bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐resolution study of the helix–coil transition of poly(L‐glutamic acid): Spectroscopic data correlation and the discovery of a new transition
Authors: Hayashi Hidechika , Wada Akiyoshi 
Published: December 2004

AbstractThis article reports on both (1) the precision and capability of a computerized multidimensional spectrophotometric system recently developed in our laboratory and (2) the high‐resolution study of the helix–coil transition of poly(L‐glutamic acid)[poly(Glu)], especially with regard to the discovery of an overlooked transition which is attributable to order–disorder rearrangement of the poly(Glu) side chain in the α‐helical conformation. This study was made possible by the high performance of the system used. The simultaneous and continuous measurement of the circular dichroism, the absorbance and light‐scattering intensity, and the pH titration curve of poly(Glu) in aqueous salt solution was carried out under continuous scanning of pH ranging from 8 to 2. Besides the well‐known random coil to α‐helix transition that occurs at about pH 5.5, a highly cooperative transition, which is indicated as a small but definite step in several spectral dimensions, is observed for the first time at pH 4.3. The transition is ascribed to an order–disorder conversion of the side chain on the α‐helix backbone.
Binding of ligands to a one‐dimensional heterogeneous lattice. I. General model for the calculation of binding isotherms by a Monte Carlo approach
Authors: Sturm Jean 
Published: December 2004

AbstractA Monte Carlo method is presented to calculate equilibria for the binding of ligands to one‐dimensional heteropolymers. Equivalency with other methods suitable for particular cases was verified (i.e., matrix and combinatorial methods). The principal interest of this Monte Carlo method is in its facility for adaptation to any physically conceivable binding model and that it gives access to the parameters accounting for partial binding to each different type of site. General properties of binding isotherms with excluded‐site effects and relations between partial binding ratios and partial free site ratios are discussed. An effective calculation is presented for illustration of the method.
Binding of ligands to a one‐dimensional heterogeneous lattice. II. Intercalation of tilorone with DNA and polynucleotides
Authors: Sturm Jean , Schreiber Lisbeth , Daune Michel 
Published: December 2004

AbstractThe interaction of tilorone with DNA and five synthetic polydeoxyribonucleotides [(I): poly[d(A‐T)]·poly[d(A‐T)]; (II): poly[d(A‐C)]·poly[d(G‐T)]; (III): poly[d(G‐C)]·poly[d(G‐C)]; (IV): poly(dG)·poly(dC); and (V): poly(dA)·poly(dT)] has been investigated. Binding isotherms for the homopolymers were obtained by microdialysis equilibria using 14C‐labeled tilorone and interpreted with different models: exclusion effect, associated or not associated with cooperativity, or variable exclusion. Affinity appears to be related more to local structure than to base composition and decreases in the following order: (I) > (II) > (III) > (IV) > (V). Intercalation in circular DNA was demonstrated by electrophoresis migration and electron microscopy, which yielded an average unwinding angle of 7° per bound dye. The behavior observed in CD and UV spectroscopy shows a sequence similar to the affinities. Tilorone seems to be less intercalated in (IV) and not at all in (V). The experimental binding isotherm of tilorone to DNA was well fitted on the basis of a model where DNA acts as a heterogeneous lattice built with the six different possible couples of adjacent base pairs, each potential site behaving as if it were in the corresponding homopolymer. The results are discussed in terms of specificity of alternating Pyr‐Pur sequences and related to theoretical calculations on intercalation energies of DNA.
Gel filtration studies of methylene blue–heparin interactions in aqueous solution
Authors: Kadokura Satoru , Miyamoto Takeaki , Inagaki Hiroshi 
Published: December 2004

AbstractThe gel filtration method was applied to the study of the interaction of the metachromatic cationic dye methylene blue (MB) with heparin in aqueous solution. This method requires the determination of the total MB concentration in the effluent. It was found that (i) MB in aqueous solution can be extracted quantitatively with benzyl alcohol (BzlOH), (ii) the metachromatic effect of MB is not observed in BzlOH, and (iii) the presence of heparin in aqueous solution does not interfere in the BzlOH extraction of MB. Accurate determination of MB concentration in the effluent can be made by extraction of MB with BzlOH, followed by the usual absorption spectroscopy. In addition, the use of the spectrophotometric method with this procedure entailed no serious problem relating to adsorption of MB on the glass walls. Gel filtration binding experiments were successfully carried out on a Sephadex LH‐20 column using 0.005M acetate buffer as effluent. The binding data obtained were analyzed in terms of the cooperativity parameter according to the method of Schwarz. The thermodynamic parameters for the binding process of MB were also evaluated. It is shown that the binding of MB to heparin is highly cooperative, exothermic, and stabilized by entropic factors.
Optical anisotropies of amides and peptides in dioxane
Authors: Khanarian G. , Mack P. , Moore W. J. 
Published: December 2004

AbstractThe molar Kerr constants mK, molar refractions mR, and dipole moments μ are reported for the N‐methylacetamides CX3CONHCH3 (X = H, CH3, F. CI, Br) and acetamides CX3CONH2 (X = H, F, Cl, Br). The components of the polarizability tensor α are deduced for N‐methylacetamide and acetamide on the basis of the bond additivity approximation. This α is found to be considerably more anisotropic than was indicated in previous determinations by other methods. The data for N‐methylacetamide were used to calculate mK, μ, and γ2 (anisotropy squared) of N‐acetyl‐N′‐methylglycine amide and N‐acetyl‐N′‐methyl‐alanine amide as functions of the torsional angles (ϕ,Ψ). The statistical mechanical averages of mK, μ, and γ2 were calculated from conformational energies obtained by the methods of Scheraga.
Electrostatic interactions in ionic homopolypeptides in solutions of moderate ionic strength
Authors: Santiago German , Maroun Rachid C. , Hawkins Erin R. , Mattice Wayne L. 
Published: December 2004

AbstractAt sufficiently high ionic strength, long‐range electrostatic interactions in a polyelectrolyte such as poly(L‐glutamic acid) might be adequately approximated in matrix calculations by use of statistical weights representing second‐order interactions. The validity of this assumption has been investigated making use of experimental observations (CD spectra and titration curves) for poly(L‐glutamic acid) as a function of temperature in 0.1–0.5M sodium chloride. Theoretical analysis, using a statistical weight matrix proposed by Warashina and Ikegami, is based on the Zimm‐Rice theory. Implementation differs from that of Warashina and Ikegami in one respect. Refinement of the initial estimates is achieved using a form of the configuration partition function which does not assume diagonalization of the statistical weight matrix. This difference is of no consequence for the values of σ and s, but it does produce somewhat different values for the statistical weights used to represent the electrostatic interactions. The method used to treat electrostatic interactions in poly(L‐glutamic acid) in 0.1M sodium chloride can be viewed as successful in that it properly reproduces the helix–coil transition and titration curves in this solvent and the molecular‐weight dependence of the titration curves yields values for s in harmony with those obtained using a treatment which is independent of model, and gives a reasonable ionic‐strength dependence for the electrostatic parameters. Furthermore, the model can account for measured helix–coil transitions and titration curves in homopolypeptides in which the side chain is —(CH2)xNHCO(CH2)yCOOH. The model, however, is not exact. It does not properly account for the molecular‐weight dependence of the helical content for polymers of low degree of polymerization.
Analysis of the ionization constants and heats of ionization of reduced and oxidized horse heart cytochrome c
Authors: Marini M. A. , Martin C. J. , Berger R. L. , Forlani L. 
Published: December 2004

AbstractSimultaneous curve fitting for the ionization parameters of oxidized and reduced horse heart cytochrome c in 0.15M KCl and 20°C yields values for the ionization constants (as pK′) and the heats of ionization (ΔHi) which can reconstruct either the potentiometric or thermal titration curves. Reduced cytochrome c requires 8 sets of groups, whereas oxidized cytochrome c requires 10 sets of groups. The additional groups in the oxidized preparation appear to involve the ferriheme (pK′, 9.25; ΔHi, 13.7 kcal/mol) and a tyrosine (pK′ ≃ 10.24) that is not present in the reduced form. The potentiometric and thermal difference curves (reduced – oxidized) involve the appearance of 17 kcal/mol centered at pH 9.7 and 5.8 kcal/mol centered at pH 4.9. The carboxyl groups in both species appear to be normal for the hydrogen‐bonded form. Only one histidine has normal ionization properties (pK′, 6.7; ΔHi, 7.5 kcal/mol), as do 17 of the lysine residues (pK′, 10.8; ΔHi, 11.5 kcal/mol).
Induced circular dichroism and mode of binding of acridine orange adsorbed on β‐form poly(S‐carboxyethyl‐L‐cysteine) in aqueous solutions
Authors: Ikeda Shoichi , Yoshida Tomohiko , Imae Toyoko 
Published: December 2004

AbstractThe absorption spectra and circular dichroism (CD) have been measured for aqueous solutions of acridine orange of a constant concentration, [D] = 5 × 10−5M, mixed with poly(S‐carboxyethyl‐L‐cysteine) in various mixing ratios, [P]/[D], ranging from 330 to 11, at different pH. The absorption spectra of the dye–polymer solutions are hypochromic, and the main band is located at 470 nm, accompanying a shoulder at 500 nm. At alkaline pH, no CD is induced in the visible region. At neutral and acidic pH, where the polymer is in the β‐conformation, CD is induced in the visible and near‐uv regions. A pair of CD bands is located at the region around 450 nm, when the pH is around the neutrality, while it appears at the region around 500 nm at acidic pH. Thus, the optically active species of bound dye changes from dimer to monomer on lowering the pH. These species form dissymmetric arrays along a polypeptide chain. The fraction of bound dye forming dissymmetric sequences is not high, but most of bound dye is adsorbed randomly on the ionized carboxyl groups of polypeptide chain and gives rise to hypochromism only. A dissymmetric structure of dye–polymer complexes is presented, in which the polymer has the β‐conformation and the dye cations, either dimeric or monomeric, bind to its side chains, in such a way that the longer axes of molecular planes of bound dye form a two‐fold, right‐handed helix along the extended polypeptide chain. A zeroth‐order calculation of CD based on the coupled oscillator model leads to the result that each dissymmetric array of dye consists, on the average, of two dimeric or monomeric cations. This low number of bound cations in a dissymmetric array and the large fraction of randomly adsorbed dye suggest that the hydrophobic interaction of dye with the polymer is strong, so that dye cations are adsorbed sparsely on both sides of the extended polypeptide chain.
Modification of the reactivity of a small molecule by reversible association with a synthetic polymer. Inhibition of the hydrolysis of cationic esters by polyanions
Authors: Morawetz Herbert , Shafer Jules A. 
Published: December 2004

AbstractThe base‐catalyzed hydrolysis rate of the cationic esters obtained by quaternization of N,N,N′,N′‐tetramethylethylenediamine with phenylbromoacetate was studied in buffers and in solutions of partially neutralized polymeric acids. The polyanions were found to be powerful inhibitors of the reaction. This effect was interpreted as due to the association of the ester with the polyanion, from which the catalytically active hydroxyl groups are repelled. It is shown that kinetic data may be interpreted by a procedure similar to the Lineweaver‐Burk plot to yield the reactivity of the bound ester and the dissociation constant of the polymer–ester complex.
Polyelectrolyte behavior of charged polyamino acids in aqueous solutions
Authors: Ascoli F. , Botré C. 
Published: December 2004

AbstractThe conductivity and activity coefficient of counterions of sodium salts of some charged polyamino acids, as poly‐L‐glutamic acid, poly‐L‐aspartic acid, and poly‐L‐cysteic acid, were measured in aqueous solution. The results show that the degree of binding of small counterions to the charged macroions shows a characteristic dependence on dilution and temperature which is not common for other simple polyelectrolytes. Such behavior is very likely related to conformational changes induced by the above factors.
Raman scattering of some synthetic polypeptides: Poly(γ‐benzyl L‐glutamate), poly‐L‐leucine, poly‐L‐valine, and poly‐L‐serine
Authors: Koenig J. L. , Sutton P. L. 
Published: December 2004

AbstractThe Raman spectra of poly‐γ‐benzyl‐L‐glutamate, poly‐L‐leucine, poly‐L‐valine, and poly‐L‐serine are reported. For the α‐helical polymers, the conformationally sensitive amide I, II, and III modes are observed in the Raman as, well as the infrared. For the β form, the Raman effect, supplies the infrared inactive inphase motion which is useful for the determination of a parallel or antiparallel chain alignment. Modes characteristic of the specific polypeptide are also observed which are insensitive to conformation.
The lattice energetics of some polypeptide chains
Authors: Hopfinger A. J. 
Published: December 2004

AbstractThe interchain energetics of alpha, beta, and PGII conformations of polyglycine, the PPII and left‐handed 3.30 fold helical conformations of trans poly‐L‐proline, and the Yonath and Traub triple helix and left‐handed three fold helices of poly(gly‐pro‐pro) were investigated. Intra‐ and inter‐chain stabilization energies appear to be inversely related, and the interchain stabilization energy can be as large its the intrachain energy. The minimization of the interchain energy can be described by the simultaneous optimization of interchain hydrogen bonding and intermolecular‐sidechain digitation. The stability of the poly(gly‐pro‐pro) triple helix can be readily explained in terms of these two factors. In all cases the experimentally observed lattice packing is predicted, although the calculated lattice constants are slightly larger than those observed. The small differences between observed and predicted lattice constants probably reflect small errors in present conformational potential functions. Homopolymers are probably the best systems to use in the refinement of conformational potential functions because solvent effects arc minimized and the experimentally observed lattice constants provide a check on the configurational calculations.
Dielectric disperison of linear polyelectrolytes
Authors: Michael Schurr J. 
Published: December 2004

AbstractA three‐dimensional (gaussian) model is formulated that permits evaluation of the one‐dimensional fourier cosine transform of the counterion‐counterion coulombic interaction energy ϕk. It is shown that ϕkis much larger for small k than was assumed by Oosawa; consequently, the magnitude of his dielectric increment, and also his relaxation time, must be drastically revised to smaller values. Evidently, the self‐field of the fluctuation is large enough to seriously depress the amplitude of the spontaneous fluctuations, and to force Ohmic conduction of the ions at a rate far in excess of the rate of translational diffusion. Finally, it is noted that in highly conducting bulk solvents, where both positive and negative counterfoils coexist in the ion‐atmosphere, one might expect to observe a low‐frequency component of the dielectric relaxation arising from unequal rates of diffusion of the positive and negative species, in analogy with the situation for spherical colloidal particles. In such a circumstance, the basic counterfoil fluctuation mechanism proposed by Oosawa would acquire a new validity.
Theory of the influence of oligonucleotide chain conformation on double helix stability
Authors: Delisi C. , Crothers D. M. 
Published: December 2004

AbstractWe consider theoretical aspects of reactions that form base pairs in a double helix. The equilibrium constant for such reactions depends on the probability of finding the two bases in the correct orientation for pairing. This probability can be expressed in terms of the spatial and angular distribution of one micleotide around the other. In this paper we use Monte‐Carlo techniques to calculate the distribution of distances between chosen phosphates in nonhclical oligonucleotide backbones, using crystallographic data for bond lengths and angles, and a screened Coulomb potential for phosphate–phosphate interactions. The model chosen is one that predicts correctly the observed dimensions of an unperturbed polynucleotide chain. Knowledge of distance distribution functions permits calculation of the dependence on loop size of the probability of closing a single backbone strand into a hairpin helix. Our results agree roughly, although not exactly, with the semiempirical ring‐weighting functions determined by Schefller. Elson, and Baldwin. Further results are a comparison of intramolecular and bimolecular helix nucleation equilibrium constants and a calculation of the stacking free energy in a double helix.
Circular dichroism calculation for random‐coil polypeptide chains
Authors: Zubkov V. A. , Birshtein T. M. , Milevskaya I. S. , Volkenstein M. V. 
Published: December 2004

AbstractA method of calculation of the circular dichroism (CD) of random‐coil polypeptides has been developed by means of a Monte‐Carlo approach to the treatment of statistical systems and exciton theory of optical activity of polymers. The contribution of π–π* and n–π* amide transitions to the CD has been taken into account. The π–π* transition gives rise to two CD bands: a negative short‐wavelength band and a weak positive long‐wavelength one. The n–π* transition gives rise to one negative CD band.
Thermodynamic parameters of helix–coil transition in polypeptide chains. II. Poly‐L‐lysine
Authors: Barskaya T. V. , Ptitsyn O. B. 
Published: December 2004

AbstractThe helix–coil transitions for poly‐L‐lysine (PL) were investigated by the methods of spectropolarimetry, viscometry and potentiometric titration in 0.2M NaCl at different temperatures as well as in 0.2MNaBr, 1MKCl, and in mixtures of 0.2MNaCl or NaBr with methanol at room temperature. The enthalpy and entropy differences between the helical and coillike states of uncharged PL molecules in 0.2.M NaCl were determined from the potentiometric titration curves. The cooperativity parameters σ for PL in different solvents were determined by two methods (from the sharpness of the transition and from the dependence of the intrinsic viscosity on the helical content in the transition region). In 0.2MNaCl σ has a value of (2.3 ± 0.5) × 10−4 and does not depend on temperature, i.e., the cooperativity of the helix‐coil transition, as for PGA, is mainly of an entropy origin (the initiating of the helical region is accompanied by the entropy decrease ΔSi = −12 eu/mole of helical regions). A comparison of the obtained results for PGA and PL with the molecular theories of the helix‐coil transitions shows that the role of dipole‐dipole interactions of nonneighboring peptide groups is greatly overestimated in these theories, leading to a considerable enthalpy contribution to the free energy of initiating helical regions which is not observed in the experiment.
Stepwise synthesis of oligopeptides with N‐carboxy α‐amino acid anhydrides. II. Oligopeptides with some polar side chains
Authors: Katakai Ryoichi , Oya Masanao , Uno Keikichi , Iwakura Yoshio 
Published: December 2004

AbstractThe reaction of NCA's with some amino acids having a nucleophilic functional group on the side chain was studied in a heterogeneous reaction medium (acetonitrile‐water). Glutamic acid and aspartic acid, having a free carboxyl group on the side chain, were successfully used to synthesize oligopeptides without interactions of the γ‐ and β‐carboxyl group with NCA's. Two products were obtained by the reaction of NCA with L‐lysine, which contains a free amino group on the side chain. ε‐Protected lysine was used to prepare α‐peptides as a nucleophile in the reaction. No racemization was observed in the synthesis of peptides by the NCA method in the heterogeneous solvent system. Oligopeptides with some polar side chains were synthesized by the NCA method.
Simplified force field calculations of the low‐frequency motions of the α‐helix
Authors: Fanconi Bruno , Peticolas W. L. 
Published: December 2004

AbstractUsing valence force field constants and a highly simplified model of the α‐helix consisting of only two masses per repeat unit we have been able to very nearly reproduce the low frequency phonon dispersion curves which we had obtained earlier with the use of a seven mass model and a Urey‐Bradley force field. Since the frequencies obtained from this latter model agree well with the observed Raman frequencies it appears that the low frequency chain motions of polypeptide chains may be calculated from a very simple model involving the amino acid residues as essentially a single mass. Such techniques appear to offer the possibility of making normal mode calculations for the chain dynamics of polypeptide chains of low symmetry such as proteins.
Electrostatic contributions to oligonucleotide transitions
Authors: Delisi Charles , Crothers Donald M. 
Published: December 2004

AbstractIn a previous paper we employed Monte Carlo techniques to calculate distribution functions for distances between charged phosphates of randomly coiled oligonucleotides in solution. The average energy of the random coil, as well as the loop weighting function and bimolecular nucleation parameter, was obtained as a function of chain length and salt concentration. In the present paper we apply the results to a consideration of the electrostatic dependence of the helix–coil transition in oligonucleotides. By considering the equilibrium among three species: hairpin, dimer, and random coil, we have calculated (1) the variation in melting temperature of dimer, hairpin, and the dimer‐hairpin mixture with salt concentration and chain length, (2) the variation in the equilibrium between dimer and hairpin as a function of salt concentration, temperature, and length, (3) the variation in the transition breadth with salt concentration and chain length.