bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of DNA base compositions from melting profiles in dilute buffers
Authors: Owen R. J. , Hill L. R. , Lapage S. P.
Published: May 2005

Equations were determined for the dependency of the melting temperature (Tm) of DNA upon the logarithm of the sodium ion concentration, for four DNA samples of widely different base compositions (θGC). The slopes of these Tm versus log M equations wore found to decrease with increasing θG Cof the samples. An empirical equation relating Tm, log M (Na+) and θG C was derived, which also accounts for differences in Tm versus log M slopes. Data from the literature for some synthetic polynucleotides and for the crab(Cancer pagarus) satellite poly AT are discussed in relation to the above finding. The changes in Tm versus log M slopes with θG C are interpreted in terms of changes in the thermodynamic parameters ΔS and ΔH with base composition.
Conformational studies on a modified poly‐L‐tryptophan: Circular dichroism and optical rotatory dispersion of poly‐2‐(2‐nitrophenylsulfenyl)‐L‐tryptophan and of random copolymers of L‐tryptophan and 2‐(2‐nitrophenylsulfenyl)‐L‐tryptophan
Authors: Peggion Evaristo , Fontana Angelo , Cosani Alessandro
Published: May 2005

Optical rotatory dispersion (ORD) and circular dichroism (CD) measurements were carried out on a block copolymer, (γ‐ethyl DL‐glutamate)160 (L‐Trp)32, in which the tryptophan sequence has been modified to various extents by using 2‐nitrophenylsulfenyl chloride. The CD spectrum of the completely modified copolymer exhibits bands in some of the regions of maximum absorption of the sidechain chromophores. In the peptide absorption region the spectrum is similar to that reported in the literature for polypeptides in the α‐helical conformation. When the extent of modification of the tryptophan sequence is progressively reduced, there is a gradual change in the ORD spectra of the copolymers. On the basis of these data the assumption was made that no conformational change occurs on proceeding from the pure unmodified tryptophan sequence to the completely modified sequence. The results are discussed in connection with the study of possible conformational effects arising from selective chemical modification of tryptophan residues in proteins.
Optical rotation of some α‐1,4‐linked glucopyranosides in the system H2O–DMSO and solution conformation of amylose
Authors: Dintzis F. R. , Tobin R.
Published: May 2005

The specific rotation of starch components, corrected for refractive index variation, exhibits a discontinuity in the region of the water–dimethyl sulfoxide (H2O–DMSO) system that corresponds to the composition of the complex 2H2O–DMSO. This discontinuity is a property dependent upon the presence of a number of consecutively linked α‐1,4 glucose units and, therefore, must reflect a change in symmetry of a segment, of polymer chain. The optical rotation of amylose between 26.5 and 92.5°C. does not change in DMSO and is only slightly lowered in water at the higher temperature. The behavior of amylose in both DMSO and H2O is like that of a random coil, as indicated by viscosity and sedimentation measurements. These results may be interpreted either as being compatible with models of amylose in solution in which the polymer backbone has helical twist, or as indicating removal of strong interactions between polymer chain segments by a good solvent.
Matching of single‐strand breaks to form double‐strand breaks in DNA
Authors: Freifelder David , Trumbo Bruce
Published: May 2005

Single‐strand breaks (ssb) in opposite strands of DNA can be sufficiently near that a double‐strand break (dsb) results. A theory is presented by which the maximum number h of base pairs which cannot prevent double‐strand breakage can be determined from the rates of production of ssb and dsb. The assumptions required to derive the necessary equations as well as the range of validity of the equations are discussed in detail. In the experiments ssb and dsb were produced by x‐irradiation in buffers which do not eliminate indirect effects and were measured by analytical ultracentrifugation. Values of h have been determined in low and high ionic strength and in low ionic strength over a range of temperatures. The values, 2.64 and 15.8, were obtained for high and low ionic strength, respectively.
Helix sense of poly‐γ‐p‐chlorobenzyl L‐glutamate
Authors: Erenrich Eric H. , Andreatta Rudolph H. , Scheraga Harold A.
Published: May 2005

Poly(γ‐p‐chlorobenzyl L‐glulamate), for which theoretical calculations have shown only a small difference in energy between the left‐ and right‐handed α‐helices, has been synthesized and its screw sense determined by ORD in various solvents. In all solvents studied, a right‐handed α‐helix has been observed.
The Lifson‐Allegra theories of the helix–coil transition for random copolymers: Comparison with exact results and extension
Authors: Poland Douglas , Scheraga Harold A.
Published: May 2005

The theories of the helix–coil transition of Lifson, Lifson and Allegra, and Allegra for random copolymers are compared with the exact results of Lehman and McTague, as was done by Fink and Crothers in an earlier test of the approximate theories of Fixman and Zeroka, Reiss et al, and Montroll and Goel. The Fixman‐Zeroka theory is the best approximation to the exact result (under the conditions used), and the Allegra theory is next best, the calculated slope of the transition curve in the Allegra theory being too small by a factor of two. An alternative derivation of the Allegra approximation, using the method of sequence generating functions, is given, and the resulting equations are of very simple form. A hybrid method, based on the work of Lifson and Allegra, is also developed here; it involves a technique of successive approximations, and reduces to the Allegra theory in first order. The fourth‐order approximation gives a slope that is too small by 10%; however, the value of the slope, extrapolated to infinite order of approximation, converges to the exact result‐ of Lehman and Mc‐Tague. By using illustrative calculations of helix–coil transition curves, some physical insight into the behavior of a copolymer in the transition region is provided: it is found that an important feature determining the shape of the transition curve is the variation in composition over the correlation length. The question of the application of copolymer theory to DNA is discussed.
Optical anisotropy of synthetic polynucleotides. II. Calculation of π‐electron polarizability of uracil and adenine
Authors: Takashima Shiro
Published: May 2005

The π‐electron polarizability of conjugated base molecules such as uracil and adenine are calculated semiempirically by using molecular orbital theories. The Hüekel method and the self‐consistent‐field (SCF) theory are used in the present calculation. The theoretical values obtained by the Hüekel method are consistently larger than the experimental results. The values obtained by the SCF theory are in good agreement with observed values. It is clearly demonstrated that the SCF method is better than the Hükel method for the calculation of polarizability. The polarizability of the adenine–uracil pair is calculated as the sum of the polarizabilities of adenine and uracil and also calculated by solving the eigenvalue problem for the A–U pair as an entity. The second method gives considerably larger polarizability than the first method. Discussions are presented and it is demonstrated that the second method is the correct way to calculate the polarizability of the A–U pair.
Binding of alcohols to the peptide CO‐group of poly‐L‐proline in the I and II conformation. I. Demonstration of the binding by infrared spectroscopy and optical rotatory dispersion
Authors: Strassmair H. , Engel J. , Zundel G.
Published: May 2005

The binding of n‐butanol, benzyl alcohol, and trifluoroethanol to polyproline I (all peptide bonds in cis configuration) and II (all peptide bonds in trans configuration) has been demonstrated. It was found by infrared spectroscopy that hydrogen bonds are formed between the CO groups of the polymer and the OH groups of the alcohols. Their strength increases from n‐butanol via benzyl alcohol to trifluoroethanol. The binding of benzyl alcohol could also be followed by optical rotatory dispersion due to the fact that the electronic transitions of the benzyl ring are rendered optically active by the binding to the polymer.
Deformation behavior of erythrocyte ghost
Authors: Blais J. J. B. P. , Geil P. H.
Published: May 2005

Biological membranes consist mainly of lipids and proteins. At present, the structure of the lipid phase appears to be established, but hypotheses on the molecular organization of the protein are difficult to support. Thus the deformation behavior of whole human erythrocyte ghosts, ghosts after the selective removal of lipids and ghosts stripped of lipids as well as nonlipid components have been examined in the hope of securing indirect information on the organization of the protein. It has been found that large localized deformations result in partial membrane failure and long uniformly wide fibrils, frequently in excess of 3000 Å, are drawn across the rupture. These data are interpreted in terms of currently favored membrane models and the possibility of a fibrous membrane framework consisting predominantly of protein is reviewed. The behavior of the membrane in its various stages of extraction is compared and contrasted to that of synthetic polymer films of known organization.
Effect of pressure on the temperature‐dependent association of β‐casein
Authors: Payens T. A. J. , Heremans K.
Published: May 2005

The effect of pressure on the temperature‐dependent association of β‐casein was studied by the method of light scattering. Between 1 and 1500 kg/cm2, β‐casein is reversibly depolymerized, indicating an increase in partial specific volume of the protein with association. Possible mechanisms for association are discussed. At still higher pressures reversible reassociation is observed, which is ascribed to conformational changes in the β‐casein molecule.
Optical anisotropy of oriented deoxyribonucleic acid films of different water content
Authors: Wetzel H. , Zirwer D. , Becker M.
Published: May 2005

Ultraviolet absorption and dichroism measurements on oriented films of calf thymus deoxyribonucleic acid (DNA) at varying degrees of hydration show a structural hysteresis which occurs within a relative humidity of 0 to 65% RH. This hysteresis is interpreted on the basis of a model which assumes the existence of structure‐stabilizing hydrogen water bridges in the DNA double helix.
Solution properties of synthetic polypeptides. V. Helix–coil transition in poly(β‐benzyl L‐aspartate)
Authors: Hayashi Yoshihisa , Teramoto Akio , Kawahara Kazuo , Fujita Hiroshi
Published: May 2005

Simple approximate expressions have been derived from the theory of Zimm and Bragg for use in the analysis of experimental data on the helix‐coil transition in polypeptide. On the basis of the resulting expressions practical procedures are proposed to determine two basic parameters characterizing a thermally induced transition, i.e., helix initiation parameter σ and enthalpy change for helix formation, ΔH. They have been applied to the data for poly(β‐benzyl L‐aspartate) (PBLA) with the result: σ = 1.6 × 10−4 and ΔH = −450 cal/mole for PBLA in m‐cresol; σ = 0.6 × 10−4 and ΔH = 260 cal/mole for PBLA in chloroform containing 5.7 vol‐% of dichloroacetic acid. This result gives evidence that σ may change not only from one polypeptide to another but also for a given polypeptide in different solvents. The change in limiting viscosity number [η] accompanying the transition was measured in the same solvents. The curve of [η] versus helical content had a relatively monotonic shape for the chloroformdichloroacetic acid solutions as compared with that for the m‐cresol solutions, indicating that [η] depended largely on σ. Provided that [η] is a direct measure of the mean‐square radius of gyration, 〈S2〉, the results are consistent with the theoretical predictions of Nagai and of Miller and Flory for 〈S2〉.
Changement de structure de la poly‐L‐proline à l'état solide par hydratation: Etude par spectrométrie infra‐rouge
Authors: De Lozé C. , Josien M. L.
Published: May 2005

Films of poly‐L‐proline I and II have been hy drated by water vapor and their infrared spectra analysed between 1250 and 3500 cm−1. Forms I and II behave differently. Water binds to the carbonyl of form II through hydrogen bridges and, when released by drying, leaves the polypeptide conformation unchanged. In form I, complex formation with water seems to proceed through a different mechanism involving more than the carbonyls. Hydration of form I yields a partial irreversible transition to form II. Successive hydration and drying of the film brings the transition to completion. This I → II transition in the solid state has a cooperative character; its mechanism is discussed. Poly‐L‐prolines I and II also absorb vapors of aliphatic alcohols but not change in conformation is observed.
Stereochemistry of nucleic acids and polynucleotides. IV. Conformational energy of base‐sugar units
Authors: Lakshminarayanan A. V. , Sasisekharan V.
Published: May 2005

In this paper, the preferred conformations of the bases with respect to the sugar in various base‐sugar units are worked out using criteria of potential energy. The van der Waals type of intercations between nonbonded atoms is represented by a 6‐12 function and the electrostatic interactions have been calculated in the monopole approximation using Coulomb's law. The torsional contributions to the total energy have been neglected. It is found that in general the pyrimidines have preferred anti contributions (as described by Donohue and Trueblood) and purines have both syn and anti and conformations. Certain differences between differently puckered riboses in regard to the above general tendency are discussed. The conclusions, in general, conform with the results obtained by us earlier with the use of hard‐sphere potential and are also supported by observations on conformations of nucleotides and nucleotides in crystal structure.
Acoustical properties of aqueous solutions of oxygenated and deoxgenated hemoglobin
Authors: Schneider F. , Müller‐Landau F. , Mayer A.
Published: May 2005

The acoustical relaxation spectrum of aqueous solutions of oxygenated and deoxygenated hemoglobin solutions was investigated in the frequency range 0.5–1000 MHz. The abrupt high frequency cut off of the broad absorption spectrum is consistent with a heavily weighted, shortest relaxation time of 2 × 10−9 sec. Both the high‐frequency cut‐off and high frequency residual absorption appear to be slightly different for oxygenated and deoxygenated hemoglobin solution.
Spectroscopic properties of oligonucleotides excised from the anticodon region of phenylalanine tRNA from yeast
Authors: Maelicke Alfred , Haar Friedrich Von Der , Cramer Friedrich
Published: May 2005

Ultraviolet absorption and static fluorescence properties of hexanucleotide (Gm‐A‐A‐Y‐A‐ψp) and a dodecanucleotide (A‐Cm‐U‐Gm‐A‐A‐Y‐A‐ψ‐m5C‐U‐Gp) excised from the anticodon region of phenylalanine tRNA from yeast have been studied with respect to temperature, pH, ionic strength, and Mg2+ concentration. At low temperature these oligomers have a largely stacked structure. Only the melting data of the dodecanucleotide in absence of Mg2+ fit a two‐state model. From the different melting behavior of the oligonucleotides after excision of base Y, a rodlike structure of the hexanucleotide produced by stacking interactions can be concluded. The Y fluorescence increase produced by Mg2+ has been used to evaluate the binding equilibria between Mg2+ and the oligonucleotides. One strong binding site per oligonucleotide and a greater number of weak binding sites have been found. The fluorescence of the free base Y is not influenced by Mg2+. The dodecanucleotide enhances the ethidium fluorescence to the same extent as tRNAPhe and produces comparable shifts in the excitation and emission spectra. Therefore a double helical structure for this oligomer under the assay conditions is suggested. Only weak binding of ethidium to the hexanucleotide is observed, indicating that intercalation of the dye into its structure is not favored. The data show the decisive role of the nucleobase Y in maintaining a rigid stacked structure of the anticodon nucleotides. This structure is stabilized by high ionic strength, Mg2+, and ethidium.
Conformational analysis of an ionizable polydipeptide
Authors: Hiltner W. A. , Hopfinger A. J. , Walton A. G.
Published: May 2005

A semi‐empirical conformational energy calculation has been performed on the ionizable polydipeptide poly(Glu‐Ala). The results indicate that; (1)the ionized polymer assumes the lefthanded extended helix conformation is aqueous solution; (2) the poly(Glu‐Ala) extended helix is less stable than that of polyglutamic acid; (3) the unionized polydipeptide will preferentially assume the “β‐helical” conformation (isolated 21 degenerate helix) in aqueous solution. These conclusions are supported by experiment.
Effect of degree of polymerization and steric configuration of poly(2‐vinylpyridine) as catalyst in the polymerization of phenylalanine NCA
Authors: Imanishi Yukio , Nagaoka Shoji , Suzuoki Kazuhiro , Higashimura Toshinobu
Published: May 2005

Despite its being weaker base poly(2‐vinylpyridine) polymerized DL‐β‐phenylalanine NCA at a much faster rate than pyridine and α‐picoline. Poly(2‐vinylpyridine) adsorbs NCA by hydrogen bonding with the cooperation of a few pyridine groups. This results in a high local concentration of NCA. The syndiotactic configuration of pyridine group seemed to be least suitable for the cooperative hydrogen bonding. Adsorbed NCA is activated to form an “activated” NCA which in turn reacts with an NCA adsorbed on the same polymer chain. Since the polymer chain is flexible, this intramolecular reaction takes place frequently, resulting in the acceleration of polymerization. The intramolecular reaction along the polymer chain is dependent on the degree of polymerization of polymer catalyst. A suitable model was proposed for the intramolecular reaction to explain the effect of degree of polymerization.
The conformational characteristics in solution of the synthetic cyclic hexapeptide
Authors: Tonelli Alan E. , Brewster A. I. Richard
Published: May 2005

An attempt to elucidate the solution conformation(s) of the synthetic cyclic hexapeptide 5L‐ala·D‐ala is described. Nuclear magnetic resonance (nmr) spectra are recorded for the purpose of measuring the vicinal coupling constant between the amide and α‐protons in each residue and to observe the deuterium exchange rate and temperature dependence of the chemical shift of each amide proton. Low‐energy cyclic conformations, whose individual residues are in conformations consistent with the observed amide to α‐proton coupling constant, are searched for in an approximate theoretical treatment. The two lowest energy, all trans peptide bond conformations generated are distinguishable by the presence or absence of a single intramolecular hydrogen bond. The observed temperature independence of the chemical shift of one of the amide protons is consistent with the presence of a single intramolecular hydrogen bond, while the observation of similar deuterium exchange rates for each of the amide protons indicates their comparable availability to solvent. Consequently, it is concluded that 5L‐ala·D‐ala is in rapid equilibrium between conformations with and without a single internal hydrogen bond and possesses considerable conformational flexibility in solution.
Origins of the differences between the circular dichroism of DNA and RNA: Theoretical calculations
Authors: Moore Dexter S. , Wagner Thomas E.
Published: May 2005

Theoretical calculations of the circular dichroism of double‐helical DNA and RNA by the method of Johnson and Tinoco were performed in order to investigate the origins of the optical activity spectral differences between these polynucleotides. Calculations were performed using transition moment directions arising from molecular orbital calculations as well as a transition moment directions in agreement with experimental directions. The results of these calculations indicate that the conservative circular dichroism spectrum of B‐form DNA and the nonconservative spectrum of RNA (and A‐form DNA) arise as a consequence of the distance between the paired bases and the helix axis. The negative nonconservative spectrum of C‐form DNA was calculated and shown also to result from the distance of the paired bases from the helix axis. Several other conspicuous geometric parameters of DNA and RNA were investigated and were found to be less significant in their effects upon the spectral differences. Theoretical calculations on a four‐stranded DNA model which has paired bases similarly related to the helix axis as RNA and A‐form DNA was found to yield a low intensity, nonconservative circular dichroism spectrum.
Etude Potentiométrique de l'α‐Poly(acide‐L‐glutamique) et de ses Oligomères. II
Authors: Rinaudo M. , Domard A.
Published: May 2005

Potentiometric neutralization of oligomers represented by the general formula shown was studied.
magnified image
The intrinsic pK of carboxyl function was found to be 4.40 at 25°C; the variation of the apparent pKa, ΔK(α), was studied as a function of the degree of neutralization: the influence of the degree of neutralization on the accumulation of ionic sites along the chain is clearly shown.

The experimental curves of polyglutamic acid allowed us to deduce the sequence of ionic selectivity and the energy of conformational transition. The theoretical interpretation of the results was proposed in terms of the rod like model from Katchalsky's theory. The intrinsic pKo for the polymer was set equal to the value experimentally obtained on oligomers. By activity measurements on Na+ and Ca2+ counterions in salt‐free solutions, the free fraction of counterions was deduced on the different samples. The results were interpreted with the electrostatic model previously proposed; in this view, the oligomers are assimilated to imaginary polyelectrolytes. This allowed us to determine the values of ΔpK and the fraction of free ions at the same time.
Cooperative and thermodynamic parameters for oligoinosinate—polycytidylate complexes
Authors: Springgate M. W. , Poland Douglas
Published: May 2005

The cooperative nature of the binding between polycytidylate and the oligoinosinates I(pI)5–10 has been determined. Using the data of Tazawa, Tazawa, and Ts'o, it is shown that knowledge of the slope of the adsorption isothern allows one to determine the oligomer‐polymer binidng constant, the oligomer–oligomer interaction constant, and the average degree of association (cooperative clustering) of the oligomers on the polymer. Knowledge of the above equilibrium constants as a function of temperature yields the respective thermodynamic parameters; no assumptions need to be made about the nature of the equilibrium constants or the thermodynamic parameters. For very long chains of polycytidylate, simple, explicit relations are given for the determination of the equilibrium constants involved. For finite chains of polycytidylate, the calculation of a single graph for each oligomer and polymer size allows the equilibrium constants to be determined for all experimental conditions of temperature and concentration. We find that the enthalpy and entropy of binding an oligomer n, bases to be δHn = ±13.7 − n(6.65) and δSn = +32.5 − n(18.8) given, respectively, in kcal/mole and e.u.; these parameters predict a melting temperature of 81°C for the poly(I)·poly(C) complex compared with the experimental value of 75°C. If the enthalpy is interpreted as arising from a sum of hydrogen bonding and stacking interactions, then the enthalpy of stacking is −13.7 kcal/mole while the enthalpy of hydrogen bonding is +7 ± 4 kcal/mole; the positive enthalpy of hydrogen bonding presumably is a result of the fact that in the inosine‐cytosine base pair, only two of the three sites on cytosine can hydrogen bond, the third being blocked from hydrogen bonding with water. The enthalpy of interaction between neighboring bound oligomers is found to be −10.4 kcal/mole while the corresponding entropy is −26.1 e.u. The binding is bound to be cooperative, though the extent of clustering varies markedly with temperature; the average number of oligomers in a cluster on the polymer is found to about five at a melting temperature of 25°C. The approach and equations given have generally applicability to oligomer‐polymer associations.
Conformational studies on pyrimidine 5′‐monophosphates and 3′,5′‐diphosphates. Effect of the phosphate groups on the backbone conformation of polynucleotides
Authors: Yathindra N. , Sundaralingam M.
Published: May 2005

In continuation of our studies on the effect of the base and the phosphate groups on the glycosyl and the sugar‐phosphate backbone conformation, we have carried out semi‐empirical potential energy calculations on the common 5′‐ and 3′5′‐ribopyrimidine mono‐ and diphosphates by considering simultaneous rotations about the glycosyl (χ) and the C(4′)–C(5′) (ψ) bonds. This calculation provides an assessment of the nature and orientation of the base on the sugar–phosphate backbone conformation of nucleotides and polynucleotides. It is found that the attractive inetractions between the 5′‐phosphate group and the base mutually stabilize the antiand the gauche‐gauche (gg) conformations about χ and ψ, respectively, in 5′‐ribopyrimidine nucleotides. The introduction of the 3′‐phosphate group as in 3′,5′‐ribopyrimidine diphosphates, still leaves the anti‐gg as the most favored conformation with the important difference that the probability of occurrence of the anti, gauche‐trans (gt) is how substantially increased. This is dependent to a large extent on the sugar conformation and to a lesser extent on the base. Uracil and thymine show a greater probability for the anti‐gt than cytosine. The syn conformation is considerably less likely and its occurrence is also dependent on the base type, cytosine showing a lesser tendency than uracil and thymine. For the syn base, the most favourec conformation for ψ is gt, since gg is sterically disallowed and tg is destabilized by electrostatic repulsive interactions between the 3′ and 5′‐phosphate groups. Thus, there is a striking correlation between the glycoysl and the backbone C(4′)–C(5′) bond conformations. The rest of the bonds of the backbone are considerable less dependent on the glycosyl conformation. These studies reveal that in poly‐ribopyrimidine nucletides the majority of the nucleotide residues are expected to occur in the anti‐gg conformation.
Influence of isopropanol‐water solvent mixtures on the conformation of poly‐L‐lysine
Authors: Barteri M. , Pispisa B.
Published: May 2005

The helix–coil transition of poly‐L‐lysine (PLL) in water–isopropanol solvent mixtures has been investigated at room temperature by circular dichroism measurements. Within the range of 70%–80% isopropanol concentration (by volume), the polymer undergoes a sharp transition, characterized by the formation of a fully charged α‐helical structure. On the basis of some experimental evidence the role of the organic component in solution appears more complicated than that of strengthening the intramolecular hydrogen bonds in the polymer. By analogy with the distribution of the components of alcohol–water mixtures in simple ionic systems, it is thought that only an high co‐solvent concentration brings about an extensive and possible cooperative depletion of the clusters of firmly‐bound water molecules in the domain of the polylelectrolyte, favoring the transition to the α‐helical structure. On the other hand, CD spectral patterns show that the addition of NaCl in the alcohol‐rich–water mixtures of charged poly‐L‐lysine gives rise to a transition from the α‐helical to a β‐structures conversion obeys a first‐order rate law at all times, with a rate constant dependent on solvent composition and ionic strength. In these conditions, the rate of the process is close to that found for the thermally induced α–β transition. Higher polymer concentration and/or ionic strength cause a phase separation of β‐PLL, suggesting that in this case interchain reactions (where hydrogen bonding should play the major role) predominate. Titration experiments on charged α‐helical poly‐L‐lysine in 85% or 90% isopropanol mixtures confirm the occurrence of a conformational transition, which takes place within a degree of dissociation α of 0.2–0.75. The transition is accompanied by a visible turbidity, which increases as the titration proceeds. Implications of the solvent distribution around the macroion on the observed conformational phenomena are also discussed.
The effect of polydispersity on the nuclear magnetic resonancxce spectra of ply‐Y‐benzyl‐L‐glutamate
Authors: Milstien Julie B. , Ferretti James A.
Published: May 2005

The effect of poly dispersity on the nuclear magnetic resonance spectra of samples of poly‐γ‐benzyl‐L‐glutamateein the helix–random coil transition is studied. In the transitionregion the α‐CH proton resonance shows two peaks whose behavior does not change appreciably upon fractionation by gel permeation chromatography. Theoretical spectra were computed with both a polydispersity model of the transition and a model for slow nucleationof helix from completely random coil molecules. The results suggest that the double peak behavior in the nmr spectra results from a slow rate of helix nucleation rather than polydispersity.
Optical activity of simple peptides. I. Glycine oligopeptides with internal L‐alanyl or ‐L‐glutamyl residues
Authors: Lord Richard S. , Cox David J.
Published: May 2005

Oligopeptides containing glycine and one or two L‐alanyl or L‐glutamyl residues have been studied by circular dichroism (CD) and optical rotatory dispersion (ORD) in aqueous solution at pH 1.0, pH 6.0, and pH 10.0 and in aqueous ethanol. Two glycyl residues are required to remove effects of α‐carboxyl or amino titration on the optical activity of the internal alanyl or glutamyl residues. The CD spectra of the alanyl and protonated glutamyl residues are similar, having two regions of negative ellipticity around 215 nm resulting in a spectrum reassembling that of poly‐α‐L‐glutamic acid (PGA) at high pH. Another large positive band below 190 nm was observed for gly2‐glu2‐gly2 in water at pH 6 and 10 and for several peptides in aqueous ethanol. Residue ellipticities were approximately additive in every case except for peptides containing intrenal glutamyl residu at pH 6.0.
Induced optical activity in poly‐L‐lysine–methyl orange system
Authors: Hatano M. , Yoneyama M. , Sato Y. , Kawamura Y.
Published: May 2005

The absorption and cicular dichroism spectra of the complex of poly‐L‐lysine (PLL) in the random coil form with methyl orange (MO) have been measured in aqueous solution. A new absorption band is observed at the shorter wavelength compared with that of the free dye. Although MO does not show a formation of dimer or aggregation with an increase in concentration, circular dichroism bands are observed at the wavelength corresponding to the wavelength of the new absorption band. These induced circular dichroism bands may arise from the dimeric MO molecules bound to PLL in the random coil form. The main contribution to the interaction between MO molecules is shown to be the electro static interaction. The observed circular dichroism spectra and the configuration of dimeric MO molecules bound to PLL can be explained by the dipole couping mechanism.
On the electric polarization of DNA
Authors: Goswami D. N. , Gupta N. N. Das
Published: May 2005

Dielectric dispersion of DNA was studied in the frequency range 100 Hz–100 kHz at four different temperatures (6–30°C). The dielectric increment ε0–ε∞ increased with the rise of temperature. The relaxation time, on the other hand, decreased. Both the increase in dielectric increment and the decrease in relaxation time could not be explained on the basis of the counterion polarization theory. Dipole moment was estimated from Kirkwood theory. It was found to decrease systematically with temperature. Even at 0°C there was a dipole moment of 104D.
Random‐phase calculation of poly‐L‐proline II circular dichroism
Authors: Pysh E. S.
Published: May 2005

Recent experiments have shown that the circular dichroism of poly‐L‐proline II is negative from 130 to 220 nm. Therefore, calculations based on exciton interactions alone cannot give the observed spectrum.

The present calculations were carried out in the framework of the random‐phase approximation. It includes exciton coupling of π‐π* transitions. It also couples the π‐π* transitions to the higher energy density of states (1) of the polymer chain via atomic polarizabilities, and (2) of bound solvent molecules. The relative importance of (1) and (2) is discussed in light of available experimental evidence.

Qualitatively, (1) and (2) modify the excition‐only results in the same way: the negative band near 200 nm shifts to longer wavelengths and increases in intensity; the crossover near 215 nm shifts to longer wavelengths; and the positive band near 225 nm shifts to longer wavelengths and decreases in intensity.
The structure of water absorbed in collagen. I. The dielectric properties
Authors: Hoeve C. A. J. , Lue P. C.
Published: May 2005

The dielectric constant and the loss factor of water in collagen are measured for various water, NaCl, and HCl contents at frequencies ranging from 102 to 105 Hz and at temperatures ranging from −70° to +23°C. For all measurements, both the dielectric constant and the loss decrease monotonically as the frequency increases, or the temperature decreases; the absence of a maximum in the loss curves as a function of temperature and frequency indicates an extremely broad spectrum of relaxation times. By shifting the curves obtained for the dielectric constant and the loss factor along the log–frequency axis, all data, obtained at different temperatures, can be represented on master curves valid for 23°C.

In order to explain these results, water molecules are assumed to be hydrogen bonded to each other in long chains. All water molecules in a chain can, cooperatively, be oriented in two different directions along the channel, resulting in large, reversible, dipole moments. These chains are not rigid, but are flexible liquid‐like structures. Diffusion of chains as entities is assumed to be the rate‐limiting step for dipole reorientation. Although the rate of diffusion decreases inversely proportional to chain length, the activation energy is independent of chain length. At lower temperatures, diffusion becomes slower, until at the glass point, approximately −100°C, it ceases.
The influence of temperature variations and pressure treatment on proteins and DNA in the solid state
Authors: Rossiter V.
Published: May 2005

Low‐frequency dielectric measurements have been made in the temperature range from −180°C to +110°C on DNA and a number of proteins in the solid state. The results suggest that a molecular rearrangement may occur in the temperature interval +60°C to +80°C. In terms of these measurements the transition appears to be reversible in DNA if the material remains at +20°C for longer than 60 hr. Such a time‐dependent recovery has not been observed for proteins. The application of a pressure of ∼150 MN m−2 for a 3‐min. period appears to be capable of reversing the thermal transition in at least some of the proteins studied. These results are compared with the results available from studies of the influence of temperature and pressure variations on similar biological materials in aqueous solutions.
A quantitative model of cooperative effects in aspartate transcarbamylase and related hybrid molecules
Authors: Diesendorf Mark
Published: May 2005

The hypothesis is made that cooperative (homotropic) effects in aspartate transcarbamylase (ATCase) and closely related hybrid molecules can be treated on the same basis, by expressing the effects in terms of cooperative interactions between catalytic sites. Then, provided the hybrid CnnnCsss[R] exhibits cooperativity experimentally, it is deduced that at least two parameters are required for a consistent description of cooperative effects in ATCase.

On this basis, a quantitative model is proposed that has cooperative interactions of two types: (1) a cooperative interaction of strength U between a pair of native catalytic sites situated in different catalytic trimers, and joined by a regulatory dimer; (2) an indirect cooperative interaction Ū, between any pair of native catalytic sites in the same catalytic trimer, which is transmitted via two regulatory dimers. The model is consistent with the observation that the isolated catalytic trimer does not exhibit cooperativity, and that cooperative effects require the integrity of the regulatory dimers.

In this model, the hybrid molecule CnnnCsss[R] becomes simply a one‐dimensional Ising model for three sites with pair interactions Ū, and the hybrid CnssCnss[R] becomes an Ising model for two sites with interaction U/3. The model of native ATCase is essentially two Ising systems (the catalytic subunits), each with three sites having intrasubunit pair interactions Ū, coupled together with three intersubunit pair interactions U.

The parameters Ū and U can be determined by comparing the exact solutions for the saturation curves of the two Ising models with the curves obtained from cooperativity measurements on the corresponding hybrid molecules. The theory can be readily tested, when accurate experimental data become available, by substituting the values of Ū and U determined from the hybrids into the model of native ATCase, or into models of other hybrids.
Oligonucleotide conformations. III. Comparative optical and thermodynamic studies of uridylyl‐3′‐5′‐nucleosides containing ribose, deoxyribose, or 2′‐deoxy‐2′‐fluororibose in the uridine moiety
Authors: Catlin Joseph C. , Guschlbauer Wilhelm
Published: May 2005

The synthesis of uridylyl‐3′‐5′‐nucleosides containing ribose, deoxyribose, or 2′‐fluoro‐2′‐deoxyribose in the uridine‐3′‐bound moiety and adenosine, guanosine, cytidine or uridine in the 5′‐nucleoside is reported. The temperature dependence of the circular dichroism of these dinucleoside phosphates in 0.06 M phosphate buffer at pH 7 was analyzed by the two‐state model and the oscillating dimer model. From the former, apparent thermodynamic parameters were determined by means of an iterative computer method. The comparison between the three different dinucleoside phosphates in each series indicated that the fluororiboside and the riboside resembled each other and were more stacked than the analogue containing deoxyribose. It further appeared that the similarity between the fluororiboside and the riboside is influenced by the nature of the neighboring 5′‐bound base. The interaction between the 3′‐bound sugar moiety and the 5′‐bound base is evoked as a possible stabilization mechanism.
The structure of the anticodon loop of tRNAPhe from yeast as deduced from spectroscopic studies on oligonucleotides
Authors: Maelicke Alfred , Von Der Haar Friedrich , Sprinzl Mathias , Cramer Friedrich
Published: May 2005

The hexanucleotide Gm‐A‐A‐Y‐A‐ψp excised from the anticodon loop of yeast tRNAPhe and its constituent oligonucleotides have been studied by ultraviolet absorption spectroscopy, static fluorescence, and circular dichroism. Gm‐Ap has a melting point of 45°C and a high melting enthalpy when compared with G‐Ap; hence 2′‐O‐methylation seems to stabilize stacking interactions. The nucleobase Y adjacent to the 3′‐side of the anticodon triplet interacts stronger with its 3′‐neighboring A than with its 5′‐neighboring A. It is concluded that the base Y disconnects the stack of the anticodon itself from the stack of the anticodon stem, thereby setting a reading frame for the mRNA in the course of protein biosynthesis. From the opposite signs of the short‐wavelength Cotton effects in the spectra of Gm‐A‐A‐Y‐Ap and Gm‐A‐A‐Y, it is concluded that Y after removal of its 3′ neighbor undergoes a dramatic change in its conformation. The fluorescence of the nucleobase Y upon addition of Mg2+ is enhanced in oligonucleotides longer than two. An identical enhancement is observed for tRNAPhe, indicating that this Mg2+ effect is a property of an oligonucleotide segment and does not reflect conformational changes of the whole tRNA. The data presented here reveal that the basic structural features of the anticodon loop are already present in the hexanucleotide Gm‐A‐A‐Y‐A‐ψp and are not determined by the overall structure of tRNA.
Electric birefringence in concentrated solutions of tobacco mosaic virus
Authors: Asai Hiroshi , Watanabe Nozomu
Published: May 2005

A tentative and phenomenological analysis of negative electric birefringence, which has often been observed as an anomalous birefringence phenomenon in a concentrated solution of rodlike macromolecules, is presented. Tobacco mosaic virus (TMV) was used as a typical example for the investigation. It was found that if the applied electric field is sufficiently high, the steady‐state birefringence becomes becomes positive even at a very high concentration of TMV. From this finding and analysis of the time course of birefringence transients, it was suggested that the TMV (common strain, OM type), which originally has no inherent permanent dipole, behaves as if it possesses a permanent dipole perpendicular to its long axis. Supporting evidence was also obtained from birefringence experiments on concentrated solutions of the HR strain of TMV, which has an inherent permanent dipole along its long axis. Other possibilities, for example, the effects of the walls of electrodes or of polymerization of TMV molecules, were excluded.
Na+ effects on transitions of DNA and polynucleotides of variable linear charge density
Authors: Record M. Thomas , Woodbury Charles P. , Lohman Timothy M.
Published: May 2005

A range of linear charge densities of the ordered and disordered forms of DNA or polynucleotides can be obtained experimentally by acid or alkaline titration, or by the investigation of unusual complexes involving protonated bases or three‐stranded helices. The variation of melting temperatures with Na+ concentration for various of these systems is known and in some cases is complemented by structural and thermodynamic information. We have extended the condensation–screening theory of Manning [Biopolymers, 11, 937–955 (1972)] to these systems. The stabilizing and destabilizing effects of Na+ (condensation and screening, respectively) and be independently varied, and the theory is successful in predicting the qualitative (in some cases, quanittative) behaviour that is observed. Comparison of theory and experiment indicates that the axial phosphate distance b for single‐stranded polynucleotides increases with increasing pH. Values of the critical parameter ξ are obtained for the various polynucleotide structures. These values are essential for an understanding of ionic effects on charged ligand–polynucleotide interactions.
Interaction between collagen and adenosine 5′‐triphosphate
Authors: Fung B. M. , Hillson Randall A. , Lee Garland G. , Nunnery Arthur W. , Bradford Reagen H.
Published: May 2005

A quantitative study was made of the adsorption of adenosine 5′‐triphosphate (ATP) on collagen by following the change in the absorbance at 258 nm of ATP in the soaking solution. The amount of ATP adsorbed decreased exponentially with the increase of pH up to pH 8 and fell off more rapidly at higher pH values. At a given pH, when the concentration of ATP was increased, the amount of ATP adsorbed increased following the pattern of a Langmuir isotherm. The adsorption was independent of the cation present. The adsorption of adenosine 5′‐diphosphate was essentially the same as that for ATP. For tendons deposited with calcium phosphate, the amount of ATP adsorbed decreased compared to natural tendons.

The adsorption of ATP on collagen fibers inhibited the contraction caused by calcium chloride, calcium bromide, and lithium bromide. In solution, ATP had very little effect on the denaturation of acid‐soluble collagen caused by calcium chloride.
Nmr studies of aqueous solutions of tetra and branched peptides. I. Sequence determination of amino‐acid residues and the assignment of peptide hydrogen signals
Authors: Sheinblatt M. , Rahamim Y.
Published: May 2005

Sequential determination of glycyl residues (and in several cases different amino‐acid residues) in tetra and branched peptides using the nmr technique is reported. The method is based on changes in the nmr spectra of (1) the peptide hydrogens of the different residues and (2) the methylene groups of the glycyl residues, as a result of increasing the rate of the base‐catalyzed exchange reaction of the peptide hydrogens. Hence, the spectral changes are pH dependent. However, the exact pH dependence is a function of the location of the residue in the peptide molecule. Thus, it is possible to determine the sequence of the amino‐acid residues by studying the changes in the spectra with pH.

For peptide molecules of known sequences, the above method can be used for unequivocal assignment of the peptide hydrogen signals.
Circular dichroism and structure of the complex of acridine orange with poly(L‐glutamic acid)
Authors: Imae Toyoko , Ikeda Shoichi
Published: May 2005

Circular dichroism and absorption spectra have been measured on solutions of acridine orange and poly(L‐glutamic acid) mixed at two molar ratios of carboxyl group‐to‐dye, P/D 25 and 0.8, and at different pH's. Characteristic circular dichroism is induced at the absorption bands of acridine orange when the P/D is 25 and the solution is acidic. Another type of circular dichroism is manifest at neutral and alkaline pH when P/D is 0.8. For the induction of the former type of circular dichroism, a helical array of acridine‐orange dimers bound to the α‐helix is postulated, in which the dye molecular planes are almost perpendicular to the helical axis. Assuming the helical geometry and optical parameters, combined with the observed magnitude of transition electric moment, the rotatory strength of the complex is calculated to the zeroth order approximation, and the observed circular dichroism spectra have been reproduced.
Moments of the probability distribution of moving molecules undergoing reversible isomerization, with applications to experiments
Authors: Mitchell R. M.
Published: May 2005

Exact expressions are obtained for the mean position and the variance about the mean of macromolecules which are moving in an electrostatic or centrifugal field and which, at the same time, are switching back and forth between two isomeric states. Comparison with experiment then yields the forward and backward switching rates. The following special cases are considered: (a) only one species present initially; (b) both species present initially but not in their equilibrium proportions; (c) both species present initially in their equilibrium proportions. It is shown that in the first two cases we need only measure the mean position of all the molecules in order to measure the absolute switching rates k1 and k2. In the third case, however, we must measure the variance (mean‐square deviation) of the position in order to obtain k1 and k2. The first two situations arise when “jumps” (e.g., in temperature or pressure) are made, while the third situation is obtained if the experiment is conducted with the species in chemical equilibrium throughout the experiment.