bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformations and interactions of excited states. II. Polystyrene, polypeptides, and proteins
Authors: Longworth J. W. 
Published: December 2004

AbstractPrevious fluorescence and phosphorescence studies of aromatic model compounds have been extended to polymers: “atactic” and isotactic polystyrene, seven aromatic poly‐(amino acids), and two proteins. We have confirmed previous observations that both forms of polystyrene exhibit strong excimer fluorescence emission at room temperature but not at 77°K. Of the poly(amino acids) (all observed in helix‐supporting solvents), poly‐L‐phenylalanine, poly(α‐benzyl‐L‐aspartic acid), and poly‐1‐benzyl‐L‐histidine likewise show excimer emission at room temperature but not at 77°K., while poly‐L‐tyrosine, poly‐L‐tryptophan, poly(γ‐benzyl‐L‐glutamic acid), and poly‐S‐benzyl‐L‐cysteine exhibit no excimer emission at either temperature. The aromatic residues of bovine serum albumin exhibit only “normal” fluorescence, but, lysozyme appears to be unique among proteins in showing excimer‐like tryptophan emission in the native state; its luminescence becomes “normal” upon denaturation. It appears very probable that none of these polymers has a ground‐state conformation in which the aromatic groups have face‐to‐face orientations appropriate for excimer interaction. It is concluded that at room temperature absorption of light can cause local “melting” of regular (usually helical) structures and thus, in some polymers, permit the attainment of a face‐to‐face arrangement of aromatic rings within the radiative lifetime of their excited singlet states. In certain other polymers (for reasons not clear at present), and in all polymers at 77°K., this does not occur. This concept is extended to provide a bettor basis for understanding the mechanism of formation of the photodimer of thy mine in irradiated DNA.
Some aspects of stereochemistry and hydrogen bonding of carbohydrates related to polysaccharide conformations
Authors: Sundaralingam M. 
Published: December 2004

AbstractSome general rules governing hydrogen bonding at the ring oxygens of furanosides, pyranosides, and bridge oxygens of glycosides have been formulated from existing data on crystal structures of carbohydrates. Ring oxygens of the majority of the glycopyranosides in the hemiacetal or acetal form are involved in hydrogen bonding such that the hydrogen bond direction is usually equatorial to the ring plane and not axial. In contrast, there are no known examples of ring oxygens of glycofuranosides and methyl‐glycopyranosides displaying hydrogen bonding in the crystal. Also, the bridge oxygens of glycosides are not involved in hydrogen bonding. The observed shortening in the exocyclic and endocyclic anomeric C(1)O bonds and the geminal CO bonds indicate that compounds with two oxygen atoms attached to the same saturated carbon atom may participate in double‐bond‐no‐bond resonance interaction in the same manner as difluoromethane. It is also possible that under these circumstances the carbon atom exhibits greater than tetracovalency. The “anomeric effect” may also be related to (a) the differences in the “double bonding” or bond shortening in the anomeric CO bonds of the anomeric glycopyranosides, (b) the shorter intramolecular O(1)…︁O(5) non‐bonded interaction, and (c) the smaller O(1)C(1)O(5) valence angle in the equatorial anomer compared to the axial anomer. An analysis has been made of the energetically preferred conformations about the glycosyl and glycosidic bonds of 1,4‐ and 1,3‐polysuc‐charides. In the 1a, 4e‐glycopyranosides the projected angle ϕ1 [O(5)C(1)OR, where R = C or H] is positive, while it is negative in the 1e, 4e‐glycopyranosides. Angle ϕ2 [C(1)OC(4′)C(3′)] is positive in both the 1,4‐anomeric polyglycosides. 1e, 4e‐ and 1a, 4e ‐polysaccharides are stabilized by intramolecular O(5)…︁HO(3′) and O(2′)…︁O(3′) hydrogen bonding, respectively, and generate linear and helical (cyclic) structures, respectively. 1e, 3e‐ and 1a, 3e‐polysaccharides may be stablized by one of two possible intramolecular hydrogen‐bonding schemes such that the 1a, 3e ‐polysaccharides generate helical structures while the 1a, 3e‐polysaccharides generate nonhelical structures. The conformation about the C(5)C(6) bond in the pyranosides falls into two groups where the angle ϕ00 [O(5)C(5)C(6)O(6)] is either positive, ∼+60 ± 30°, or negative, ∼–60 ± 30°, the former conformation being found more frequently. In the furanosides the latter conformation is preferred.
Topography of nucleic acid helices in solutions. III. Interactions of spermine and spermidine derivatives with polyadenylic–polyuridylic and polyinosinic–polycytidylic acid helices
Authors: Glaser Robert , Gabbay Edmond J. 
Published: December 2004

AbstractThe synthesis of spermine derivatives (II), \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm R}_1 {\rm R}_{\rm 2} {\rm R}_{\rm 3} \mathop {\rm N}\limits^ + \left( {{\rm CH}_2 } \right)_3 \mathop {\rm N}\limits^ + {\rm R}_{\rm 1} {\rm R}_{\rm 2} \left( {{\rm CH}_2 } \right)_2 ]_2 \cdot 4{\rm X}^ - $\end{document}, and spermidine derivatives (III), \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm R}_1 {\rm R}_{\rm 2} {\rm R}_{\rm 3} \mathop {\rm N}\limits^ + \left( {{\rm CH}_2 } \right)_4 \mathop {\rm N}\limits^ + {\rm R}_{\rm 1} {\rm R}_{\rm 2} \left( {{\rm CH}_2 } \right)_3 \mathop {\rm N}\limits^ + {\rm R}_{\rm 1} {\rm R}_{\rm 2} {\rm R}_3 \cdot 3{\rm X}^ - $\end{document}, are reported. The effects of these salts on the helix–coil transition of rA–rU and rI–rC helices were examined. Increasing the size of the hydrophobic substituents, R1, R2, and R3 lowers the degree of stabilization of the helical structure. The disproportionation reaction, 2rA–rU→rA–rU2 + rA occurs readily with salts II and III, especially when the substituents, R1, R2, and R3 are small, i.e., H or Me. Spermine is found to stabilize the rA–rU2 and rI–rC helices to approximately the same extent; however, large differences between the degree of stabilization of rA–rU2 and rI‐rC helices are observed when the substituents R1, R2, and R3 are large hydrophobic groups. Similar results are also obtained for the spermidine series. Finally, differences in the interactions of the salts II and III with rA–rU2 and rI–rC helices suggest that the latter helix is denser.
Photoelectric effects of deoxyribonucleic acid
Authors: Snart Ronald S. 
Published: December 2004

AbstractStudies have been made of the d.c. semiconductive behavior of fibers and solid gels of DNA. The semiconductive behavior under high vacuum is similar in solid gels of DNA and stretched fibers of DNA measured along and across the fiber axis. Photoelectric effects have been studied, and an action spectrum is reported which agrees with the absorption spectrum of DNA. No photoelectric effects are observed at wavelengths corresponding to the thermal energy gap. The temperature dependence of the photocurrent has been determined, and the effects of air, oxygen, and nitrogen at different pressures on the photocurrent have been measured.
Steric structure of L‐proline oligopeptides. II. Far‐ultraviolet absorption spectra and optical rotations of L‐proline oligopeptides
Authors: Okabayashi H. , Isemura T. , Sakakibara S. 
Published: December 2004

AbstractThe results of the measurement of the far‐ultraviolet absorption spectra of L‐proline oligomers in water and acetonitrile are summarized as follows. The monomer has an absorption maximum at 182.5 mμ in acetonitrile. The absorption maximum of the dimer is found at 185 mμ and a shoulder appears around 200 mμ, that is, splitting of the absorption spectrum is observed in the dimer. As the degree of polymerization increases, the position of the shoulder shifts toward the wavelength of the absorption maximum of poly‐L‐proline II, with an accompanying increase in intensity. We may describe the absorption peak around 203 mμ of poly‐L‐proline II as identical with the shoulder with an increased intensity. By measurements of optical rotatory dispersion and circular dichroic spectra, it was also confirmed that the appearance of the helical conformation commences at the tetramer. When the number of residues is five or greater, the conformation of the helical structure of poly‐L‐proline II seems to be completed.
Kinetics of primer‐dependent polynucleotide phosphorylase synthetic reactions
Authors: Cantor Charles Robert 
Published: December 2004

AbstractThe kinetics of a model for the primer‐dependent, polynucleotide phosphorylase‐catalyzed synthesis of oligo‐ and polynucleotides is developed. Numerical solutions are presented which correspond to a wide variety of possible reaction conditions. The model seems capable of explaining the types of behavior which have been experimentally observed for polynucleotide phosphorylase reactions. The most unusual of these is the presence of a transient intermediate of high molecular weight polynucleotide chains which is subsequently degraded to an equilibrium mixture of short oligonucleotides. Methods of estimating the time of occurrence and maximum size of the polymer are discussed. Analytical solutions are developed for the concentrations of free enzyme and unreacted nucleoside diphosphate. In conjunction with equilibrium data these may permit the rate constants required by the model to be determined.
Calculation of kinetic curves for the helix–coil transition of polypeptides
Authors: Craig Mary E. , Crothers Donald M. 
Published: December 2004

AbstractMethods for calculating the rate of cooperative transitions on a linear lattice, for which the helix–coil transition of polypeptides is an example, are reported. The problem is to determine the kinetic characteristics of the transition given the rate constants for a set of elementary steps: in this case, the transformations of individual segments between the helix and coil states. The most straightforward method is to store the state of a long lattice (in which helix and coil segments are represented by 1′s and 0′s) in a computer and to use random‐number techniques to generate its behavior as a function of time. This is, in principle, a solution to the problem, but it requires very large amounts of computer time. We have devised a matrix iteration procedure which allows much faster computation while reproducing the results of the random‐number method accurately. In this procedure the computer operates repeatedly with a transition probability matrix on a vector which represents the time‐dependent state of a finite group of units. The choice of a finite group neglects kinetic correlations between the state changes of units inside and outside the group, but comparison with the random‐number method indicates that these correlations are not important. Thus it is possible to generate the kinetic behavior of the model under essentially any conditions, for either relaxation or large perturbations. Examination of these calculated curves suggests a simple and quite generally applicable solution to the inverse problem—that of evaluating the rate constants from kinetic curves. The initial slope is well defined in almost every case, and since an analytic equation can be written relating this to the rate constants, these can be obtained directly from the initial rate. This latter is therefore the most convenient single measure of transition rate.
Temperature‐dependent optical properties of a torsional oscillator model for dinucleoside phosphates
Authors: Glaubiger Daniel , Lloyd David A. , Tinoco Ignacio 
Published: December 2004

AbstractA torsional oscillator model is proposed, as an alternative to the two‐state model, to explain the temperature dependencies of the optical properties of the dinucleoside phosphates. The assumptions upon which the model is based are discussed, and the predicted temperature dependencies of the optical properties of ApA are compared with the experimental results of Davis and Tinoco. A brief discussion of other models of this type is included.
Transient electric birefringence studies of T2 bacteriophage and T2 ghost
Authors: Maestre Marcos F. 
Published: December 2004

AbstractThe transient electric birefringence behavior of bacteriophage T2 and the T2 ghost or protein coal was studied. The field free relaxation measurements show both the intact virus and its ghost to have two rotary diffusion coefficients. These coefficients have values of 555 ± 54 and 111 ± 22 sec.−1 for the intact virus and 688 ± 89 and 161 ± 29 sec.−l for the ghost. The equivalent ellipsoids for the fast and slow relaxation coefficients were obtained by use of Perrin's equation and were related to the bacteriophage structure in terms of a possible extension of the tail fibers or an enlargement of the head structure. The saturation of the specific birefringence of the phage and the ghost when compared with the specific birefringence of the free nucleic acid gave an average optical orientation of 10 to 18% of the nucleic acid parallel to the main axis of the phage. The analysis of the birefringence versus applied field strength in the Kerr region gave the following values for the anisotropy of the polarixability. αe,33 – αe,11 and intrinsic dipole, μ, of both phage and ghost : for T2 phage αe,33 – αe,11 = 5.0 × 10−14 cm.3 and μ = 64,400 Debyes; for T2 ghost αe,33 – αe,11 = 7.9 × 10−14cm.3 and μ = 57,200 Debyes. The high intrinsic dipole for phage and ghost is interpreted as to be associated with the mechanisms of the virus for attachment, to the host cell wall.
Hydration of polyacids
Authors: Ikegami Akira 
Published: December 2004

AbstractThe hydration of several polyacids has been investigated with special attention to the effects of neighboring charged groups and hydrophobic groups on the hydration regions. The molar volume change due to the structural change of water by the hydration was obtained by the method of refractivity measurement. The polyacids employed were poly(acrylic acid), poly(methacrylic acid), poly(L‐glutamic acid), and a copolymer of maleic acid and vinyl acetate. The measurement of the refractive index was performed for the solutions of these polymers neutralized to varying degrees by tetrabutyl‐ammonium hydroxide and sodium hydroxide. The results confirm the characteristics of the previous model of the hydration of polyelectrolytes, that is, the cooperative action of neighboring charged groups induce the second hydration region in addition to the intrinsic hydration region. The stiff structure of water in these regions restricts the mobility of counterions forced to enter into these regions by the strong electrostatic potential of polyions. The results indicate also that hydrophobic groups induce an additional hydration region around their neighboring charged groups. Small but negative volume changes were observed for conformational changes of poly(L‐glutamic acid) and poly(methacrylic acid) induced by the neutralization of carboxyl groups.
Anomalies in the sedimentation behavior of high molecular weight DNA isolated from Proteus mirabilis
Authors: Triebel Hans 
Published: December 2004

AbstractThe sedimentation properties of a P. mirabilis DNA sample have been investigated at different concentrations and rotor speeds. Pronounced speed effects occurred at high angular velocities. The s

value evaluated from low‐speed experiments amounts to 61 S., indicating a mean molecular weight of 105 million. Anomalous concentration distributions in the ultracentrifuge cell have been observed at low speeds. At the boundary, a pile‐up of concentration occurs which exceeds the total plateau concentration. The concentration elevation decreases with increasing time due to convection which is caused by the existence of a negative density gradient. Despite this convection, accurate mean sedimentation coefficients could be obtained even at extremely low concentrations. A careful analysis of sedimentation coefficient distributions shows, however, that the lending and trailing tails of the boundaries are disturbed by convection. Thus it may be expected that the effect produces difficulties in determining true sedimentation coefficient distributions of polydisperse DNA samples of very high molecular weight.
Possible formation of the left‐handed α‐helix of poly‐L‐serine
Authors: Sarathy K. P. , Ramachandran G. N. 
Published: December 2004

AbstractA conformational study of poly‐L‐serine has shown that it can exist in the left‐handed α‐helical form. A study of a pair of peptide units with the serine sidegroup attached to the α carbon atom linking the two units showed that OH ⃛O hydrogen bonds between the OH group of the side chain and a carbonyl oxygen of the first peptide group in the backbone can occur in two regions of ϕ, namely, ϕ = 15°–30° for χ1 = 300° and for ϕ = 225°‐230° for ϕ = 60°. The latter is close to a possible left‐handed helix of poly‐L‐serine, stabilized by NH ⃛O hydrogen bonds. From a study of contact criteria, the best conformation for this helix is found to be ϕ = 227°, Ψ = 238°, χ1 = 65° which has n = 3.65, h = 1.51 A. The NH ⃛O hydrogen bond has a length of 2.90 A. (6°) and the OH ⃛O hydrogen bond is of length 2.60 A. (0°). There are no other bad short contacts in the structure. The cylindrical coordinates of the atoms, as well as a perspective view of the structure arc given in this paper.
Kinetics of reversible reactions on linear lattices with neighbor effects
Authors: Silberberg A. , Simha R. 
Published: December 2004

AbstractAs a model for a variety of reaction processes on long chain molecules, for example, helix formation, a kinetic theory on a linear lattice is presented. Each reaction site can undergo reversible transitions between two states (0 and 1) with rates depending on the slate of its nearest neighbors. The system of coupled rate equations for the frequencies of specified runs of 0's and 1's is infinite for an infinite chain. In contrast to the case of irreversible processes, the system cannot, be written down by inspection. A procedure for the systematic derivation of the rate equations is developed which can be programmed on a computer. Explicit expressions for runs up to length four, involving runs up to length five are obtained without recourse to the computer. For the solution of the rate equations a closure must necessarily be imposed, and a possible procedure is pointed out. Furthermore the equilibrium relations following from the model are considered. The well‐known equilibrium results for nearest‐neighbor interactions represent a special case of these equations.
Studies on the conformation of protonated DNA
Authors: Zimmer Ch. , Luck G. , Venner H. , Frič J. 
Published: December 2004

AbstractExperiments were made to demonstrate the predominant protonation effects and structural changes of the ordered double helical DNA structure and denatured state of DNA. Spectrophotometric titrations performed at different wavelengths indicate that cytosine can be protonated in the DNA double helical molecule to a high extent without breakdown of the secondary structure. With DNA heat‐denatured under severe conditions the protonation of cytosine can be measured at 280, 295, and 300 mμ: the apparent pK value obtained was ∼4.6. The protonated double helical conformation of the DNA molecule differs from the unprotonated state, which follows from the decrease of the thermal stability and from changes in the ORD curves. The ORD of a GC‐rich DNA indicates a novel Cotton effect with positive rotations at ∼260 mμ in 0.02M KCl below pH 4.0 to pH 3.3. The occurrence of the new peak parallels the extent of protonated cytosine measured by the spectrophotometric titrations. It is concluded that the protonated cytosine in the double helical structure is responsible for the difference between the protonated DNA conformation and the native state at neutral pH.
Calculation of binding isotherms for heterogeneous polymers
Authors: Crothers Donald M. 
Published: December 2004

AbstractThe matrix method of statistical mechanics is used to calculate equilibria for the binding of small molecules to polymers. When there is only one kind of binding site the problem is simple; some examples are given for illustrative purposes. If, however, the binding sites are not all equivalent and the bound molecules interact or interfere with each other, the problem is no longer trivial, being formally analogous with calculation of the helix–coil transition equilibrium in a heterogeneous polypeptide. Particular difficulties arise when the sequence of binding sites is aperiodic; most naturally occurring materials fall in this class. The purpose of this paper is to point out that problems of this type are readily solved with good accuracy by use of random‐number methods on a high‐speed digital computer. One such calculation is presented for illustration. The methods developed are applicable to such systems as the binding of actinomycin, Hg–, and acridine dyes to DNA.
Low‐angle light‐scattering instrument for DNA solutions
Authors: Harpst J. A. , Krasna Alvin I. , Zimm B. H. 
Published: December 2004

AbstractA light‐scattering instrument capable of measurements on native DNA at angles as low as 10° is described. The major features of the instrument, which make it capable of low‐angle measurements, are the use of an intense light source in which the incident beam is monitored directly and the use of a long, rectangular sample cell in which the scattered light can be measured at low angles with no interference from the incident beam. Methods for calibrating the instrument and for determining scattering correction factors are described. Procedures for the preparation and use of various calibration standards are given.
Specific aggregation of poly(α‐L‐glutamic acid) and hysteresis effects in aqueous solutions. I. Influence of temperature‐dependent aggregation on the optical rotation of PGA
Authors: Jennings B. R. , Spach G. , Schuster T. M. 
Published: December 2004

AbstractThe instability of aqueous solutions of poly(α‐L‐glutamic acid) (PGA) at low pH is due to two distinguishable phenomena: precipitation, favored above 40°C., and aggregation, favored below 20°C. The aggregated form of PGA can be isolated by gel permeation chromatography. Both aggregation and precipitation increase with decreasing pH, i.e., with decreasing ionization of the side chain carboxyl groups. Temperature‐induced aggregation and disaggregation give rise to a reproducible hysteresis loop which can be followed by optical rotation, light scattering, sedimentation, viscosity, and chromatography. Hysteresis has been observed with different PGA samples, and in several aqueous buffered or unbuffered solvents and organic‐aqueous solvent mixtures and in the pH range 4.1–4.5. Aggregation manifests itself as an increase in negative optical rotation in the visible and ultraviolet spectral range. The specific relation at 233 mμ is sensitive to aggregation and also reflects the hysteresis. Measurements of optical rotatory dispersion indicate that a0 reflects the hysteresis but b0 does not, the latter revealing only reversible changes with aggregation and disaggregation. The helix‐coil equilibrium is apparently unperturbed by aggregation, as is the thermal stability of the helix structure. For fully aggregated PGA it is estimated that a0 increases by about 300 degrees, which suggests that a0 may be a sensitive parameter to measure aggregation in other systems. The rate of aggregation increases with decreasing temperature. The disaggregation, upon heating, is more rapid. However, kinetics measurements have not yet been done. The temperature M at which all aggregates are disrupted increases with decreasing pH, but is independent of total PGA concentration, at constant pH. No molecular weight dependence of M was detected in the range 20–100 × 103. The shape and size of the hysteresis loop depends upon pH and molecular weight, which is interpreted as a dependence on the extent of aggregation. One branch of the loop, representing the helix–coil transition of isolated molecules, is reversible, while the others, representing the formation and disruption of the aggregates, are not. The system exhibits both ascending and descending scanning curves, which are typical of a true hysteresis.