bluuebunny/crossref_metadata_2025 huggingface dataset:
Infrared spectrum of a DNA–RNA hybrid
Authors: Higuchi Shigesada , Tsuboi Masamichi , Iitaka Yoichi
Published: May 2005

The infrared absorption spectrum in the 4000–400 cm− region of an oriented film of a DNA–RNA hybrid in its undeuterated and deuterated states was observed with the polarized radiation. Most of the stronger bands found in the double‐helical DNA's and double‐helical RNA's are identified in the spectrum of the hybrid. The absorption band at 1225 cm−1 shows a perpendicular dichroism and that at 1085 cm−1 shows almost no dichroism. These facts indicate that the orientation of the group with respect to the helix axis in the hybrid structure is not entirely the same as that in the double‐helical Na DNA at, 75% RH., although the x‐ray diffraction pattern of the hybrid is quite similar to that of the DNA A form. The PO2− orientation is not the same as that in the double‐helical RNA either. The observed dichroism is explained, however, by considering that the PO2− group in the RNA moiety takes nearly the same orientation as that in the double‐helical RNA, and the PO2− group in the DNA moiety takes nearly the same as that in the double‐helical DNA.
Polymerization of amino acid derivatives by polymer catalysts. I. Polymerization by poly‐2‐vinylpyridine
Authors: Suzuoki Kazuhiro , Imanishi Yukio , Higa‐Shimura Toshinobu , Okamura Seizo
Published: May 2005

Polymerizations of D,L‐β‐phenylalanine, p‐nitro‐D,L‐β‐ phenylalanine, and o,p‐dinitro‐D,L‐β‐phenylalanine NCA's were carried out with the use of α‐picoline or poly‐2‐vinyl‐pyridine as initiator. Polymerizations induced by the polymer catalyst were always faster than those with α‐picoline in the same base concentrations. Furthermore, the polymer effect was more marked when the number of nitro groups in the NCA's increased. It was considered that the polymer catalyst interacts with the NCA's primarily by hydrogen bonding and increases the effective concentration of NCA along the chain. The increase of the NCA concentration in the vicinity of the polymer catalyst wits also achieved through charge‐transfer complexes between nitrophenyl groups in the NCA's and pyridine groups in the polymer catalyst. As the polymer chain is flexible, a collision between an adsorbed NCA and a pyridine unit in the same polymer chain is favored, thus increasing the polymerization rate.
Dielectric properties of hemoglobin and myoglobin. I. Influence of solvent and particle size on the dielectric dispersion
Authors: Schlecht P. , Mayer A. , Hettner G. , Vogel H.
Published: May 2005

Dielectric dispersion measurements with aqueous solutions of hemoglobin and myoglobin have been performed in the frequency range from 100 kcps to 15 Mcps. The influence of preparation, particle size, and solvent conditions was studied. The results are analyzed in terms of an orientational polarization mechanism.
Sedimentation, diffusion, and osmotic pressure of sodium DNA in salt‐free solution
Authors: Auer Henry E. , Alexandrowicz Z.
Published: May 2005

The osmotic, sedimentation, and diffusion coefficients of sonicated sodium DNA in aqueous solutions which were rendered rigorously free of salts have been obtained in order to study the polyelectrolyte effect on these parameters. Both native and heat denatured DNA's were studied. All three parameters were found to be independent of concentration between 2 and 10 mmole/1. The osmotic coefficient gives the fraction of counterions not immobilized by the polyelectrolyte potential, under conditions of equilibrium. The value (ca. 0.18) obtained for this fraction agrees very well with that predicted by a theory of rodlike polyelectrolytes. A simplified model that permits the computation of fractions of mobile ions from sedimentation and diffusion coefficients, when applied to the experimental data, showed that under these conditions of flow between 0.5 to 0.9 of counterions are not immobilized. The experimental data also showed that for native DNA the translation frictional coefficient seems to have different values in sedimentation and diffusion, which agrees with a finding reported for another saltfree polyelectrolyte. For denatured DNA, however, the values were found to be equal: no satisfactory explanation could be found for this difference of behavior.
Raman spectra of polyglycines
Authors: Smith M. , Walton A. G. , Koenig J. L.
Published: May 2005

The laser‐excited Raman spectrum of helical polyglycine II has been obtained. Oligomers of polyglycine are in the planar zigzag conformation and their Raman spectra are indicative of the spectrum of polyglycine I. The Raman spectra of polyglycines have bands complementary to the infrared which are sensitive to the conformation of the chain. The spectra of the oligomers have bands sensitive to the length of the polyglycine. The Raman spectra of di‐ and triglycine in aqueous solution suggest the conformation is neither planar nor helical.
Etude, par spectroscopie infra‐rouge, de la conformation de quelques composés peptidiques modèles
Authors: Avignon M. , Huong P. V. , Lascombe J. , Marraud M. , Neel J.
Published: May 2005

Some experimental data are given on the infrared spectra between 3300 and 3500 cm−1 of dilute solutions in carbon tetrachloride of three types of model compounds: CH3−CONH‐CH(R1)‐CONH(R2), (I); CH3‐CON(CH3)‐CH(R1)‐CONH(R2), (II) and CH3‐CONH‐CH(R1)‐CON(R2)2, (III). In studying the N‐H stretching bands, it was found that there are two types of intramolecular hydrogen bonds in these molecules; these result in two different cyclized conformations, C5 and C7, which contain respectively, five and seven atoms in the ring. By using model substances I, II, and III, in which the nitrogen atoms are unequally substituted, it is possible to identify the N‐H stretching bands which are to be ascribed to the N‐H oscillators included in the two different chelated conformations. It is found also that the stretching frequency of a free N‐H oscillator depends upon the substituent on the nitrogen atom. Thus, it is possible to observe, with some of the model compounds I, four different absorption bands located at 3340, 3420, 3440, and 3460 cm−1. The first two are ascribed to the N‐H oscillators included in the Hbonds which lock the C7 and C5 conformations; the last two correspond to free N‐H which differ with the substituent on the nitrogen atom.
Low‐frequency infrared bands and chain conformations of polypeptides
Authors: Masuda Yukio , Fukushima Kunio , Fujii Toyoko , Miyazawa Tatsuo
Published: May 2005

Infrared spectra of polypeptides were measured in the region of 1800–400 cm−1. For the α‐helical form, disordered form, and antiparallel‐chain β‐form, amide V band‐ arising from N‐H out‐of‐plane bending models were observed at 610–620, around 650, and 700–705 cm−1, respectively, and amide V′ bands arising from N‐D out‐of‐plane bending modes were observed at 455–465, around 510, and a 515–530 cm−1, respectively. These correlations are useful for conformation diagnoses, particularly for copolyamino‐acids or proteins which are not oriented. The nature of low‐frequency amide bands are discussed with reference to potential energy distributions calculated for the α‐helical form and β form.
Mise en évidence d'une relation entre la longueur el la constante de sédimentation des molécules de DNA en solution
Authors: Nicolaíeff Anatole , Litzler Robert
Published: May 2005

A comparative study on sonicated calf thymus DNA was made by using electron microscopy and sedimentation methods. The length distribution, established by electron microscopy by using Kleinschmidt's technique, is related to the sedimentation curve obtained with the same solution. The relation permits a determination of the sedimentation constant corresponding to a given length up to 8000 Å and vice versa.
Helix–coil transition of poly‐N5‐(3‐hydroxypropyl)‐L‐glutamine: Thermodynamic and statistical analysis
Authors: Lotan Noah , Bixon Mordechai , Berger Arieh
Published: May 2005

The thermally induced conformational changes of poly‐N5‐(3‐hydroxypropyl)‐L‐glutamine in water and in methanol–water (3:7 v/v) have been analyzed in terms of the Lifson‐Roig theory. The transitions in both solvents can be described by using v = 0.017. The thermodynamic parameters for the random coil‐to‐helix transition of one amino acid residue at room temperature were found to be: in water, ΔH = − 130 cal/mole and ΔS = − 0.45 e.u.; in methanol–water (3:7 v/v), ΔH = − 170 cal mole and ΔS = − 0.45 e.u. The size distribution of helical segments is broad, and the results of numerical calculations are presented for three degrees of polymerization (DP = 100, 300, and 750).
Conductivity and photoconductivity of NaDNA in the solid state
Authors: Šubertová E. , Prosser V. , Drobník J.
Published: May 2005

The d. c. conductivity of five samples of NaDNA in dry state was investigated. All specimens show similar behavior, with specific resistivity at 40°C of the order of 1013–1014 ohm‐cm and an energy gap of Ec = 2.04–2.25 eV. Based on the Eley's model for conductivity mechanism, the possibility of conservation of an ordered structure in the dry state (temperature range 20–80°C) is discussed. This is ascribed to the interaction of electron systems of individual bases. From the activation energy values it may be estimated that 17–19 π‐electrons take part in the interaction. Photoconductivity measurements indicated activation energies Ef of 0.88–0.96 eV in the visible region.
Morphological evidence for the folding of polyproline II helices
Authors: Andries J. C. , Walton A. G.
Published: May 2005

Spherulites of poly‐L‐proline II were grown by film casting from a dilute formic acid solution. Electron diffraction indicated that the molecular axis was parallel to the surface and essentially normal to the face of the lamellae. The molecular length was five times greater than the width of the lamellae. This is considered to he substantial evidence for the molecular folding of poly‐L‐proline II. A correlation between the molecular conformation of poly‐L‐proline in solution and the observed morphological form in the solid state has been determined. As the solution mutarotates from form I to form II, the solid morphology varies from an indistinetly shaped spherulite with little inner detail to a well formed crystalline spherulite complete with lamellae.
Persistence length of DNA
Authors: Hays John B. , Magar Magar E. , Zimm Bruno H.
Published: May 2005

In the wormlike chain (Kratky‐Porod) model of DNA the stiffness of the chain is determined by the persistence length, a. The persistence length may be evaluated from light‐scattering measurements of the molecular weight and the mean‐square radius if the samples are not polydisperse or if the polydispersity can be quantitatively determined. The persistence length can also be evaluated with the aid of hydro dynamic theory from measurements of intrinsic viscosity and sedimentation coefficient. Data taken from the literature and from other studies by the authors are examined by these methods. The light‐scattering method yields a value of a of 900 ± 200 Å the hydrodynamic data yield 600 ± 100 Å. These values are considerably larger than those obtained by most previous authors.
Interactions of metallic ions with DNA. V. DNA Renaturation Mechanism in the Presence of Cu2+
Authors: Richard Hélène , Schreiber J. P. , Daune M.
Published: May 2005

New experimental data were obtained by means of circular dichroism, melting, renaturation, and kinetic experiments, upon Cu2+ binding to DNA, poly dAT, and poly dGdC. They enable us to propose a model of binding giving a satisfactory explanation to all of the data found in the literature. Two types of binding sites are proposed: (a) a “sandwich” of Cu2+ between two adjacent G‐C pairs giving a charge‐transfer complex, and (b) a chelate between a phosphate group and a nitrogen atom of the bases (N7 of guanine and N3 of cytosine at room temperature, N3 of adenine after thermal opening of A‐T pair). Type (a) stabilizes the helix and keeps the two strands linked. Type (b) destabilizes the helix and explains why the kinetic rate of renaturation is the same as that of copper release.
Ultrasonic absorption studies of poly‐benzyl‐L‐aspartate in mixed solvents, in relation to the helix–coil transition
Authors: Zana R. , Lang J.
Published: May 2005

Ultrasonic absorption measurements were carried out on solutions of polybenzyl‐L‐aspartate (PBLA) in chloroform–dichloroacetic acid (DCA) and in 1,2‐dichloroethane (DCE)–DCA, in the range 3.9–155 MHZ. The helix–coil transition of PBLA produces an increase of absorption which is larger in CHCl3–DCA than in DCE–DCA solutions. The influence of the solvent on the excess ultrasonic absorption suggests that solvation processes may be involved in these changes of absorption. The plots of the absorption vs. the volume fraction of DCA do not show any absorption maximum. This indicates that the ultrasonic absorption is not sensitive to the helix–coil equilibrium of PBLA in the frequency range investigated. A maximum value of 109 S−1 has been obtained for the rate constant of growth of a helix region.
Different conformations of double‐stranded nucleic acid in solution as revealed by circular dichroism
Authors: Ivanov V. I. , Minchenkova L. E. , Schyolkina A. K. , Poletayev A. I.
Published: May 2005

Conformation of two‐stranded DNA in H2O–methanol, H2O–ethanol, H2O–isopropanol, and H2O–dioxane solutions at different concentrations of alkaline ions has been studied with the aid of circular dichroism. The following conclusions are drawn:

The conformation of DNA in H2O and H2O–methanol belongs to a family of B forms (B, C, T forms are the representatives of the family). The magnitude of the winding angle between adjacent base pairs (θ) is determined by the concentration and type of the cations. In H2O the cation action is nonspecific and leads to an increase in θ value. In 80% methanol the ions act specifically, Cs+ being to stabilize a form with a greater θ value, and Li+ being with a lesser one. The total θ change is likely within the limits of 33° ⩽ θ ⩽ 45°.

At high content of ethanol, isopropanol, or dioxane (∼80%), but not with methanol, and in low ionic strength the conformation of DNA belongs to a family of A forms (A form is one of the members of the family) and is specified by the concentration and type of cation involved. The two‐stranded regions of RNA in H2O are also of A type and winds with the rise of cation concentration. The range of θ variation is not narrower than 30° ⩽ θ 33°.

The conformational transitions within the families (induced by ions) are of non‐cooperative pattern, wheras the transitions between the families (induced by nonpolar component) are of cooperative pattern. The effect of cations, when specific, is discussed on the basis of steric correspondence between the width of DNA narrow groove and the size of a hydrated cation.
Electric permittivity of alfalfa mosaic virus in aqueous solutions
Authors: Touw F. Van Der , Briedé J. W. H. , Mandel M.
Published: May 2005

The electric permittivity of alfalfa virus particles in buffer solutions of three different concentrations at pH 7 was studied between 10 kHz and 100 MHz. The experimental results could be described with one single dispersion curve of the Cole‐Cole type characterized by a concentration independent specific dielectric increment and mean relaxation time. The results were interpreted semi‐quantitatively in terms of counterions–atmosphere polarizability, neglecting counterion repulsion.
Interaction of the polyelectrolyte heparin with copper(II) and calcium
Authors: Lages Bruce , Stivala S. S.
Published: May 2005

The binding of copper(II) ions by heparin was investigated using equilibrium dialysi techniques, and the effects of this binding on solution properties determined. In neus tral Tris buffer solutions, heparin binds a maximum of twenty‐three to twenty‐four copper ions in two classes of sites, one containing three to four binding sites, the other containing twenty to twenty‐one sites. Cooperative binding is associated with the larger class of sites. In more acidic citrate buffer solution, only one class of sites is observed, containing about four to five binding sites. Association constants are calculated for the classes and the possible chemical nature of the sites is discussed. The binding of calcium ions in neutral buffer is also examined, and these ions appear to be bound by a group of twenty to twenty‐one binding sites, with a larger association constant than that for the copper ions. Definite effects on the solution properties of heparin, such as intrinsic viscosity, sedimentation coefficients, and partial specific volume, can be observed only in the cooperative binding of copper ions in neutral buffer. The interpretation of these solution properties in terms of molecular size and shape is analyzed, and it is concluded that the metal ion interactions cause no major change in the apparently random coil conformation of heparin in buffered solution, although some minor changes can be associated with the cooperative uptake of copper ions.
Proton magnetic resonance studies of the conformational changes of dideoxynucleoside ethyl phosphotriesters
Authors: Kan Lou S. , Barrett James C. , Miller Paul S. , Ts'O Paul O. P.
Published: May 2005

PMR investigations on the diastereomeric phosphate methyl protons of the dinucleoside ethyl phosphotriesters Tp(C2H5)T, dA, and dIp(C2H5)dI have been used to study the conformational changes of these dimersin solution. In D2O (273°K), the diastereomeric phosphate‐methly groups of Tp(C2H5)T appear as a triplet. The methyl resonances of dIp(C2H5)dI and dAp(C2H5)dA appear as two sets of triplets and their chemical shift differences (δ1 − δ2), decrease with increasing temperature, finally becoming zero at 292°K and 333°K, respectively. The same phenomenon is observed for dAp(C2H5)dA in CD3OD; in this detacking solvent, the difference (δ1 − δ2) diminishes to zero at a lower temperature (261°K). At room temperature in D2O, the chemical shift of the phosphate methyl of Tp(C2H5)T appears at lower field than those of dIp(C2H5)dI or dAp(C2H5)dA. The differences between the chemical shifts of these groups (δI − δT or δA − δT) increase with increasing temperature, and reach maximal values at 301°K and 333°K, respectively. The results suggest that at low temperature the largest fraction of the dimer population exists in a stacked state, with the phosphate‐ethyl groups outside the stack. Increasing temperature causes an oscillation of the bases and a shift in the dimer population away from the stacked state. Finally at high temperature, the planar bases rorate with respect to one another and in the case of dIp(C2H5)dI and dAp(C2H5)dA, the ethyl groups experience shielding by the anisotropic ring current of the five‐membered ring of the bases. Thus, the current pmr studies and those reported earlier from our laboratory support an “oscillation‐rotation model” for the unstacking process of the dimers. The relationship of this model and the “two‐state model” is discussed.
Etude Phsicochimique des Copolymères Triséquencés Poly(γ‐L‐glutamate de benzyle)/Poly(oxyéthylène)/Poly(γ‐L‐glutamate de benzyle). Rǒle de la Polydispersiteé dans la Détermination de la Conformation des Molécules en Solution Diluée
Authors: Reibel Léonard , Spach Gérard , Dufour Claude
Published: May 2005

We have prepared a series of three‐block copolymers containing the same central block of poly(ethylene oxide) (POE) and two side blocks poly(γ‐L‐glutamate) (PBLG) of variable lengths. These molecules could present an unusual conformational model when dissolved in solvents where PBLG exhibits a helical structure: a helical structure: a gaussian chain connected at each end to a rigid rod. We checked this hypothesis by light scattering, viscosimetry, and dielectric adsorption measurements.

In order to take into account the possibility that the orientations of the two rods may not be completely independent, we have introduced in the calculations the angle θ, formed by the two rigid segments. We have mainly considered three types of conformation which can be described by assimilating the lods of PBLG of two vectors having their origin at the juncture with the POE chain: depending whether cos θ (the average value of cos θ) is equals to −1,0, or +1 ( where the two vectors are antiparalles, oriented independently, or parallel, respectively). We have tried to establish a theoretical expression for the molecular size obtained by each method of investigation, as a function of cos θ. We corrected this value to account for the effect of the polydispersity on the molecular size and then compared the theoretical values thus calculated with the experimental results. The measurements of the radius of gyration, R, by light scattering does not permit the unambiguous determination of cos θ. As soon as the system is not perfectly monodisperse, the variation of R as a funciton of cos θ is not very large. The viscosity results are also difficult to interpret because the effect of the polydispersity on the viscosity cannot be established fo each conformational model. However, a clear answer can be obtained by the dielectric absorption technique for two reasons: the variation of the dielectric absorption as a function of cos θ is very important and the influence of the polydispersity on the measurements is weaker than for the two former methods. The results show that cos θ is equal to −1, demonstrating that the two vectors are antiparallel.

From the dielectric dispersion, one sees that the total length of the molecule is roughly equals to the sum of the lengths of the two rigid blocks. To explain this result we propose a new conformational model. Since it is known that in some solvents and mixtures of solvents the molecules of PBLG tend to associate, we assume that the two rigid rods are antiparallel and partly associated. The associated part of the molecule is assumed to be surrounded by the mixture of POE and solvent, which acts as a poor solvent (ef. Fig. 2.).
A model for solvent contributions to polypeptide and protein circular dichroism
Authors: Pysh E. S.
Published: May 2005

The possibility of bound solvent contributing directly to the circular dichroism of polypeptides and proteins is discussed. The model presented is based on the requirement of a breakdown in the planar symmetry of the amide environment. This symmetry breakdown is described in terms of the conformational states of the chain, and leads to necessary, but not sufficient, conditions for observable solvent contributions. Application of the model leads to the conclusion that, while some chain conformations are intrinsically incapable of roviding the required breakdown in the symmetry of solvent perturbations, other conformations force such a breakdown, notably poly‐L‐proline II and disordered chains.
Energy transfer in tRNAPhe (Yeast). The solution structure of transfer RNA
Authors: Blumberg W. E. , Dale R. E. , Eisinger J. , Zuckerman D. M.
Published: May 2005

In the preceding paper, the dependence of the dipolar orientation factor κ2, which governs long‐range (Förster) energy transfer, on the relative orientation and reorientational freedom of the donor and acceptor chromophores is examined. The analysis given there is employed to derive minimum and maximum values of 〈κ2〉 for energy transfer from the Y base of tRNAPhe (yeast) to an acriflavine acceptor attached to the 3′ terminus of the tRNA using estimates for the reorientational freedom of the donor derived from a combination of steady‐state and time‐dependent polarized emission measurements. The acceptor motion is estimated from data in the literature. From these limiting values of 〈κ2〉 and Beardsley and Cantor's determination of the long range energy‐transfer efficiency for this donor–acceptor pair, the interchromophore distance R is calculated to be between 34 and 61 Å, this range being independent of the particular model chosen to described the reorientational freedom of the donor and acceptor. While this large range in R is of little help in establishing the solution structure of tRNA, the analysis illustrates the potential of polarized energy‐transfer experiments, particularly when transfer depolarization experiments are possible.
Water sorption on deoxygenated hemoglobins CC, SC, SS, AS, and AA
Authors: Killion Philip J. , Cameron Bruce F.
Published: May 2005

Five human hemoglobins whose genetic relationship to one another involves one set of alleles, hemoglobins CC, SC, SS, AS, and AA, were studied in the deoxygenated form within a McBain gravimetric sorption system at 28°C. Water was used as the adsorbate at relative vapor pressures ranging from 0.11 to 0.39. The results of this study are reported and compared with a similar study on the ferric form of these same five hemoglobins. For both forms of hemoglobin studied, a slight increase was measured in the number of polar sites accessible to H2O vapor for those genotypes in which the substituent in the sixth position from the N terminus of the two β chains had a positively charged side chain, i.e., hemoglobin C. Those samples containing hemoglobin S (less soluble in the deoxy form) show an increased BET monolayer coverage in the deoxy as compared to the ferric form. For each genotype, the deoxygenated form had more polar sites accessible to H2O vapor than its ferric form. This finding is in agreement with an increase in the size of the central cavity as shown by crystallographic analysis.
Intensities and other spectral parameters of infrared amide bands of polypeptides in the α‐helical form
Authors: Chirgadze Yu. N. , Brazhnikov E. V.
Published: May 2005

Intensities and other spectral parameters of infrared amide I and II bands of α‐helical polypeptides in solutions have been determined for poly(γ‐benzylglutamate), poly(γ‐ethylglutamate), and polymethionine in chloroform, polylysine, poly(glutamic acid), and fibrillar protein tropomyosin from rabbit muscles in heavy water. The majority of spectral parameters are characteristic. The half‐width of the amide I band was found to vary in the range of 15–40 cm−1 for different polypeptides in the different solutions. The correlation between this parameter of the amide I band and the stability of the α‐helix was estimated. A new weak band near 1537 cm−1 of unknown origin was observed for the hydrogen form of polypeptides in the α‐helical state.
Energy bands and electronic delocalization in the sugar‐phosphate backbone of DNA
Authors: Suhai Sándor
Published: May 2005

The results of a CNDO/2 all‐valence electron crystal orbital study are reported for the sugar‐phosphate chain of DNA. The valence and conduction bandwidths are found to be large enough to make electronic delocalization through this backbone possible. Different mechanisms for charge carrier transport in DNA are compared on the basis of the electron and hole effective masses. Conduction along the backbone seems to be at least as probable as through the aperiodic system of the superimposed nucleotide bases.
The state of water on hydrated collagen as studied by pulsed NMR
Authors: Fung B. M. , Witschel John , McAmis Lavon L.
Published: May 2005

The spin‐lattice relaxation time (T1) of water adsorbed on collagen fibers was determined at six frequencies and temperatures varying from 25° to −80°C. Care was taken to eliminate the contributions to the signal of protons other than those in the adsorbed water. Quantitative calculations were made on T1 and the results were compared with the experimental data. It is suggested that a maximum of about 0.50–0.55 g water per g collagen forms a hydration layer, which cannot be frozen down to −90°C and exhibits a distribution of motional correlation times. For collagen samples containing a larger quantity of adsorbed water, the additional water molecules behave like ordinary isotropic water, having a single correlation time and a freezing temperature of about −10°C.
Evaluation of kinetic parameters of thermal decomposition of native collagen by thermogravimetric analysis
Authors: Lim Jong J. , Shamos Morris H.
Published: May 2005

The kinetic parameters associated with the thermal decomposition of native collagen have been obtained by thermogravimetric techniques. In order to achieve this a thermogravimetric analysis was carried out in the temperature range of 25°C to about 1000°C. In this temperature range, it had been found that the differential primary weight loss curve had yielded three distinct peaks for the tendon collagen. The thermal decomposition corresponding to each peak was analyzed to retrieve its kinetic parameters. The peak temperature associated with the first peak decreased as the water content in a sample increased, while that of the second peak was independent of its hydration condition. It is believed that the first and the second peaks are, respectively, results of: (1) dissociation of water from collagen, and (2) of breaking of the collagen molecule itself. The third peak has not been easily identified so far. The activation energy and the order of water decomposition are obtained by various known methods. The results obtained by these different approaches agree reasonably well. The kinetic parameters of second and third peak are also obtained and reported here.
Raman spectroscopic study of tropomyosin denaturation
Authors: Frushour B. G. , Koenig J. L.
Published: May 2005

Raman spectra of the pH denaturation of tropomyosin are presented. In the native state tropomyosin has an alpha‐helical content of nearly 90%, but this value drops rapidly as the pH is raised above 9.5. The Raman spectrum of the native state is characterized by a strong amide I line appearing at 1655 cm−1, very weak scattering in the amide III region around 1250 cm−1, and a medium‐intensity line at 940 cm−1. When the protein is pH‐denatured, a strong amide III line appears at 1254 cm−1 and the 940 cm−1 line becomes weak. The intensities of the latter two lines are a sensitive measure of the alpha‐helical and disordered chain content. These results are consistent with the helix‐to‐coil studies of the polypeptides.

The Raman spectra of α‐casein and prothrombin, proteins thought to have little or no ordered secondary structure, are investigated. The amide III regions of both spectra display strong lines at 1254 cm−1 and only weak scattering is observed at 940 cm−1, features characteristic of the denatured tropomyosin spectrum. The amide I mode of α‐casein appears at 1668 cm−1, in agreement with the previously reported spectra of disordered polypeptides, poly‐L‐glutamic acid and poly‐L‐lysine at pH 7.0 and mechanically deformed poly‐L‐alanine.
Raman studies of nucleic acids. XII. Conformations of oligonucleotides and deuterated polynucleotides
Authors: Prescott B. , Gamache R. , Livramento J. , Thomas G. J.
Published: May 2005

Laser Raman spectra of the trinucleoside diphoshate ApApA and dinucleoside phosphates ApU, UpA, GpC, CpG, and GpU are reported and discussed. Assignments of conformationally sensitive frequencies are‐facilitated by comparison with spectra reported here of poly(rA), poly(rC), and poly(rU) in deuterium oxide solutions. The significant spectral differences between ApU and UpA, and between GpC and CpG, reveal that the sequence isomers have nonidentical conformations in aqueous solution. In UpA at low temperature the bases are stacked and the backbone conformation is similar to that found in ordered polynucleotide structures and RNA. In ApU no base stacking can be detected and the backbone conformation differs from that found in UpA, both in the orientation of phosphodiester linkages and in the internal conformation of ribose. At the conditions employed neither ApU nor UpA exhibits base pairing in aqueous solutions. In both GpC and CpG the bases are stacked and the phosphodiester conformations are similar to those encountered for UpA and RNA. However, major differences between spectra of GpC and CpG indicate that the geometries of stacking and ribosyl conformations are different. In GpC the Raman data favor the formation of hydrogen bonded dimers containing GC pairs. Protonation of C in GpC is sufficient to eliminate the ordered conformation detected by Raman spectroscopy. Despite the ordered backbone conformation evident in GpU, this dinucleoside apparently contains neither stacked nor hydrogen bonded bases at the conditions employed here. The Raman data also confirm the stacking interactions in ApApA, poly(rA), and poly(rC) but suggest that the backbone conformation in poly(rC) differs qualitatively from that found in most ordered polynucleotide structures and is thermally more stable. The present results demonstrate the sensitivity of the Raman technique to sequence‐related structural differences in oligonucleotides and provide additional spectra–structure correlations for future conformational studies of RNA by laser Raman spectroscopy.
Recursion relation generation of probability profiles for specific‐sequence macromolecules with long‐range correlations
Authors: Poland Douglas
Published: May 2005

The problem of calculating detailed probability profiles giving the probability of each unit in the chain to be in the ordered state (and all other average quantities as well including the fraction of strand association) for specific‐sequence macromolecules requiring statistical weights that correlate up to the total number of units in the chain (e.g., DNA, collagen) is formulated in terms of recursion relations for appropriate a priori and conditional probabilities, thus generalizing the approach of Lacombe and Simha for nearest‐neighbor correlations in specific sequence macromolecules. The technique allows the probability profiles for chains of thousands of units to be calculated in minutes making no approximation in the basic model.
Cooperative elution of oligoadenylic acid in poly U immobilized chromatography
Authors: Okada Shozo , Husimi Yuzuru , Tanabe Sachiko , Wada Akiyoshi
Published: May 2005

Characterization of polyU immobilized chromatography was performed in order to use this technique as an analytical device. A method of analysis of the elution profile related to thermodynamic parameters was also developed.

Sites of attachment of polyU to agarose gel activated by cyanogen bromide were studied using uridine diphosphate and adenine. Independent equilibrium dialysis of ApA for different states of polyU, in solution and immobilized in gel, were carried out. These results show that the immobilized polyU is attached to agarose only at the 5′‐terminal phosphate groups and behaves as it does in solution.

Column chromatography of ApA with the immobilized polyU was performed at several temperatures and concentrations. To analyze the elution profile, the theory of cooperative binding of oligonucleotides to polynucleotides was extended to the frame‐work of plate theory. A computer simulation for the elution profiles was performed using thermodynamic parameters obtained by equilibrium dialysis. This simulation duplicated the experimental results. This fact shows that the peculiar leading form of elution profile is due to the cooperative binding. The thermodynamic parameters of the polyU–ApA system were obtained from the “peak trajectory.”
The ESR determination of protein α‐helicity
Authors: Lvov K. M. , Kim Yu. A.
Published: May 2005

Experimental data are summarized on decay kinetics of uv‐induced paramagnetic centers in globular proteins. The PC decay rate in the absence of oxygen in α helical regions is shown to differ always by about two orders from that in nonhelical regions of the polypeptide chain. This effect can be utilized to estimate the degree of α helicity in the dry state, in solution, and in the frozen solution of proteins.
Fluorescence correlation spectroscopy and Brownian rotational diffusion
Authors: Aragón S. R. , Pecora R.
Published: May 2005

A theroy relating rotational Brownian motion to the time autocorrelation function of the intensity of radiation from a fluorescent system composed of spherical rotors is presented. The calculation shows three relaxation times, two associated with the rotational diffusion, and the third associated with the natural decay of the fluorescence. The correlation function contains terms that relax independently of the fluorescence decay time, thus arbitrarily extending the time range over which rotational diffusion can be studied by fluorescence.
The solution conformation of poly(L‐lysine). A Raman and infrared spectroscopic study
Authors: Painter Paul C. , Koenig Jack L.
Published: May 2005

The Raman and infrared spectra of poly(L‐lysine) and poly(DL‐lysine) in solution are reported and the effects of various salts are investigated. The results demonstrate that α‐helix formation in solution is induced by specific salts and the spectral data support the hypothesis of regions of local order for poly(L‐lysine) in aqueous solutions of low ionic strength.
Thickness and density of protein films by optical mixing spectroscopy
Authors: Uzgiris E. E. , Fromageot H. P. M.
Published: May 2005

The adsorption of protein films on polystyrene latex spheres was studied by optical mixing spectroscopy. With this technique, we show that both the hydrodynamic thickness of protein films and their optical density can be measured. Thus, we found that films of the glycoproteins isolated from the human erythrocyte membrane were four times as thick as films of either human serum albumin or bovine serum albumin for about the same surface coverage. This result suggests an end‐on orientation for the adsorbed glycoprotein molecules, which is consistent with the model proposed by others for the orientation of these molecules at the surface of the red blood cell itself.
Salt effects on the denaturation of DNA. V. Preferential interactions of native and denatured calf thymus DNA in Na2SO4 solutions of varying ionic strength
Authors: Fu Joseph C. C. , Gruenwedel Dieter W.
Published: May 2005

Precision density measurements were performed at 25°C on Na‐DNA‐Na2SO4 mixtures in the presence of either 0.005 m cacodylic acid buffer (pH 6.8) or in the presence of 0.1 m NaOH (pH 12.3). From measurements executed under equilibrium dialysis conditions, the so‐called “density increments” (∂ρ/∂c2)μ0 for native (pH 6.8), heat‐denatured (pH 6.8), and alkali‐denatured (pH 12.6) Na‐DNA were evaluated as a function of Na2SO4 concentration. (∂ρ/∂c2)μ0 for native DNA was found to decrease almost linearly with ionic strength I1/2 of the supporting electrolyte. The density increment for Na‐DNA at pH 12.6, on the other hand, increases in more or less linear fashion with I1/2. (∂ρ/∂c2)μ0 for heat‐denatured DNA at pH 6.8 is not affected very much by increasing salt strength. From density measurements performed on the Na‐DNA–Na2SO4 mixtures at fixed concentrations of diffusible components, the partial specific volumes ν2° of native (pH 6.8), heat‐denatured (pH 6.8), and alkali‐denatured (pH 12.6) Na‐DNA were determined as a function of Na2SO4 concentration. All ν2° values, irrespective of the secondary structure of the DNA, increase with increasing salt concentration although the increase for heat denatured DNA (pH 6.8) is barely noticeable. ν2° of both native and heat‐denatured DNA (pH 6.8) extrapolates to a value of 0.50o ml/g at vanishing salt concentration; ν2° of DNA in 0.1 m NaOH, on the other hand, assumes the value 0.2o ml/g.

Distribution coefficients of diffusible components, expressed in terms of preferential water and salt interaction, were evaluated from the (∂ρ/∂c2)μ0 data, solvent densities, and partial specific volumes of all solution components. All interaction parameters depend strongly on salt concentration and on the conformation of DNA. From data collected and from information available in the literature it is concluded that Na2SO4, for instance, displaces water of hydration from native DNA much more readily with increasing salt concentration than does NaCl. The solvation properties of the denatured forms of Na‐DNA are rather complex but appear to be in harmony with whatever information can be gathered from the literature.
Length and dipole moment of TMV by laser signal‐averaging transient electric birefringence
Authors: Newman Jay , Swinney Harry L.
Published: May 2005

Transient electric birefringence experiments have been performed on well‐characterized highly monodisperse samples of tobacco mosaic virus (TMV). Experiments and calculations are presented that show that the sensitivity and accuracy of the traditional transient electric birefringence technique can be enhanced by several orders of magnitude through the use of a low‐powered laser and crystal polarizing optics, signal averaging, and digital data processing. Measurements of the field‐free decay of the birefringence yield for the rotational diffusion coefficient, DR = 318 ± 3 sec−1. The length of the rodlike virion, calculated from the Broersma equation with this value of DR and a rod diameter of 15 nm, is 292.5 ± 1.0 nm. Measurements of the growth of the birefringence when an electric field is applied across the sample yield μ2/kT(α∥ − α⊥) = 0.47 ± 0.07, where μ is the permanent dipole moment (assumed parallel to the symmetry axis of the virus) and α∥ − α⊥ is the electrical polarizability anistropy of the virus. Using the value of α∥ − α⊥ measured by O'Konski et al., we then obtain μ = 2.5 × 10−14 esu cm.
Analysis of derivative binding isotherms. Theoretical considerations
Authors: Sturgill T. , Biltonen R. L.
Published: May 2005

The basic theoretical groundwork for the use of derivative binding isotherms in the analysis of ligand binding is presented. The derivative binding isotherm is defined as Γ (Y) = df/dy where f = fractional degree of saturation and y = natural logarithm of the free ligand concentration. Since Γ (y) is a positive function, which goes to zero as y → ±∞, the mean value of y, 〈y〉, and the second and third moments, μ2 and μ3 about 〈y〉 are well defined.

For a macromolecular system consisting of N equivalent and independent binding sites, Γ (y) is a symmetrical bell‐shaped function with one maximum. The maximum occurs when y = −ln Kassoc; μ2 = π2/3, and μ3 = 0. For multiple sets of independent binding sites, Γ (y) is a superposition of Γ‐type functions. If the sets are sufficiently well separated in binding free energy, multiple extrema may be seen at positions corresponding to the logarithms of the dissociation constants for the individual sets. In any case, 〈y〉 is equal to the mean value of the logarithms of the dissociation constants for the sets; μ2 > π2/3 and equal to π2/3 plus the variance of the logarithms of the dissociation constants about their mean value; and μ3 is, except by coincidence, not equal to zero and equals the third moment of the distribution of logarithms of the dissociation constants about their mean value.

Analysis of Γ(y) for the case of cooperative interactions within a set of binding sites was investigated by examining (1) the Hill model (whose mathematical representation is equivalent to that used to describe antibody heterogeneity except that in the latter case the parameter a, the Sips, constant, is constrained (0 < a ≤1);(2) a common model for cooperativity in which the cooperative free energy is a linear function of the fraction bound; and (3) a general representation of cooperative interactions within a set of sites in terms of ϕ(f), a smooth function that gives the interaction free energy in units of RT.

For the Hill model (or Sips model) Γ(y) is a symmetrical function with one maximum at y = (−1)/a)lnK, μ2 = π2/3a2; and μ3 = 0. For the case in which the cooperative free energy is a linear function of f [ϕ(f) = cf], 〈y〉 = −ln K0 + (c/2); μ2 = (π2/3) + c[(c/12) + 1] where c > −4; and μ3 = 0. General expressions for the moments in terms of ϕ(f) are derived. In general, μ2 < (π2/3) for positive cooperativity and μ2 > (π2/3) for negative for negative cooperativity. Γ(y) will be symmetrical if and only if the cooperative free energy is introduced symmetrically about f = 0.5.
Generation of continuous ligand–macromolecule binding isotherms. Use of exponential concentration gradients
Authors: Mountcastle Donald B. , Freire E. , Biltonen R. L.
Published: May 2005

Continuous exponential concentration gradients, accurate, precise, and reproducible to better than 1% over at least a 103–104 concentration range, can be easily produced. In fact, it appears that these gradients may be substantially better than this. Such gradients have been used to generate a continuous ligand binding isotherm for the system Mg++ + Eriochrome Black T over a 106 ligand concentration range. This continuous isotherm is shown to be sufficiently precise to provide a first derivative function Γ(y), which is precise to 0.4%. The moments of Γ(y) were calculated and found to be extremely accurate. For example, the second moment about the mean was calculated to be 3.32 and 3.30 for two different experiments compared to a theoretical value of 3.29. The general application of these techniques to generate continuous ligand binding isotherms is discussed.
1H Nuclear magnetic resonance studies of histidine‐containing di‐ and tripeptides. Estimation of the effects of charged groups on the pKa value of the imidazole ring
Authors: Tanokura Masaru , Tasumi Mitsuo , Miyazawa Tatsuo
Published: May 2005

The nmr titration curves of chemical shifts versus pH were observed for the protons of various histidine‐containing di‐ and tripeptides. With these results, the macroscopic pKa values and the chemical shifts intrinsic to each ionic species were determined by a computer curve‐fitting based on a simple acid dissociation sequence. The pKa value of the imidazole ring in N‐acetyl‐L‐histidine methylamide was assumed to represent the intrinsic (or unperturbed) pKa of the imidazole rings of histidine having peptide linkages at both the CO and NH sides. The pKa values of the imidazole rings observed for most di‐ and tripeptides were reasonably reproduced by simple calculations using the intrinsic value and the perturbations due to the CO2− and NH3+ groups located at various positions. Some other factors affecting the pKa value of the imidazole ring are also discussed.
Cooperative ligand binding by ferrihemoglobin: An experimental artifact?
Authors: Anusiem Alphonso C. I. , Beetlestone John G.
Published: May 2005

We have carried out a detailed study of ligand binding of ferrihemoglobins under various conditions. Our results show that n varies with time and that this variation is paralleled by changes in the spectrum of methemoglobin. This suggests some form of structural perturbation. The time‐dependent value of n is discussed in terms of the observed spectral changes accompanying prolonged equilibration.
The spatial configuration of ordered polynucleotide chains. I. Helix formation and base stacking
Authors: Olson Wilma K.
Published: May 2005

A single virtual bond scheme set forth previously for the treatment of average properties of randomly coiling polynucleotides is here applied to the calculation of helical parameters which characterize a regularly repeating polynucleotide molecule. Only a fraction of the enormous number of conformationally feasible helixes fulfill the geometric criteria of vertical base stacking usually associated with ordered polynucleotide chains. Detailed examination of the nature and mode of base stacking feasible in a single helical backbone structure indicates that the handedness of a base stacking arrangement does not correlate either quantitatively or qualitatively with the handedness of the polymer backbone. A number of polynucleotide chains which exhibit lefthanded base stacking patterns in nmr and CD studies may, in fact, be righthanded helixes.