bluuebunny/crossref_metadata_2025 huggingface dataset:
X‐Ray diffraction of ethylenediamine–amylose complex
Authors: Simpson T. D.
Published: December 2004

Solutions of amylose in ethylenediamine yield a crystalline film complex upon evaporation of solvent. The x‐ray analysis indicates the presence of a tetragonal‐shaped cell with a symmetry approximating that of space group P212121. The amylose sixfold helix has a diameter of 13.3 Å and a translation period of 8.0Å. Chemical and physical analyses support a complexing ratio of one ethylenediamine molecule to every two glucose units. The structure is nearly identical to any amylose–dimethyl sulfoxide complex previously examined. The square mode of packing arrangement appears to result from complexation between amylose chains. Such complexing indicates a much greater degree of amylose interaction than is observed in amylose complex structures having a hexagonal close‐packing arrangement.
Oligonucleotide interactions. IV. Conformational differences between deoxy‐ and ribodinucleoside phosphates
Authors: Warshaw Myron M. , Cantor Charles R.
Published: December 2004

The circular dichroism spectra of all 16 ribodinudeoside phosphates containing the bases adenine, uracil, cytosine, and guanine have been measured at room temperature and neutral pH. These results are compared with the circular dichroism spectra of the corresponding deoxy compounds. From the optical properties it is clear that the geometry of the base‐stacked conformation of ribo compounds must differ substantially from that of deoxy compounds. Because of this, it is not possible to draw firm conclusions about the relative extent of stacking in most ribo and deoxy compounds. The optical rotatory dispersion of about a dozen deoxy and ribodinucleoside phosphates has been studied as a function of temperature. These results confirmed the conclusions drawn earlier from measurements at a single temperature. Several dinucleoside phosphates containing a 2′ → 5′ phosphodiester bond have also been examined. These compounds have a substantial degree of base stacking at room temperature. The geometry of the stacked conformation is different from that of either the normal ribo dimer or the deoxy dimer. The role of the 2′‐hydroxyl group in stabilizing base stacked geometries has been examined by studies on C‐2′‐O‐methyl‐pC. This compound has optical properties almost identical to those of CpC. This suggests that the effect of the 2′ hydroxyl is felt indirectly through its perturbation of the geometry of the sugar ring rather than directly by hydrogen bonding. It is not possible at present to identify precise conformational differences among deoxy‐, ribo‐and 2′ → 5′ ribodinucleoside phosphates.
Raman spectra of poly‐L‐lysines
Authors: Koenig J. L. , Sutton P. L.
Published: December 2004

The Raman spectra of poly‐L‐lysine hydrochloride and poly‐ϵ‐carbobenzoxy‐L‐lysine in the solid state have been obtained and are consistent with the presence of an α‐helical structure. The Raman spectrum of poly‐L‐lysine in aqueous solution suggests the presence of random coil structures.
Conformational studies of linear β‐D‐1,4′‐mannan and galactan
Authors: Sundararajan P. R. , Rao V. S. R.
Published: December 2004

The nonbonded interaction energy of disaccharides, mannobiose and galactobiose and polysaccharides mannan and galactan have been computed as a function of dihedral angles (ϕ,ψ). The conformation (40°, −20°) has been preferred for the mannan chain from nonbonded interaction energy considerations. The O5…O3′ type of intramolecular hydrogen bond has been found to be possible in the above conformation. Comparison of the allowed region of mannan with those of cellulose and xylan indicates that the monomer unit, in mannan chain has slightly higher freedom of rotation than that of cellulose and less than that of xylan. As in cellulose and mannan, the freedom of rotation of the monomer units in β‐1,4′ galactan is highly restricted. Unlike mannan (which prefers an extended conformation) the β‐1,4′ galactan prefers a helical conformation similar to amylose. Just as in amylose the O2…O3′ type hydrogen bond between contiguous residues is also possible in β‐1,4′ galactan.
Conformational and kinetic studies of synthetic polypeptides by NMR
Authors: Warashina Akira , Iio Takayoshi , Isemura Toshizo
Published: December 2004

The α‐helix–coil transition of poly‐L‐leucine, poly‐L‐alanine and poly‐L‐methionine in chloroform–trifluoroacetic acid system was studied by nuclear magnetic resonance (NMR) and optical rotatory dispersion (ORD). The kinetics of the hydrogen–deuterium exchange in the peptide was also followed in these polymers by means of NMR. Two types of the NMR spectra and the hydrogen–deuterium exchange reaction were found, corresponding to the high and low molecular weight polypeptides. In high molecular weights, the NH and α‐CH resonance lines gave single peaks and the hydrogen–deuterium exchange was expressed as a single first order reaction. In low molecular weights, the NH and α‐CH lines were separated into two peaks, corresponding to helical and random‐coiled states, respectively, and the exchange react ion was expressed as super‐position of a very rapid exchange reaction in the random‐coiled part and another slow exchange reaction of the first order in the helical part. These results suggest that the helix–coil interconversion of low molecular weight polypeptides has a longer relaxation time (⩾ 4.5 × 10−3 sec) than that of high molecular weight polypeptides.
Critical comparison of the experimental optical activity of helical polypeptides and the predictions of the molecular exciton model
Authors: Cassim Joseph Y. , Yang Jen Tsi
Published: December 2004

The predictions of the presently accepted molecular exciton model for the optical activity of helical polypeptides are in reasonable agreement with experimental spectra in the accessible wavelength range. However, crucial verification requires the detect of a significant negative rotatory hand just below the accessible range. A computer‐oriented method is utilized to obtain information concerning the inaccessible range. Optical rotatory dispersion computed by evaluation of the Kronig‐Kramers integral transform from the experimentally determined circular dichroism of several helical homopolypeptides in solution are compared with the experimentally determined optical rotatory dispersion. Computed and experimental curves are congruent within an uncertainty approaching that of the experimental technique, whatever the polypeptide sample lot, side chains, and solvent. It is shown that t his agreement is not a computational or experimental artifact. These results can be interpreted in two ways: (1) that the predicted band does not exist, and (2) that the perturbation of the predicted band is being negated by other inaccessible bands in the vacuum ultraviolet. Arguments are presented to show that the first of these two possibilities is more probable.
Instability in pressure‐dependent sedimentation of monomer—polymer systems
Authors: Johnson Michael , Yphantis David A. , Weiss George H.
Published: December 2004

The possibility of convection in velocity sedimentation studies on pressure dependent associating systems is known both experimentally and theoretically. We present accurate numerical solutions to the Lamm equation to illustrate this phenomenon for monomer–polymer systems. An approximate theory based on the absence of diffusion is then developed to predict the onset of convection. Comparison of the theory with the numerical solutions shows it to be quite accurate.
A rapid method for the preparation of amino acid resin esters for merrifield solid‐phase peptide synthesis
Authors: Monahan Michael W. , Gilon Chaim
Published: December 2004

An improved method for the preparation of Merrifield resin esters is presented. This method is rapid, is free of racemization, and is not complicated by a quaternization side reaction. Chloromethylated resin beads, t‐butoxycarbonyl amino acid, and potassium t‐butoxide are heated at 80 °C in dimethylsulfoxide for one‐half hour to yield resin esters of suitable substitution for solid‐phase petide synthesis. All twenty of the BOC protected common amino acids were esterified to the resin by this method. Resin substitution values lie in the range of 0.13 meq/g (BOC‐Glu (NH2)) to 0.66 meq/g (BOC/Pro), with most of the amino acids yielding 0.3–0.4 meq/g (on a resin containing 0.8 meq Cl/g).
Effect of temperature on the induced cotton effects of acid polysaccharide–basic dye complexes
Authors: Nakajima Kazuko , Matsumura Go
Published: December 2004

The induced Cotton effect of some acid polysaccharide–thiazine dye complexes were studied at various temperatures. When the equivalent ratio of the anionic site of the polymer to the cationic dye was near unity, all the complexes examined showed remarkable Cotton effects corresponding to their absorption bands in the visible and ultraviolet regions, at neutral pH and room temperature. Although the structure of the hyaluronate complex resembles the carbohydrate backbone, the sign of the Cotton effects was opposite that of chondroitin sulfate complexes.

When the temperature was raised, the hyaluronate–toluidine blue complex decreased the metachromatic shift in the absorption spectrum gradually; the amplitude of the Cotton effects of this complex decreased also. With a polysaccharide which has a carboxylate group as its only anionic site (such as carboxymethylcellulose or pectic acid), a similar effect of temperature was observed on its induced Cotton effects.

With the chondroitin 4‐sulfate–toluidine blue complex, some reverse of the metachromatic shift was observed at higher temperature. However, the amplitude of its Cotton effects decreased up to 70 °C, then the sign of the effects reversed and the amplitude subsequently increased. A similar inversion of the sign of the Cotton effects was found with the chondroitin 6‐sulfate–toluidine blue complex, but at a lower temperature (about 40 °C).

Charonin sulfate, a highly sulfated cellulose‐like glucan from a marine mollusca, showed a marked metachromatic effect on methylene blue even at the elevated temperature. The induced Cotton effects of this complex were also affected by temperature and the inversion of the sign was observed.

When the pH was lowered, the amplitude of the Cotton effects of the hyaluronate‐toluidine blue complex decreased and diminished at pH 3, at room temperature. With chondroitin 4‐sulfate, the induced Cotton effects were remarkable at such a low pH; however, the amplitude of the effects decreased with elevated temperature and no inversion was observed. The optical rotatory dispersion of the chondroitin 6‐sulfate–toluidine blue complex was reversed by acidifying to pH 3, and the amplitude of the Cotton effects decreased by elevating the temperature.
Conformational aspect of polypeptide structure. XLIV. Conformational transitions of poly(N‐methyl‐alanines) induced by trifluoroacetic acid
Authors: Goodman Murray , Chen Fu , Prince Frank R.
Published: December 2004

The synthesis of poly(N‐methyl‐L‐alanine) and poly (N‐methyl‐DL‐alanine) are described. The polymers were examined by 220 MHz high‐resolution nuclear magnetic resonance (nmr) and circular dichroism (CD). The results demonstrate that poly(N‐methyl‐L‐alanine) exists as an ordered helical structure with all the amide bonds in the trans configuration in appropriate solvents. As trifluoroacetic acid (TFA) is added to the solutions of the polymer in helix‐supporting solvents, resonances corresponding to both trans and cis amide conformations of N‐methyl, C‐methyl, and α‐CH are observed. The presence of both the trans and the cis peptide bonds in a polymer chain disrupts the ordered structures. Our conclusions from CD data are in agreement with the nmr results. Ultracentrifugation shows that degradation of the polymer chain does not occur during the TFA treatment.
Kinetic study on unzippering of polynucleotides and order–order transition in polypeptides
Authors: Chay Teresa Ree , Stevens Charles L.
Published: December 2004

Solutions are presented for N + 1 sequential and reversible first‐order reactions for which the magnitude of the reverse rate constant, kb, for all steps except the last is identical. Also the magnitude of the forward rate constant, kf, for all steps except the first and last is identical. The initial and final steps are nucleation reactions; therefore, the initial and final kf are modified by the factors σ′ and γ respectively. The final kb is modified by the factor γ σ. The ratio kb/kf is defined as s, which has the same meaning as s in the Zimm‐Bragg theory. The mathematical model is intended to apply to polymeric molecules of N segments and allows the calculation of the mole fraction of molecules in state i at any time t, Ci(t). A molecule in state i has i unreacted segments and N – i reacted ones. Because the reactions are sequential, all reacted segments are contiguous. Our numerical results show that when σ′ is much less than unity and the forward reaction is favored, the relaxation curve is sigmoidal. If, however, the forward and reverse reactions are equally favored (i.e., s ≃ 1) the relaxation curve is a straight line. When s and σ′ are near unity, the curve is exponential for a considerably large fraction of the reaction. Further, in the exponential for a considerably large fraction of the reaction. Further, in the exponential phase of the reaction, the relaxation time is proportional to N2 for highly cooperative systems (i.e., Nσ ≪ 1). As found by Pipkin and Gibbs, if N is sufficiently large and s is less than unity (e.g., N ≳ 50 and s ≃0.9) the relaxation curve is largely linear with a slope inversely proportional to N. Applications are given for the unwinding of double‐helical poly(A·U) and the order–order transition in poly‐L‐proline.
Dielectric properties of polyelectrolytes. V. Dielectric dispersion of heavy meromyosin
Authors: Minakata Akira , Kobayashi Shoyu
Published: December 2004

Dielectric constant and dielectric loss of heavy meromyosin (HMM) were measured with varying pH. HMM showed a broader dispersion pattern than that with a single relaxation time especially on the high‐frequencey side. The dielectric increment increased sharply with pH, above pH 6, whereas the mean relaxation time and whole dispersion pattern were unchanged in the same region. The values of the increment and the mean relaxation time were much larger than those of usual globular proteins. The dispersion profile, pH dependence, and values of the increment are well explained by Oosawa's counterion fluctuation theory. Other mechanisms are more or less inadequate to our results. In the low pH region below the isoelectric precipitation region, both the increment and the mean relaxation time decreased; this is probably due to partial denaturation and suppression of the dissociation of carboxyl groups. An experiment on a urea‐denatured sample supports this assumption. The biological significance of the pH dependence is discussed.
Rigidity of α‐helical polypeptides. A new method of obtaining the persistence length from viscosimetric data
Authors: Morcellet M. , Loucheux C.
Published: December 2004

The hydrodynamic properties of α‐helical poly(L‐glutamic acid), (Glu)n in aqueous solutions and in mixtures of water with organic solvents have been interpreted in terms of the persistence length of the macromolecule. A modification of the method of Vitovskaya and Tsvetkov has been proposed in order to allow a more accurate determination of this parameter. The addition of an organic solvent increases strongly the rigidity of the helical conformation of (Glu)n. A comparison is made with some data of the literature of poly[N5‐(3‐hydroxy propyl)L‐glutamine], [Gln(CH2)3OH]n, and poly(γ‐benzyl‐L‐glutamate), [Glu(OBzl)]n.
Packaging of DNA in bacteriophage Heads: Some considerations on energetics
Authors: Riemer Steven C. , Bloomfield Victor A.
Published: December 2004

We have made quantitative estimates of some of the energetic factors to be considered in packaging of double‐stranded DNA in virus particles. Numerical calculations were made using parameters appropriate for T4 bacteriophage. The unfavorable factors, and the Gibbs free energies per mole virus at 20°C associated with them, are bending, 1.5 × 103 kcal/mol; conformational restriction upon condensation, 5.1 × 102 kcal/mol; polyelectrolyte repulsion, 2.1 × 105kcal/mol; and melting or kinking, 6.9 × 103 kcal/mol. These must be counterbalanced in the assembled phage by noncovalent bonding interactions between protein subunits in the phage‐head shell; by interactions between the DNA and polyvalent cations, especially putrescine and spermidine; nad perhaps by repulsive excluded volume and electrostatic interaction between the DNA and acidic polypeptides. Indeed, a rough estimate of the standard free energey of interaction between T4 DNA and the putrescine and spermidine contained in the head is ‐‐2.1 × 105 kcal/mol. In the absence of the other two sources of stabilization, each head protein subunit must contribute about 210 kcal/mol of binding energy.
Proton transfer in and polarizability of hydrogen bonds coupled with conformational changes in proteins. II. IR investigation of polyhistidine with various carboxylic acids
Authors: Lindemann Rainald , Zundel George
Published: December 2004

Polyhistidine‐carboxylic acid systems are studied by ir spectroscopy. It is shown that OH ⃛N ⇌ O−…H+N bonds formed between carboxylic groups and histidine residues are easily polarizable proton‐transfer hydrogen bonds when the pKaof the protonated histidine residues is about 2.8 units larger than that of the carboxylic groups. From these results it bis concluded that OH ⃛N ⇌ O−⃛H+N bonds between glutamic or aspartic acid histidine residues in proteins may be easily polarizable proton‐transfer bonds. Furthermore, it is demonstrated that water molecules shift the proton‐transfer equilibria in these hydrogen bonds in favor of the polar structure, i.e., due to water or polar environments OH ⃛N ⇌ O−⃛H+N bonds with smaller ΔpKavalues become easily polarizable proton‐transfer hydrogen bonds. A consideration of the amide bands of polyhistidine shows that it can be present in five different conformations. It is shown that these conformational changes are strongly related to the degree of proton transfer. Hence, the degree of proton transfer, the degree of hydration, and conformation are not independent of each other, but are strongly coupled. Further proof for the interdependence of proton transfer and conformational changes are hysteresis effects, which are observed with studies of polyhistidine dependent on carboxylic acid, adsorption and desorption. OH ⃛N ⇌ O−⃛H+N bonds between aspartic and glutamic acid and histidine residues are present in hemoglobin, in ribonucleases, and in proteases, whereby this type of bond is preferentially found in the active centers of these enzymes. It is pointed out that hydrogen bonds with such interaction properties should be of great significance for structure and especially functions of proteins in which they are present.
Interaction of polyadenylic acid with methylated xanthines
Authors: Davies R. J. H. , Davidson N.
Published: December 2004

Polyadenylic acid forms both 1 : 1 and 2 : 1 complexes with 3‐methylxanthine under appropriate conditions. While the binding isotherms for formation of these complexes are typical of strongly cooperative processes, their melting profiles are anomalous and indicate that intermediate species are present during the thermal dissociation process. Theobromine and theophylline do not form complexes with polyadenylic acid under similar conditions, and they do not hydrogen‐bond very strongly with 9‐ethyludenine in chloroform solution.
Physical behavior of gelatin gels: A simple model for connective tissue
Authors: Preston B. N. , Meyer F. A.
Published: December 2004

The swelling behavior of gelatin gels when immersed in buffer or in osmotically active solutions of dextran 500 has been studied, and the results can be described by means of the Flory‐Rehner theory of the thermodynamic properties of three‐dimensional network structures. The density of crosslinkages formed in the gel is found to be related to the concentration of gelatin at which gelation occurs. Values of rigidity moduli are estimated from the density of crosslinkages by use of the statistical thermodynamic theory of rubber elasticity. These values are in excellent agreement with direct measurements.
Effects of temperature on the polymerization of γ‐ethyl DL‐glutamate N‐carboxy anhydride in DMF initiated by tri‐n‐propylamine
Authors: Terbojevich M. , Cosani A. , Peggion E. , Scoffone E.
Published: December 2004

Polymerization of γ‐ethyl DL‐glutamate N‐carboxy anhydride (NCA) in DMF has been carried out at various temperatures and with the use of tri‐n‐propylamine as the initiator. It was found that on decreasing the polymerization temperature the reaction rate is lowered but the molecular weight and the helix content of the final polymer are enhanced. An overall activation energy of ∼4 kcal/mole has been found for the polymerization process. Preliminary experiments carried out on the polymerization of γ‐benzyl D‐glutamate NCA in DMF and with tri‐n‐propylamine as the initiator showed a strong depressing effect of the CO2 evolved during the polymerization, both on the reaction rate and on the molecular weight of the polymer. All data are interpreted in terms of the Bamford‐Swarc mechanism.
Hétérogénéité des Sites de Fixation de la Proflavine sur le DNA
Authors: Bidet R. , Chambron J. , Weill G.
Published: December 2004

The desorption and melting with temperature of proflavine–DNA complexes has been studied by spectrophotometry and spectrofluorometry. Two methods are described to determine at each temperature the concentration of free and bound dye. The first one is based on the quenching of fluorescence of the free dye by the iodine ion, the second on fluorescence polarization measurements. It is shown that the sites where the bound dye fluoresces are thermally less stable than those where it is quenched, in such a way that a redistribution of the dye between the two types of sites occurs at intermediate temperatures, leading to a drop in the total fluorescence. This confirms the nature of the “emitting” sites which correspond to AT‐rich region, while “quenched” sites correspond to GC‐rich region. The first have a larger binding constant at room temperature, but only the latter are stabilized by dye intercalation. The desorption and melting have also been followed through the relative changes of absorption. The curves obtained at different wavelengths are not superimposed which is at variance with what is observed with complexes of proflavine with poly dAT and poly dG.dC. The beginning of the desorption process corresponds to minor variations at 445 nm, the maximum of absorption of the free dye, but large changes occur at 460 nm, the maximum of the difference spectrum of the complexes proflavine–poly dAT and proflavine‐poly dG.dC. The spreading of the melting curves for different wave lengths must therefore reflect the dependence of the absorption spectra of the dye on the nature of the neighboring bases. However, the action spectrum of the fluorescence, which gives the absorption spectrum of the “emitting” sites only, is identical with the total absorption spectrum of the bound dye.
Conformation of amylose in aqueous solution: Optical rotatory dispersion and circular dichroism of amylose–iodine complexes and dependence on chain length of retrogradation of amylose
Authors: Pfannemüller B. , Mayerhöfer H. , Schulz R. C.
Published: December 2004

The dependence on chain length of two characteristic properties of amylose, i.e., retrogradation and complex formation with iodine, have been studied by using enzymatically synthesized, homodisperse amyloses. The association rates of amyloses in water containing 5% dimethyl sulfoxide have a sharp maximum at a degree of polymerization P̄n of 80; shorter and longer molecules are much more soluble. The iodine complexes of amylose exhibit a strong Cotton effect in the range of the long‐wave absorption maximum (position depending on chain length) and two weaker Cotton effects at 480 and 350 nm. The long‐wave Cotton effect is most intense at about P̄n 50 and decreases rapidly for shorter and longer chains. This behavior is unexpected and is not in accordance with the further increase of λmax and λmax. The experiments can best be interpreted by assuming well ordered, stiff chains in the low molecular weight range (P̄n 50–80). For longer chains, the findings are discussed in the light of current concepts of amylose conformation in aqueous solution, namely the model of the broken helical chain (alternating stiff helical segments and unordered regions) and the model of a flexible coil without a significant helical content. However, according to the results given in this paper, a wormlike helical chain seems to be the most adequate model for amylose conformation in neutral solution.
Molecular weights and hydrodynamic properties for homogeneous native DNA, derived from diffusion, sedimentation, and viscosity measurements on polydisperse samples
Authors: Reinert K. E. , Strassburger J. , Triebel H.
Published: December 2004

The diffusion, sedimentation, and viscosity behavior of native DNA has been studied as a function of molecular weight absolutely determined by diffusion and sedimentation measurements between 106 and 20 × 106 Daltons. Only data for monodisperse subfractions of the polydisperse DNA samples investigated have been compared. They were derived by means of calculations based on individual sedimentation constant distribution and polymer parameters. The inconstancy of these parameters for the semi‐rigid DNA molecules over the range of different sub‐fractions of the polydisperse samples has been taken into account. A detailed description of the corresponding mathematical background as well as of the diffusion measurements has been given in the two preceding papers. For the homologous series of monodisperse native DNA molecules, three‐parameter equations have been determined representing the s0–[η], s0–M, and [η]–M relations as well as the D0–s0 and D0–M interdependence over the entire molecular weight range of interest. Furthermore a simple equation is given describing the molecular weight dependence of the Mandelkern‐Flory‐Scheraga parameter β in terms of s0 and [η]. The asymptotic value β∞ has been determined, primarily by measurements at finite molecular weights, to be 2.39 × 106, resulting in β values near 2.50 × 106 at M = 108 Daltons. The hydrodynamic properties of our two calf thymus DNA samples of highest molecular weight proved to be influenced by residual protein interactions resulting in a more compact conformation. Further data are given demonstrating the influence of the individual polydispersity of the investigated samples on diffusion constant and molecular weight averages.
Deuterium NMR and EPR of hydrated collagen fibers in the presence of salts
Authors: Fung B. M. , Trautmann Patricia
Published: December 2004

A new model for hydrated collagen fibers is postulated. According to this model, a part of the water adsorbed is bound to the collagen fiber through hydrogen bonding, and the rest is randomly reorienting. The two types of water are in chemical exchange. The observed dipolar splitting for H2O and quadrupolar splitting for D2O are time‐averaged values. The deuterium quadrupole splitting of D2O in oriented collagen fibers decreases in the presence of salt. The phenomenon can be explained either by a change in the structure of collagen or by the blocking of the water binding sites by the ions. In the EPR spectra of collagen presoaked in Mn(II) and Cu(II) sulfates, the line widths decrease with the increase of water content, indicating the coordination of the cations to water. The change in the hyperfine splitting (from 70 gauss in dry fibers to 96 gauss in fibers equilibrated at 100% RH) of Mn(II) with water content is explained by the change in the symmetry of its environment.
Kinetic and hydrodynamic studies of the complex of proflavine with poly A·poly U
Authors: Schmechel D. E. V. , Crothers D. M.
Published: December 2004

Relaxation kinetic experiments reveal general similarity between the mechanism of binding of proflavine to poly A·poly U and DNA. There are differences in detail, however. For example, the rate constants are roughly an order of magnitude smaller for the former, and the thermodynamic parameters of the individual steps are also different. The total heat and free energy for intercalation of free dye are quite similar in the two cases. As was the case with DNA, considerable dye (up to 25% of the bound form) is attached externally to the double helix, even in the strong binding region of the isotherm. Sedimentation measurements on small, rodlike fragments of poly A·poly U reveal a length increase on binding proflavine of a magnitude similar to that found with DNA. This length increase seems to become smaller under conditions (high temperature) where the relaxation measurements indicate a higher fraction of externally bound dye.
Conformational studies on concentrated solutions of poly(γ‐benzyl L‐glutamate)
Authors: Puett D. , Ciferri A.
Published: December 2004

We have studied the effect of polypeptide concentration on the helix–coil transition of poly(γ‐benzyl L‐glutamate) (PBLG) in both dichloroacetic acid (DCA) and DCA–chloroform (CHF) mixtures. In agreement with other reports, we find the van't Hoff transition enthalpy to be strongly dependent on PBLG concentration. Also, an apparent effect of polypeptide concentration was noted on the transition temperature; however, corrections for finite PBLG concentration on the mole fraction of DCA seem to remove this effect. In order to explain our data, as well as some calorimetric data in the literature, we consider the transition free energy and enthalpy as a sum of three partial terms. These represent the thermodynamic parameters associated with: (1) conformational changes of the polypeptide, e.g. formation or disruption of intramolecular hydrogen bonds; (2) binding by the strong acid to the nonhelical segments of the polypeptide; (3) an overall (weak) interaction of the polypeptide with the nonbound solvent giving rise to dilution parameters that are dependent on the polypeptide conformation. The latter effect is generally ignored, since it is assumed that solvent interactions, other than specific binding, are similar for both the helical and the nonhelical conformation. Striking effects of water (small amounts) and solution aging on the formation of PBLG helices was observed. Water, as expected, acts as a helicogenic solvent when combined with DCA. The processes occurring during solution aging are not known, although the net effect is to stabilize the helical conformation. Finally, we present some rather unique thermally induced transitions of concentrated PBLG (about 200 mg/ml) in DCA. At low temperatures the soluble randomly coiled conformation is present. Heating produces first an isotropic gel, followed at higher temperatures by an isotropic solution consisting of about 70% α‐helicity.
Binding of alcohols to the peptide CO group of poly‐L‐proline in the I and II conformation. II. Binding constants from infrared measurements in solution
Authors: Strassmair H. , Engel J. , Knof S.
Published: December 2004

Trifluoroethanol, benzyl alcohol, and n‐butanol bind to the peptide and acelyl CO groups of poly‐O‐acetyl‐L‐hydroxyproline in dichloromethane via hydrogen bonds. The binding aflinity decreases from trifhioroelhanol to n‐buitanol. For the acelyl CO groups the binding does not depend on the conformation of the polymer but for the peptide CO groups the binding constants are larger by a factor of two to five time when it is in the helix II conformation (all peptide bonds trans) than when it assumes the helix I conformation (all peptide bonds cis). This preference is explained by the higher accessibility of the peptide CO groups in the II helix. The small additional energy which results from the preferential binding is sufficient, to induce a complete I → II transition because of the very high cooperativily of the system. The quantitative dependence of the equilibrium constant s for the propagation step of the transition on solvent composition (ratio of trifluoroethanol or benzyl alcohol to n‐butanol) is derived from the binding data. It agrees satisfactorily with the empirical relation obtained from a best fit to transition curves of Ganseret al. The I ⇌ II conversion of poly‐L‐proline is therefore an example of a conformational transition whose solvent dependence can be explained by a binding mechanism.
The crystal structure of the 2:1 intermolecular complex containing 1‐melhyl‐5‐flourouracil and 9‐ethyl‐2,6‐diaminopurine
Authors: Chandross Ronald , Rich Alexander
Published: December 2004

Two molecules of 1‐methyl‐5‐fluorouracil complex with one molecule of 9‐erthyl‐2, ‐6‐diaminopurine and crystsallize in a triclinic unit cell. The crystal structure was solves by analysis of 3‐dimensional x‐ray diffraction data. Asharpened Patterson map was used to dertermine the structure with apsuedo‐heavy atom technique. The three molecule from a planar hydrogen bonded Watson‐Crick pair with the purine while the other pyrimide forms hydrogen bond to adenine through the imdazole nitrogen. The network is compeleted by purine‐purine hydrogen bond.
Density‐gradient sedimentation equilibrium of DNA and the effective density gradient of several salts
Authors: Schmid Carl W. , Hearst John E.
Published: December 2004

The various treatments of sedimentation equilibrium are compared on a theoretical and an experimental basis. Particular attention is paid to the polyelectrolyte nature of the problem and the choice of a neutral component. The effective density gradients of several cesium salts for DNA are measured. Two previous theories for the effective density gradient are shown to be equivalent, and the experimental values are interpreted with respect to these theories. It is clear t hat sedimentation equilibrium in a density gradient may be used for the determination of unambiguous molecular weights.
Cooperative nonenzymic base recognition II. thermodynamics of the helix‐coil transition of oligoadenylic + oligouridylic acids
Authors: Pörschke Dietmar
Published: December 2004

The properties of oligonucleotide helices of adeuylic‐ and uridylic acid oligomers have been investigated by measurements of hypo‐and hyperchromieity. High ionic strengths favor the formation of triple helices. Thus, the double helix‐coil transition can be studied (without interference by triple helices) only at low ionic‐strength. A “phase diagram” is given representing the Tm‐values of the various transitions at different ionic strengths for the system A(pA)17 + U(pU)17. Oligonucleolides of chain lengths <8 always form both double and triple helices at the nucleotide concentrations required for base pairing. For this reason the double helix‐coil transition without coupling of the triple helix equilibrium can only be measured for chain lengths higher than 7. Melting curves corresponding to this transition have been determined for chain lengths 8, 9, 10, 11, 14 and 18 at different concentrations. An increase in nucleotide concentration leads to an increase in melting temperature. The shorter the chain length the lower the Tm‐value and the broader the helix‐coil transition. The experimental transition curves have been analysed according to a staggering zipper model with consideration of the stacking of the adeuylic acid single strands and the electrostatic repulsion of tlip phosphate charges on opposite strands. The temperature dependence of the nucleation parameter has been accounted for by a slacking factor x. The stacking factor expresses the magnitude of the stacking enthalpy. By curve fitting xwas computed to be 0.7, corresponding to a stacking enthalpy of about S kcal/mole. The model described allows the reproduction of the experimental transition curves with relatively high accuracy. In an appendix the thermodynamic parameters of the stacking equilibrium of poly A and of the helix‐coil equilibria of poly A + poly U at neutral pH are calculated (ΔHA = −7.9 kcal/mole for the poly A stacking and ΔH12 = −10.9 kcal/mole for the formation of the double helix from the randomly coiled single strands). A formula for the configurational entropy of polymers derived by Flory on the basis of a liquid lattice model is adapted to calculate the stacking entropies of adenylic oligomers.
Investigations on spectra and orientation of dipole moments of uracil and thymine by electrochromism
Authors: Seibold K. , Labhart H.
Published: December 2004

The direction of the ground stale dipole moment with respect to the transition moment to the lowest excited singlet state as well as the dipole moment in this excited state could be determined from the influence of an electric field on the light absorption of uracil and thymine in solution. By making use of results on the orientation of the transition moment in the molecular framework, the orientation of the ground‐and excited‐state dipole moments can also be fixed and compared with theoretical predictions. The agreement is fair. The measurements show that in both compounds a weak band is hidden under the longest‐wavelength absorption band.
Kinetics of sedimentation in a density gradient
Authors: Dishon Menachem , Weiss George H. , Yphantis David A.
Published: December 2004

Two models of sedimentation in a density gradient are analyzed. The first is for sedimentation in cylindrical sector geometry and contains the assumption that diffusion can be neglected. The second treats sedimentation in a rectangular field and includes diffusion, although the boundaries are not treated exactly. In both of these models we approximate the time dependence of the gradient by a relaxation form. We derive exact results for both models. It is also shown that the sedimentation coefficient can be calculated from data by following the motion of the position of the maximum (or minimum) of the concentration gradient.
Variation of the NH–CαH coupling constant with dihedral angle in the NMR spectra of peptides
Authors: Ramachandran G. N. , Chandrasekaran R. , Kopple Kenneth D.
Published: December 2004

Proton magnetic resonance data and conformational calculations of a series of model compounds containing a NH‐CαH group substituted as in peptides have been used to generate a proton–proton coupling constant–dihedral angle relation for the peptide unit. For those substances used in which the dihedral angle about the N‐Cα bond is not fixed, the angle distribution was calculated from conformational theory. Using eight examples in which the number of theoretical assumptions were least, the best values of the coefficients A, B, and C in the expression J(θ) = Acos2θ + B cosθ + Csin2θ were found by a least‐squares procedure to be 7.9, −1.55, and 1.35, respectively. This relation gives reasonable values for the dihedral angles ϕ in cyclic oligopeptide structures for which the availability of both NMR data and other structural information allow comparison. When applied to N‐acetylamino acid N‐methylamides having side chains extending beyond Cβ, however, agreement with the calculated conformational distribution was found for Leu, Met, and Trp, but observed values of J were larger than expected for Val, He, Phe, and Tyr, These disagreements are considered to be the result of interactions not yet taken into account in the usual conformational calculations.
Spectroscopic study of the self‐association of myosin
Authors: Herbert Thomas J. , Carlson Francis D.
Published: December 2004

Homodyne and heterodyne measurements have been made of the spectrum and intensity of laser light scattered from solutions of skeletal muscle myosin at high salt concentrations. The spectral broadening and intensity measurements are consistent with the hypothesis that a myosin monomer‐dimer equilibrium exists in these solutions. Values have been calculated for molecular weight and radius of gyration of the myosin monomer, virial coefficients, and diffusion constants of both monomer and dimer, and equilibrium constant of the reaction to form dimer. Diffusion constant measurements yield an approximate length of 1481 Å for the monomer and 2121 Å for the dimer. The significance of these lengths is discussed in terms of the models of Huxley and Pepe for the structure of the myofilament.
β‐carbonylamides in peptide chemistry. II. Ultraviolet absorption and circular dichroic properties of azlactones derived from N‐acetoacetyl amino acids
Authors: Di Bello Carlo , Filira Fernando , Toniolo Claudio
Published: December 2004

Ultraviolet absorption and circular dichroism spectra of azlactones derived from N‐acetoacetyl amino acids are examined. A number of model compounds of the isomeric forms possibly present in the equilibrium mixtures of these azlactones have also been prepared and their spectral properties compared. The reported data permit, structural and stereochemical assignments on these amide compounds.
“Renaturation” des solutions cuivriques de DNA. I. Analyse phenomenologique
Authors: Richard H. , Pacault A.
Published: December 2004

A study of the kinetics of renaturation of cupric DNA solutions has been carried out by two physical properties methods. The use of a purely phenomenological analysis leads nevertheless to interesting conclusions concerning the transformation mechanism. We have found that: in the presence of Cu++ ions, different. DNA samples exhibit an equivalent kinetic behavior; the system can be decomposed into two parts: DNA and copper ions, and the rate of formation of DNA should be faster than that of copper ions; the mechanism of transformation may be bimolecular, but further investigation is necessary to confirm this.
A non‐perturbation method for the optical properties of helical polymers
Authors: Loxsom F. M. , Tterlikkis L. , Rhodes William
Published: December 2004

The optical absorption and circular dichroism (CD) of poly‐L‐alanine in an α‐helical conformation are computed in terms of monomer properties by use of Bogoliubov exciton theory (a non‐perturbation method). It was shown earlier that a proper formulation of the theory of CD for large molecular systems permits the use of periodic boundary conditions, a feature which greatly simplifies calculations as well as conceptual understanding. If is found that the shape of the observed CD spectrum can be explained in terms of the two rotational strength components and an electric dipole strength component referred to as the helix term. Comparisons of the results of perturbation theory and Bogoliubov exciton theory show that perturbation theory is valid for absorption but is inadequate for CD if the coupling among monomers is sufficiently large lo predict the observed hypochromism.
The effect of adjacent charges on the kinetics of rotation of the peptide bond
Authors: Gerig J. T.
Published: December 2004

The kinetics of rotation of the peptide (amide) bond in dimethylacetamide, glycine dimethylamide, N‐acetylsarcosine, and glycylsarcosine have been studied in basic, neutral, and acidic aqueous solutions by proton magnetic resonance spectroscopy. The data indicate that the presence of nearby negative or positive charges do not greatly perturb the energetics of conformational equilibration about the amide carbon‐nitrogen bond. In N‐acetylsarcosine and glycylsarcosine two distinguishabe conformers are present; their relative abundance is essentially 50%/50% except at low pH. It is suggested that intramolecular hydrogen bonding is responsible for deviations from this population ratio. The activation enthalpies (ΔH‡) for rotation appear to be linearly related to the corresponding activation entropies (ΔS‡) leading to an isokinetic temperature of about 400°K.
Light scattering and hydrodynamic properties of linear and circular bacteriophage lambda DNA
Authors: Dawson J. R. , Harpst J. A.
Published: December 2004

Low‐angle light scattering, sedimentation velocity, and intrinsic viscosity measurements have been made on circular and linear forms of lambda (λ) bacteriophage DNA. Available equations, used to relate hydrodynamic parameters of both forms to the molecular weight, give relatively consistent values of particle weights which essentially agree with the light‐scattering results. An average molecular weight of (34 ± 3) × 106 for λ DNA was obtained in good agreement with literature values of (31–33) × 106. The linear λ DNA has a larger root‐mean‐square radius than the circular molecule, when determined by light scattering, but the difference does not appear to be us large as expected from hydrodynamic data. The two forms also show significantly different angular distrbutions of scattered light intensities which agree only qualitatively with those derived from existing theory. The light‐scattering results suggest that further experiments and modifications of available theories should be undertaken.
Poly(γ‐p‐nitrobenzyl‐L‐glulainate): synthetic aspects, sedimentation, and viscosity studies
Authors: Feyen J. , De Groot K. , De Visser A. C. , Bantjes A.
Published: December 2004

A series of poly(γ‐p‐nitrobenzyl‐L‐glutamates), PNBG, has been synthesized by the polymerization of N‐carboxyanhydride (NCA) derivatives of γ‐p‐nitrobenzyl‐L‐glutamate, NBG, using triethylamine as an initiator. We studied the influence of (a) the solvents dioxane, nitrobenzene, dimethylformamide (DMF), and DMF–1,2‐dichloroethane mixture and (b) the anhydride–initiator ratio (A/I) for the polymerization in nitrobenzene (A/I varying from 50 to 750) on the properties of the polymers obtained. In order to improve its synthesis, NBG, was prepared by three different methods. Ten samples of PNBG, ranging in Mw from 10,000 to 50,000, were examined viscometrically in DMF and dichloroacetic acid (DCA) and by ultracentrifugation in DMF. The data for [η] and So (limiting sedimentation coefficient) as functions of Mw for PNBG in DMF were utilized, applying theories of Kuhn and Kuhn,13 Schachman,14 and Perrin, 15 for the estimation of the length per monomeric residue h. Viscosity data gave a h value of about 2.3 Å, Whereas sedimentation yielded 1.5 Å. Treating viscosity and sedimentation data for poly(γ‐benzyl‐L‐glutamate), PBLG, in the same way leads to somewhat higher hvalues (2.4 Å and 1.7 Å, respectively).

Although a nitroaromatic effect was shown to be absent for PNBG in DMF, it can be concluded that in this medium PNBG has a somewhat more compact structure than PBLG.