bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nmr studies on linear homo‐oligopeptides: A perspective view
Authors: Goodman Murray , Saltman Robert P. 
Published: May 2005

AbstractThe use of high‐resolution nmr to determine the structure of linear homo‐oligopeptides in solution is described. Complete assignments of NH and α‐CH resonances were elucidated based upon a guest–host series of compounds and selective α‐deuteration of residues in the chain. The conformations for oligomethionines and oligoglutamates in dimethylsulfoxide, chloroform, and trifluoroethanol are discussed, and molecular models are described. Recent studies of L‐glutamate peptides attached to polyoxyethylene are also included. These peptide–polyoxyethylene conjugates are soluble in a broad range of solvents, such as dimethyl‐sulfoxide, chloroform, trifluoroethanol, and water. Preliminary conclusions are drawn concerning the effects of amine terminal end groups and the nature of the solvent on the conformations of these peptide derivatives.
Some aspects of the relationship between the structure of a bitter diketopiperazine and its receptor
Authors: Shiba Tetsuo , Uratani Hiroshi , Kubota Ichiro , Sumi Yoshihiko 
Published: May 2005

AbstractA conformation of a diketopiperazine, cyclo(L‐leucyl‐L‐tryptophyl), was determined by nmr and x‐ray analysis. The receptor for this bitter diketopiperazine neither recognizes chirality nor requires a strict conformation of the substrate. A good correlation was found between the bitterness of diketopiperazine and its hydrophobicity. Experiments using liposome as a model of the receptor membrane suggested that a lecithin‐like lipid is a candidate for a binding site of the bitter diketopiperazine. Furthermore, affinity chromatography using cyclo(L‐leucyl‐L‐phenylalanyl) as a bitter ligand indicated that phosphoglycerides of the lipids tested showed a particular affinity to the bitter diketopiperazine.
Tobacco mosaic virus as a carrier for small molecules: Artificial receptor antibodies and superhormones
Authors: Schwyzer Robert , Kriwaczek Verena Marly 
Published: May 2005

AbstractPeptide agonists covalently attached to tobacco mosaic virus exhibit such unusual properties as superpotency, superaffinity, enhanced resistance towards enzymic degradation, and prolonged action at the target cell. These properties can be exploited for the isolation by density‐gradient centrifugation of membrane vesicles bearing specific receptors for the peptides and for radioactive and fluorescent labeling of cell‐surface receptors. Our observations can be explained by cooperative–affinity phenomena caused by the deployment in space of the agonist molecules.
Helix–coil transition of poly‐γ‐N‐carbobenzoxy‐L‐α,γ‐diaminobutyrate and poly‐δ‐N‐carbobenzoxy‐L‐ornithine
Authors: Gaskin Felicia , Yang Jen Tsi 
Published: May 2005

AbstractThe helix–coil transition of poly‐γ‐N‐carbobenzoxy‐L‐α,γ‐diaminobutyrate (PCLB) and poly‐δ‐N‐carbobenzoxy‐L‐ornithine (PCLO) in chloroform–dichloroacetic acid mixtures was followed by optical rotatory dispersion. PCLB displays a “normal” temperature‐induced transition, but PCLO an “inverse” one. The thermodynamic parameters for helix formation of the two polymers were determined using the Zimm‐Bragg theory. The enthalpy for adding an amide residue to a helical region, ΔH, and the initiation factor σ were ΔH = −180 cal/mole and σ = 9.2 × 10−5 for PCLB and ΔH = +490 cal/mole and σ = 1.9 × 10−5 for PCLO.
Permeability of synthetic polypeptide membranes. I. Poly‐D,L‐leucine‐co‐D,L‐methionine
Authors: Klein E. , May P. D. , Smith J. K. , Leger N. 
Published: May 2005

AbstractD,L‐Leucine‐NCA and D,L‐methionine‐NCA were copolymerized in varying mole fractions by using primary base initiation. The methionine segments were oxidized to both sulfoxide and sulfone functions by using peroxide oxidation. The compositions of the resulting polymers were established with the aid of 60 MHz NMR. The transport properties of aqueous solutes through membranes formed from these polymers were studied by means of a diffusive dialysis measurement. The transport of NaCl, urea, creatinine, uric acid, and bacitracin were found to be strongly dependent on the degree of hydration of the polymers. The relative rates of transport of these solutes were affected by interaction with the polymers, when the degree of hydration was not excessive. The degree of hydration was a function of the extent of methionine oxidation.
Optical rotary dispersion of mucopolysaccharides III. Ultraviolet circular dichroism and conformation al specificity in amide groups
Authors: Stone Audrey L. 
Published: May 2005

AbstractThe circular dichroism of glycosaminoglycans and ganglioside in distilled water are described, showing two bands in the region of amide and carboxyl transitions. The first, negative hand is common to all polymers and the amino sugar derivatives. The characteristics of the second band depend upon polymer structure. Those containing 4–1‐linked amino sugars show a second, positive, resolved band about 190 mμ, while those with 3–1‐linked amino sugars show a second, negative band less resolved from the first usually ≤185mμ, but clearly centered at 188mμ for dermatan sulfate. Ultraviolet optical absorption from 300 to ∼183 mμ showed inflection regions around 190 mμ for most compounds.
Stereoselective polymerization of γ‐Benzyl Glutamate NCA
Authors: Williams Fred D. , Eshaque M. , Brown Ronald D. 
Published: May 2005

AbstractThe polymerization of γ‐benzyl glutamate NCAs has been investigated. The results indicate that a coil‐to‐helix transformation is not responsible for the kinetic data. The results were rationalized by assuming formation of polymer aggregates coupled with the stereoselective adsorption of monomer onto growing polymer prior to reaction. From kinetic data a ratio of equilibrium constants for adsorption was determined. Independent data confirmed the assumption that adsorption of monomer onto polymer occurred. Equilibrium constants were evaluated, and their ratio was found to be comparable with that obtained from the kinetic data.
Solute binding curves for (two polymer + solute)–complex systems I. “one‐solute‐stack” systems
Authors: Schmitz Kenneth S. 
Published: May 2005

AbstractThe matrix method is used for calculating the grand partition function for the reaction: 2 polymer + solute = complex. The homogeneous polymers are assumed to have two types of sites within each nucleotide unit: sites for the polymer–polymer association, i.e., (p‐p) sites; sites for polymer–solute association i.e., (p‐s) sites. The respective binding parameters, P and F, and nearest‐neighbor interaction parameters, W and S, are assumed independent. Complications due to ring entropy are avoided by rest riding the model to one‐solute‐stack systems, which are physically realizable when the reciprocal of the solute cooperativity parameter is much larger than the number of nucleotides in the polymer. The 4 × 4 generating matrix is shown to be a tensor product of two 2 × 2 matrices, each the generating matrix of a particular type of site. The scalar product of the 4 × 4 matrix is shown to be equivalent to the scalar product of a 2 × 2 matrix in the weak interaction limit, W ≈ 0. Calculations are presented for the general case which restricts the (p‐s) association to occur only with (p‐p) associated nucleotide units. The nature of the binding curve in relation to partitioning the total interaction energy (F + P + S + W) among the parameters is discussed. Also presented is a criterion for neglecting possible states in the calculation of the grand partition function.
Hydration of DNA: A neutron scattering study of oriented NaDNA
Authors: Dahlborg U. , Rupprecht A. 
Published: May 2005

AbstractA preliminary neutron‐scattering study of wet‐spun oriented NaDNA samples with various contents of H2O or D2O has been performed to obtain information about the hydration of NaDNA. The preferred orientation was in the direction of the crystallographic c axis. Perpendicular to this direction the samples could be regarded as poly‐crystalline. It has been found that the preferred crystallite orientation was also reflected in the water structure. This fact, taken together with the small energy widths of the measured near‐elastic peaks indicates that water molecules in the sample are relatively strongly bound to the DNA helix either directly or via other water molecules. Angular distribution measurements of elastically scattered neutrons were performed with the momentum transfer vector directed along and perpendicular to the DNA helix axis. Different Debye‐Waller factors were obtained, indicating different water dynamics in the two directions. Comparison between the H2O and D2O measurements suggests that the difference is caused by motions of rotational nature. The shape of the frequency distribution function for the H2O molecules in the NaDNA sample was somewhat similar to that which has been measured in ice.
Dichroism of TMV in pulsed electric fields
Authors: Allen F. S. , Van Holde K. E. 
Published: May 2005

AbstractThe linear dichroism induced in a solution of electrically anisotropic molecules by a pulsed electric field has been studied. Equations have been obtained which express the dichroism as a function of dipole moment, excess polarizability, field strength, and the angle α between the dipole moment and the transition moment for the absorption band. These expressions have been related to the experimentally observed difference signal in such a way that when the dichroism is measured as a function of field strength the permanent moment, excess polarizability and angle a can be determined.Experiments have been carried out on tobacco mosaic virus (TMV), which is similar in its properties to the theoretical model. The polarizability anisotropy and rotary diffusion constant for the monomer and dimer of TMV have been obtained from these experiments. In addition to the molecular parameters mentioned above, the saturated electric dichroism of the virus was measured as a function of wave length and the presence of an n–π* transition in the tryptophan spectrum was indicated.Further experiments measuring dichroism as a function of pH demonstrated the general denaturation of the virus at high pH (10–11) but also the existence of a stable fraction which is not fragmented even at the high pH involved.
Statistical length of DNA from light scattering
Authors: Schmid Carl W. , Rinehart Frank P. , Hearst John E. 
Published: May 2005

AbstractAn analysis of hydrodynamic data of DNA by use of the wormlike coil model gave a statistical length of 1300 Å, in the absence of excluded volume corrections. The worm‐like coil model and this hydrodynamically observed statistical length adequately describe the light scattering properties of DNA.
Kinetic studies of interaction between acridine orange and DNA
Authors: Sakoda Mitsuaki , Hiromi Keitaro , Akasaka Kazuyuki 
Published: May 2005

AbstractThe interaction between acridine orange (AO) and deoxyribonucleic acid (DNA) was studied by the stopped‐flow method. The spectral change of AO due to interaction with DNA was followed over the wavelength range 350–600 nm at various concentration ratios of DNA phosphate to dye. The spectral change observed by the stopped‐flow method was found distinctly different from that, during the dead‐time, leading to a conclusion that the binding of AO to the outside of DNA occurs much faster than the intercalation into base pairs of DNA. The dependence of the rate of reaction on the reactant concentration and on the salt, concentration of the solution was also studied. The results are consistent with the mechanism that the intercalation proceeds via the outside bound state.
Circular dichroism of superhelical DNA
Authors: Maestre Marcos F. , Wang James C. 
Published: May 2005

AbstractThe circular dichroism (CD) spectra of a number of superhelical DNA's have been measured. The introduction of negative superhelical turns causes an increase in magnitude of the positive band around 280 mμ, while the trough around 250mμ is little affected. For two samples of λb2b5c DNA (20 Mdalton) containing different number of negative superhelical turns, the magnitude of the positive band relative to that of the nicked control increases with increasing number of superhelical turns. In 2M NaCl, the small (1.45 Mdalton) superhelical DNA from E. coli 15 shows an unusually large difference in CD compared with that of the same DNA with a few single‐chain scissions per molecule. This large difference is not observed in a medium containing p. 0.11M NaCl. These results indicate that the double helix in a superhelical DNA is perturbed somewhat due to the bending and torsional forces in such a molecule. The magnitude of such structural alteration seems to depend on the number of superhelical turns per unit length, the size of the DNA molecule, as well as the ionic medium.
Morphological and structural studies of poly(gly‐gly‐ala)
Authors: Andries J. C. , Anderson J. M. , Walton A. G. 
Published: May 2005

AbstractThe ultrastructural morphology and x‐ray and electron diffraction of poly (Gly‐Gly‐Ala) have been studied. The polymer has two forms; the first, form I possesses a super‐folded cross‐β structure, long fibers of which show some twisting and intertwining. Form II precipitates in a less distinct fibrous form from aqueous solution. The x‐ray diffraction and oriented electron diffraction data suggest that form II is a polyglycine II helix situated in a monoclinic cell with dimensions a = 8.86 Å, b = 22.0 Å, c = 9.42 Å, and β = 90°. Combined with the morphological evidence it appears likely that form II is also in an antiparallel superfolded array.
Conformations of model compounds of proteins II. Infrared spectra of n‐acetyl‐amino acid methylamides
Authors: Koyama Yasushi , Shimanouchi Takehiko , Sato Motomu , Tatsuno Takashi 
Published: May 2005

AbstractN‐Acetyl‐amino acid methylamides CH3CONHCHRCONHCH3 were prepared from L‐ and DL‐alanine, L and DL‐α‐amino‐n‐butyric acid, L‐ and DL‐norvaline, DL‐norleucine, L‐ and DL‐methionine, L‐ and DL‐leucine, L‐aspartic acid and DL‐phenylalanine. The deuterium homologs of the type CH3CONDCHRCONDCH3, CD3CONHCHRCONHCH3, and CH3CONHCHRCONHCD3 were also prepared. The infrared spectra of these compounds were measured down to 300 cm−1 in the crystalline state. The infrared spectra of N‐isopropylacetamide CH3CONHCH(CH3)2, N‐methylisobutyramide (CH3)2CHCONHCH3 and their deuterium homologs were also measured. The CO in‐plane and out‐of‐plane bending vibration bands of the CH3CONHCα group (amide IVa and VIa) and those of the –CαCONHCH3 group (amide IVb and VIb) were assigned from these data. Two crystalline modifications, form I and form II, were found for the compounds prepared from L‐alanine, DL‐leucine, L‐aspartic acid and DL‐phenylalanine. The two forms show quite different skeletal vibrations, which suggest, rotational isomerism. Two distinct patterns were found as to the positions of the amide IVa and VIa bands for the above compounds. The two amide bands were found near 630 and 600 cm−1 in form I, whereas they were found near 600 cm−1 in form II. The crystals of the remaining compounds were also classified into form I or form II on the basis of the arrangement of the amide bands. The X‐ray structure analyses suggest that these two forms have different hydrogen‐bond structures.
A statistical mechanical theory of unfolding of globular proteins induced by preferential binding of solvent components in water‐organic solvent systems
Authors: Shindo Yohji 
Published: May 2005

AbstractA statistical mechanical model was developed for use in connection with the problem of preferential binding of solvent components to proteins and of conformational transition in water‐organic solvent systems. The model is a statistical one for the conformational transition of globular proteins induced by the adsorption of solutes in the solution, considered as a nearest‐neighbor problem in statistical mechanics. Although a few illustrative examples are given, the actual interpretations of the experimental data using this theory are reserved for a later paper.
Stereochemistry of nucleic acids and polynucleotides III. Electronic charge distribution
Authors: Renugopalakrishnan V. , Lakshminarayanan A. V. , Sasisekharan V. 
Published: May 2005

AbstractCalculation of σ‐ and π‐charges were made on nucleotides and nucleic acids. The σ‐charges were calculated using LCAO MO method suggested by Del Re, making use of Berthod and Pullman parameters. The π‐charges were calculated by Hückel's method, making use of suitable parameters which gave a good qualitative correlation of calculated bond orders with experimentally determined bond lengths. General features of the charge distribution are discussed.
The reaction between neutral salts and fibrous proteins. I. The model system sodium poly‐L‐glutamate‐LiBr‐H2O
Authors: Baddiel C. B. , Chaudhuri D. , Stage B. C. 
Published: May 2005

AbstractThe effects of concentrated aqueous solutions of a neutral salt, lithium bromide, on randomly coiled sodium poly‐L‐glutamate have been followed using high resolution infrared and nuclear magnetic resonance spectroscopy. The results suggest that two processes are taking place. First, at low concentrations 0–4M LiBr, a simple electrolyte effect occurs in which some water is removed from the polymer by an electrostriction effect. Second, a more intense interaction (>4M LiBr), apparently cooperative, occurs in which the competition for the available water in the system forces the electrolyte to form an association with the peptide group either as a fully or partially hydrated species. It is proposed that the anion is associated with the nitrogen atom of the peptide group and the cation is situated within the vicinity of the carbonyl oxygen.
Allosteric interactions in phospkorylase B
Authors: Bresler S. , Firsov L. 
Published: May 2005

AbstractAn allosteric model of phosphorylase B is proposed based on the following assumptions. The enzyme consists of two sub‐units and undergoes a concerted transition from the inactive T to the active R state. The binding of substrates, phosphate, and glycogen is regarded as exclusive, but the binding of the activator AMP is nonexclusive. The enzyme model is of the K, V type, i. e., the activator AMP is important, not only for the T‐R transition and the substrates binding, but also for the formation of the active site. Therefore, it displays a big influence on the maximal reaction rate. Calculations based on this model lead to an equation containing 5 constants, which can be easily computed from kinetic data. All kinetic measurements fit the expressions derived from the model. Independent methods for the measurement of all the constants involved were developed. They are based on the study of binding of phosphorylase with the substrates and the activator. These measurements are in satisfactory agreement with the data obtained from enzyme kinetics.
Optical properties of the polyglycine II helix
Authors: Rippon W. B. , Walton A. G. 
Published: May 2005

AbstractThe circular dichroism spectrum obtained from a dilute aqueous solution of poly (ala‐gly‐gly) resembles that described for charged polypeptides such as the salt form of poly glutamic acid. A similar spectrum is found for films cast from aqueous solution where x‐ray studies reported elsewhere have indicated a poly‐glycinc II conformation. Evidence is presented for a heat induced poly‐glycine II to unordered state transition similar to that described for collagen. The interpretation of this, the first observation of the optical properties of a poly‐amino acid in the poly glycine II conformation, is further rationalized on the basis of spectra obtained from a number of polypeptides whose conformation approaches that of a 31 helix.
Comparaison entre oligoribonucleotides et oligodesoxyribonucleotides. I. Formation des doubles helices
Authors: Mauriuzot J. C. , Blicharski J. , Brahms J. 
Published: May 2005

AbstractThe ability of oligodesoxyribonucleotides of various chain lengths to form complexes has been compared with that of oligoribonucleotides. Four series of oligonucleotidcs were prepared and investigated, i.e., dCn at acid pH versus rCn, dAn and dTn versus. rAn and rUn at neutral pH. The results indicate that in dilute solution, the formation of complexes is greatly facilitated in the case of desoxyoligomers and occurs for shorter oligomere than in the corresponding ribooligomers. The spectrophotometric titration of deoxyribooligo C indicates the appearance of two pK values in the 4–5 pH region characteristic of the double‐stranded form, which occurs for much shorter dCn than rCn. The circular dichroism (CD.) spectra of deoxycytidylies in dilute solution starting from the trimer are conservative, characteristic of the double‐stranded helical form of poly C at acid pH. In contrast, the CD spectra of a series of corresponding ribo Cn, under identical conditions is of nonconservative character similar to that of the single‐stranded form of poly C at neutral pH, but differs in the band position. This spectrum is called intermediate. Only at higher concentrations of oligonucleotidcs (i.e., 10−3Minstead of 10−4M) does the circular dichroism spectrum of longer ribocytidylics assume conservative character. Thermal denaturation of deoxycytidylces at acid pH are strongly dependent on chain length and concentration, its one would expect for a cooperative helix‐coil transition. The circular dichroism spectra measured at different temperatures shows one isosbestic point. In dilute solution, the standard‐state enthalpy change found was 5–6 kcal/mole for higher oligomers (dC7). These properties are all in agreement with a structural transition from the d‐Cn double‐stranded form to a coil for n > 3. Studies of dAn and dTn in solutions of high ionic strength at low temperature indicate that complex formation occurs already at the level of trimer and for high oligomers. Under identical conditions a complex between rAn and rUn is detected only for oligomers longer than the hexamer. The nature of the “intermediate” form of oligoribo C at acid pH and low temperature was investigated by sedimentation and circular dichroism. A model of rCn is proposed of linear molecules which are partially double‐stranded and partially single‐stranded, which probably are slowly rearranged by “slippage” into a regular‐double‐stranded helical form.
Conformational energy calculations on alginic acid I. Helix parameters and flexibility of the homopolymers
Authors: Whittington S. G. 
Published: May 2005

AbstractConformational energy maps have been calculated for the 1‐4‐linked dimers of β‐D‐mannuronic acid and α‐L‐guluronic acid. Helix parameters have been calculated for poly(mannuronic acid) and for poly(guluronic acid), which are in reasonable agreement with data from x‐ray fiber diffraction studies of these polysaccharides. The flexibility of the homopolymers was investigated by calculating the characteristic ratios, i.e., the ratio of the mean‐square end‐to‐end lengths of the unperturbed chains to the product of the number of residues in the chains and the virtual bond lengths. The general conclusions are that both polymers are very stiff and extended, but that poly(mannuronic acid) is less extended than poly(guluronic acid).