bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polarography of polynucleotides. IV. Effect of the molecular weight of poly(U) on its adsorption at a charged surface
Authors: Janik Borek , Sommer Ronald G. 
Published: December 2004

AbstractEffects of molecular size on the adsorption properties of poly(U) were studied using alternating current polarography as a technique and a dropping mercury electrode (d.m.e.) as a model interface. The measurements were carried out on fractions (by molecular weight) of poly(U) characterized by sedimentation and viscosity measurements. The data indicate that the rate of poly(U) adsorption is controlled by diffusion. The adsorption equilibrium can be established during the drop‐life at higher concentrations of poly(U) where the electrode is fully covered, while at low concentrations corresponding to the linearized isotherm, the time τ for the establishment of the adsorption equilibrium is much longer than can be obtained with d.m.e. The time τ increases with increasing chain length, n (in monomeric units). From the concentration dependence of the course of current time, I ∼t, curves, or of the current values at the end of the drop life, a constant K was calculated which depends on n. In the range of molecular weights studied (25 × 103 to 564 × 103) the data obeys the relationship log n = a + b log K (where a and b are constants). Area, A, occupied by the monomer of an adsorbed poly(U) molecule was calculated from experimental values of K and D (diffusion coefficient). The decrease of A with increasing n was explained in terms of the looping of longer poly(U) chains out from the electrode surface.
Studies on cyclic peptides. I. Cyclodisarcosyl–metal salts complexes
Authors: Sugihara Toshiharu , Imanishi Yukio , Higashimura Toshinobu 
Published: December 2004

AbstractThe complexes of cyclodisarcosyl (N,N′‐dimethyldiketopiperazine) have been synthesized with copper perchlorate, lithium perchlorate, barium perchlorate, silver perchlorate, silver nitrate, and boron trifluoride. It has been shown by infrared absorption spectra that the metal cations coordinate to carbonyl groups of the peptide to form insoluble complexes. It has been suggested that the complexation takes place by ion–dipole interaction. Since a linear analog of the peptide formed no insoluble complex with the metal salts, conformation of cyclodisarcosyl seems to play an important role in the complex formation. Examination of the molecular model and X‐ray analysis suggest that the copper perchlorate complex of the cyclic peptide has a “2:1‐sandwich” structure.
Synthesis and electron microscopic investigation of model polyacryloylnucleosides
Authors: Mosevitsky M. I. , Panarin E. F. 
Published: December 2004

AbstractUsing the interaction of polyacrylic anhydride with uridine or N‐acetyl derivatives of adenosine, cytidine, and guanosine, the water‐soluble copolymers, polyacryloylnucleosides, were obtained. The acryloylnucleoside units to acrylic acid units ratio in the copolymer was usually about 1:20. The attaching of nucleosides to the polymer occurs mostly through the 5′‐hydroxyl group of the sugar.The prominent feature of all polyacryloylnucleosides obtained is their fibrous structure at an ionic strength 0.2 and neutral pH. At concentrations <200 μg/ml the separate strands with a length of 0.2–1.0 μ and diameter of 30–40 Å are distinguishable. Evidently they are formed by side association of two molecules of copolymer or by folding of one molecule on itself. At higher concentrations branched multistranded structures are formed. In the same conditions polyacrylic acid alone does not form the fibrous structures.Heating of polyacryloylnucleoside solutions at 100°C and fast cooling in ice water, or raising of the pH to 12 turned the stranded structures to coils. After annealing or neutralization the stranded structures reformed. These transformations are similar to those which occur with nucleic acids. The results show that the fibrous structure of the copolymers depends on the hydrogen bonds formed by purine and/or pyrimidine bases.
Macromolecular structure and organization of alpha keratin
Authors: Harget P. J. , Krimm S. 
Published: December 2004

AbstractThe small‐angle equatorial X‐ray scattering of alpha keratin (African porcupine quill) was studied using a direct type of analysis, which allows the separation of the intermicro‐fibrillar interference effects from those of the intramicrofibrillar scattering without the use of prior assumptions. X‐ray data were obtained from 470–21 Å; their analysis by the above method resulted in a z‐axis projection of the microfibrillar electron density, which extends over a diameter of 80 Å and has a core region surrounded by a peak located at a radius of 28 Å. The macromolecular organization of the 80‐Å‐diameter microfibrils was found to be an arc‐like layer type of aggregation and not a pseudohexagonal packing. When the specimen was subjected to silver staining the aggregation of the microfibrils did not change except for a slight contraction. The z‐axis projection of the stained microfibril, however, was significantly different. The silver appears to build up slightly around the outer periphery of the microfibril, stains the peripheral region very little, deposits on the inside of the peripheral region, and outlines the core area.
Isothermes de partage de DNA, rRNA et RNA rapidment marqués dans un système solvant salin
Authors: Garel Jean‐Pierre 
Published: December 2004

AbstractPartition isotherms of DNA, rRNA, and rapidly labeled RNA in a salt solvent system are determined. In the salt solvent system PMB (potassium phosphate buffer 1.50 M pH 7.0:2‐methoxyethanol:2‐butoxyethanol; 3:1:variable volume), equilibrated at the temperature T, the partition isotherms of animal ribosomal RNA and DNA form a series of straight lines according to the basic relation log k = B − AT(BuO), where k is the partition coefficient, B and AT are parameters depending upon the base composition, the molecular weight, the helix content, and conformation of nucleic acids, and (BuO) refers to the 2‐butoxyethanol amount in volume percent. This relation is also valid for other nucleic acid compounds (bases, nucleosides, nucleotides, oligoribonucleotides, and transfer RNA). For RNA fractions distributed in different Kirby salt solvent systems, log k is proportional to the relative levels of adenine and guanine expressed as the A/(A+G) ratio.Partition isotherms of high molecular weight RNA from mouse plasmocytoma, labeled during a few hours, are not straight lines. This behavior indicates a heterogeneous RNA population. By plotting the specific activity of this mixture (rRNA and rapidly labeled RNA) determined in the top phase of our salt solvent system as a function of the 2‐but‐oxyethanol content, we obtained a sigmoidal curve, which characterizes the nature of the RNA population investigated. Formulas are given for the calculation of the specific activities of rRNA and rapidly labeled RNA and for the calculation of their relative ratio.
Sequential oligopeptides. Synthesis and characterization of the oligopeptides and a polypeptide with the repeating sequence L‐norvalyl‐glycyl‐L‐proline
Authors: Bonora Gian Maria , Toniolo Claudio 
Published: December 2004

AbstractThe synthesis and characterization of a series of oligopeptides (from the tripeptide to the octadecapeptide) with the repeating sequence L‐norvalyl‐glycyl‐L‐proline and a polytripeptide with this sequence are reported. The oligomers were synthesized step by step using the mixed anhydride method. All the products were chemically and optically pure. The polymer was prepared by the active ester method, using the p‐nitrophenyl ester as the polymerizable tripeptide derivative. Good yield of relatively high average molecular‐weight polymer was obtained. In the accompanying paper conformational investigations, both in solution and in the solid state, on the oligomers and the polymer are described.
Solution properties of synthetic polypeptides. XVIII: Helix–coil transition of poly‐N5‐(2‐hydroxyethyl)L‐glutamine
Authors: Miyake Michihisa , Akita Shuichi , Teramoto Akio , Norisuye Takashi , Fumita Hiroshi 
Published: December 2004

AbstractThe helix–coil transition of poly‐N5‐(2‐hydroxyethyl)L‐glutamine (PHEG) in aqueous isopropanol was examined by means of optical rotatory dispersion (ORD) and intrinsic viscosity [η] measurements. The Zimm–Bragg parameters σ and s for the transition were determined from the ORD data as a function of molecular weight. It was found that the transition was characterized by a relatively low cooperativity; the values of \documentclass{article}\pagestyle{empty}\begin{document}$ \sqrt \sigma $\end{document} were in the range from 0.039 to 0.066, depending on the solvent composition. These σ values are much larger than those reported for other polypeptide–solvent systems. The transition enthalpy was negative and its magnitude varied with the solvent composition, with a maximum of 620 cal/mol at 40 wt% isopropanol. The curve of [η] versus helical content for a high‐molecular‐weight sample exhibited a very broad minimum, and this behavior was attributed to the low cooperativity of the transition.
Conformational change of poly‐Nε‐glutary‐L‐lysine and poly‐Nε‐succinyl‐L‐lysine in aqueous salt solutions
Authors: Murai Norio , Sugai Shintaro 
Published: December 2004

AbstractThe conformational changes of poly‐Nε‐glutaryl‐L‐lysine (PGL) and poly‐Nε‐succinyl‐L‐lysine (PSL) in various salt solutions were studied by use of ORD and potentiometric titration measurements. The addition of alkali metal salts to the fully ionized PGL or PSL solution caused helix formation. The helical content of the polymers increases in the following sequences: at salt concentration 0–2 M, CsCl < KCl < LiCl < NaCl; and at 2–3 M, LiCl < CsCl < KCl ∼ NaCl. The preferential binding of the solvent components with various alkali metal salts of PGL or PSL was measured in LiCl, NaCl, and KCl solutions by means of equilibrium dialysis and differential refractometry. It was found that with increasing salt concentration, the polymers were preferentially hydrated in NaCl and KCl soultions; however the salt was preferentially bound to the polymers in LiCl solution. Such preferential binding was suggested to be closely related to conformational change. The addition of CaCl2 to polymer solutions led to the stabilization of the helical structure of PGL or PSL.
Polymerization of optical isomers of phenylalanine N‐carboxyanhydride by poly (N‐methylalanine) diethylamide
Authors: Imanishi Yukio , Kugimiya Kazuya , Higashimura Toshinobu 
Published: December 2004

AbstractIn the polymerization of phenylalanine N‐carboxyanhydride (NCA) using poly(N‐methyl‐L‐or DL‐alanine) diethylamide as initiator, the polymerization rate was L‐NCA ≃ D‐NCA > DL‐NCA. This is a new type of selective polymerization and indicates the incompleteness of earlier investigations to study the asymmetrically selective polymerization without D‐NCA. Neither secondary structure nor optical activity of the polymeric initiator is a reason for the selectivity. Hence the cause for the selectivity was sought in the properties of the NCA's in solution. However, the selectivity was not observed in the polymerization initiated by poly(L‐phenylalanine) dimethylamide. The importance of the initiator being a secondary amine type was suggested. The experimental results are discussed on the basis of these considerations.
Dielectric studies of electrolytic poly(α‐amino acid)s in aqueous solutions
Authors: Aiuchi Toshihiro , Murai Norio , Sugai Shintaro 
Published: December 2004

AbstractThe dependence of the dielectric constant and dielectric loss of aqueous solutions of poly‐ε, N‐succinyl‐L‐lysine on its degree of polymerization, degree of neutralization, concentration of the polymer, and counterion type was studied in a frequency range from 300 Hz to 5 MHz. Regardless of the conformation, a low‐frequency dispersion in a frequency range lower than 10 kHz and a high‐frequency dispersion in a range higher than 100 kHz were found. The large value of the dielectric increment, its nonlinear dependence on concentration, its remarkable dependence on counterion type, and its dependence on the degree of polymerization suggest that the low‐frequency dispersion is mainly due to the polarization of loosely bound counterions. These data were found for both the helical and coiled forms. The rotational motion of the electric dipole on the molecule could not have been primarily responsible for these results. On the other hand, the high‐frequency dispersions may be attributable to the Maxwell–Wagner‐type effect.The results were compared with the dispersions of poly(L‐glutamic acid), poly(L‐lysine), and their salts reported previously.
Intermolecular orientations of adenosine‐5′‐monophosphate in aqueous solution as studied by fast fourier transform 1H nmr spectroscopy
Authors: Evans Frederick E. , Sarma Ramaswamy H. 
Published: December 2004

AbstractProton magnetic resonance spectra of 5′AMP were taken in the concentration range of 0.001–2.2M. The concentration profiles of all the nonexchangeable protons were determined. The data for 5′AMP was compared to those of adenine, adenosine, and poly(A). Theoretically computed isoshielding lines of the adenine moiety were used to qualitatively predict a preferred stacking geometry of 5′AMP in aqueous solution. It is concluded that 5′AMP at pH 8 forms multistacked aggregates at high concentration levels and that a preferred orientation is such that the bases are aligned face to back with considerable, though less than 100%, base overlap; and that the ribose moieties of adjacent molecules are near one another with the phosphate groups well separated. Mn(II) ion binding studies show that the stacks are not restricted to one unique orientation type. Specific evidence is given showing that base‐stacking orientations in the solid state may in some cases be considerably different from that in aqueous solution, due in part to numerous hydrogen bonding differences, and this is shown to be the case for base‐stacked adenosine. In the case of 5′AMP the stacking orientations between the solid and liquid states are also different, except in this comparison the solid‐state structure carries a positive charge.
Conformational properties of methionine homo‐oligopeptides in solution
Authors: Bonora Gian Maria , Toniolo Claudio 
Published: December 2004

AbstractA conformational analysis was carried out in solution on a series of L‐methionine oligomers having the general formula \documentclass{article}\pagestyle{empty}\begin{document}$ {\rm BOC\rlap{--} (L - Met\rlap{--})}_n {\rm OMe (}n = 2 - 7)$\end{document}. We examined these oligopeptides in TFE, HFIP, EG, and mixed organic–water media. The critical size for helix formation was found to be seven residues in TFE, whereas the β‐associated structure appears at the pentamer in EG and TFE–water (20 : 80, v/v). In HFIP, however, the oligomers exist essentially in an unordered conformation.
Optical activity of doubly ordered macromolecules
Authors: Tenenbaum A. , Triolo L. 
Published: December 2004

AbstractIn order to analyze the optical activity of poly‐N‐γ‐carbobenzoxy‐L‐α,γ‐diaminobutyric acid, the microscopic model we have previously worked out is here further developed. Comparison with experimental data allows us to formulate a hypothesis on the stereochemical interaction between the side chains and the backbone of the macromolecule, and on the dependence of the optical activity on the conformational state of the backbone itself. Finally, the thermodynamic parameters concerning the side chains are estimated.
Conformational change of the triple‐helical structure. II. Conformation of (Pro‐Pro‐Gly)n and (Pro‐Pro‐Gly)n(Ala‐Pro‐Gly)m(Pro‐Pro‐Gly)n in an aqueous solution
Authors: Sutoh Kazuo , Noda Haruhiko 
Published: December 2004

AbstractMeasurements of the molecular weight of (Pro‐Pro‐Gly)n and (Pro‐Pro‐Gly)n(Ala‐Pro‐Gly)m(Pro‐Pro‐Gly)n, which were synthesized by the solid‐phase method, revealed that they formed a trimer in an aqueous solution, and dissociated into single‐stranded chains on warming. Accompanying the transition, a large decrease of optical rotation was observed, like the collagen–gelatin transition. The shape of the trimeric molecule was rodlike, and the dimensions were 12 Å in diameter and 2.8 Å per residue in length, regardless of the length of Ala‐Pro‐Gly sequences in a peptide chain. The data indicate that both Pro‐Pro‐Gly sequences and Ala‐Pro‐Gly sequences from the triple‐helical structure similar to that of collagen in aqueous solution. All optical rotational dispersion (ORD) curves of solutions of the peptides were represented by a single‐term Drude equation, and the Drude constant λc was 200 nm for all peptides regardless of the length of Ala‐Pro‐Gly sequences. The resemblance between the helical structure formed by Pro‐Pro‐Gly sequences and that by Ala‐Pro‐Gly sequences was also suggested by the formation of the hybrid triple helix from two kinds of peptide chains with different lengths of Ala‐Pro‐Gly sequences.
The precipitation of poly‐L‐glutamic acid. I. α‐Precipitation
Authors: Zimmerman S. S. , Mandelkern L. 
Published: December 2004

AbstractStudies have been made of the precipitation of poly‐L‐glutamic acid from dilute aqueous solutions, over the pH range where the α‐helical conformation is maintained. The major purpose is to establish the molecular conformation in the precipitate and to outline the mechanism of the precipitation. Utilizing molecular‐weight fractions, it is shown that there are two distinctly different precipitation regions, which depend on temperature, concentration, and pH. In one of these regions, the α‐region, a variety of physical properties demonstrate that precipitation occurs without any conformational change. The temperature coefficient of the precipitation process in this region indicates that it is nucleation‐controlled.
Conformation of tetranactin in solution
Authors: Kyogoku Yoshimasa , Ueno Masaharu , Akutsu Hideo , Nawata Yoshiharu 
Published: December 2004

AbstractThe conformation of tetranactin, an ionophore, in chloroform was investigated by infrared and Raman spectra and by proton and 13C magnetic resonances. The infrared spectra show that the structure of its K+ complex in the solution is quite similar to that in crystals. The proton spin–spin coupling constants are explained well by assuming that the crystalline structure is retained in solution. The spin–lattice relaxation times of the 13C nuclei of the K+ complex indicate that its framework is rigid. The correlation time of the overall reorientation of the molecule was calculated to be 9 X 10−11 sec. On the other hand, the conformation of the complexed form in chloroform differs from that in crystals. Despite the geometrical nonequivalence of the four subunits in the crystalline state, the nuclear magnetic resonance spectra show their magnetic equivalence in the solution. The proton spin–spin coupling constants have values that are averaged by rapid internal rotation. The spin–lattice relaxation times of the 13C nuclei in its framework are unexplained by the overall reorientation of the molecule, and reveal the existence of internal motion in the framework. The rate of the local motion of the framework is between 102–1010 sec−1. By comparison of the infrared spectra, it can be said that the mean conformation of the fluctuated framework of the uncomplexed tetranactin in the solution is similar to that of nonactin in the crystalline form, which has an S4 symmetry axis through the center of the macrocyclic ring.
The structure of V amylose dehydrate: A combined X‐ray and stereochemical approach
Authors: Murphy Vincent Gerard , Zaslow Bert , French Alfred Dexter 
Published: December 2004

AbstractVisually integrated, flat‐plate film data were collected from oriented filaments of V amylose dehydrated made from dimethyl sulfoxide–amylose; and X‐ray diffraction and stereochemical methods were used to search a multidimensional parameter space for the most satisfactory description of the crystal and molecular structure. Results indicate that the helical chains are left‐handed and that they pack into the unit cell in an antiparallel arrangement conforming to space group P212121. Packing is very compact with several O …. O contacts in the range 2.70–2.85 Å between both parallel and antiparallel pairs of chains. Other characteristics of the final model are residue geometry similarity to residue 3 from potassium acetate–cyclohexamylose, O(2)i–O(3)i+1 distance of 2.75 Å, O(6) gg, and O(6)i–O(2)i–6 distance of 2.84 Å. Proton magnetic resonance studies of dried, crystalline V amylose dehydrate powder showed only 0.15 water per glucose residue.
Estimation of the circular dichroism exhibited by statistical coils of poly(L‐alanine) and unionized poly(L‐lysine) in water
Authors: Mattice Wayne L. , Harrison William H. 
Published: December 2004

AbstractThe circular dichroism of Ac‐(Ala)x‐OMe and H‐Lys‐(Lys)x‐OH with x = 1, 2, 3, and 4 has been measured in aqueous solutions. The oligomers with x = 4 show similar circular dichroism spectra in water when the lysyl amino groups are protonated, and they respond in similar fashion to heating and to sodium perchlorate. Both oligomers at 15°C exhibit a positive circular dichroism band at 217–218 nm, which is eliminated by the isothermal addition of 4 M sodium perchlorate or by heating. The positive circular dichroism of the lysine oligomer is also eliminated when the pH is elevated to deprotonate the amino groups. Positive circular dichroism is still observed for Ac‐(Ala)4‐OMe at elevated pH. Circular dichroism spectra have been estimated for poly(L‐alanine) and poly(L‐lysine) as statistical coils under the above conditions, based on the trends established with the oligomers. Poly(L‐lysine) and poly(L‐alanine) are predicted to exhibit similar circular dichroism behavior in aqueous solution so long as the lysyl amino groups are protonated. The circular dichroism of the statistical coil of poly(L‐lysine), but not poly(L‐alanine), is predicted to change when the pH is elevated sufficiently to deprotonate the lysyl amino groups. These results suggest that the unionized lysyl side chains participate in interactions that are not available to poly(L‐alanine). Hydrophobic interactions may occur between the unionized lysyl side chains. Protonation of the lysyl amino groups is proposed to disrupt these interactions, causing poly(L‐alanine) and protonated poly(L‐lysine) to have similar circular dichroism properties.
The conformational analysis of adenosine triphosphate by classical potential energy calculations
Authors: Millner O. E. , Andersen Jon A. 
Published: December 2004

AbstractThe conformational analysis of adenosine triphosphate was conducted by using classical potential energy calculations. All rotatable bonds were examined, i.e., no dihedral angles were fixed at predetermined conformations except for the ribofuranose ring, which was held in the C(3′)‐endo conformation—the conformation observed for adenosine in the crystal state.The energy terms included in the total energy expression consist of nonbonded pairwise interaction, electrostatic pairwise interaction, free energy of solvation, and torsional bond potentials.Two separate approaches were used in the conformational analyses. The first consisted of a sequential fragment approach were four bonds were rotated simultaneously at 30° increments. Each fragment overlapped the preceding one by at least one bond. All rotors were then simultaneously examined at their minima and at ±15°. The second approach consisted of a coarse grid search where all rotors were examined simultaneously, but only at staggered positions. The low‐energy conformations thus obtained were then used as starting conformations for a minimization routine based on the method of conjugate directions. The first approach required about 40 hr of central processing unit (CPU) computer time, while the coarse grid/minimization approach required about 4 hr of CPU time.Both the sequential fragment approach and the minimization approach yielded lowest‐energy conformations which are remarkably similar to the solid‐state conformation of C(3′)‐endo ATP.