bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermal transitions in mixtures of polydeoxyribodinucleotides
Authors: Hayes F. N. , Lilly E. H. , Ratliff R. L. , Smith D. A. , Williams D. L.
Published: December 2004

Oligo d(C‐A) and oligo d(T‐G) of known average lengths, prepared by a combination of chemical and enzymatic procedures, have been mixed in 0.02 M and 0.07 M Na+, and absorbance has been studied as a function of increasing temperature. The transitions have been analyzed for the temperature of maximum slope Tm, the breadth of the transition, the value of the slope at Tm, and the maximum hyperchromicity. Linear expressions have been found relating the inverse of the length in nucleotide units (n−1) of the shorter oligomer, irrespective of its identity, to Tm and also to the transition breadth. From a difference in slope between the Tm versus n−1 expressions for the two molarities, the entropy and enthalpy of melting have been calculated as a function of n−1.
Stepwise synthesis of oligopeptides with N‐carboxy α‐amino acid anhydrides
Authors: Iwakura Oshio , Uno Keikichi , Oya Masanao , Katakai Ryoichi
Published: December 2004

Oligopeptides were synthesized in high yields by the controlled coupling reaction of N‐carboxy α‐amino acid anhydrides (NCA's) with amino acid and peptide sodium salts in the heterogeneous reaction medium of acetonitrile–water which contained sodium carbonate. In this solvent, it could be considered that the reaction could occur at the interface of acetonitrile and aqueous layers, and that NCA's could be protected by the organic layer from side reactions such as hydrolysis and polymerization. The careful control of reaction conditions such as pH of the solution was not necessary when the heterogeneous mixed solvent was used. Sodium carbonate which had not been used for a reaction of this kind could be satisfactorily used for stabilizing the carbamate intermediates in the aqueous layer of the heterogeneous reaction medium.
Heat of denaturation of lysozyme
Authors: O'Reilly J. M. , Karasz F. E.
Published: December 2004

The enthalpy of denaturation of lysozyme was determined by measuring the heat, capacity of an aqueous solution of this protein in the vicinity of the transition temperature, 46 °C at pH 1. Within experimental error the calorimetric, heat (56 ± 8 kcal/mole) was found to agree with the van't Hoff transition enthalpy (63 ± 6 kcal/mole) determined from optical rotation measurements as a function of temperature. This indicates that denaturation of this protein can be interpreted in terms of a two‐state model. Successive measurements of the same sample showed, from several lines of evidence, that the transition was about 80% reversible for the particular environmental conditions and thermal history involved in the study.
Transient electro‐optic Kerr effect in spheroidal particles
Authors: Wright A. Kent , Keefe William E.
Published: December 2004

Benoit's theory of the time dependence of the birefringence transient in the Kerr cell following sudden removal of the orienting field has been examined and shown to hold only for spherical part ides and not ellipsoids of revolution. This observation is in agreement with the methods of dielectric dispersion and depolarization of fluorescence which yield two rotary diffusion constants, while Benoit's theory yields only one. A new theory is presented here which contains two rotary diffusion constants and reduces to the Benoit equation in the limiting cases of spheres and infinitely thin rods. Also the theoretical extensions of Tinoco and Ridgeway have been examined and compared to the resulting theory.
On the double peak of NMR in the helix—coil transition region
Authors: Nagayama Kuniaki , Wada Akiyoshi
Published: December 2004

To attempt to resolve the controversy over “fast” and “slow” helix–coil transition rates in polypeptides, nuclear magnetic resonance spectra were measured for monodisperse poly‐γ‐benzyl‐L‐glutamate (PBLG). These results were compared with simulated line spectra which were computed by taking the molecular‐weight distribution into consideration. Broad but single peaks have been observed in 220 mHz nmr for the α‐CH and NH proton resonance spectra in the transition region. The shape of the line changes with the extent of polydispersity. Assuming a fast conversion rate, a molecular model of the helix–coil transition simulates these results. Consequently, the double peak which has been observed in the nmr of polypeptides at the helix–coil transition region is shown to result from the polydispersity in molecular weight.
Interaction of metal ions with polynucleotides and related compounds. XXII. Effect of divalent metal ions on the conformational changes of polyribonucleotides
Authors: Shin Yong Ae
Published: December 2004

Changes in the conformation of poly(G), poly(C), poly(U), and poly(I) in the presence of divalent metal ions Mg2+, Ca2+, Mn2+, Co2+, Ni2+, Cu2+, Cd2+, and Zn2+ have been measured by means of ORD and u.v. spectra. Mg2+ and Ca2+ ions stabilize helical structures of all the polynucleotides very effectively at concentrations several orders of magnitude lower than the effective concentration of Na+ion.

Cu2+ and Cd2+ destabilize the helical structure of polynucleotides to form random coils. Zn2+, Ni2+, Co2+, and Mn2+ions do not behave in such a clear‐cut manner: they selectively stabilize some ordered structures, while destabilizing others, depending on the ligand strength of the nucleotide base as well as the preferred conformation of that polynucleotide.
Kinetics of thermal unfolding of lysozyme
Authors: Segawa Shin‐Ichi , Husimi Yuzuru , Wada Akiyoshi
Published: December 2004

A reversible unfolding of lysozyme has been studied by means of the temperature‐jump method by measuring the absorbance change of pH indicator p‐nitrophenol (p‐NP). In the presence of 4.5M lithium bromide three relaxation processes were found. The fastest process with a relaxation time τ of about 30 μsec is found to come from the proton‐transfer reaction between p‐NP and His 15 in lysozyme. Only the slowest process (τ ≃ 15 sec) is a first‐order reaction and attributable to the unfolding of lysozyme. These results suggest that the all‐or‐none model can be applied to the unfolding of lysozyme as a fairly good approximation. This shows good agreement with the result of Tanford et al. (J. Mol. Biol., 15, 489 (1966); J. Mol. Biol., 73, 185 (1973)). The enthalpy, entropy, and specific heat change between a native and a denatured form are found to be close to 53 kcal/mol, 168 cal/mole/°K, and 2.1 kcal/mol/°K, respectively. The enthalpy and entropy of activation and the specific heat change for the unfolding and the folding are also obtained from kinetic experiments. In the folding reaction, the enthalpy of activation is negative. In the unfolding reaction, the specific heat change is nearly equal to zero. These results suggest that a number of intramolecular hydrogen bonds are broken, but most residues remain tightly folded in the activated state. Our results in concentrated LiBr solutions are compared with those of Tanford in concentrated GuHCl solutions.
Hydrophobic interaction and a model for the elasticity of elastin
Authors: Gosline John M.
Published: December 2004

The thermodynamics of the elastic process in the rubberlike protein elastin have been investigated by microcalorimetery. The results indicate that the reversible heat liberated upon the extension of water‐swollen elastin at room temperature is much largerthan the stored elastic energy, indicating a large than the stored elastic energy, indicating a large, negative internal energy change for stretching. The ratio of the measured internal energy change to the stored energy varies inversely wiht extension, and at 22° C it is −91 for 2% extension and −3 for 70% extension. The interanl energy change also varies dramatically with temperature over the range of 2–65° C it is zero.

The temperature dependence for internal energy change is virtually identical to the temperature dependence for internal energy changes associated with the breaking of hydrophobic interactions, and it is suggested that the measured internal energy change can be attributed entirely to hte absorption of water onto nonpolar groups in the elastin network. Calculatons based on this assumption indicate that the free‐energy change associated with this solvent–polymer process is large and positive. It is concluded that the absorption of water onto hydrophobic groups contributes to the elasticity of elastin, particularly at extensions of less than about 70%. The implications of this elastic mechanism are discussed in terms of the random‐network model for elastin structure.
Conformational studies of bacterial polysaccharides. II. Optical activity of some bacterial capsular polysaccharides
Authors: Wolf Ch. , Elsässer‐Beile U. , Stirm S. , Sutton G. G. S. , Burchard W.
Published: December 2004

The optical activity of the Klebsiella capsular polysaccharides of serotypes K1, K5, K6, K8, K11, K56, and K57 has been studied in aqueous solution. Measurements of ORD in the range 185–450 nm reveal anomalous ORD with Cotton effects near λ0 = 195nm. The results are evaluated quantitatively according to hte Moffitt‐Yang and the Drude equations. Straight lines are obtained in the Moffitt‐Yang plots, while the corresponding Drude plots yield bent curves. The b0 values, calculated from the slope of the stright lines in the Moffitt‐Yang plot, range from 90 to 270 and suggest a helical superstructure for the capsular polysaccyharides. Positive b0 values have been found for K1, K5, and K6 and negative b0 values for K8, k11, K56, ad K57. Circular dichrosim has been mesured, but the CD curves are found to be truncated at the lower‐wavelength end due to the 185‐nm limit of the spectrometer used. Measurements of the temperature dependence of the specific optical rotation [α] reveal in all cases cooperative order–disorder transitions at temperatures, Tm, fro m298 to 323°K. The van′t Hoff enthalpies derived from the width of the transition curves are found to be similar in value to those of polypeptieds in aqueous solution. The K8 polysaccharide shows a two‐step transition. The results are discussed in relation to the known primary structure and x‐ray data from oriented and partially crystalline films. A model is suggested for the two‐step transition in the K8 polysaccharide.
Dynamic structure of polyriboguanylic acid in neutral aqueous solution. A proton and phosphorus‐31 NMR study
Authors: Yamada Atsuko , Akasaka Kazuyuki , Hatano Hiroyuki
Published: December 2004

An NH proton signal was observed in neutal D2 solution (pH 5.8 ± 0.2) of poly (G) (Mr > 150,000) that had been lyophilized from H2O. This NH proton is slowly exchanged with deuterium with a rate constant of 5 × 10−5 sec−1 at 29.5° C. This proves that poly(G) exists in a relatively rigid multistranded form after lyophilization in neutral aqueous solution. The number of NH protons, observedis approximately 0.5 per nucleotide, indicating that this multistrand would not be a complete four‐stranded form as suggested by x‐ray works [Zimmerman et al. (1975) J. Mol. Biol. 92, 181–192: and Arnot et al. (1974) Biochem. J. 141, 537–543]. The large difference between phosphorus‐31 spin–spin relaxation time (T2) measured with the spin‐echo method and that calculated from the line width suggests that there is a distribution of rotational angles about the phosphodiester bond. The rate of conversion among different conformatonal states is slow in the nmr time scale and is estimated to be less than 300 sec−1 at 28° C.

For both phosphorus and H8 proton, spin‐‐lattice relaxation time (T1) and T2 show opposite temperature dependence and the ratio of T1 to T2 gives the correlation time τr of 5 × 10−8 sec and 7 × 10−8 sec (at 27° C) for H8 and phosphorus, respectively. These correlation times are considerd to represent the slow rotional diffusion of the multistranded form of poly(G).
Dilute solution properties of proteoglycan fractions from bovine nasal cartilage
Authors: Kitchen Robert G. , Cleland Robert L.
Published: December 2004

Fresh proteogycans (adult bovine nasal cartilage) isolated from the densest portion of a dissociative density gradient had a weight‐average molecular weight of ca. 106 in 4M guanidine hydrochloride (GdnHCI) by light scattering. Fractions of such material obtained by elution with 4M GdnHCI from 2% agarose gel, both normal and cross‐linkd, has proteoglycan subunit molecular weights ranging from 0.8 to 2.6 × 106 and root‐mean‐square radii ranging from 35 to 52 nm in the same solvent. The protein molecular weight per proteoglycan subunit was about 1.2 × 105 and that of keratan sulfate about 1.8 × 105, both independent of total molecular weight. A random‐flight “graft copolymer” model having uniform side chains of chondroitin sulfate (40 disaccharides) and keratan sulfate (15 disaccharides) and a random‐coil polypeptide back bone was used to estimate the unperturbed radius, whihc was about 19 nm for a mol wt of 1.5 × 106. Experimental light‐scattering data for fractions were fitted very well by theoretical curves for the particale scattering factor for both linear and appropriate branched polymers. Examination of coil expansion on the basis of perturbation calculations for branched polymer models suggested that expansion did not account for the experimentally observed radii in terms of unperturbed radii calculated from the model. A possible explanation is that substantial local stiffening of the polypeptide chain due to substitution of side‐chain clusters increases the unperturbed radii. The intrinsic viscosity [η] is 4M GdnHCI ranged from 120 to 180 ml/g, and could be interpreted in terms of th eequivalent sphere model; the Flory number has approximately its normal value for flexible linear polymers. The treatment of the sedimentation coefficient by this is less successful, since the Man delkern‐Flory parameter β apparently increases with increasing molecular weight; average value are similar to those for flexible polymers, but the variation in β makes this method useful only for rough estimation of molecular weight of proteoglycans. Molecular weights of purified proteoglycans are the same in 0.2M NaCI as in 4M GdnHCI, while crude preparations gave higher molecular weights in 0.2M NaCI, probably because of association due to incomplete removel of “linking” proteins.
Kinetics of large‐ligand binding to one‐dimensional lattices: theory of irreversible binding
Authors: Epstein Irving R.
Published: December 2004

Exact solutions are obtained for the time dependence of the extent of irreversible binding of ligands that cover more than one lattice site to a homogeneous one‐dimensional lattice. The binding may be cooperative or noncooperative and the lattice either finite or infinite. Although the form of the solution is most convenient when the ligand concentration is buffered, exact numerical or approximate analytical solutions, including upper and lower bounds, can be derived for the case of variable ligand concentration as well. The physical reason behind the relative simplicity of the kinetics of irreversible as opposed to reversible binding in such systems is discussed.
Degree of polymerization and polydispersity of xylan from the cell wall of the green seaweed Penicillus dumetosus
Authors: Mackie W. , Sellen D. B.
Published: December 2004

Xylan was extracted from the cell wall of green seaweed penicillus domutosus using a very mild procedure. Xylan dinitrate samples were prepared and their degrees of polymerization found to depend markedly on temperature, of nitration, the best compromise between yield and degradation being at about −20°C. Two samples, one obtained under optimum conditions and one highly degraded, were investigated in detail by using light‐scattering, osmometry, gel‐permeation chromatography, and viscosity techniques. The results show that there are xylan chains present, in the cell wall having degrees of polymerization above 10,000. This figure is much higher than those previously found for other similar xylans. The light‐scattering results show that the xylan dinitrate molecule is much smaller than the molecules of the trinitrates of other structural polysaccharides (cellulose and mannan) for the same degree of polymerization. The effective bond length b is 16 Å, assuming a linear chain.
A proton magnetic resonance study of the interaction of adenylyl (3′ → 5′) adenosine with polyuridylic acid
Authors: Kreishman George P. , Chan Sunney I.
Published: December 2004

The interaction of adenylyl (3′ → 5′) adenosine (ApA) with polyuridylic acid in D2O solution at neutral pD has been studied by high resolution proton magnetic, resonance spectroscopy. At temperatures above ∼32°C, no evidence was obtained for the interaction of ApA with poly U. Below this temperature, a rigid triple‐stranded complex involving a stoichiometry of 1 adenine to 2 uracil bases is formed, presumably via specific adenine–uracil base‐pairing and cooperative base stacking of the adenine bases in a manner similar to that previously reported for the adenosine–poly U complex.
Syntheses of poly[β‐(l)‐menthyl D‐ and L‐aspartates] and their secondary structures
Authors: Yamamoto Hiroyuki , Hayakawa Tadao
Published: December 2004

β‐(l)‐Menthyl D‐ and L‐aspartates were prepared by a fusion reaction of N‐phthalyl D‐ and L‐aspartic anhydrides with l‐menthol, followed by hydrazinolysis. The monomers were then polymerized to poly[β‐(l)‐menthyl D‐ and L‐aspartates] by the N‐carboxyanhydride method. These polymers were soluble in many organic solvents, such as diethyl ether, tetrahydrofuran, chloroform, n‐bexane, and dioxane. From the results obtained by a study of the optical rotatory dispersions and circular dichroisms, poly [β‐(l)‐menthyl D‐aspartate] was found to be a β form structure in solution. On the other hand, poly[β‐(l)‐menthyl L‐aspartate] was a random‐coil structure. These results suggest that the asymmetry of the l‐menthyl chromophore in the side chain interacts with the polypeptide main chain and causes an extraordinary optical rotation.
Helix–coil transition in copolypeptides. II. Poly(γ‐benzyl L‐glutamate‐co‐ε‐carbobenzoxy‐L‐lysine)
Authors: Roig A. , Blanco F. García , Cortijo M.
Published: December 2004

The thermal helix–coil transition of poly(γ‐benzyl L‐glutamate‐co‐ε‐carbobenzoxy‐L‐lysine) copolypeptides was studied in solvent mixtures of different compositions. The cooperativity parameter v changes linearly with polymer (and solvent) composition, whereas the heat of the transition shows a very pronounced minimum as a function of polymer composition. This minimum cannot be due only or mainly to the solvent changes and must be attributed to the effect on the transition of the side chains of the polypeptides.
Optico‐hydrodynamic properties of high molecular weight DNA. II. Effect of aqueous glycerol solvents
Authors: Harrington Rodney E.
Published: December 2004

The optical and hydrodynamic properties of T2 bacteriophage DNA have been determined by steady‐state flow birefringence and viscosity in glycerol–aqueous buffer solvents at 25°C. Flow birefringence and extinction angle data were obtained over a velocity gradient range of 0.1 to 5 sec−1 and at concentrations from 3 to 55 μg/ml in solvents containing approximately 30, 42, and 48 vol‐% glycerol. Large optical backgrounds were observed in the mixed solvent flow birefringence studies which presented special experimental difficulties; these are described and their effect upon the flow birefringence data are discussed. The data on extinction angle provide no evidence for an internal viscosity effect on the stationary‐state hydrodynamic properties of high molecular weight DNA over a range of solvent viscosity from 0.9 to 4.6 cP. Both the optical and hydrodynamic properties under present conditions of measurement appear to be self‐consistent in terms of the values for these quantities in neutral aqueous buffer solution. Interpretation of the birefringence is complicated by uncertainties inherent in calculating the form anisotropy of DNA in non‐aqueous solvents, but the data imply no large changes in helical structure with increasing glycerol concentration. Both intact and slightly degraded DNA samples were investigated, and no significant polydispersity effects were observed under the experimental conditions described.
Potentiometric and circular dichroic measurements of poly(L‐glutamic acid) in aqueous solutions of organic and inorganic electrolytes at ambient temperature
Authors: Steigman Joseph , Cosani Alessandro
Published: December 2004

Titration of an aqueous solution of sodium poly‐L‐glutamate with a strong acid usually produces turbidity and precipitation before the equivalence point is reached. In 1M sodium p‐toluenesulfonate and 1M sodium methylcyclohexanesulfonate aggregation was delayed for days to months. In very concentrated tetra‐n‐butylammonium chloride and bromide the polymeric acid dissolved and could be titrated with NaOH. However, potentiometric titration curves in these solutions did not yield information (by way of plots of apparent pK versus the degree of neutralization) about the helix‐to‐coil transition of the polymer. It was argued in addition that the apparent pK of a weak polyelectrolyte should not be calculated from titrations in concentrated salt solutions since it is a mixed or composite quantity. It contains not only the effect of the salt on the dissociation of the weak electrolyte but its effect on the activity coefficient of hydrogen ions as well.

Circular dichroic spectra were therefore measured a t various degrees of neutralization of poly(L‐glutamic acid) in a number of aqueous salt solutions and mixtures of organic solvents with water. It was found that the undissociated polymer in the concentrated methylcyclohexanesulfonate and quaternary ammonium halide solutions had the spectrum of a right‐handed α helix. The n → π* band at 222 mμ was used as a measure of the fraction of polymer in the helical conformation. The value of − Δε for the undissociated polyacid in these organic electrolyte solutions was 11.4. By means of this value and a number of assumptions, the fraction of helix (fh) as a function of α, the degree of polyacid neutralization, was calculated for the different solvent mixtures. An empirical equation was used to describe the variation of fh with α, fh = 1/(1 + e−a+bα), in which b represents the degree of cooperativeness of the transition, and a is a measure of the effect of the medium on the onset of the transition. The values of b did not differ very much from one another, suggesting that the cooperativeness of the transition was not sensitive to changes in the medium. On the other hand, the value of a (or its equivalent, the value of α at the halfway point in the transition) was more dependent on the solvent. Comparisons of these results with those of some other workers were made by means of the empirical equation.
Amylose optical rotation in some mixed solvent systems
Authors: Dintzis F. R. , Tobin R. , Babcock G. E.
Published: December 2004

This paper extends a previous study in which a discontinuity in the specific rotation of open chain α‐l,4‐linked glucopyranosides in the water–dimethyl sulfoxide (H2O–DMSO) system was attributed to a symmetry change about a polymer chain segment. Optical rotation of amylose, cyclohexamylose, methyl β‐maltoside, and dextran was measured in the following mixed solvent systems: formamide–dimethyl sulfoxide (F‐DMSO), ethylenediamine–dimethyl sulfoxide (E–DMSO), and hexamethylphosphoramide–dimethyl sulfoxide (HMPA–DMSO). Refractive index measurements were used in an attempt to detect hydrogen bonding between solvent components. The specific rotation of amylose corrected for variation in refractive index (CSR), as a function of solvent composition, showed a discontinuity at solvent compositions corresponding to about 1 mole F to 2 moles DMSO and to 1 mole E to at least 8 moles DMSO. A discontinuity in the CSR function of amylose in the H2O‐DMSO mixed solvent that occurs at 25°C is not observed at 70°C. The CSR function of methyl‐β‐maltoside exhibits a discontinuity in solvent composition corresponding to mole ratios between 2F–DMSO and 3F–DMSO. Present results indicate that an amylose chain segment may undergo a symmetry change in solvent compositions corresponding to mole ratios between F–DMSO and F–2DMSO. Our CSR measurements of amylose and model compounds in E–DMSO and HMPA–DMSO do not permit us to distinguish between possible changes in amylose chain segment symmetry and solvent interactions that could affect symmetry properties of the glucopyranose ring.
Experimental thermodynamics of the helix–random coil transition. IV. Influence of the base composition of DNA on the transition enthalpy
Authors: Klump H. , Ackermann T.
Published: December 2004

The helix–coil transition of DNA of various base compositions has been followed by measuring the heat capacity and the ultraviolet absorption as a function of temperature through the transition region. The results of these measurements indicate that the transition enthalphy ΔH for a given pH value and salt concentration depends considerably on the base composition of the various DNA samples. The values of the transition enthalpies vary from ΔH = 7.73 kcal/mole base pair (MBP) for 31% GC base pairs to ΔH = 8.52 kcal/MBP for 72% GC base pairs. The results of the heat capacity measurements are discussed in relationship to the theoretical models suggested by various authors. Some peculiarities of the measured heat capacity versus temperature curves are reported. The correlation between these peculiarities and the results of the transcription experiments of DNA is discussed.
Effects of alkali ions on myosin conformation
Authors: Cheung Herbert C. , Cooke Roger
Published: December 2004

We have used two probes to study the effects of alkali ions on the conformation of myosin. One was paramagnetic, the “spin label” N‐(1‐oxyl‐2,2,6,6‐tetramethyl‐4‐piperidinyl)‐maleimide, which binds primarily to SH groups; and the other was fluorescent, l‐anilino‐8‐naphthalenesulfonate, which binds to an apolar niche. The bonding of the spin label to myosin was carried out in 0.6M LiCl, 0.6M NaCl, or 0.6M KCl, and the resulting labeled myosin was studied in the same medium in which the myosin was labeled as well as in other alkali chlorides. The electron paramagnetic resonance spectra of the spin label showed that the structure of myosin in the vicinity of the labeled groups differed in the various salts. The protein surface in the region of the labeled groups restricted the rotational freedom of the spin label more in KCl than in any of the other salts. Although ions are known to influence the properties of myosin, our results show that these ions also effect the molecular structure. The fluorescence of l‐anilino‐8‐naphthalenesulfonate, noncovalently attached to myosin in the presence of alkali chlorides, decreased progressively with increasing size of the cations, again showing the protein structure near the probe attachment to be a function of the cation, in the solvent. Ca2+ quenched the fluorescence of the bound probe, indicating an interaction between Ca2+ and the myosin molecule. The effect of Ca2+ on the fluorescence was greatest in KCl.
Minor nucleosides in RNA: Optical studies of dinucleoside phosphates containing inosine
Authors: Formoso Carl , Tinoco Ignacio
Published: December 2004

From the study of circular dichroism (CD) spectra and hypochromism we conclude that the dinucleoside phosphates IpA, ApI, and IpI stack, while IpU stacks very little. Studies with various concentrations of IpI in low salt, and 1M NaCl indicate that the stacking geometry of this compound is sensitive to the ionic strength of solution. The CD of poly I is presented and compared to the data for IpI. Little change was found in the CD of poly (G,I) (1 : 1) with change of salt concentration, and we conclude that, unlike Poly I, there is no major structural change. From the CD of poly (G, I), IpI, and GpG, the CD of IpG plus GpI is calculated by using the nearest‐neighbor approximation. From the calculated spectrum, we tentatively conclude that there is stacking in either IpG or GpI or both.
Synthesis and physicochemical properties in aqueous solution of the sequential polypeptide poly(Tyr‐Ala‐Glu)
Authors: Ramachandran Janakramana , Berger Arieh , Katchalski Ephraim
Published: December 2004

A polypeptide having the repealing sequence (Tyr‐Ala‐Glu)n was synthesized by the polymerization of the N‐hydroxysuccinimide ester of O‐benzyl‐L‐tyrosyl‐L‐alanyl‐γ‐benzyl‐L‐glutamate, followed by the removal of the benzyl groups by means of hydrogen bromide. The main fraction obtained on gel filtration had an average molecular weight of over 60, 000, corresponding to over 500 amino acid residues per polypcptide chain. The polymer is soluble in water above pH 5.5, and precipitates on lowering the pH. The x‐ray powder photographs show features of an α‐helical structure. The dependence of the ultraviolet absorption spectrum, the optical rotatory dispersion, and the fluorescence of poly(Tyr‐Ala‐Glu) on pH, in salt‐free as well as in salt‐containing aqueous solutions, was compared with the corresponding properties of a copolymer containing equimolar proportions of tyrosine, alanine, and glutamic acid in a random sequence. From these measurements it was concluded that poly(Tyr‐Ala‐Glu ) has a helical con formation at low pH and a random coil conformation at high pH, the transition taking place at pH 6 in the absence of salt and pH II in the presence of salt. Thus, in the range pH 7 to l0. random coil‐to‐helix transition can be achieved by merely increasing the ionic strength. A model is proposed for the structure of the helical poly peptide which accounts for the Stability of the helical conformation by assuming hydrogen bonding between the carboxylate group of the ith glutamic acid residue and the hydroxyl group of the (i + 4 )th tyrosine residue. The complex ORD of helical poly(Tyr‐Ala‐Glu) is explained as being due to a superposition of the ORD of an α‐helix and that of a regular array of phenolic ehroniopholes originating from the immobilization of the aromatic rings in the specific structure of the polymer.
Ionic polysaccharides. V. Conformational studies of hyaluronic acid, cellulose, and laminaran
Authors: Cleland Robert L.
Published: December 2004

Hindered rotation was studied for the disaccharides composed of basic β‐glucopyranose units A (linked at O1 and O4) and B (linked at O1 and O2) in Cl conformation. The van der Waals' interactions were calculated for the Lennard‐.Jones, Buckingham, and Kitay‐gorodsky interatomic potential functions, including a study of the effect of minimization of the first two functions for each atomic pair k, m (a) at the sum rkm* of the usual crystal atomic radii rk* + rm* and (b) at rkm* + 0.2 Å. Values of the ratio of unperturbed to free‐rotation root‐mean‐square end‐to‐end distance σ, were calculated for chains composed of the unsolvated disaccharide repeating units: AA (cellulose), AB and BA (hyaluronic acid), and BB (laminaran). For cellulose and hyaluronic acid, σ increases markedly with both assumed atomic radii rk* and θ, the supplement of theglycosidebond angle. Energy contributions from dipole–dipole and side‐chain interactions cause relatively small dimensional changes for hyaluronic acid: for cellulosic polymers bulky side groups attached near the glycoside carbon atom may increase or decrease unperturbed dimensions, depending on the potential function chosen. Inclusion of bond torsional potentials increases σ for cellulose and hyaluronic acid and decreases σ for laminaran. Hydrogen‐bonding ellects normally increase calculated σ values for unsolvaled polymers. The predicted influence of temperature on σ is small. The large decrease in σ with increasing temperature which appear to occur experimentally for cellulosic polymers are prc.‐umably due to conformational effects of solvation.
Theory of friction‐limited DNA unwinding
Authors: Crothers D. M. , Spatz H. C.
Published: December 2004

The theory of friction‐limited DNA unwinding is developed explicitly for moderate tind large perturbations. This extension of the earlier theory of the relaxation kinetics is necessary because of the complex nature of the rate limitation for small perturbations. The assumption of the theory that is violated under relaxation conditions is that base pairing reactions occurring at a constant local degree of twist of the strands are fast compared to the net unwinding of the molecule. However, these reactions that are slow for small perturbations have a large activation energy, and become faster than friction‐limited un winding for large enough temperature jumps and sufficiently large DXA molecules. Thus only the rate for moderate and large perturbations is clearly limited by frictional resistance to turning the molecule in solution. The model used is a diffusional unwinding of the two strands, driven by the accompanying decrease in free energy. For large perturbations a numerical solution of the diffusion equation is required, since the diffusion coefficient is not constant. Two new parameters must be introduced into the equilibrium statistical theory to describe friction‐limited unwinding kinetics. These are the force constant b, for winding up coil regions and the frictional coefficient per base pair βcfor rotating coil regions in solution. We find by fitting the theory to experiment that b = 1.8 × 10−13 ergs/ rad2‐ and βc = 3.5 × 10−21 erg see/base pair, both for DNA melted in alkali at 0.4.M Na + and ∼30 °C. The latter value is in agreement with predictions based on the viscosity of single stranded DNA in alkali. The quoted value of bcan be interpreted to mean that the number of conformational states of a nucleolide is reduced by an average factor of 1.55 when it is wound around another strand to the degree of twist in a double helix, but without forming a base pair.
Sedimentation characteristics of DNA multiply crosslinked by a difunctional alkylating agent, mustard gas
Authors: Edwards P. A. , Shooter K. V.
Published: December 2004

It is confirmed from sedimentation studies that only a small fraction of diguaninyl derivatives formed on reaction on reactions of native DNA with mustard gas crosslink the two DNA chains. It is also apparent that heavily alkylated DNA can be studied in the denatured form in dimethyl sulfoxide without the gross degradation that results if denaturation is effected by alkali.
Specificity in the genetic code: the role of nucleotide base–amino acid interaction
Authors: Rendell Marc S. , Harlos J. P. , Rein Robert
Published: December 2004

The mechanism of the unique and specific association of a given amino acid to its t‐RNA is investigated by theoretical methods. Several possible schemes are proposed to explain specificity. The physical forces which act within these mechanisms are illustrated by the computer simulation of probable interactions between glycine and nucleotide bases and base pairs. It is demonstrated that glycine has direct and selective affinities for the nucleotide bases and that these interactions are principally determined by the polar groups. Energies have been calculated for the interaction of glycine with several base pairs. From these, the possibility that specificity arises through direct complexing of an amino acid with its anticodon is evaluated.
Thermodynamic parameters of helix‐coil transition in polypeptide chains I. Poly‐(L‐glutamic acid)
Authors: Bychkoya V. E. , Ptitsyn O. B. , Barskaya T. V.
Published: December 2004

The helix‐coil transitions for poly(L‐glutamic acid) (PGA) in 0.2M NaCl and in its mixture with dioxane were studied by the methods of spectropolarimetry, viscometry, and potentiometric titration at different temperatures from 8 to 50°C. The enthalpy and entropy differences between the helical and coillike states of uncharged PGA molecules were determined from the curves of potentiometric titration. The temperature dependence of the cooperativity parameter σ was determined by two methods: from the sharpness of transition and from the dependence of the intrinsic viscosity on the helical content in the transition region. In 0.2MNaCl, σ= (2.5 ± 0.5) × 10−3 and practically does not depend on temperature, i.e., the cooperativity of the helix‐coil transition is connected mainly with the entropy decrease in initiating helical regions (ΔSi ≈ −12 is mole of helical regions). On the contrary, initiation of a helical region in the water‐organic solvent mixture is accompanied by a considerable enthalpy increase.
Biosynthèse de la cellulose bacterienne deutériée: étude par R. M. N. du taux d'incorporation et de la localisation du deutérium
Authors: Barnoud Fernand , Gagnaire Didier , Odier Léon , Vincendon Marc
Published: December 2004

The use of the NMR spectra (250 MHz) of cellulose triacetate allows the determination of the percentage of deuterium bonded to each of the six carbon atoms of the monomer residue (except for H−1 and one of the protons bonded to C6 where the signals overlap). Deuterated derivatives of D‐glucose and/or deuterated water were used for the biosynthesis of bacterial cellulose by Acetobacter xylinum. Analysis of NMR spectra of acetylated samples gives the following results. About 90% of the protons linked to C1 and C6 come from the D‐glucose used in the nutrition medium, whereas 10% are exchanged with other sources of protons. Over 40% of the protons linked to C2, C3, C4, and C5 arise from the water of the nutrition medium. Discrepancies between results of biosynthesis from deuterated water and from deuterated D‐glucose can only be explained if more than one enzymatic process is involved in the biosynthesis of bacterial cellulose.
Eleclrooptical study of the electric polarizability of rodlike fragments of DNA
Authors: Hornick C. , Weill G.
Published: December 2004

The anisotropy of electrical polarizability of rodlike fragments of DNA has been studied by a number of electro‐optical methods: Kerr effect (combined with flow birefringence), light scattering, diehroism, and fluorescence in an electric field. The most sensitive technique (Kerr effect) has been used to study the variation of the polarizability with the nature and concentration of counteroins. DNA fragments constitute a truly rigid polyelectrolyte of known structure. The value obtained can then be quantitatively compared to the predictions of those of the theories of the longitudinal polarizability of rigid polyelectrolytes which are based on true molecular parameters. The comparison emphasizes the role of the counterion–counterion repulsion. Oosawa's theory seems to represent the best approach but fails to explain the differences observed between monovalent and divalent ions.
Far‐infrared spectra of some globular proteins
Authors: Buontempo U. , Careri G. , Fasella P. , Ferraro A.
Published: December 2004

The far‐infrared absorption spectrum (40–400 cm−1) of solid pellets and films of several globular proteins (lysozyme, myoglobin, hemoglobin, serum albumin, ribonuclease, chymotrypsinogen, subtilisin) and of some representative polypeptides [nylon 66, poly (γ‐benzyl L‐glutamate)] have been investigated by using a Michelson interferometer. While polypeptides are known to present several peaks which can be assigned mostly to hydrogen‐bond modes, all the investigated globular proteins display only one broad, intense baud in the 100–200 cm−1 region. The origin of this band, which persists even after denaturation or partial digestion, is discussed.
Light‐scattering and potentiometric‐titration studies of poly‐L‐tyrosine in aqueous solution
Authors: Senior Marilyn B. , Gorrell Sandra L. H. , Hamori Eugene
Published: December 2004

Aqueous solutions of poly‐L‐tyrosine were studied by potentiometric titrations, light‐scattering measurements, and infrared spectroscopy in order to characterize the conformational changes the macromolecules exhibit when the hydrogen‐ion concentration of the solutions is varied. It was found that when the pH of the system at 25°C is lowered from a value of about 13 the poly‐L‐tyrosine molecules undergo a random‐coil to β‐structure conformation change at pH 11.5. It appears, that under the experimental conditions used, the formation of the β structure is an intramolecular process which involves the folding of the polymer backbone into several hairpins of antiparallel β structure. On further lowering of the pH of the solutions aggregation (pH 11.35) and subsequently precipitation (pH 11.2) takes place. Since the apparent pK of the polymer does not show a drastic change during the random‐coil to β‐structure conformation change, it was concluded, that the therinodynamic driving force for this conformation change is mainly due to the electrostatic effect of the partially charged side chains of the poly‐L‐tyrosine molecules.
The binding of Mg++ ions to polyadenylate, polyuridylate, and their complexes
Authors: Krakauer Henry
Published: December 2004

The binding of Mg ++ to polyadenylate (poly A), Polyuridylate(poly U), and their complexes, poly (A + U) and poly (A + 2U), was studied by means of a technique in which the dye eriochrome black T is used to measure the concentration of free Mg−. The apparent binding constant KX = [MgN]/[Mg++][N], N = site for Mg++ binding (the phosphate group of the nucleotide), was found to decrease rapidly as the extent of binding increased and, at low extents of binding, as the concentration of Na− increased in poly A, poly (A + U), and poly (A + 2U), and somewhat less so in poly U. Kx is generally in the range 104 > KX > 102. The cause of these dependences is apparently, primarily, the displacement of Na+ by Mg++ in poly U and poly (A + U) on the basis of the similarity of extents of displacement measured in this work and those measured potentiometrically.

was calculated and was found to approach zero as the concentration of Na+ increased. In poly U, poly (A + U), and poly (A + 2U) at low ΔH′ v.H. > 0, about + 2 kcal/“mole.” In poly A, also at low salt, ΔH′ v.H. ≈ −4 kcal/“mol” for the initial binding of Mg++, and increases to +2 kcal/“mol” at saturation. This enthalpic variation probably accounts for the anticooperativity in the binding of Mg++ not ascribable to the displacement of Na++.
Volume changes accompanying the complex formation of polyadenylic and polyuridylic acids
Authors: Noguchi Hajime , Arya Suresh K. , Yang Jen Tsi
Published: December 2004

The complex formation of polyadenylic acid (poly A) and polyuridylic acid (poly U) in 0.1M NaCl solution containing 0.01M sodium cacodylate was followed by dilatometric measurements at various mixing ratios of poly A and poly U. The volume changes, ΔV, accompanying the formation of poly A. poly U and poly A.2poly U were + l.5 and + 2.5 ml per mole of the nucleotide residue, respectively. This increase in volume was probably due to the increased counterion binding when the single‐stranded polynucleotides were converted into the double‐ and triple‐stranded helices, since depletion of charged species from the solvent proper would lessen the effect of electrostriction, thus resulting in a positive ΔV. The conversion of a single‐stranded poly A to a double‐stranded helix in acidic solution led to a ΔV of + 3.8 ml per mole of the nucleotide residue. This increase in volume was attributed to the charge neutralization as a result of protonation of the adenine bases.
Potentiometric titration of poly‐S‐carboxyethyl‐L‐cysteine
Authors: Maeda Hiroshi , Ikeda Shoichi
Published: December 2004

Potentiometric titration curves have been determined for aqueous solutions of poly‐S‐carboxyethyl‐L‐cysteine, which is subject to the β‐coil transition by a change in pH. Reversibility and time dependence of the titration curves are examined by different methods in order to establish the conditions for obtaining equilibrium curves. The β‐coil transition is manifest, at some region on the equilibrium titration curve, if pH – log (α/1 – α) is plotted against α. Assuming a value, 4.00, for pKint, the free‐energy change for the β‐coil transition of uncharged polymer has been evaluated from the extrapolation of the observed titration curves and is found to depend on the ionic strength and polymer concentration. The Henderson‐Hasselbach plot of the titration curve yields clearer distinction between the β‐form and random coil, and it permits estimation of the content of β‐form at, a given pH. Comparison of the conformational titration curve with the circular dichroic measurements leads to a value of −10,000° for [θ]223 for the pure β‐structure. Precipitation which occurs at low degrees of ionization and, especially, at high ionic strength does not reveal any discontinuous change of the titration curve, which suggests that, the degree of ionization of the precipitated β‐form is not very different from that in solution.
Nuclear magnetic resonance and optical spectroscopic studies of block copolymers of polypeptides. I. Block copoly[(benzyl‐L‐glulamate)n: (benzyl‐L‐aspartate)m]
Authors: Paolillo L. , Temussi P. , Trivellone E. , Bradbury E. M. , Crane‐Robinson C.
Published: December 2004

In a study of A–B type block copolymers of γ benzyl‐L‐gultamate and β‐benzyl‐L‐aspartate use has been made of the observations: (1) that for poly aspartate esters the chemical shifts of the α‐CH and NH resonances are sensitive to the helix sense, (2) that in both helical and random coil conformations the same resonances of poly‐γ‐benzyl‐L‐glutamate are well separated from those of poly aspartates. Since the sense of poly‐β‐benzyl‐L‐aspartate is very sensitive to the inclusion of γ‐benzyl‐L‐glutamate residues, the degree of overlap between the blocks can be studied by monitoring the helix sense of the aspartate. The ability of the NMR method to make separate observation of the two blocks removes the necessity of relying on an overall ORD parameter such as b0. The copolymers studied include those having lefthanded, righthanded, and mixed‐sense aspartate, corresponding to differing degrees of overlap.
Ca2+‐induced conformational transitions of phosphorylated peptides
Authors: Hollöasi M. , Ötvös L. , Ürge L. , Kajt´ar J. , Perczel A. , Laczkó I. , Vadász ZS. , Fasman G. D.
Published: December 2004

CD spectroscopic studies on protected peptides containing lysine and serine, or phosphoserine, and on serine‐containing fragments of the neurofilament protein midsized subunit, both in the unphosphorylated and phosphorylated form, are reported. The introduction of the phosphoryl group was not found to have a significant spectral effect in aqueous solution. In trifluoroethanol (TFE), spectral shifts toward unordered (type U) spectra or the appearance of distorted spectra likely reflect the adoption of aperiodic polypeptide conformations due tosalt bridge(s)between negatively charged phosphoserine and positive lysine side‐chain groups. A turn‐stabilizing effect of phosphorylation was also observed.

CD‐monitored titration experiments in TFE revealed a high conformational sensitivity of phosphopeptides toward Ca2+ions. The appearance of the unordered spectra or spectral shifts were the sign of a bulkdisorderingeffect of Ca2+ions. Spectra with specific spectroscopic features reflect the formation of Ca2+complexes and the adoption of ordered unique backbone conformations.

When ordered structures were obtained on addition of Ca2+ions, the observed CD curves showed a resemblance to the spectrum of β‐pleated sheets. This may originate fromchain extensionand the formation of β‐pleated sheet segments fixed by Ca2+bridges between PO3Hgroups of adjacent peptide chains. The data clearly show that the effect of the Ca2+ions is highly specific: the sequence, chain length, presence and distribution of charged side‐chain groups, degree and site of phosphorylation, and environmental factors appear to be determining in the process of chain extension or β‐sheet formation. © 1993 John Wiley & Sons, Inc.