bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformation of poly(L‐lysine) homologs in solution
Authors: Tseng Yuen‐Wen , Yang Jen Tsi 
Published: December 2004

AbstractThe effect of the number of methylene groups in the side chains on the conformation of polypeptides is assessed for three poly(L‐lysine) homologs with R = –(CH2)nNH2. Circular dichroism studies show a pH‐induced helix–coil transition in 0.05 M KCl with midpoints at 9.6, 9.0, and 8.7 for n = 5, 6, and 7, respectively, as compared with 10.1 for (Lys)x (n = 4). Homologs with n = 6 and 7 could be partially helical even when the side groups are fully charged (with n = 7, the compound is highly aggregated above pH 9.1). Thus, the longer the number of methylene groups the more stable is the helical conformation of these homologs. Potentiometric titration of the n = 5 homolog gives a ΔG° of −310 cal/mol (residue) for the uncharged coil‐to‐helix transition at 25°C. The corresponding ΔH° and ΔS° are −1740 cal/mol (residue) and −4.8 e.u./mol (residue). Unlike (Lys)x, the uncharged helix‐to‐β transition is slow and incomplete even after heating at 80°C for 1 hr. Addition of methanol enhances the helical formation in neutral solution with midpoints at 72, 52, and 27% methanol (v/v) for n = 5, 6, and 7, respectively [cf. 88% for (Lys)x]. Addition of sodium dodecyl sulfate induces a coil‐to‐helix transition for all three homologs in contrast with the β form of (Lys)x under similar conditions.
Block copolymers of amino acids. I. Synthesis and structure of copolymers of L‐alanine or L‐phenylalanine with D,L‐lysine‐d7 or D,L‐lysine
Authors: Cardinaux F. , Howard J. C. , Taylor G. T. , Scheraga H. A. 
Published: December 2004

AbstractWater‐soluble block copolymers of the type (A)m‐(B)n‐(A)p, where (A)m,p was either poly(D,L‐lysine‐α,β,β,γ,γ,δ,δ‐d7) or poly(D,L‐lysine) and (B)n was either poly(L‐alanine) or poly(L‐phenylalanine), were synthesized for conformational studies by proton magnetic resonance spectroscopy. Analytical determination of the amount of the initiator fragment (n‐hexylamine) at the C‐terminus of the copolymers was used to obtain the number‐average degrees of polymerization, DPn, and thereby, together with the amino acid composition, to establish the covalent structures of the polymers. The values of DPn were found to be much lower than those deduced from sedimentation equilibrium or form viscosity measurements. These deviations, which also are thought to have arisen in similar studies reported in the literature, are attributable to intermolecular aggregation; the relation of such aggregation to covalent structure (and its effect on the polymerization reaction) is discussed in terms of the conditions and mechanism of synthesis of block copolymers of amino acids.
Block copolymers of amino acids. II. Physicochemical data on copolymers containing L‐alanine or L‐phenylalanine
Authors: Howard J. C. , Cardinaux F. , Scheraga H. A. 
Published: December 2004

AbstractThe water‐soluble block copolymers, whose syntheses were described in the preceding paper, were subjected to ultracentrifugation, viscosity, optical rotatory dispersion circular dichroism, fluorescence, proton magnetic resonance, and infrared measurements. Discrepancies between Mn and Mw, and line broadening in the proton magnetic resonance spectra (attributed to the formation of rigid structures), support the conclusion (drawn in the preceding paper) that the block copolymers are aggregated in aqueous solution. It is shown that similar block copolymers reported in the literature are also aggregated.
Hydrodynamic shielding of spherical subunits in macromolecular complexes
Authors: Schmitz Kenneth S. 
Published: December 2004

AbstractThe Garcia de la Torre‐Bloomfield hydrodynamic interaction tensor was used to calculate the shielding coefficient matrices for each spherical friction bead in the rigid arrays of a rod and helix. Negative values for the average shielding coefficient result for small beads adjacent to large beads, suggesting premature truncation in the series expansions employed in the hydrodynamic interaction tensor. Numerical analysis also suggests that the magnitude of geometric asymmetry is not a good measure of the extent of friction asymmetry of the molecule due to extensive hydrodynamic shielding by other subunit beads.
Conformational studies on polynucleotide chains. II. Analysis of steric interactions and derivation of potential functions for internal rotations
Authors: Tosi Camillo , Clementi Enrico , Matsuoka Osamu 
Published: December 2004

AbstractIn the first paper of this series we showed that the total electronic energy, computed ab initio in the Hartree‐Fock approximation for both independent and coupled rotations of the five torsional angles in the sugar–phosphate–sugar complex C10H18O8P, can be reproduced with reasonable accuracy by a Lennard‐Jones 6‐12 potential, with different attractive and repulsive parameters assigned to the four oxygens of the phosphate group, on one hand, and the four oxygens of the sugar rings and the hydroxyl groups, on the other. The conclusion was reached on the basis of some attempts at the derivation of analytical expressions capable of correctly describing the energies obtained with the quantum mechanical computations. An analysis of the barriers to internal rotation for the angles φ and ψ indicated the possibility of improving the description through addition of further terms, in particular of an intrinsic torsional potential. In order to obtain a fit based on all internal rotations of the sugar–phosphate–sugar molecules, and coupling numerical accuracy with physical significance, we made a study of the possible contributions to the conformational energy: intrinsic torsional energy, electrostatic interactions, London attractions, van der Waals repulsions. The results of this study show that the best description of ab initio energies is offered by a potential containing a Lennard‐Jones 6‐12 term and an intrinsic torsional term.
Dehydrated circular DNA: Circular dichroism of molecules in ethanolic solutions
Authors: Gray Donald M. , Taylor Thomas N. , Lang Dimitrij 
Published: December 2004

AbstractWe have measured the ultraviolet CD spectra for covalently closed and linear forms of phage PM2 DNA in solution. We find that increased concentrations of salt or ethanol (up to 50% ethanol by weight) depress the long‐wavelength positive CD bands in the spectra of both forms of DNA, although the spectrum of the native covalently closed DNA always has a slightly larger magnitude of these bands than does the spectrum of the linear DNA. In addition, both DNAs are equally capable of undergoing a transition to the A conformation in 70–80% ethanol at low Na+ concentrations. Thus, the constraint imposed by the covalent closure of a DNA molecule does not seem to hinder its conformational response to these changing solution conditions. Lang [(1973) J. Mol. Biol. 78, 247–254] has found by electron microscopy that T7 DNA has an inherent ability to condense into compact particles, suggested to be supercoils of multiple order. Both covalently closed and linear forms of PM2 DNA also become condensed when the DNA, in 0.2M ammonium acetate and 1 mM EDTA, is exposed to ethanol and subsequent drying on specimen grids [Lang, D., Taylor, T. N., Dobyan, D. C. & Gray, D. M. (1976) J. Mol. Biol. 106, 97–107]. Under similar conditions, in solutions of 0.2M ammonium acetate and 1 mM EDTA to which ethanol is added, we have measured the CD spectra of both covalently closed and linear forms of DNA. Below ethanol concentrations at which the DNA obviously precipitates, the CD spectra of both forms have reduced long‐wavelength positive CD bands.
A semiempirical extension of polyelectrolyte theory to the treatment of oligoelectrolytes: Application to oligonucleotide helix‐coil transitions
Authors: Record M. Thomas , Lohman Timothy M. 
Published: December 2004

AbstractThe interaction of counterions with a suitably long, charged oligomer appears susceptible to treatment in the context of polyelectrolyte theory by the introduction of an end‐effect parameter that reflects the reduced association of counterions with the terminal regions of the oligo‐ion. Use of a physically reasonable value for the end‐effect parameter provides excellent agreement between theory and the experimental data of Elson, Scheffler, and Baldwin [J. Mol. Biol. 54, 401–415 (1970)] on the dependences of melting temperature on salt concentration and chain length for a series of hairpin helices formed by d(TA) oligomers. The differences in behavior expected for hairpin, dimer, and oligomer‐polymer helices are discussed. The salt dependence of the end‐joining equilibrium investigated for λ DNA by Wang and Davidson [Cold Spring Harbor Symp. Quant. Biol. 33, 409–415 (1968)] is treated as an oligomer–polymer interconversion. The dependence of equilibrium constant for this reaction on counterion concentration is in good agreement with that predicted by theory for an end‐region totalling 24 nucleotides, the known length of the λ ends.
Oxygenation of cobalt(II) protoporphyrin IX dimethyl ester bound to copolymer of 4‐vinylpyridine and styrene
Authors: Nishide Hiroyuki , Hata Seiji , Mihayashi Keiji , Tsuchida Eishun 
Published: December 2004

AbstractThe polymeric cobalt(II) porphyrin complexes were prepared from cobalt(II) protoporphyrin IX dimethyl ester(Co(II)P) and copolymers of 4‐vinylpyridine and styrene(PSP), and their binding ability of molecular oxygen was studied in toluene solution. The five‐ and six‐coordinate structure of CoP‐PSP complexes were confirmed by esr spectra. The esr parameters for the CoP‐PSP complexes were not affected by the molecular weight and the vinylpyridine‐unit content of PSP‐ligand. The 1:1 dioxygen‐Co complex was reversibly formed when the solution of CoP‐PSP was exposed to oxygen atmosphere at low temperature. While the visible spectra and esr parameters for the dioxygen complexes of CoP‐PSP were the same as those of the CoP‐pyridine complex, the equilibrium constant for the oxygen binding increased with the vinylpyridine‐unit content of the PSP‐ligand. The larger entropy change was observed for the oxygenation in the CoP‐PSP system especially, of which the vinylpyridine‐unit content was large.
The low‐ temperature mechanical relaxation of elastin. II. The solvated protein
Authors: Scandola M. , Pezzin G. 
Published: December 2004

AbstractThe low‐temperature dynamic mechanical relaxation of ox Ligamentum nuchae elastin, swollen with water and ethylene glycol at various swelling ratios, has been investigated by means of the Rheovibron DDV II viscoelastometer, at frequencies from 3.5 to 110 Hz. The peak location on the temperature scale, its intensity and activation energy have been studied as a function of solvent content and it has been found that the two solvents influence the dynamic mechanical behavior in a quite different way. A similar interaction of the solvent molecules with the backbone peptide groups is assumed for both solvents, and the differences in the mechanical spectra, which are more marked the higher the solvation degree, are explained in terms of the different size of the protein–solvent relaxing units.
Molecular states in single‐stranded adenylate chains by relaxation analysis
Authors: Pörchke Dietmar 
Published: December 2004

AbstractThe single‐strand helix‐coil transition in various oligo‐ and polyadenylates is characterized by means of an improved cable temperature‐jump technique. In all the polymers studied {poly(rA), poly(dA), poly[A(m2′)] and poly[A(e2′)]} helix‐coil relaxation is observed in the time range from 30 to 1000 nsec. Relaxation‐time constants observed at wavelengths λ<280 nm (τα) are different from those found at λ >280 nm (τβ), indicating the presence of more than two conformational states. The time constants τα increase in the series poly(dA), poly[A(m2′)], constants τβ/τα is approximately 2.5, except in poly(dA) where τβ/τα ≈ 9. Relaxation measurements with r(A)n‐ oligomers show a decrease in conformational mobility with increasing chain length. The relaxation curves also demonstrate that “internal” residues have lower reaction rates than residues at the ends of the oligomer chain. Measurement in D2O reveal a solvent isotope effect for τα of +87% for poly(rA), and of +53% for poly(dA), whereas no isotope effect is found in τβ. The absence of “slow” relaxation processes in the model compound 9,9′ ‐trimethylenebisadenine shows that the relatively low rate of the single‐strand helix‐coil transitions is due to the coupling of base stacking with the folding of the sugar–phosphate chain. The absence of a seprate relaxation process (corresponding to τβ) in 9,9′‐trimethylenebisadenine, as well as in the dinucleotides ApC and CpA, suggests that this relaxation process is dependent upon the presence of both the sugar–phosphate chain and of adjacent adenine bases. The experimental data provide evidence that there is more than one ordered conformation in various single‐stranded oligo‐ and polyadenylates and that the transition between these conformations is influenced by the sugar conformation.
Fluorescence correlation spectroscopy. III. Uniform translation and laminar flow
Authors: Magde Douglas , Webb Watt W. , Elson Elliot L. 
Published: December 2004

AbstractWe extend fluorescence correlation spectroscopy to systems that undergo translation or laminar flow in a sample cell. We include theoretical and experimental results; we consider uniform and nonuniform velocity profiles. Concentration correlation analysis extracts microscopic rate parameters from measurements of the spontaneous concentration fluctutations, which occur even at equilibrium. Fluorescence is one of the most sensitive means of monitoring these fluctuations. Analysis of flowing or translating systems (1) offers a method of measuring number concentrations of selected species, for example, of aggregates or polymers, (2) provides a nonperturbing velocity probe, (3) sometimes allows one to circumvent photolytic degradation, (4) has proved extremely helpful in testing and aliging apparatus for fluorescence correaltion measurement and in verifying theoretical analyses, and (5) may be required for interpretation of results obtained on systems in motion, even though that motion is undesired or initially unsuspected. We include both theoretical and experimental results for combined Poiseuille flow and diffusion in the geometry which is of most practical interest. Theoretical expressions for the much simpler cases of nondiffusive Poiseuille flow as well as uniform flow or translation with or without diffusion constitute limiting cases which are displayed explicitly.
Dynamic light‐scattering studies of internal motions in DNA. I. Applicability of the rouse‐zimm model
Authors: Lin S.‐C. , Schurr J. Michael 
Published: December 2004

AbstractThe intermediate scattering function G(K,t) for any polymer model obeying a linear separable Langevin equation can be expressed in terms of the eigenvalues and eigenvectors of its normal coordinate transformation. An algorithm for the extract numerical evaluation of G(K,t) for linear Rouse‐Zimm chains in the presence of hydrodynamic interaction has been developed. The computed G(K,t)2 were fit to C(t) = A exp(−t/τA) + B, and apparent diffusion coefficients calculated according to Dapp ≡ 1/(2τAK2). G(K,t)2 was surprisingly well‐fit by single‐exponential decays, especially at both small and large values of Kb, where K is the scattering vector and b the root‐mean‐squared subunit extension. Plots of Dapp vs K2 in‐variably showed a sigmoidal rise from D0 at K2 = O up to a constant plateau value at large K2b2.Analytical expression for G(K,t), exact in the limit of short times, were obtained for circular Rouse‐Zimm chains with and without hydrodynamic interaction, and also for free‐draining linear chains, and in addition for the independent‐segment‐mean‐force (ISMF) model. The predicted behaviors for G(K,t) at large Kb (or KRG) was found in all cases to be single‐exponential with 1/τ ∝ K2 at large Kb, in agreement with the computational results. A simple procedure for estamating all parameter of the Rouse‐Zimm model from a plot of Dapp vs K2 is proposed.Experimental data for both native and pH‐denatured calf‐thymus DNA in 1.0M Nacl with and without EDTA clearly plateau behavior of Dapp at large values of K, in harmony with the present Rouse‐Zimm and ISMF theories, and in sharp contrast to previous predictions based on the Rouse‐Zimm model.
The triple helix‐coil transition of cyanogen‐bromide peptides of the α1‐chain of the calf‐skin collagen
Authors: Saygin Oe. , Heidemann E. , Klump H. 
Published: December 2004

AbstractThe thermal triple helix‐coil transition of the CNBr peptides of the α1‐chain of calf‐skin collagen was studied optically and calorimetrically. Besides α1CB5, all the peptides were able to form triple‐helical structures at low temperatures. The peptides with longer chain lengths showed, under the experimental conditions, hysteresis in the transition range depending on the direction of the successive temperature changes. The detailed thermodynamic analysis of the optical transition curves was only possible for the two small peptides α1CB2 and α1CB4. We observed a higher stability of α1CB2 relative to α1CB4 (α1CB2 has higher imino acid content), accompanied with increased values of both denaturation enthalpy and entropy. Further, we observed a linear relationship between the calorimetrically determined denaturation enthalpy of all the CNBr peptides and their imino acid content. Although this behavior is qualitatively in accordance with the observation of Privalov and Tiktopulo on various kinds of native collagen, the CNBr peptides showed much lower values of the thermodynamic parameters ΔH0 and ΔS0 and differed also in the rate of their change with imino acid content. These differences are interpreted as being caused by misalignment in the helical form of the CNBr peptides resulting in a rupture of the specific interactions in the native form.
The electronic structure of cytosine, 5‐azacytosine, and 6‐azacytosine
Authors: Raksányi K. , Földváry I. , Fidy J. , Kittler L. 
Published: December 2004

AbstractThe normal and vacuum uv spectra of cytosine, 5‐azacytosine, and 6‐azacytosine thin layers were determined. The spectra were resolved into a series of Gaussian bands and the experimental band positions and oscillator strengths were compared with the calculated values. The calculations were carried out with the PPP‐SCF‐CI method. The agreement of the calculations with those of others and with the experiment is discussed.
Opticohydrodynamic properties of high‐molecular‐weight DNA. III. The effects of NaCl concentration
Authors: Harrington Rodney E. 
Published: December 2004

AbstractExcluded volume and persistence length of high‐molecular‐weight DNA from T2 bacteriophage have been evaluated over a range of NaCl concentrations from 0.005 to 2.0M using low‐shear flow‐birefringence and intrinsic‐viscosity data. Uncertainty in persistence length due to ambiguity in the assignment of intrinsic birefringence has been avoided by calibrating the data at 0.2M NaCl using a recently reported persistence‐length value based upon photon correlation spectroscopy [Jolly, D. & Eisenberg, H. (1976) Biopolymers 15, 61]. Results at high salt concertrations are in satisfactory agreement with other estimates of excluded volume and chain flexibility in the literature, but at very low salt concentrations they reflect greater chain expansion than has heretofore been reported. The extinction‐angle data imply a transition from a nondraining chain with excluded volume at 0.1M NaCl to an almost freely draining chain at 0.005M NaCl. Over this same salt range, the experimental persistencelength data agree very well with Flory's thermodynamic chain‐expansion theory [Flory, P. J. (1953) J. Chem. Phys. 21, 162], but are in generally poor agreement with other theoretical treatments. A detailed comparison of the results with other data in the literature suggests that the combined flow‐birefringence‐intrinsic‐viscosity technique employed here may be more sensitive to the distribution of chain stiffness and excluded volume in polyelectroytechain expansion of DNA than are othe rhydrodynamic methods such as sedimentation or intrinsic viscosity alone.
Spatial configuration of ordered polynucleotide chains. V. Conformational energy estimates of helical structure
Authors: Olson Wilma K. 
Published: December 2004

AbstractSemiempirical potential energy functional used previously to account successfully for the mean‐square unperturbed dimensions and nmr coupling constants of randomly coiling polynucleotides are used, after modifications, to account for base stacking and interstrand hydrogen bonding, and to evaluate the conformational energies of single‐ and double‐stranded polynucleotide helices. Attention is focused upon the variety of A‐genus helices with local backbone conformations resembling the known double‐helical structures of RNA. Distinct structural differences between single‐ and double‐stranded helices are predicted from the energy calculations. A second point of interest is the apparent failure of two conformationally identical left‐handed polynucleotide chains to form a left‐handed duplex. The third major observation of the study is the wide morphological variety of theoreticaly allowed right‐handed polynucleotide duplexes. In addition to the familiar double helix stabilized by horizontal base stacking and hydrogen bonding, an unusual vertical double helix is predicted to form between complementary bases fixed in the unusual but not energetically forbidden high anti glycosyl conformation. Experimental results bearing upon the theoretical predictions are discussed.
Relaxation and electrophoretic effects in polyelectrolyte solutions. II. Polyelectrolyteplus‐salt solutions
Authors: Schmitt A. , Meullenet J. P. , Varoqui R. 
Published: December 2004

AbstractElectrophoretic mobilities are studied in polyelectrolyte‐plus‐salt solutions, using linear irreversible thermodynamics and the concepts of relaxation and electrophoretic effects discussed in paper I. If ionic interactions are treated within the Debye‐Hückel approximation, co‐ions contribute significantly to the relaxation field experienced by polyions. Moreover, through self‐diffusion and electrophoretic measurements, the effective valance of the polyion becomes an experimentally accessible parameter. It should provide another method to check the concept of ion condensation.
Preresonance Raman studies of poly(L‐lysine), poly(L‐glutamic acid), and deuterated N‐methylacetamides
Authors: Sugawara Yoko , Harada Issei , Matsuura Hiroatsu , Shimanouchi Takehiko 
Published: December 2004

AbstractThe Raman spectra of poly(L‐lysine) with various structures, ionized poly(L‐glutamic acid), and deuterated N‐methylacetamides have been observed using visible and the 257.3‐nm laser lines as the light source. Most of the Raman bands with significantly enhanced intensities in the uv‐excited spectra of the polymers have been assigned to the vibrations associated with the CO and C–N stretching modes, the amide I, II, III, I′, II′, and III′, with reference to the results obtained for simple amide molecules including the deuterated N‐methylacetamides. Several amide frequencies have been newly identified and the structures of the polymers have been discussed through the comparison of the Raman and ir amide frequencies.