bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonactin, monactin, dinactin, trinactin, and tetranactin. A Raman spectroscopic study
Authors: Phillies George D. J. , Asher Irvin M. , Stanley H. Eugene 
Published: December 2004

AbstractRaman spectra are reported for crystalline nonactin, monactin, dinactin, trinactin, and tetranactin and their solutions in CCl4, CHCl3, CH3OH, and 4:1 (v/v) CH3OH:CHCl3. The macrotetrolide nactins selectively bind a wide variety of cations, and are important model compounds for the study of ion complexation. The conformations of nonactin, monactin, and dinactin in solution are similar. Their conformations are found to be sufficiently open to permit the ester carbonyl groups to form hydrogen bonds with CH3OH; this gives rise to characteristic changes in the vibration frequencies associated with the ester groups. Nonactin, which is the least soluble of the nactins in CH3OH, is also the least effective at forming hydrogen bonds with CH3OH. The greater ability of the higher nactins to form hydrogen bonds with CH3OH may be due to the increased inductive effect of ethyl over methyl side chains, which may increase the dipole moment of the ester carbonyl groups. Spectra of crystalline nonactin, monactin, and tetranactin are fairly similar, while the spectra of dinactin and trinactin comprise a second, distinct family. This is consistent with X‐ray crystallographic studies, which show that nonactin and tetranactin form monoclinic crystals, while trinactin is triclinic.
A triple‐helical model for (Gly‐Pro‐Hyp)n with cis peptide units
Authors: Bansal M. , Ramakrishnan C. , Ramachandran G. N. 
Published: December 2004

AbstractSynthetic regular polytripeptides of the type (Gly‐R2‐R3) where R2, R3, or both, are imino acids have been widely studied as model compounds for collagen. One such polytripeptide is poly(Gly‐Pro‐Hyp), since triplets with this sequence constitute about 10% of collagen. Recently, a new model has been proposed for this polytripeptide in which one of the three peptide bonds in the tripeptide unit is in the cis conformation, and the γ‐hydroxyl group of hydroxyproline forms a direct interchain hydrogen bond within the triple helix. We have confirmed this structure by model building using computer techniques, and the helical parameters obtained by us are close to the experimentally observed values. The model is also found to be comparable in stability with other models from energy considerations.
The interaction of glutaraldehyde with poly(α,L‐lysine), n‐butylamine, and collagen. I. The primary proton release in aqueous medium
Authors: Blauer G. , Harmatz D. , Meir E. , Swenson M. K. , Zvilichovsky B. 
Published: December 2004

AbstractThe interaction between poly(α,L‐lysine) (DP = 180) and glutaraldehyde was investigated in dilute aqueous solution by measurement of the kinetics of proton release at constant pH and temperature and at various concentrations of the reaction components. Under various conditions, the release of protons at constant pH appeared kinetically to be composed of at least two steps: an initial zero‐order reaction, followed by a slower reaction.At excess of polylysine amino groups, the pH optimum for the rates of reaction was at pH 9–10 (24–25°C). Under the conditions used and at pH 8, the initial rate of the second kinetic step was proportional to the glutaraldehyde concentration and was practically independent of polylysine concentration at pH 8 and 8.6, at an excess of amino groups. At pH values of 7, 8, and 8.6 the apparent overall energy of activation for the second kinetic step was 18–19 kcal/mole (temp. range 4–40°C). Comparing acetaldehyde with the difunctional glutaraldehyde, it was found that the rate of proton release was much smaller in the case of acetaldehyde. Comparing n‐butylamine with the macromolecular polylysine at equal concentrations of amino groups, the rates of proton release were much smaller in the case of n‐butylamine. Collagen in aqueous medium also interacted with glutaraldehyde in a manner analogous to polylysine, although the conditions were not quite comparable. In the case of collagen, the initial fast proton liberation step was relatively much larger than in the case of polylysine.A reaction scheme for the initial reaction steps is being proposed which includes primary complex formation between glutaraldehyde and polylysine. This dialdehyde–polyamino acid system is considered to serve as a model for tanning processes of hides and for fixation procedures.
Kinetic studies on the cyclization of T7 and T1 DNA's
Authors: Lee C. S. , Pyeritz R. E. , Thomas C. A. 
Published: December 2004

AbstractThe rates of cyclization of two terminally repetitious phage DNA molecules, T7 and T1, were determined and compared with earlier studies of λ DNA. Though differing over 200‐fold in the number of complementary nucleotides in the single‐chain terminals, these three DNA's cyclize at about comparable rates, suggesting that excluded volume effects are significant. The first order rate constants for T7 and T1 are strictly dependent on solvent viscosity, consistent with a diffusion limitation of the rate determining step. Whole molecules with exposed single‐chain terminals were shear‐broken to half‐molecules and the second order rate constants for joining were measured. The rates for T7 and T1 were nearly equivalent and some tenfold slower than predicted, suggesting that the long double‐helical region appended to the renaturing regions and perhaps other undetermined factors retard the rate of joining of half‐molecules.
Polypeptide models of collagen. Solution properties of (Gly‐Pro‐Sar)n and (Gly‐Sar‐Pro)n
Authors: Ananthanarayanan V. S. , Brahmachari Samir K. , Rapaka Rao S. , Bhatnagar Rajendra S. 
Published: December 2004

AbstractOur studies on the solution conformation of (Gly‐Pro‐Sar)n and (Gly‐Sar‐Pro)n synthesized as polypeptide models for collagen are reported. It is found that, while (Gly‐Pro‐Sar)n exists in ordered triple‐helical conformation, (Gly‐Sar‐Pro)n remains as a disordered random coil in water. Addition of certain helix‐promoting solvents seems to generate order in (Gly‐Sar‐Pro)n.
Buoyant and potentiometric titrations of synthetic polypeptides. II. Five copolypeptides and two nonionizable homopolypeptides in CsCl solutions
Authors: Sharp Dan S. , Almassy Robert , Lum Lawrence G. , Kinzie Kathleen , Zil John S. V. , Ifft James B. 
Published: December 2004

AbstractThe buoyant density titrations of five ionizable copolypeptides in concentrated CsCl solutions have been determined. The results are used to formulate models for predicting the buoyant density titration behavior of copolypeptides and proteins using the previously reported homopolypeptide buoyant density titration curves. It was determined for these copolypeptides that the best predictive model must include not only the buoyant densities of the constituent amino acid residues and the relative composition, but also hydration and salt binding.Hydrations determined for the homopolypeptides are used in the copolypeptide predictive model. The hydrations of the neutral homopolypeptides were readily calculable since their buoyant densities are thermodynamically defined in terms of their partial specific volumes and hydrations. For the case of a charged macromolecule, an expression for the buoyant density as a function of the number and nature of the bound ions, its partial specific volume, and its relative hydration has also been available for some time. This heretofore intuitive relationship is now derived from thermodynamic principles and allows calculations of hydrations to charged macromolecules which bind either cations, anions, or both.The potentiometric titrations of three of the five copolypeptides in concentrated CsCl solutions were determined in order to study the effect of residue interaction and solvation effects on their ionization behavior. The potentiometric results are also combined directly with the buoyant density titration results to determine the correlation of the buoyant density with the degree of ionization. As in the cases of poly(Glu) and poly(His), the buoyant density of the copolypeptides changed linearily with the degree of ionization.The buoyant density titrations of two nonionizable homopolypeptides, poly(Gly) and poly(Ala), were determined in concentrated CsCl solutions. The buoyant density was found to increase with increasing pH, despite the fact that side chains do not contain ionizable groups. This is the first evidence from homopolypeptide or copolypeptide data that buoyant density changes can be observed from effects other than side‐chain ionizations.
Proton magnetic resonance investigation of interactions between L‐tryptophan and dinucleoside phosphates at low pD
Authors: Kolodny N. H. , Neville A. C. , Coleman D. L. , Zamecnik P. C. 
Published: December 2004

AbstractInteractions between mononucleoside and dinucleoside phosphates containing adenine and/or cytosine and L‐tryptophan have been studied at low pD by proton magnetic resonance (pmr) spectroscopy. The results of those studies indicate that, despite extensive protonation of ring positions, and resulting electrostatic repulsion, ring stacking does occur between both like and unlike molecules. Geometries for stacked complexes are proposed and the extent of complex formation between L‐tryptophan and adenosine or cytidine in 3′ or 5′ esterified positions is discussed qualitatively.
Co‐oligopeptides of aromatic amino acids and glycine with a variable distance between the aromatic residues. V. pH‐Dependent conformational changes in peptides containing two adjacent tryptophyl residues as evidenced by circular dichroism studies
Authors: Rizzo Vincenzo , Luisi Pier Luigi 
Published: December 2004

AbstractThe influence of pH upon CD spectra of H‐Trp‐Trp‐OH, H‐Trp‐Trp‐Gly‐OH, and H‐Gly‐Trp‐Trp‐OH is investigated and data are compared with those obtained for peptides containing only one tryptophyl residue. A negative Cotton effect at around 225 nm, which in previous work has been related to an increase of the conformational rigidity in compounds having the sequence ‐CO‐Trp‐Trp, is also observed in the case of H‐Trp‐Trp‐OH and H‐Trp‐Trp‐Gly‐OH upon deprotonation of the terminal α‐amino group. These data, together with observations arising from solvent and temperature effects, give evidence that H‐Trp‐Trp‐OH undergoes a conformational change upon going from acid to alkaline conditions, where the two aromatic side chains become conformationally more rigid relative to each other. This rigidity generates an exciton coupling between the Bb transitions of the two indoles. Hydrophobic forces, including stacking interactions, do not appear important in stabilizing this conformationally rigid structure. Rather, intramolecular electrostatic interactions (e.g., hydrogen bondings or polar interactions between the aromatic side chain and the peptide backbone) as well as interactions with the OH group(s) of the solvent, are suggested to be the salient forces. Possible structures which obey these requisites are discussed.
Enzymic activity and conformational properties of native and crosslinked glucose oxidase
Authors: Solomon Beca , Lotan Noah , Katchalski‐Katzir Ephraim 
Published: December 2004

AbstractGlucose oxidase has been modified by reacting it with glutardialdehyde. The products obtained are water soluble and merely intramolecularly crosslinked; they exhibit high enzymic activity and good stability towards denaturing agents. Comparative circular dichroism studies have been performed with the native and crosslinked enzymes, as well as with the corresponding apoenzymes. The results suggest that the FAD coenzyme is not a gross structural determinant of glucose oxidase.
Calorimetric determination of the heat capacity changes associated with the conformational transitions of polyriboadenylic acid and polyribouridylic acid
Authors: Suurkuusk J. , Alvarez J. , Freire E. , Biltonen R. 
Published: December 2004

AbstractThe heat capacities of the single‐stranded and double‐stranded forms of polyadenylic acid, polyuridylic acid, and poly(uridylic and adenylic acid) were determined with a drop heat capacity calorimeter. In addition, the temperature dependence of the apparent partial heat capacity (ϕCp) was measured with a newly developed differential scanning calorimeter. The calculated ΔCp at 28°C for the transition poly(A)·poly(A) ⇄ 2 poly(A) was found to be 165 ± 24 cal/Kmol‐base pair, compared with a value of 140 ± 28 for the transition poly(A)·poly(U) ⇄ poly(A) + poly(U). The temperature dependence of ϕCp of single‐stranded poly(U) was consistent with the conclusion that it is totally unstacked at temperatures above 15°C. The temperature dependence of ϕCp of single‐stranded poly(A) was used to determine the base‐stacking parameters for poly(A). The experimental results are consistent with a stacking enthalpy change of −8.5 ± 0.1 kcal/mol bases and a cooperativity parameter σ of 0.57 ± 0.03 for the stacking of adenine bases. These results demonstrate that the heat capacity of single‐stranded polynucleotides is greater than that of the double‐stranded forms. This increased heat capacity is mainly the result of the temperature dependence of the base‐stacking interactions in the single‐stranded form.
Conformation of adenosine 5′‐monophosphate in aqueous solution as studied by nmr‐DESERT method
Authors: Imoto Toshiaki , Shibata Susumu , Akasaka Kazuyuki , Hatano Hiroyuki 
Published: December 2004

AbstractThe molecular conformation of adenosine‐5′‐monophosphate (5′‐AMP) in D2O (pH 8.1) has been investigated by the method of “DESERT” proposed earlier by Akasaka et al. [J. Magn. Reson. 18, 328 (1975)]. The reciprocal sixth‐power‐averaged distances r̄i′8 between H(8) of the adenine ring and H(i′) (i′ = 1′, 2′, and 3′) of the ribose moiety have been deduced directly from the differential spin‐lattice relaxation rates of these ribose protons upon deuterium substitution for H(8) and the rotational correlation times of the molecule estimated from carbon‐13 T1 values, by utilizing the pulse Fourier transform nmr method. The r̄i′8 values have been found to change significantly with the concentration of 5′‐AMP. The values of r̄1′8, r̄2′8, and r̄3′8 at infinite dilution have been determined to be 3.14, 2.45, and 3.37 Å, respectively, whereas those corresponding to the infinite concentration have been determined to be 3.84, 2.80, and 3.01 Å, respectively.The interproton distances obtained for infinite dilution are not consistent with any single conformation with respect to the rotation about the glycosidic torsional angle and to the ribose puckering, but can be explained well by approximately an equal mixture of three groups of conformers showing an intercorrelation between the ribose puckering and the glycosidic torsional angle, i.e., 3′‐endo‐anti, 2′‐endo‐syn, and 2′‐endo‐intermediate. The increase of r̄1′8 and r̄2′8 and the decrease of r̄3′8 with increasing concentration of 5′‐AMP can be explained well quantitatively by the preferential stabilization of anti conformers for both ribose states with formation of a base‐stacked dimer. The present results are compared with those obtained previously by other workers using a variety of methods.
Proton magnetic resonance and model peptides conformations
Authors: Forchioni A. , Abillon E. , Thiéry J. M. , Le Barny P. , Loucheux‐Lefebvre M. H. 
Published: December 2004

AbstractDerivatives and peptides of β‐nitrobenzyl‐L‐aspartates were studied with high‐field nmr. Differences were observed between the chemical shifts of protons located near the extremity of the principal chain as a function of the terminal group. These differences are explained by conformational calculations which exclude the existence of an hydrogen bond and demonstrate the influence of the aromatic ring position on the protons of the main chain. Both nmr experiments and conformational analysis indicate that conformations are nearly the same for ortho, meta, and para nitro substitution. These conclusions are in good agreement with Karplus relationship applied to the α and β protons.
Block oligopeptides (L‐lysyl)m‐(L‐alanyl)n‐L‐Tyrosyl‐(L‐Alanyl)n‐(L‐Lysyl)m. II. Circular dichroism and pulsefluorimetry conformational studies
Authors: Mayer R. , Gauduchon P. , Spach G. , Wahl Ph. 
Published: December 2004

AbstractThe conformation of chromatographically pure block oligopeptides (L‐lysyl)m‐(L‐alanyl)n‐ L‐tyrosyl‐(L‐alanyl)n‐(L ‐lysyl)m with n = 3 and m = 6 or 3 is investigated. By circular dichroism it is shown that these peptides may exhibit a partially α‐helical structure depending upon pH, ionic strength, solvent, and temprerature. An attempt is made to describe the helical content of these small peptides by utilizing the data obtained on high‐molecular‐weight poly(L‐lysine). By measurement of the quantum yield and the decays of the peptides fluorescence, it is shown that, in aqueous solution, at neutral pH, the fluorescence of the peptides is quenched by interactions with the peptide carbonyl groups. The decays are multiexponential, which shows the presence of several conformations of the phenolic chromophore relative to the peptide chain. The addition of methanol, which induced the helix formation, decreases the quenching of the fluorescence and the multiexponential character of the decays. In presence of sodium hydroxide, which further increases the helical content of the peptides, a dynamic quenching occured that can be attributed to interactions between the phenol hydroxyl group of tyrosine (ith residue) and the ε‐amino groups of the (i+4)th and (i ‐4)th lysyl residues.
Different families of double‐stranded conformations of DNA as revealed by computer calculations
Authors: Zhurkin V. B. , Lysov Yu. P. , Ivanov V. I. 
Published: December 2004

AbstractAn algorithm has been developed that permits one to find all possible conformations of the sugar‐phosphate backbone for any given disposition of DNA base pairs. For each of the conformations thus obtained, the energy of the helix was calculated by the method of atom‐atom potentials. Several isolated regions in the space of the bases′ parameters (Arnott's parameters) have been found for energetically favorable helical structures. Two parameters, the distance of a base pair from the helix axis, D, and the windling angle, τ, allow one to subdivide possible conformations into the families of closely related forms. Two regions (ravines) on the (D, τ) map correspond to the know A and B families. In the B family a continuous transition has been obtained in which the double helix undergoes increasing winding, while the base pairs are moving toward the major (nonglycosidic) groove.Interrelationships between the variables, characterizing the spatial structure of the double helix, D, τ, TL and χ, when going along the bottom of the B ravine, were also obtained.Besides the Known A and B families, several new ones were found to be energetically possible. Among these the strongly underwound helices with the negative D values, as well as the forms with the C4‐C5 angle in a trans position, should be mentioned.Biological roles of the different double‐stranded conformations, in particular, in protein‐nuclei acid interaction are discussed.
Statistical mechanical deconvolution of thermal transitions in macromolecules. II. General treatment of cooperative phenomena
Authors: Freire Ernesto , Biltonen Rodney L. 
Published: December 2004

AbstractIn the preceding article1 we demonstrated that the partition function of a system is experimentally accessible from scanning calorimetric data. In this article the general results of the deconvolution theory are applied to the general case of cooperative transitions in macromolecules. It is demonstrated that, in the limit of very large systems, all the relevant molecular averages and molecular distribution functions can be directly obtained from the experiment. In doing this, the method of the grand partition function is used. It is shown that in the case of homopolymers, only one parameter, the stability constant, needs to be explicitly specified for a complete description of the system. Since the partition function is directly evaluated from the experiment, no special assumptions or artificial constraints directed to obtain a mathematically solvable model are required. This result offers the unique opportunity of having direct experimental access to statistical averages of systems in which the partition function cannot analytically be solved. Consequently, the theory can be extended to cooperative transitions occurring in two and three dimensions by introducing cluster distribution functions.
Statistical mechanical deconvolution of thermal transitions in macromolecules. III. Application to double‐stranded to single‐stranded transitions of nucleic acids
Authors: Freire Ernesto , Biltonen Rodney L. 
Published: December 2004

AbstractThe statistical mechanical deconvolution theory for macromolecular conformational transitions is extended to the case of nucleic acids transitions involving strand separation. It is demonstrated that the partition function, Q, as well as all the relevant thermodynamic quantities of the system, can be calculated from experimental scanning calorimetric data. In particular, it is shown that important thermodynamic parameters such as the size of the average cooperative unit during strand separation, the mean helical segment length, and the mean coil‐segment length can be calculated from the average excess enthalpy function 〈ΔH〉. The theory is applied to the double‐stranded to single‐stranded transition of the system poly(A)·poly(U) at different salt concentrations. It is shown that the mean helical segment length is a monotonically decreasing function of the temperature well before strand separation occurs. On the other hand, the mean coil segment length remains practically constant until temperatures very close to Tm. Both experimental findings clearly indicate that the unfolding of poly(A)·poly(U) proceeds through the formation of many short helical sequences. The cooperative unit for the strand separation is calculated to be about 120 base pairs and essentially independent of the salt concentration. The existence of a minimum helical segment length of 10 ± 2 base pairs within the double‐stranded form is calculated.
Application of thin film dialysis to the determination of equilibrium constants
Authors: Russo Salvatore F. , Engel Randall G. 
Published: December 2004

AbstractA theoretical basis for thin‐film dialysis involving binding between a ligand and nondialyzing species is presented. A general differential equation that applies to the case of equivalent, noninteracting sites is derived relating [A]F, [A]T, [P]T, and K. Numerical solutions to this equation are used to develop a series of escape curves corresponding to specific values of the parameters [P]T, [A]i, K, and k0. A general method for determining an equilibrium binding constant from thin‐film dialysis data is given. A comparison of thin‐film dialysis results predicted by this theory with literature data shows essential agreement.
Conformation of amino acid residue contiguous to helical polypeptide
Authors: Nakata Yoshiro , Akaike Toshihiro , Inoue Shohei 
Published: December 2004

AbstractThe calculation of the conformational energy of the terminal D‐ or L‐alanine residue contiguous to an α‐helical polypeptide, polyalanine, was made. Both L‐and D‐residues contiguous to the carboxyl terminal of α‐helical poly(L‐alanine) are considered to prefer the α‐helical conformation due to the effect of the α‐helical structure of the polymer. The residue at the amino terminal is found to be less affected by the α‐helical structure of the polymer.