L‐proline
Authors: Applequist Jon 
Published: December 2004

AbstractA treatment of the Finite one‐dimensional Ising model is given in which four possible nearest‐neighbor interactions are taken into account, as well as the effect of the absence of neighbors at the ends of the chain. This represents the most general situation possible when interactions are limited to nearest neighbors and when the number of accessible states of a single residue is two. Some previous treatments of the Ising model are shown to be special cases of this problem. From the symmetry of the partition function it is found that the equilibrium transition curves for chains of all lengths intersect at their midpoints if and only if the free energy of both residue states is modified to the same extent when located at an end of the chain. The shift in transition midpoints with chain length generally observed for various one‐stranded systems is thus largely a measure of an end effect, and not a junction effect, as might seem to be the case from the theory of helix–coil equilibria. These considerations appear to be important in the cis—trans equilibrium in poly‐L‐proline, where the observations of Engel on short‐chain samples suggest that the effects at junctions and at chain ends must differ significantly. It is concluded from his observations that a cis unit at the end of a chain has a less favorable free energy than a trans unit at the end. This is attributed to the fact that there are no van der Waals contacts between three residues at the end of the relatively compact cis helix and the missing adjacent turn of the helix, while the residues in the relatively open trans helix are little affected by their location at the end of the chain.
A theory on the effect of low molecular salts on the dissociation of linear polyacids
Authors: Oosawa Fumio 
Published: December 2004

AbstractA theoretical analysis is given on the effect of low molecular salts on the titration behavior of partially neutralized linear polyacids or polybases. On the basis of the additivity law experimentally and theoretically established on the activity of counterions in polyelectrolyte solutions containing salts, the chemical potential of alkali added for neutralization of polyacids is derived as a function of the salt concentration. The relation between the pH and the salt, concentration at constant degree of neutralization is expressed by pH(cs) − pH(0) = ({[∂ (γpCa)/∂Ca]/γos} − 1) ln [1 + (γosCs/γpCA)] where Ca is the concentration of alkali, C8, the concentration of salts, γp is the activity coefficient of counterions in the absence of salts and γos is that in the absence of polyelectrolytes. This relation is found to be in good agreement with experimental data obtained in synthetic linear polyelectrolytes as well as in rodlike charged proteins. Therefore, it is concluded that the titration behavior of linear polyions can be understood from the special feature of the integrated coulomb interaction between linear polyions and small ions which was essential for the additivity law. In addition, the screening effect of salts on the electric potential around the polyion is discussed.
Fluorescence of proflavine–DNA complexes: Heterogeneity of binding sites
Authors: Thomes J. C. , Weill G. , Daune M. 
Published: December 2004

AbstractMeasurements of the relative quantum yield of fluorescence of proflavine bound to DNA as a function of the number of bound dyes per nucleotide and the ionic strength allow the determination of the binding constants and respective number of the two types of sites previously postulated. It is demonstrated that 2–3% of the base pairs form sites where the dye is strongly bound and fluoresces normally while in the other set of sites the binding constant is 3–4 times weaker and the fluorescence completely quenched. Comparison with complexes of Pro with double stranded polynucleotides poly (A + U), poly (I + C), poly(G + C), confirm that the strong binding sites correspond to A‐T‐rich regions of the DNA while the quenched sites seem to require the presence of a neighboring guanine. The role of charge transfer in quenching of fluorescence and mutagnic action is considered. An original method for the determination of free dye and bound dye, based upon the use of an external quencher is described in the Appendix.
Optical properties of polypeptides in the β‐conformation
Authors: Woody Robert W. 
Published: December 2004

AbstractThe rotational strengths and oscillator strengths of the nπ* band and ππ* exciton bands have been calculated for antiparallel and parallel β‐structures of varying length and width. The results are compared with experiment and with previous theoretical treatments of β‐structures. The generally good agreement of calculations on the antiparallel β‐structure with experimental results on poly‐L‐lysine and poly‐L‐serine indicates that these systems are indeed in the antiparallel conformation. It is found that the exciton component strongest in absorption shifts to longer wavelengths as the width of an antiparallel structure increases, and it is suggested that the position of the ππ* absorption band may be a useful criterion of sheet width. The results also reconcile the linear dichroism measurements of Rosenheck and Sommer on poly‐L‐lysine films with an anti‐parallel structure. Calculations on parallel β‐structures indicate that the CD spectra of this form will be rather similar to that of the antiparallel form. However, the major absorption band in the antiparallel form is associated with a small positive CD band, while in the parallel form it coincides with a large negative CD band. Finally, it is pointed out that the large positive CD bands predicted for single‐stranded parallel and antiparallel β‐structures at about 200 mμ render unlikely the suggestion that random‐coil polypeptides contain a substantial fraction of extended chain.
Some optical properties of myosin and tropomyosin
Authors: Rainford Patricia , Rice Robert V. 
Published: December 2004

AbstractThe optical rotatory dispersion (ORD), and to a lesser extent the circular dichroism (CD) of the proteins tropomyosin and myosin have been extensively studied. The effect of aging and of certain reagents on these optical properties, relating to helical contents, were observed. As expected, spectra typical of right‐handed, α‐helices were found, with helical contents of 60–65% for myosin and 97–100% for tropomyosin. Studies were made to find which aqueous salt solutions would permit rotation observations in the far ultraviolet and also dissolve these proteins. The presence or absence of sulfhydryl groups (SH) were found to have no effect on helicity, and it is suggested that both proteins have an identical helical portion of 40%.
Optico‐hydrodynamic properties of high molecular weight DNA from steady‐state flow birefringence and viscosity at extremely low velocity gradients
Authors: Harrington Rodney K. 
Published: December 2004

AbstractThe flow birefringence, extinction angles, and shear‐dependent viscosity over a velocity gradient range of approximately 0.1–3 sec−1 have been obtained for T2 bacteriophage DNA at low concentration in neutral aqueous buffer. The data are found to be interpretable and self‐consistent in terms of subchain dynamical theory, including hydrodynamic, interactions and excluded volume, and the parameters characterizing these phenomena are in good agreement with the results of other hydrodynamic experiments and theoretical calculations. No necessity for modification of the subchain model in terms of limited extensibility or internal viscosity is found for high molecular weight DNA at the velocity gradients studied, although the latter cannot be ruled out on the basis of the present data. The Kuhn statistical segment length is determined from the intrinsic optical anisotropy and is estimated as 930 Å. Implications of these findings and their relation to appropriate dynamical models for DNA are discussed.
Investigations on the resolving power of hydroxyapatite columns
Authors: Kawasaki Tsutomu , Bernardi Giorgio 
Published: December 2004

AbstractAn investigation on the resolving power of hydroxyapatite columns is reported. The macromolecules chosen for this investigation have been five proteins endowed with a rigid structure and of different sizes: cytochrome c, lysozyme, β‐lactoglobulin A, collagen, and T2 phage. The following points have been investigated in detail: (1) the dependence of the elution molarity upon column length and slope of the gradient; (2) the dependence of the elution molarity and the width of the protein peak upon the load and the presence of other chromatographic components; (3) the optimal conditions for the resolution of macromolecules having the same size or different sizes.
Heterogeneity of tropocollagen as investigated by chromatography on hydroxyapatite columns
Authors: Kawasaki Tsutomu , Bernardi Giorgio 
Published: December 2004

AbstractThe chromatography of native acid‐soluble tropocollagen from calf skin on hydroxyapatite columns has been investigated. Resolution of a number of chromatographic peaks has been obtained by using shallow slopes of the eluting phosphate gradient. The results obtained suggest a heterogeneity of tropocollagen molecules which might be due to different distributions of absorbing sites on the molecules. The results obtained have also been used to study the mechanism of chromatography of proteins on hydroxyapatite and the resolving power of the columns.
Interlocked DNA rings. II. Physicochemical studies
Authors: Wang James C. 
Published: December 2004

AbstractSeveral species of topologically interlocked λb2b5c DNA rings (catenanes) have been prepared in vitro. The sedimentation behavior of dimeric catenanes containing 0, 1, or 2 covalently closed duplex rings has been studied as a function of the superhelical density of the covalently closed ring or rings. In general, if XtpY represents rings X and Y topologically interlocked, the sedimentation coefficient of this species, SXtpY, is related to the sedimentation coefficients SX and SY of the component rings by the empirical relationship SXtpY/SY = [(MX + MY)/MY] [1 + (MX/MY)1.78(SY/SX)1.78]−0.56This equation can also be extended to the case where three monomeric rings are topologically linked in a chain. For two topologically interlocked monomeric rings with neither ring covalently closed, the sedimentation coefficient is 1.35 times that of the monomeric ring. This is different from results reported for mitochondrial and P22 catenanes by others. Several possibilities are discussed to account for this discrepancy. The sedimentation coefficient of a species containing one covalently closed duplex ring and a single‐stranded ring was also measured in an alkaline medium. This species, which can be easily derived from a dimeric catenane containing two covalently closed duplex rings, is particularly useful for the identification of covalently closed dimeric catenanes. Some electron microscopic studies of these interlocked rings are presented in an accompanying paper.
Location of proline derivatives in conformational space. II. Theoretical optical activity
Authors: Madison Vincent , Schellman John 
Published: December 2004

AbstractThe coupling of theoretical optical calculations with experimental data provides a check of the validity of the theory or provides conformational information. The theory was validated by studies in which the approximate conformation was located independently. These studies have shown that a theory restricted to the two lowest energy transitions for each chromophore gives qualitative agreement with experiment. On the other hand, for some of the proline derivatives, the theoretical treatment allows detailed conformational assignments. Both successes and failures in correlating theory with experiment are discussed. The results presented provide a basis for assessing the prospects for relating protein and polypeptide optical activity to their conformations.
Cooperativity of the helix–random coil transition determined from hydrodynamic data
Authors: Hagnauer Gary , Miller Wilmer G. 
Published: December 2004

AbstractThe approximations in the equation relating the viscosity of partially helical molecules to the cooperativity of the helix–random coil transition are investigated. Of the several approximations considered, only the neglect of long‐range intramolecular interactions in the random coil leads to significant error. This is a result of the inverse fourth‐power relationship between the assumed expansion factor and the cooperativity determined from analysis of experimental data. Upon approximately accounting for the random coil expansion, the experimental data of Ptitsyn et al. yield an ionic strength‐independent cooperativity in agreement with other methods.
Solution properties of synthetic polypeptides. VI. Helix–coil transition of poly‐N5‐(3‐hydroxypropyl)‐L‐glutamine
Authors: Okita K. , Teramoto A. , Fujita H. 
Published: December 2004

AbstractA new procedure for evaluating u and σ characterizing σ‐helix‐forming polypeptides in solution was derived from Nagai's theory for the helix–coil transition of such polymers. Here u is the activity for helix formation from random coil, and σ is the helix initiation parameter. The necessary data are the helical content fN at fixed solvent and temperature as a function of N, where N is the degree of polymerization of the polypeptide sample. Such data were obtained from ORD measurements on a number of fractionated samples of poly‐N5‐(3‐hydroxypropyl)‐L‐glutamine (PHPG) in mixtures of water and methanol covering the complete range of composition and at various termperatures (5–40°C). When analyzed in terms of the proposed procedure, they yielded values of σ which were in the range (3.2 ± 0.6) × 10−4, substantially independent of solvent composition and temperature. These values were much larger than those obtained recently for σ of poly(β‐benzyl‐L‐aspartate) in m‐cresol and in a mixture of chloroform and DCA. The data for [η] and s0 (limiting sedimentation coefficient) as functions of molecular weight indicated that the molecular shape of PHPG in pure methanol is essentially rodlike, whereas that in pure water is not entirely randomly coiled but rather may be regarded as an interrupted helix. These indications were consistent with the results from ORD measurements. When plotted against the corresponding values of fN, the values of [η] and [s0] for PHPG in mixtures of water and methanol of various compositions and temperatures formed smooth composite curves, and we attributed these phenomena to the fact that σ of PHPG was nearly constant under these solvent conditions. Here [s0] stands for a reduced limiting sedimentation coefficient which is equal to the inverse friction factor of the solute molecule.
Effect of side‐chain hydrophobic bonding on the stability of homopolyamino acid α‐helices: Conformational studies of poly‐L‐leucine in water
Authors: Ostroy Sanford E. , Lotan Noah , Ingwall Richard T. , Scheraga Harold A. 
Published: December 2004

AbstractThe conformational properties of block copolymers of poly‐L‐leucine in water have been examined. The degree of polymerization of the poly‐L‐leucine block was 11 and 21, respectively, for samples prepared by the Merrifield procedure, and 56 for a sample prepared by the polymerization of leucine N‐carboxyanhydride. The optical rotatory dispersion parameter b0 was used to obtain the helix content θh at various temperatures. Application of the Lifson‐Roig theory gave the following parameters for the transition of a residue from a coil to a helical state: v = 0.05–0.011, ΔH = +100 cal/mole, ΔS = +0.70–1.00 e. u. These parameters, as well as those for other polyamino acids, are accounted for by hydrophobic bonds involving the nonpolar side chains in the helical and randomly coiled forms. From the data for poly‐L‐alanine and theoretical values of the thermodynamic parameters for hydrophobic bond formation, the parameters for formation of a polyglycine helix are computed. By separating the contributions of the backbone, it is possible to obtain a set of thermodynamic parameters for the side‐chain contributions of a number of polyamino acids. Increased size of the nonpolar side chain (with a larger contribution from hydrophobic bonding) makes a larger contribution to the stability of the α‐helix which is reflected, among other ways, in a higher helix content at given temperature.
Sedimentation of ribosomal ribonucleic acid from ribonuclease treated and untreated ribosomes
Authors: Rodgers A. 
Published: December 2004

AbstractThe formation of a slowly sedimenting form of 23‐S ribosomal RNA from E. coli has been investigated by analytical ultracentrifugation and thermal denaturation in aqueous solution and in formamide. Evidence is presented that the slow form of 23‐S arises as a result of nucleate damage to the RNA in the 50‐S ribosome. The 30‐S ribosome (and 16‐S RNA), is unaffected. The slow form of 23‐S RNA cannot be demonstrated under conditions of complete denaturation in formamide, but only by partial denaturation in aqueous solution of low ionic strength (< 0.01M Na). Apparent maintenance of the integrity of 23‐S RNA in formamide after nuclease treatment suggests that this may not be a simple linear molecule. An alternative model is suggested containing a circular element in the structure.