bluuebunny/crossref_metadata_2025 huggingface dataset:
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

The 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

Studies 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

The 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

The 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

Methods 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

A 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

The 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

The 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

The 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

A 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

As 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

Experiments 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

The 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

A 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

The 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.
Poly‐α‐Acide‐L‐Glutamique en Solution Aqueuse. Agrégation Spécifique et Phénomènes d'Hystérésis. II. Agrégation et Précipitation. Analyse Chromalographique
Authors: Spach G. , Constantin D.
Published: December 2004

The aggregated form of poly(L‐glutamic acid) can be isolated by gel permeation chromatography, whereby it was found that in a polydispersed sample the lower molecular weight fractions precipitate preferentially and the higher fractions tend instead to aggregate. In addition, aggregation has the effect of retarding or inhibiting precipitation.
Interaction of antibodies specific towards the 2,4‐dinitrophenyl group and of their fragments with hapten
Authors: Zikán J. , Kotýnek O.
Published: December 2004

The interaction of hapten (ε‐DNP lys) with native and S‐sulfonated antibodies specific towards the 2,4‐dinitrophenyl group, as well as the interaction with isolated chains and a complex obtained by mixing light, (L) and heavy (H) chains of these antibodies, were followed both by polarography and by equilibrium dialysis. With the S‐sulfonated antibodies and with the mixture of H and L chains the binding heterogeneity observed in the original antibodies was much lowered or entirely removed. At the same time, the amount of active proteins in the sample decreased approximately by half. The association constants of modified antibodies were of the same order as the average association constants of the original antibodies. A slow increase of the amounts of hapten bound with proteins was observed on mixing the H and L chains and adding hapten. This slow reactivation was not obtained with the original or S‐sulfonated antibodies and with isolated chains. It was shown that the reaction determining the kinetics of this reactivation (the slowest reaction) was not the association of H and L chains but the interaction of complexes of the H and L chains with hapten. It was reported previously that H chains were nonspecifically reactivated by binding L chains. The amount of hapten bound by the complex of H and L chains increased with increasing excess of L chains following a curve resembling the Langmuir isotherm. The limiting value of the amount of hapten bound when using antibody L chains was higher than in the case of nonspecific L chains.
Viscosity and optical activity of chondroitin sulfate C
Authors: Eyring Edward J. , Yang Jen Tsi
Published: December 2004

Chondroitin sulfate C (CSC), isolated from shark vertebral mucoprotein, has a molecular weight of 0.2 × 104–5.5 × 104 in both NaCl and CaCl2 solutions. Optical rotatory dispersion and circular dichroism of CSC reveal a strong, negative, optically active band near 210 mμ, arising from the carboxylate and N‐acetyl groups. Results of similar studies of glucuronic acid and N‐acetyl‐D‐galactosamine suggest that the N‐acetyl group contributes more to the rotations of CSC than does the carboxylate group, but the acidification of the carboxylate groups largely accounts for the change in magnitude and position of the circular dichroic bands of CSC at low pH.
Induced optical activity of chondroitin sulfate c–acridine orange complexes
Authors: Eyring Edward J. , Kraus Howard , Yang Jen Tsi
Published: December 2004

Chondroitin sulfate C (CSC) and acrdiine orange (AO) formed two types of complexes at neutral pH, depending upon the order of mixing. The induced optical activity of AO was much more pronounced when the polysaccharide was added to dye than the dye to polymer (final concentration of dye was 5 × 105M). The difference in aggregation of the dye molecules is believed to be responsible for the observed peculiarities. The Cotton effects of the CSC‐to‐dye solution displayed a sharp inversion near 59°C. and the profile at 76°C. was almost a mirror image of that at room temperature. At pH 1.3, however, the order of mixing became unimportant, suggesting that the carboxylate on the polysaccharide way involved more intimately than were sulfates in the peculiarities of the Cotton effects.
Statistics of branching and hairpin helices for the dAT copolymer
Authors: de Gennes P.‐G.
Published: December 2004

At low temperatures a single strand of dAT copolymer tends to form a double helix with a loop at one end (hairpin). At slightly higher temperatures a branched structure (consisting of many hairpins connected by coiled regions) appears. The equilibrium properties of this branched structure are studied here by a propagator method. In particular the radius of gyration RG is calculated; under typical conditions, RG is expected to show a minimum at a temperature slightly below melting, in agreement with viscosity measurements. The present calculation is restricted to rather sharp transitions, for which the size of each helical region is large, even at the melting point. Then, in a rather broad range of molecular weights, M, RG is proportional to M1/4(as in the Zimm‐Stockmayer theory of simple branched polymers).
Radiationless energy transfer through a polypeptide chain
Authors: Gabor Gavriella
Published: December 2004

Electronic excitation spectra were measured on a donor‐acceptor pair which was separated by oligomers of L‐proline of gradually increasing lengths. The logarithmic plot of the transfer efficiency versus the donor‐acceptor separation, for (pro)n oligomers with n⩾5, yielded a slope of 5.8 ± 0.3 in good agreement with the theoretical value of 6, predicted by Forster. The above method is suggested as a tool for the estimation of distances between certain chromophoric groups, covalently bound to macromolecules. The use of any stereoregular polymer for calibrating a certain energy donor‐acceptor pair is discussed.
Comparison of several calculations of helix–coil transitions in hetergeneous polymers
Authors: Fink Thomas R. , Crothers Donald M.
Published: December 2004

Random number methods are used to calculate helix—coil transition curves for the model of a heterogeneous polypeptide of random sequence. These curves are compared with several other calculations. The random number computations confirm the exact calculation of Lehman; among the several approximate calculations examined only that of Fixman and Zeroka agrees closely with results of the random number method over the whole range of conditions considered. Calculations are also reported of the average length of helix and coil sections in a heterogeneous molecule of random sequence which is undergoing the helix‐coil transition.
General theoretical approach to the thermodynamic and kinetic properties of cooperative intramolecular transformations of linear biopolymers
Authors: Schwarz Gerhard
Published: December 2004

A general method to calculate experimentally accessible thermodynamic and kinetic quantities for any type of cooperative transitions is developed. Special attention has been directed to transition curves and mean relaxation times. The procedure is applied to the most general case of nearest‐neighbor cooperativity by using the linear Ising model and the matrix method of evaluation. The various potential types of end effects arid the resulting chain length dependences are discussed in detail. The significance of the theory with respect to the helix‐coil transition of polypeptides as well as to the polyproline I‐II transition is indicated.
Ionic polysaccharides. II. Comparison of polyelectrolyte behavior of hyaluronatc with that of carboxymethyl cellulose
Authors: Cleland Robert L.
Published: December 2004

Sodium hyaluronate (NaHy) and sodium carboxymethyl cellulose (NaCMC) behave similarly with respect to concentration.N 3 of an added 1 : 1 electrolyte. The second virial coefficient A2 (light scattering) is identical within experimental error at a given.N 3. The limiting viscosity number [η] also varies with N3−1/2in similar fashion for samples of similar [η] of the two polymers. Differences in Na+ activity in salt‐free solutions are interpreted on the basis of weaker Na+ binding in NaHy, presumably due to the greater charge separation along its chain backbone. Added electrolyte is excluded in dialysis more strongly by NaHy (or its acid form) than by NaCMC. The Flory parameter Φ is smaller in good solvents for NaHy, as for many other polyelectrolytes, than for nonionic polymers.
Effect of side chains on the conformational energy and rotational strength of the n–π*transition for some α‐helical poly‐α‐amino acids
Authors: Vournakis John N. , Yan Johnson F. , Scheraga Harold A.
Published: December 2004

Calculations of the dependence of the conformational energy and the rotational strength of the amide n–π* electronic transition (in a series of α‐helical polyhel‐α‐ amino acids with different side chains) on conformation have been carried out. The conformational energies were computed by procedures developed in this laboratory; the computation of rotational strengths was carried out by the method of Schellman and Oriel, with a slight modification. Polyamino acids with both nonpolar and polar side chains were considered; in the latter case, it was assumed that the only influence of the polar side chain was on the backbone conformation and on the electrostatic field which perturbs the amide chromophore of the backbone. Only conformations in the range of backbone dihedral angles of the right‐ and left‐handed a‐helices were considered, and the assumption of regularity (i.e., uniformity of dihedral angles in every residue) was made. The rotational strength per residue was found to vary markedly with chain length (in oligomers of up to 40 residues long); both the conformational energy per residue and the rotational strength per residue were found to vary significantly with the backbone conformation, which in turn depends on the nature of the side chain. The geometry of the hydrogen bond in the α‐helical backbone is the most important factor which influences the dependence of the rotational strength on conformation. The implications of these results, for the interpretation of experimental circular dichroism and optical rotatory dispersion data, are discussed.
Interchain hydrogen bonds via bound water molecules in the collagen triple helix
Authors: Ramachandran G. X. , Chandrasekharan R.
Published: December 2004

If the collagen triple helix is so built as to have one set of NH ⃛ O hydrogen bonds of the type N3H3(A) ⃛ O2(B), then it is possible to have a linkage between N1H1(B) and O1(A) through the intermediary of a water molecule with an oxygen O leading to the formation of the hydrogen bonds N1(B) ⃛ O and O (A). In the same configuration, another water molecule with an oxygen O can link two earbonyl oxygens of chains A and B forming the hydrogen bonds O O1(A) and O O0 (B). The two water oxygens also become receptors at the same time for CH ⃛ O hydrogen bonds. Thus, the neighboring chains in the triple helix are held together by secondary valence bond linkages occurring regularly sit intervals of about 3 Å along the length of the protofibril. The additional water molecules occur on the periphery of the proto‐fibril and will contribute their full share towards stabilizing the structure in the solid state. In solution, they will be disturbed by the medium unless they are protected by long side groups. It appears that this type of two‐bonded structure, in which one NH ⃛ O bond is to a water molecule, can explain several observations on the stability and hydrogen exchange properties of collagen itself and related synthetic polypeptides. The nature of the water bonds and their strength are found to be better in the one‐bonded structure proposed from Madras than in the one having the coordinates of Rich and Crick.
Crystalline structure in oriented fibers of KBr–amylose
Authors: Jackobs John J. , Bumb Robert R. , Zaslow Bert
Published: December 2004

The study of the structure of KBr–amylose begun by Senti and Witnauer has been extended by a three‐dimensional crystallographic analysis and by stereochemical considerations. Location of Br− at (0.200, 0.200, 0.000) and K+ at (0.540, 0.540, 0.000) was obtained from the three‐dimensional map of vector interactions. By using known parameters for the D‐glucose residue and accurate space‐filling models, an amylose helix was constructed to meet the fiber repeat spacing of 16.1 Å. The helix was determined to be left‐handed, and the correct space group for KBr–amylose is P43 212. Placement of the helix in the unit cell resulted from structure factor calculations; minima in the grid of R values were checked with space‐filling models to establish the final structure. Both ions are located in a waterlike environment. The oxygen atoms O(2), O(3), and O(4) from glucose residues on adjacent chains coordinate around K+.
Conformational aspects of polypeptides. XXIX. Conformationl assignments for some aromatic polypeptides by far‐uv cotton effects. New results
Authors: Goodman Murray , Toniolo Claudio , Peggion Evaristo
Published: December 2004

Recent improvements in apparatus permit the examination of circular dichroism (CD) and optical rotatory dispersion (ORD) spectra to 185 mμ. In addition, new solvents which are transparent to 185 mμ have become available for synthetic polypeptides. The spectral region 185–250 mμ is extremely important for the amide (peptide) chromophore, because of the presence at these wavelengths of the n–π* and π–π* bands,1 and of another transition, the assignment of which remains unsettled.2
Enthalpy change of the coil–helix transition of poly(γ‐benzyl L‐glutamate) in dichloroacetic acid–1,2‐dichloroethane mixtures
Authors: Kagemoto Akihiro , Fujishiro Ryoichi
Published: December 2004

By combining the heat of dilution of a poly(γ‐benzyl L‐glutamate)–dichloroacetic acid–1, 2‐dichloroethane solution with the corresponding heat of mixing of two solvents, the integrated heat of the coil–helix transition of poly(γ‐benzyl L‐glutamate) in the solution was estimated to be about 750 cal/mole.
Far‐infrared spectra of polyalanines with α‐helical and β‐form structures
Authors: Itoh K. , Nakahara T. , Shimanouchi T. , Oya M. , Uno K. , Iwakura Y.
Published: December 2004

Far‐infrared spectra of poly‐L‐alanines having the α‐helical conformation and the β‐form structure were measured. The spectra of glycine–L‐alanine copolymer, silk fibroin, and copoly‐D,L‐alanines with different D:L compositions were also measured. In addition to the bands so far reported, four bands at 190, 107, 120, and 90 cm−1were found for the α‐helix conformation and the two bands at 442 and 247 cm−1 were found for the β form. The 442 cm−1 band consists of the parallel 432 cm−1 and perpendicular 445 cm−1 bands. The 247 cm−1 band is well defined and has strong dichroism parallel to the direction of stretching. These two bands appear also for silk fibroin and glycine–L‐alanine copolymer. All the far‐infrared bands of copoly‐D,L‐alanines can be interpreted as α‐helix bands, the three peaks at 580, 478, and 420 cm−1 being ascribed to the D‐residue incorporated into the right‐handed α‐helix or to the L‐residue in the left‐handed α‐helix.
Dielectric properties of polyelectrolytes. I. A study on tetra‐n‐butyl ammonium polyacrylate
Authors: Minakata Akira , Imai Nobuhisa
Published: December 2004

Dielectric constant and loss of aqueous solutions of tetra‐n‐butyl ammonium polyacrylate ((Bu)4NPA) were measured in the frequency range from 300 Hz to 6 MHz as compared with sodium and other salts at various conditions. Our results show that there are two dispersions observed in the low‐frequency range (LFD, several ten kHz to MHz), respectively, both of which are roughly expressed as the Cole‐Cole dispersion formula with Cole parameters about 0.3. The large values of dielectric increment, its nonlinear concentration dependence, and other features suggest that both dispersions are explained by relaxations of two different ionic processes. For HFD, experimental results were qualitatively similar to those have been reported and compared with theories of the Maxwell‐Wagner‐type effect. On the other hand, LFD may be attributable to the polarization of loosely bound counterions. A model available for LFD was presented on the basis of counterion fluctuation.
Dielectric properties of polyelectrolytes. II. A theory of dielectric increment due to ion fluctuation by a matrix method
Authors: Minakata Akira , Imai Nobuhisa , Oosawa Fumio
Published: December 2004

The mean square of dipole moment of a linear macromolecule which is responsible for dielectric increment of aqueous polyelectrolyte solutions is calculated by means of a matrix method in which ion binding at discrete sites and the nearest‐neighbor interaction are taken into account. On the basis of the relationship between polarization of poly‐ion and fluctuation of bound counterions the present theory indicates that the loosely bound ions result in larger increment and otherwise smaller increment. Also, the theory predicts that the dielectric increment has a maximum at an intermediate monovalent–divalent ion ratio when both species coexist. These results are consistent with experiments on polyacrylic acid neutralized with NaOH and Ca(OH)2. At large contents of divalent ions the effect of chelation is also discussed.
Nuclear magnetic resonance spectra of poly(N‐alkylamino acid)s
Authors: Sisido Masahiko , Imanishi Yukio , Higashimura Toshinobu
Published: December 2004

220‐MHz NMR spectra of various poly (N‐alkylamino acid)s are investigated. Spectra of polysarcosine recorded in various solvents showed fine splittings of the methyl and methylene bands. Comparing the spectrum with that of its model compound, the fine structure of the methyl band of polysarcosine was assigned to four dyad sequences of the cis–trans isomeric state of the main chain amide bonds. Also the methylene band was roughly divided into cis and trans bands. From the temperature dependence of the spectra of polysarcosine, a double coalescence phenomenon was observed, in which the four dyad peaks coalesced into two peaks corresponding to cis and trans, then the two peaks coalesced into one peak. Further, the approximate value of the free energy for the internal rotation of the main chain amide bond was estimated. NMR spectra of various poly(N‐alkylglycine)s in methylene chloride solution were also obtained. From the comparsion of their methylene bands, the introduction of the bulky N‐alkyl groups was found to increase the cis content of the amide bond.
Steady‐state and pulsed NMR studies of gelation in aqueous agarose
Authors: Child T. F. , Pryce N. G.
Published: December 2004

Steady‐state and pulsed NMR techniques have been used to investigate molecular motion in sols and gels of agarose. In passing through the sol–gel transition, the molecular mobility of water molecules is reduced only by a small amount, whereas motion of the polymer chains is greatly attenuated. The results are discused in terms of the network theory of gelation, with references to the role of water in the process and the nature of the “junction zones” between polymer chains. T2 and line‐width measurements are dominated by exchange broadening. The effects of exchange rate and differences in relaxation time between the exchanging sites are discussed. The temperature hysteresis behavior of agarose gels has been investigated and the effects of “ageing” correlated with changes in nuclear relaxation times. The synergistic increase in gel strength obtained on adding locust bean gum (LBG) to agarose has been investigated. The results indicate that LBG does not form double‐helix junctions and may decrease rates of gelation by steric effects. At high agarose concentration, the LBG remains mainly in solution in interstitial water, but at low agarose concentration, it is suggested that the LBG can link gel aggregates together into a self‐supporting structure, producing a synergistic increase in gel strength. Comparisons have been made between the nature of the agarose–LBG interaction and agarose–cellulose interactions in biological systems.
A cross‐linked copolypeptide with increased affinity for cations
Authors: Kim Yung D. , Klotz Irving M.
Published: December 2004

The copolymer poly Glu42Lys28Ala30 was crosslinked by S–S bridges by reaction with butyrothiolactone followed by air oxidation of the mercaptan covalent adduct. The modified copolypeptide was more compact hydrodynamically, more resistant to the structurally disruptive effects of urea, and able to bind dye cations with much increased avidity.
The effect of charges on the melting of DNA
Authors: Nagasawa Mitsuru , Muroga Yoshio
Published: December 2004

A method of calculating both the electrostatic free energy and en tlpy changes for melting of DNA is proposed. The nonelectrostatic parts of free energy and enthalpy changes for melting of DNA are obtained by subtracting these electrostatic free‐energy and enthalpy changes from the total free‐energy and enthalpy changes of melting reported by Privalov, Ptitsyn, and Birshtein, respectively. The ionic strength dependence of the melting temperature of DNA is computed using these thermodynamic functions.
Rate studies of the amylose–iodine reaction in unfractionated starch samples of various plant origin
Authors: Hamori Eugene , Kallay Michael C.
Published: December 2004

The initial rate of the fast reaction among amylose, iodine, and iodide ions was studied in unfractionated corn, potato, rice, wheat, and arrowroot starches. It was found that the reaction followed the same rate equation as the one established in a previous study using pure amylose fractions containing no amylopectin. There were significant differences, however, among the rate constants of the various starches investigated. These variations were explained in terms of the different average molecular weights of the amylose fractions of these starches. Since whole potato starch indicated a rate constant well within the fange of those of pure amylose fraction (obtained from the same potato starch samples), it was concluded, that amylopectin did not interfere significantly with the rate of the complexation reaction.
Macromolecule‐small molecule interactions; introduction of additional binding sites in polyethyleneimine by disulfide cross–linkages
Authors: Takagishi Toru , Klotz Irving M.
Published: December 2004

Polyethyleneimine and its acyl derivatives have been thiolated with thiobutyrolactone and the SH groups introduced have been crosslinked in the presence of and in the absence of methyl orange, respectively. After crosslinking of the polymers, the bound methyl orange was removed. The resultant two kinds of crosslinked polymers have been examined for their ability to bind methyl orange. The polymer crosslinked in the presence of methyl orange shows more binding sites and stronger binding than does the polymer crosslinked in the absence of methyl orange. It seems, therefore, that the conformation of the polymer may be molded to provide sites that can accommodate a specific small molecule.
Rotatory dispersion and circular dichroism of low‐molecular‐weight poly‐γ‐benzyl‐L‐glutamate
Authors: Imae Toyoko , Ikeda Shoichi
Published: December 2004

Rotatory dispersion and circular dichroism of low‐molecular‐weight poly‐γ‐benzyl‐L‐glutamate, which was prepared from the N‐carboxyanhydride by n‐hexylamine initiation at [A]/[I] 3, 4, and 8, have been measured in ethylene dichloride and dioxane at different concentrations. The rotatory properties of the polypeptides are all characterized by a trough at 233 mμ of a negative Cotton effect or by a negative circular dichroic band at 223 mμ. With increasing A/I value or concentration, dextrorotation increases and the negative dichroic band becomes deeper. Both the trough magnitude and the negative ellipticity are linearly dependent on the content of β‐structure, and the rotatory parameters for the pure β‐structure are estimated by extrapolation of the linear relations. Circular dichroism and infrared spectra of the polypeptides have also been measured in trifluoroethanol, and the effect of solvents on the polypeptide conformation is discussed.
Independence of length and temperature effects on the rate of helix formation between complementary ribopolymers
Authors: Lee Cheng H. , Wetmur James G.
Published: December 2004

The rate of double helix formation by single stranded Poly A plus Poly U, Poly I plus Poly C, Poly G plus Poly C, and T2 DNA has been investigated as a function of both the length of the reacting strands and temperature. The length dependence of the rate is found to be independent of temperature. All of the reactions studied show a rate approximately proportional to the square root of the length of the shorter of the complementary strands. At or about 30°C below the melting temperature the ribopolymers react with about the same rate. This rate is four to five times slower than DNA renaturation rates. The effect of temperature on ribopolymer reaction rates is interpreted in terms of a steady‐state model for helix propagation.
Dielectric dispersion of the α‐helix at the transition region to random coil
Authors: Wada Akiyoshi , Tanaka Toyoichi , Kihara Hiroshi
Published: December 2004

Dielectric studies have been carried out for the helix–coil transition of poly‐β‐benzyl‐L‐aspartate with m‐cresol as a solvent. The transition of the solute molecules has been sharply reflected as a characteristic change in the dielectric dispersion curves in changing temperature. Two polarizations, one having a low and the other a high critical frequency, have appeared. According to theoretical considerations of a model of a broken helix, the former is found to come from the orientation. of helical sequences and the latter from the chemical relaxation due to the helix–coil transition. It also seems likely that the unfolded chain may have a polarizability which could not be neglected at the high‐temperature side of the transition.
An x‐ray diffraction study of poly‐L‐arginine hydrochloride
Authors: Suwalsky M. , Traub W.
Published: December 2004

An x‐ray study has been made of polyarginine hydrochloride to investigate whether, like polylysine hydrochloride, it can undergo conformational changes merely from variations in the degree of hydration. X‐ray powder and fiber photographs of specimens containing up to about five molecules of water per arginine residue show features characteristic of α‐helical structures including a 5.4‐Å layer line and a meridional 1.5‐Å reflection. Increasing the water content from 1/2 to 61/2 molecules per residue causes the a axis of the hexagonal unit cell to increase from 14.4 Å to 15.8 Å, with no appreciable change in the 27.0 Å c axis. Removal of the last half molecule of water results in a very diffuse α pattern, but on rehydration the sharp pattern reappears.

Specimens containing five to twenty water molecules per residue show quite a different pattern, the spacing of which do not vary appreciably with hydration. This pattern includes a meridional 3.4‐Å reflection, a feature commonly shown by β structures, and indeed all the reflections can be satisfactorily indexed in terms of a monoclinic unit cell with a = 9.26 Å, b = 22.05 Å, c = 6.76 Å, and γ = 108.9°. These dimensions are shown by models to be compatible with a β pleated‐sheet structure.
Pressure dependence of the helix–coil transition temperature for polynucleic acid helices
Authors: Gunter T. E. , Gunter K. K.
Published: December 2004

Thermal denaturation of DNA's and the corresponding helix–coil transformation of artificial polyribonucleic and polydeoxyribonucleic acids have been studied extensively both theoretically1–13 and experimentally. 14–30 Much less work has been carried out on the properties of these polynucleic acids at high pressure, and in particular, on the presure dependence of the helix–coil transition temperature.31–33 Light‐scattering techniques have been used in this study to measure the pressure dependence of the helix–coil transition temperature of the two‐ and three‐stranded helices of polyriboadenylic and polyribouridilic acids and of calf thymus DNA. From the slopes of the transition temperature vs. pressure curves and heats of transition obtained from the literature,20,34 the following volume changes from these helix–coil transitions have been obtained: (a) −0.96 cc/mole of nucleotide base pairs for the poly (A + U) transition, (b) +0.35 cc/mole of nucleotide base trios for the poly (A + 2U) transition, and (c) +2.7 cc/mole of nucleotide base pairs for the DNA transition. The relative magnitudes and signs of these volume changes which show that poly (A + U) is destabilized by increased pressure, whereas poly (A + 2U) and calf thymus DNA are stabilized by increased pressure, indicates that further development of the helix–coil transition theory for polynucleotides is needed.