bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photoselective synthesis of azobenzene‐containing cyclic oligosarcosine and its thermal cis → trans isomerization in solution
Authors: Sisido Masahiko , Ito Hiroshi , Imanishi Yukio 
Published: December 2004

AbstractOligosarcosines, which contain as azobenzene group at the center of the chain and amino groups at both ends [(Sar)nAzo(Sar)n], were prepared with the N‐carboxyanhydride method. The oligomers were coupled with an equimolar amount of succinyl chloride in the presence of triethylamine. When the condensation was carried out under photo irradiation, the azobenzene group assumed the cis configuration and the intramolecular reaction (cyclization) was facilitated. Intermolecular polycondensation occurred preferentially in the dark, in which case the azo group was trans. Cyclic oligosarcosine, which contains one azo group, was isolated by gel chromatography, and its thermal cis → trans isomerization was examined in dimethylformamide. The isomerization rate depended strongly on the number of sarcosine units n in the oligomer; for very small rings (n < 5), the rate constants were less than those for open‐chain analogs; for rings of medium size (n = 5 ∼ 10), they were larger than those for open‐chain analogs; and for longer chains, no significant difference was observed. This specific chain‐length dependence was explained by the conformational restrictions of the cyclic oligomers. The ring‐restricted isomerization was evidenced by an isomerization‐induced conformational change observed in 1H‐nmr spectroscopy.
Solution properties and chain flexibility of pullulan in aqueous solution
Authors: Kato Tadaya , Okamoto Toshihiro , Tokuya Tadashi , Takahashi Akira 
Published: December 2004

AbstractMolecular characteristics for pullulan, a polysaccharide produced by a fungus Aureobasidium pullulans, were measured by light scattering, viscometry, and gel‐permeation chromatography. From the experimental data the Mark‐Houwink‐Sakurada viscosity equation in water at 25°C was determined for samples having the molecular weight M ranging from 48 × 103 to 2.18 × 106 g mol−1 as [η] = (1.91 ± 0.02) × 10−2Mw0.67±0.01 (in cm3 g−1); and as molecular weight decreased, the slope of the viscosity equation decreased, although the molecular weight values below 30 × 103 g mol−1 evaluated by gel‐permeation chromatography were somewhat unreliable. The unperturbed dimensions 〈R2〉01/2 of pullulan were estimated by determining the expansion factor αs, from the theoretical combination of theories for the interpenetration function Ψ and those for αs. The 〈R2〉0/M value estimated from this procedure in 6.7 × 10−17 cm2 mol g−1. We concluded that the polysaccharide chain that is linked by the α‐1,6‐glucosidic linkage behaves like a flexible chain in aqueous solution.
Kinetic and equilibrium studies of the interactions of silver ions with poly(A)
Authors: Yakabe Yoshikuni , Sano Takayuki , Kure Naohisa , Murakami Kiyofumi , Yasunaga Tatsuya 
Published: December 2004

AbstractThe interaction of silver ions with poly(A) was studied by potentiometric titration, uv spectrophotometry, and stopped‐flow spectroscopy. For 0 < rb < 0.5, where rb is moles of silver ion bound per mole of nucleotide base, there exists only one type of binding for poly(A). Using McGhee's theory, the binding parameters, such as intrinsic binding constant, number of sites per nucleotide, and cooperativity, were determined from the potentiometric titration data. Using the stopped‐flow method, one relaxation time was observed in 0 < r0 < 0.5, where r0 is the moles of silver ions added per mole of nucleotide base. The concentration dependences of the relaxation time suggest that the binding of silver ions to poly(A) proceeds through the following mechanism:

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where M is free silver ions, P the free binding sites on poly(A), and C and C′ are two forms of the complex. The nature of the binding of silver ions to poly(A) is also discussed.
Ligand‐induced melting reaction of specific‐sequence DNA molecules
Authors: Tachibana Hideki , Wada Akiyoshi 
Published: December 2004

AbstractAn algorithm for the calculation of ligand‐induced helix–coil transitions of macromolecules of any specific sequence was derived. The probabilities of each residue to be in helix and ligand‐free, helix and ligand‐bound, coil and ligand‐free, and coil and ligand‐bound states can be calculated by extending the recursion relation formula proposed by D. Poland [(1974) Biopolymers 13, 1859–1871]. Calculations using hypothetical DNAs having block heterogeneities for melting reactions showed that cooperative binding specific to single strands weakens the effect of the heterogeneity. Fine structures in the melting profiles or cooperatively melting regions, which have so far been found in thermal melting experiments, were predicted to exist in ligand‐induced melting reactions for natural DNA fragments.
Conformation and folding in histones H1 and H5
Authors: Crane‐Robinson C. , Privalov P. L. 
Published: December 2004

AbstractDenatured histones H1 and H5 can be readily refolded on salt addition. Their digestion by trypsin leads to limit peptides of about 80 residues having the same nmr and CD spectra as those of the intact parent histones. Scanning microcalorimetry shows that (1) the folded structures of H1 and H5 are located entirely in their limit peptides; (2) both have values of the specific denaturation enthalpy typical for small globular proteins; and that (3) both exhibit a classic “2‐state” transition (ΔH = ΔH). The heat‐denaturation profiles of H5 measured using intrinsic and extrinsic Cotton effect and side‐chain nmr peaks do not coincide at all. Only the intrinsic Cotton effects give a Tm and ΔH close to that from microcalorimetry. We conclude that these proteins exhibit large‐scale side‐chain motions that precede the macroscopic cooperative transition.
NMR analysis of structure and function of snake neurotoxins
Authors: Miyazawa Tatsuo , Endo Toshiya , Inagaki Fuyuhiko , Hayashi Kyozo , Tamiya Nobuo 
Published: December 2004

AbstractThe 270‐MHz proton‐nmr spectra of short neurotoxins (erabutoxins from Laticauda semifasciata and cobrotoxin from Naja naja atra) and long neurotoxins (toxin B from Naja naja and α‐bungarotoxin from Bungarus multicinctus) have been analyzed. The conformation of erabutoxin b in solution is largely consistent with the x‐ray crystal analysis, although the environment of His‐7 in solution is definitely different from that in the crystal. The pH‐dependent transition has been found for toxin B, indicating that the conformation in neutral solution is different from that in the crystal as grown from acidic solution. The deuterium‐exchange rates of the amide protons for the four neurotoxins have been measured. The order of structural rigidity is the same as the order of the irreversibility of neuromuscular block by neurotoxins.
1H‐NMR studies on poly(oxyethylene)‐bound oligopeptides
Authors: Bode Karsten , Mutter Manfred , Saltman Robert P. , Goodman Murray , Ribeiro Anthony A. 
Published: December 2004

AbstractConformational studies on poly(oxyethylene)‐bound homo‐, oligo‐, guest‐host, and sequential peptides synthesized according to the liquid‐phase method were carried out by means of 1H‐nmr spectroscopy. The solubilizing effect of the C‐terminal polymeric support allowed a thorough investigation of the secondary structure in solution.
Insulin's structural behavior and its relation to activity
Authors: Dodson E. J. , Dodson G. G. , Hubbard R. E. , Reynolds C. D. 
Published: December 2004

AbstractThis paper discusses the hypothesis that insulin undergoes a conformational change either before or during its binding to the receptor. The evidence for this is not conclusive but allows us to reconcile the following observations: (1) no chemical modification or deletion of invariant surface residues has abolished the hormone's activity—only reduced its potency. (2) Reduction in potency follows many modifications to different side chains, both variant and invariant. (3) There are insulins with perfectly preserved structure (by the criteria of aggregation, spectroscopy, and x‐ray analysis) that have markedly reduced potency. (4) Insulins with disturbed structure still exhibit real, sometimes substantial activity.
Microheterogeneity of bovine myelin basic protein studied by nuclear magnetic resonance spectroscopy
Authors: Deber Charles M. , Cheifetz Sela , Moscarello Mario A. 
Published: December 2004

AbstractMyelin basic protein isolated from bovine white matter is known to consist of a mixture of three or more “charge isomers”, which can be separated by cation‐exchange chromatography. We are using 360‐MHz 1H‐nmr spectroscopy to establish the chemical and structural differences among them. Preliminary studies by difference spectroscopy between two of the isomers suggest (a) all aromatic residues, and probably their nearest‐neighbors, are unchanged; (b) the less cationic isomer lacks one (or two) of its C‐terminal Arg residues; and (c) a significant fraction of the two Met residues in the less cationic isomer is present as methionine sulfoxide.
Peptide factors as pharmaceuticals: Criteria for application
Authors: Wünsch E. 
Published: December 2004

AbstractThe increasing interest in the pharmaceutical use of peptide factors in human medicine presents formidable challenges for peptide chemistry. Fully reproducible multistage syntheses with a definite assessment of the degree of purity represent the crucial premise for the introduction of peptide factors as pharmaceuticals. Extensive studies of the stability of peptidic material on storage allows identification of the most suitable form of administration. Nevertheless, the high clearance rate of peptides as pharmaceuticals presents new challenges for improvement by structural modification of resistance to enzyme degradation without creating new problems related to metabolites.
Specific and nonspecific macromolecule–drug conjugates for the improvement of cancer chemotherapy
Authors: Hurwitz Ester 
Published: December 2004

AbstractAntineoplastic drugs such as daunomycin, adriamycin, methotrexate, 5‐fluorouridine, cytosine arabinoside, and platinate were bound to antibodies directly or via a polymeric bridge. The drug antibody conjugates retained most of their drug and antibody activities when tested in vitro. Daunomycin–antibody conjugates were shown to penetrate tumor cells in the conjugated form. In animals, daunomycin–antibody conjugates were at least as effective chemotherapeutically as the corresponding free drugs and considerably less toxic. In some tumor systems, the daunomycin–antibody conjugates represented an improvement over the free drug. This improvement was restricted in some tumors to a particular injection route of the tumor and the treatment.
Breathing and bending fluctuations in DNA modeled by an open‐base‐pair kink coupled to axial compression
Authors: Manning Gerald S. 
Published: December 2004

AbstractWe develop a model designed to show that flexibility in the DNA molecule can arise from relatively improbable transient opening of base pairs. The axial direction changes at the site of an open base pair. The region between open base pairs is a double helix of hydrogen‐bonded base pairs with a slightly decreased rise per residue and a slightly increased helical winding angle. An analysis of the model yields several testable predictions. For example, we predict probability 0.026 for a base pair to be open at 25°C, a value close to that measured by hydrogen‐exchange experiments. Other predictions involve matters like the variation of persistence length with ionic strength and temperature, the variation of helical winding angle with temperature, and the kinetics of heat denaturation. An additional result of the analysis is an explanation of the high degree of local stiffness of the DNA molecule. Strong resistance to bending fluctuations is provided from two sources: increased polyelectrolyte repulsion among phosphate groups in the axially compressed stacks between open base pairs and the tendency of stacking forces to oppose opening of a base pair. Stacking forces, however, also support compression of the stacks between open base pairs, so that the net effect of stacking forces on elastic bending of DNA is small relative to the polyelectrolyte effect. If the ionic charges on the phosphate groups were absent, DNA would spontaneously fold, driven by the entropy gained when about 1% of its base pairs open.
Hydrogen bonding of the carbonyl groups of uridine nucleosides
Authors: Scheiner Steve 
Published: December 2004

AbstractMolecular‐orbital calculations are used to compare the hydrogen‐bonding characteristics of the two carbonyl groups of uridine nucleosides. Various numbers of water molecules are allowed to interact with uracil. The hydrogen‐bond energies and the effects of these bonds on the electronic structure of uracil provide no evidence of a significant difference between the two carbonyls in terms of intrinsic properties. Calculations are also performed upon MMU, a derivative of the uridine nucleoside and a close analog of a system studied previously by nmr measurements. Energy minima are located on the conformational energy surface. The calculated anti‐gg global minimum is quite similar to the x‐ray structure. Electronic parameters examined in the various minima, as well as in hydrated complexes of MMU, again indicate no significant chemical differences between the two carbonyls. The theoretical data offer an explanation of the observed differences in shift of the two carbonyl 17O resonance signals when an aprotic solvent is replaced by water. Whereas the two carbonyls are found to be chemically similar, the observed difference in behaviour is attributed to steric factors. The lesser accessibility of the C2 carbonyl to solvation allows a smaller number of hydrogen bonds with water and hence a reduced shift when the solvent is changed.
Copolymerization kinetics of N‐carboxyanhydrides of some α‐amino acids: Influence of nature of amino acids
Authors: Atreyi M. , Rao M. V. R. , Kumar Satish 
Published: December 2004

AbstractStudies on copolymerization kinetics of N‐carboxyanhydride (NCA) of O‐acetyl‐L‐tyrosine (T) with NCAs of L‐valine (V) and glycine (G) were carried out in dioxane at 25°C with n‐butylamine as initiator. The reactivity ratios for the VT system were found to be rV:rT:0.57:0.22; and for the GT system, rG:rT:0.26:0.42. A comparison of this data with that obtained when L‐analine was used in place of L‐valine or glycine showed that in the three systems, the reactivity ratio of the amino acid residue with a greater tendency to form ordered secondary structure was greater than that of its comonomer. Among the variable comonomers (glycine, L‐alanine, L‐valine) of O‐acetyl‐L‐tyrosine, it is again L‐alanine, whose tendency to form helical structure is very high, that has the greater reactivity ratio.
Circular dichroism of nucleic acid monomers. II. Derivation and application to polymers of a consistent set of guanine and cytosine transition parameters
Authors: Williams Arthur L. , Moore Dexter S. 
Published: December 2004

AbstractAn approximate semiempirical procedure has been developed in order to derive nucleic acid monomer π → π* electronic transition moment parameters. Using the approximate procedure, guanine (G) and cytosine (C) transition moment parameters have been derived from agreement found between calculated weight‐averaged and measured CD spectra of cyclic‐GMP and cyclic‐CMP. The derived base transition moment parameters have been assessed in CD spectral calculations on some G‐ and C‐containing nucleic acids for which reasonably good structural information exists. An attempt was also made at evaluating the likely CD spectral contributions of G and C electric n → π* transition moments whose magnitudes were taken to be the maximum expected. Overall, the results indicate that the derived G and C π → π* transition moment parameters are more successful in nucleic acid CD spectral calculations than those used in previous DeVoe theory CD calculations. In addition, the results indicate that electric n → π* transitions may be of importance in understanding nucleic acid monomer CD spectra but appear to be relatively unimportant in understanding nucleic acid polymer CD spectra. It is concluded that the derived G and C π → π* parameters are more useful in DeVoe theory CD calculations than parameters used previously.
Dynamic light scattering from thin rigid rods: Anisotropy of translational diffusion of tobacco mosaic virus
Authors: Wilcoxon Jess , Schurr J. Michael 
Published: December 2004

AbstractAn Exact theoretical expression for the apparent diffusion coefficient Dapp(K) of a thin rigid rod with arbitrary anisotropy of its translational diffusion diffusion coefficient is derived from the first cumulant of its dynamic structure factor. Dapp(K) is predicted to reach a limiting plateau value at extermely large values of KL, where K is the scattering vector and L the rod length. Howerver, that limiting plateau value is approached only very slowly along a quasi‐plateau with a very gradual slope. Dynamic light‐scattering studies have been performed on tobacco mosaic virus from K2 = (0.4–20) × 1010 cm−2 using 632‐8‐nm laser radiation. The present data yield D0 = (4.19 ± 0.10) × 10−8 cm2/s (corrected to 20,w conditions) and, with literature data to establish L = 2980 Å and the rotational diffusion coefficient DR = 318s−1, yield also Δ ≡ D∥ − D⊥ = (1.79 ± 0.38) × 10−8 cm2/s. The experimental data closely follow the curve of Dapp(K) vs K2 calcuated for these parameters. The present value of D0 substantially exceeds all previous dynamic light‐scattering values, but is in good aggreement with previous sedimentation data, which were confirmed for the presemt sample. The anisotropy ratio Δ/D0 = 0.43 ± 0.09 is in accord with theoretical predictions based on the modified Kirkwood algorithm, despite the fact the D0 lies significantly below its corresponding theoretical value. The present data largely predlude the possibility that both D0 and Δ/D0 could simultaneously match their theoretical predictions. We present a detailed comparison of the experimental data with the calculations of Tirado and Garcia de la Torre based on the modified Kirkwood algorithm and with the Broersma formulas.
Optical properties of cyclic dimers of amino acids: An experimental and theoretical study
Authors: Bowman Richard L. , Kellerman Martin , Johnson W. Curtis 
Published: December 2004

AbstractCD spectra have been measured in the vacuum‐uv region to about 135 nm for cyclo(Lalanyl‐glycine), cyclo(Lalanyl‐L‐alanine), and cyclo(L‐prolyl‐L‐proline). In addition to the amide CD bands usually observed at wavelengths longer than 180 nm, a Independent systems calculations show that these intense short‐wavelenght bands can be attributed to σσ* transitions of the backbone. Transitions of the amide chromophore expected at wavelenghts shorter than 180 nm cannot account for the observed CD.
Correlation between chemical modification and surface accessibility in yeast phenylalanine transfer RNA
Authors: Holbrook Stephen R. , Kim Sung‐Hou 
Published: December 2004

AbstractChemical reactivities of the functional groups of yeast phenylalanine transfer RNA are compared with surface accessibilities of the groups calculated with various probe radii representing effective radii of the chemical reagents used. We observe 97% agreement with the hypothesis that the chemically modified bases are those with the greatest surface accessibility. This overall strong correlation supports the conclusion that base exposure in an important determinant of chemical modification in this polynucleotide.
Preparation of fractionated low‐molecular‐weight poly(S‐carboxymethyl‐L‐cysteine) by ion‐exchange chromatography
Authors: Maeda Hiroshi , Ito Takeshi , Suzuki Hidetoshi , Hirata Shuzo , Kako Isao , Yoshino Masachika , Ikeda Shoichi , Kobayashi Yuji 
Published: December 2004

AbstractN‐Carboxyanhydride of S‐carbobenzoxymethyl‐L‐cysteine was polymerized by the addition of ethylamine as an initiator at anhydride–initiator ratios A/I = 3, 4, 6, 8, 12, and 16. Acetylation of the amino terminal was carried out with p‐nitrophenylacetate. After debenzylation, low‐molecular‐weight samples of poly(S‐carboxymethyl‐L‐cysteine) were obtained for A/I = 8, 12, and 16. These samples were fractionated by ion‐exchange chromatography (DEAE–cellulose). About six fractions of narrow molecular‐weight distributions were obtained. Their degrees of polymerization (DP) ranged from 8 to 16, as determined from proton nmr and also estimated based on their elution volumes on the ion‐exchange chromatography at constant ionic strengths. This range of DP covered the range of interest concerning the formation of the β‐structure in aqueous solutions; a fraction did not form the β‐structure, whereas another fraction did. The results of the gel filtration (Biogel P‐10) of the fractionated samples were consistent with the estimated DPs.
Influence of conformation on the fluorescence of tryptophan‐containing peptides
Authors: Anderson Janet S. , Bowitch Gary S. , Brewster Robert L. 
Published: December 2004

AbstractConformational‐energy calculations of the zwitterionic forms of Trp, Gly‐Trp, Pro‐Trp, Phe‐Trp, Trp‐Gly, Trp‐Phe, Trp‐Trp, and Trp‐Gly‐Gly were done using an empirical energy program for peptides (ECEPP). The resulting low‐energy conformations were analyzed for the presence of hydrogen bonds, the distances between carbonyl groups and the indole ring, the distances between the N‐terminal amino group and the indole ring, the dihedral angle between the planes containing carbonyl groups and the indole ring, and for dipeptides with two aromatic side chains, the dihedral angle and distance between the planes of the aromatic rings. This information was correlated with literature data from x‐ray crystallographic studies, fluorescence lifetime studies, and quantum‐yield experiments; proposed models of intramolecular quenching are discussed in light of the peptide conformations.
An affinity scale for the interaction of amino acid residues with nucleic acids
Authors: Porschke Dietmar , Ronnenberg Jorg 
Published: December 2004

AbstractThe affinity of amino acid residues to nucleic acids is probed by measurements of melting temperatures tm for the helix–coil transition at various concentrations of amino acid amides. The increase of tm on addition of ligand is described by the equation tm = t*m + αlog(1+Ktcλ), where t*m is the melting temperature in the absence of ligand, cλ the ligand concentration, and Kt the “tm‐onset” constant, which is analogous to an equilibrium constant. It is shown that Kt is closely related to the affinity of the ligands to the double helix, whereas the slope α mainly reflects the preference of the ligand binding to the helix versus the coil form. In the case of the amino acid amides, α is found to be virtually independent of the nature of the side chain with few exceptions, e. g., aromatic amides. The tm‐onset constant, however, strongly depends on the nature of the amino acid side chain. For simple aliphatic amino acids, the relative free energy of binding decreases with increasing hydrophobic free energy, e.g., a high affinity is found for Gly‐amide and a low affinity for Leu‐amide. This relation is modified by functional groups like OH in Ser‐amide. The helices poly[d(A‐T)], ploy[d(I‐C)]. and poly[d(A‐C)]·poly[d(G‐T)] exhibit similar affinity scales with relatively small variations. Our results demonstrate that the hydrophilic character of double helices at their surface disfavors binding of hydrophobic ligands unless special contacts can be formed. From our results we establish an affinity scale for the binding of amino acids to double helices.