bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linked and threaded loops in proteins
Authors: Connolly Michael L. , Kuntz I. D. , Crippen Gordon M. 
Published: December 2004

AbstractTertiary structure of globular proteins has traditionally been analyzed in terms of the organization of secondary structure elements. This paper presents a method for systematically identifying different topological features of the convolutions of the backbone. We define a loop as a segment of chain whose end residues are in contact. We find some loops which are threaded by another segment of chain passing through the loop or actually linked with another loop. Fifty‐six loop threadings were found among the 20 proteins studied, all of them occurring in a subset of seven proteins. In our sample, threadings and linkings were generally found if and only if the protein has more than 200 residues. To account for the existence of these topological features, despite their apparent entropic unfavorability, we have proposed a number of kinetic mechanisms by which they may form without a thread actually passing through a loop. We have found that almost all loop threadings possess structural features that would make one of these mechanisms plausible.
Physicochemical studies of amylose and its derivatives in aqueous solutions: Thermodynamics of the iodine–triiodide complex
Authors: Cesàro Attilio , Jerian Edvino , Saule Silvano 
Published: December 2004

AbstractThermodynamic properties of the amylose–iodine–triiodide complex have been studied by spectrophotometry and by calorimetry using previously studied samples of amylose ionic derivatives, carboxymethylamylose and diethylaminoethylamylose. The ratio of triiodide to total molecular iodine ([I3]b/[I]b + [I2]b) in the complex is ca. 0.3 over a range of iodide concentration from 10−5 to 10−4M, and there is no evidence for an increasing charge at slightly higher iodide concentration. Direct calorimetric experiments have been carried out in different conditions of polymer, iodine, and iodide concentration in order to study the dependence of the heat of the complexation as a function of the above parameters. It is shown that the dependence of the measured ΔH on the iodide concentration simply derives from the rearrangement of the triiodide equilibrium because of the uptake of a fixed ratio of iodine and triiodide molecules in the complex.
Ultraviolet Raman spectroscopy of polyribouridylic acid: Excitation profile of the hypochromism induced by order–disorder transition
Authors: Chinsky L. , Turpin P. Y. 
Published: December 2004

AbstractRaman spectra of polyribouridylic acid excited in the uv region, from 363 to 290 nm, are reported. The conformational changes of the polymer from random coil to ordered structure with stacked bases at high and low temperature, respectively, are reflected by important changes in the Raman line intensities; this Raman hypochromism is itself a function of the excitation wavelength—its profile has been determined and shows negative values in the region of 290 nm (near resonance), i.e., hypochromism becomes hyperchromism. Thus the knowledge of the hypochromism excitation profile is important in following order–disorder transition of a polymer using resonance Raman spectroscopy. Theoretical attempts are proposed for explanation, involving not only the relative variations of the molar extinction coefficient on the order‐disorder transition of the polymer, but also the damping factors of the vibronic levels. The theoretical curve is found to fit adequately the experimental data over the excitation range, using only the frequency of the O‐O transition of uracil and a vibronic linewidth of 2200 cm−1.
Interactions of molecules with nucleic acids. III. Steric and electrostatic energy contours for the principal intercalation sites, prerequisites for binding, and the exclusion of essential metabolites from intercalation
Authors: Miller Kenneth J. , Macrea Joseph , Pycior Joseph F. 
Published: December 2004

AbstractBased on steric and electrostatic considerations, the prerequisites for binding to DNA via the intercalation mechanism are proposed. Steric contour energy curves are presented to demonstrate the region inaccessible to an intercalant. They are calculated with a 6‐n (n = 14) potential. This method is a soft potential analog of an excluded‐volume approach. Electrostatic contours on the steric surface illustrate the relatively positive and negative regions of the binding site. The principal intercalation sites, predicted to fit into B‐DNA via a tetramer‐duplex unit, and the unconstrained dimer‐duplex units, obtained in crystal structures, are examined. These contours illustrate the requirements of size, conformation, and net atomic charges necessary for intercalation and optimum binding. Based on the limited space available for intercalation by the presence of the backbone and the maximum base‐pair separation of 8.25 Å, an Essential Metabolite Exclusion Hypothesis is presented.
Interactions of molecules with nucleic acids. IV. Binding energies and conformations of acridine and phenanthridine compounds in the two principal and in several unconstrained dimer‐duplex intercalation sites
Authors: Miller Kenneth J. , Brodzinsky Richard , Hall Stephen 
Published: December 2004

AbstractThe binding positions and relative minimum binding energies are calculated for complexes of 9‐aminoacridine, proflavine, N‐methylphenanthridinium, and ethidium in theoretically determined intercalation sites in B‐DNA (sites I and II) and in unconstrained dimer‐duplex sites. The selection of site I in B‐DNA by these compounds agrees with the theoretical interpretation of studies of unwinding angles in closed circular DNA in all cases but ethidium, which is predicted to select site II. The most stable binding positions of the acridines and ethidium in unconstrained dimer‐duplex units agree with experimental results of intercalation complexes of dinucleoside monophosphate units. Base‐pair specificity for Watson‐Crick pairing is examined. The energy of an intercalation complex is partitioned into ΔE23, the energy required to open base pairs BP2 and BP3 in B‐DNA to a site, and ΔEIn, the energy change when a free molecular intercalates. ΔE23 depends strongly on the base‐pair sequence, whereas ΔEIn for the four molecules studied does not. The three most stable sequences contain (pyrimidine)p(purine) units, and this provides a rationale for the exclusive formation of crystals of intercalation complexes with these units. In spite of this selectivity, the distribution of GṁC and AṁT base pairs is equal for these three units and persists as the more unstable sequences are included. Therefore, specificity arises from the interaction between the base pairs and the 2′‐deoxyribose 5′‐monophosphate backbone for the opening of B‐DNA to an intercalation site and not from the interaction between the chromophore and the DNA.
Rǒle des electrons π des fonctions amide et ester dans les peptides et depsipeptides
Authors: Boussard G. , Marraud M. 
Published: December 2004

AbstractThe IR data for the R1 CO‐O‐CHR2‐CO‐NHR3 derivatives are interpreted in terms of a H…π interaction involving the NH bond and the π orbitals of the ester function and giving rise to a high ν(CO) frequency and a low ν frequency. The resulting molecular conformation corresponds to the angular values ϕ # −90°, ψ # 0°. The H…π interaction in MeCO‐L‐Lac‐NHMe is highly destabilized by water and aprotic solvents but is retained in methanol. Considering the high ν(CO) ester or amide frequency of the middle function in β‐folded depsipeptide or peptide sequences, it may be supposed that the residue indexed i + 2 in β turns experiences a H…π interaction which has a stabilizing effect on β turns. Some examples concerning valinomycin and some model compounds are discussed.
Polyelectrolyte contribution to the persistence length of DNA
Authors: Schurr J. M. , Allison S. A. 
Published: December 2004

AbstractThe difference between the theories of Manning, on the one hand, and of Odijk and Skolnick and Fixman, on the other, for the polyelectrolyte contribution to the persistence length of DNA is shown to arise entirely from a subtle geometrical error in the theory of Manning. The corrected theory of Manning predicts a negligible polyelectrolyte contribution in 1.0M NaCl and only 33 Å in 0.01M NaCl, thus giving a change in total persistence length by a factor of only 1.07 over that range, in agreement with Odijk. Pertinent data in the literature indicate that the persistence length must change by a factor of ≤ 1.6 between 1.0 and 0.01M NaCl, and very likely by less than a factor of 1.4. Evidently, the intrinsic rigidity of the uncharged double‐strand filament dominates the bending rigidity at NaCl concentrations above 0.01M.
Hydrodynamic behavior and molecular conformation of poly(L‐lysine HBr) in carbonate buffer solution
Authors: Kakiuchi Kinji , Akutsu Hideo 
Published: December 2004

AbstractIn carbonate buffer at pH 10.5, a transparent solution of poly(L‐lysine HBr) was obtained up to fairly high concentration of 3 g/dl at room temperature. The hydrodynamic behavior of the solution has been studied by sedimentation analyses and viscosity measurements. A dimer form for high concentrations and a monomer form for low concentrations were inferred. The dimer and monomer forms were assigned to a β‐structure and α‐helix, respectively, based on the CD and optical rotary dispersion spectra. Using CD spectroscopy, a reversible transition between α‐helix and β‐structure was observed as a function of either poly(L‐lysine HBr) concentration or temperature. An aggregated form which was assigned to the antiparallel pleated sheet appeared at 50°C on the basis of its ir spectrum.
Viscoelastic properties of protein crystals: Triclinic crystals of hen egg white lysozyme in different conditions
Authors: Morozov V. N. , Morozova T. Ya. 
Published: December 2004

AbstractA technique for the measurement of the dynamic Young's modulus E and logarithmic decrement 𝓋 of protein crystals and other microscopic samples by the resonance method modified to a microscale is described. Monoclinic crystals of horse hemoglobin and sperm whale myoglobin; triclinic hen egg white lysozyme crystals, crosslinked by glutaraldehyde; and native and crosslinked needlelike lysozyme crystals were studied, as were amorphous protein films. The E of wet protein crystals is shown to be in the range (3–15) × 103 kg/cm2, 𝓋 = 0.3–0.7. The crosslinking does not significantly affect the values. General elastic properties were analyzed for triclinic lysozyme crystals. No frequency dependence of E and 𝓋 was found over the frequency range of 2.5–65 kHz. The temperature dependence was found to be characteristic for glassy polymers; the decrement of Young's modulus was −2.4 ± 0.1%/°C. The guanidine HCl denaturation caused a 1000‐fold decrease of E, its temperature dependence becoming similar to that of rubberlike materials. Studies of pH and salt effects showed E to be influenced by ionization of the acidic groups at pH 3–4.5. A humidity decrease from 100 to 30% caused a three‐ to fourfold increase of E and a decrease of 𝓋. The final values of E = (40–60) × 103 kg/cm2 and 𝓋 ≃ 0.1 were the same for dry crystals and amorphous films, whether crosslinked or not. These values may be attributed to the protein globular material.
Monte Carlo simulation on the intrachain end‐to‐end charge‐transfer interaction on oligosarcosines
Authors: Sisido Masahiko , Imanishi Yukio 
Published: December 2004

AbstractMonte Carlo conformational calculations for oligosarcosines having terminal electron‐donor (D) and ‐acceptor (A) chromophores [A‐(Sar)n‐D, n = 2–8] were carried out. The bulkiness of the terminal chromophores, the conformational energies, and the charge‐transfer (CT) interaction energy were taken into account in the calculation. The equilibrium constant for the intramolecular end‐to‐end CT interaction was evaluated, and the result was compared with the experimental data. The alternating chain‐length dependence of the equilibrium constant observed experimentally was reproduced by the simulation and the solvent dependence of the equilibrium constant was also reasonably explained.
Interaction of Mn2+ with DNA as studied by proton‐relaxation enhancement of solvent water
Authors: Van Steenwinkel Raymond , Campagnari Francesco , Merlini Margaret 
Published: December 2004

AbstractThe binding of Mn2+ to double‐stranded DNA in solution has been studied by measuring the proton‐relaxation enhancement of solvent water. The nmr experiments were carried out on DNAs of different base composition and showed the existence of weak and tight binding sites for Mn2+. The former sites are related to the electrostatic binding of the divalent cation with two contiguous phosphate groups, and the latter appear to vary almost proportionally with the number of G·C base pairs in the DNAs. Our results agree, in general, with the emerging evidence for a specific interaction of Mn2+ with the G·C residues of DNA. Competition experiments with Mg2+ suggested that this binding of Mn2+ in DNA also involves the phosphate groups. More definitely, our data conform with the hypothesis made by Clement et al. of Mn2+ chelation between the phosphate and the nitrogen N7 of a deoxyguanyl unit of DNA.
Molecular‐weight dependence of the low‐frequency dielectric properties of aqueous solutions of gel‐fractionated DNA
Authors: Molinari Robert J. , Cole Robert H. , Gibbs Julian H. 
Published: December 2004

AbstractCombined three‐ and four‐terminal AC bridge measurements have been made at frequencies from 10 Hz to 100 KHz on samples of DNA with different molecular weight in aqueous solution under varying conditions of DNA concentrations and added salt. A method is described for the separation of large quantities of DNA fractionated according to size. A complicated pattern of dependence of the specific dielectric increment on concentration is found, and the difficulties of comparing the results from sample to sample are discussed. The dielectric properties of the fractionated samples of DNA in aqueous solution are reported for solutions sufficiently dilute that specific dielectric increment is independent of concentration. The specific dielectric increment of the solutions (with concentration measured in moles of DNA molecules/liter) is found to increase as the square of the molecular weight. The results are compared with results of polyelectrolyte theories which deal explicitly with counterion fluctuations and interactions. The frequency dependence of the dispersion is much broader than for simple Debye relaxation. It is satisfactorily fitted by the empirical Cole–Cole circular are function and the breadth of the dispersion is found to be, if anything, less for the fractionated samples than for native DNA in solution.
Noninteracting local‐structure model of folding and unfolding transition in globular proteins. II. Application to two‐dimensional lattice proteins
Authors: Abe Haruo , GŌ Nobuhiro 
Published: December 2004

AbstractThe noninteracting local‐structure model of the folding and unfolding transition in globular proteins, the formulation of which was given in the preceding paper, is applied to the analysis of the two‐dimensional lattice model of proteins. The lattice model of proteins is a theoretical tool designed to study the statistical‐mechanical aspect of the folding and unfolding transition. Its dynamics have been studied by a method of Monte Carlo simulation. The noninteracting local‐structure model reproduces the equilibrium properties of the lattice model obtained previously by computer simulation remarkably well, when the specificity of the long‐range interactions is strong. This observation indicates that the basic assumption of the noninteracting local‐structure model is equivalent to the assumption of strong specificity of intramolecular interactions. It is argued that by assuming this strong specificity, we can emphasize the correct main paths of folding and unfolding transition. The way local structures grow and/or merge along the most probable path of folding in the lattice model is discussed by the noninteracting local‐structure model.
Relationship between proton–proton nmr coupling constants and substituent electronegativities. III. Conformational analysis of proline rings in solution using a generalized Karplus equation
Authors: Haasnoot C. A. G. , De Leeuw F. A. A. M. , De Leeuw H. P. M. , Altona C. 
Published: December 2004

AbstractThe relationship between published vicinal proton–proton coupling constants and the pseudorotation properties of the pyrrolidine ring in L‐proline, 4‐hydroxy‐L‐proline, 4‐fluoro‐L‐proline, and several linear and cyclic model proline peptides is investigated. Compared to earlier studies, several important improvements are incorporated: (1) a new empirical generalization of the classical Karplus equation is utilized, which allows a valid correction for the effects of electronegativity and orientation of substitutents on 3JHH; (2) an empirical correlation between proton–proton torsion angles and the pseudorotational parameters P and τm is derived; and (3) the best fit of the conformational parameters to the experimental coupling constants is obtained by means of a computerized iterative least‐squares procedure. Two pseudorotation ranges were considered, classified as type N (χ2 positive sign) and type S (χ2 negative sign). The conformational equilibrium is fully described in terms of four geometrical parameters (PN, τN, PS, τS) and the equilibrium constant K. The present results indicate that, in general, the geometrical properties found in x‐ray studies of proline and hydroxyproline residues are well preserved in solution. Several novel features are encountered, however. It is demonstrated that the proline ring occurs in a practically 1:1 conformational equilibrium between well‐defined N‐ and S‐type forms. Introduction of an amide group at the C‐terminal end has no observable effect on this equilibrium, but the formation of a peptide bond at the imino nitrogen site results in a pronounced, but not exclusive, preference for an S‐type form which is roughly 1.1 kcal/mol more stable than its N‐type counterpart. The hydroxyproline ring system in neutral or acidic medium displays a pure N‐type state, but N‐acetylation results in the appearance of a minor (S‐type) conformation. Cyclic proline dipeptides similarly exist in a biased conformational equilibrium. The major form (77–88%) corresponds to the N‐type conformer observed in the solid state; the minor S‐form has not been observed before. In contrast, cyclic hydroxyproline dipeptides display complete conformational purity. Ranges of endocyclic torsion angles deduced for the various classes of pyrrolidine derivatives in solution are presented. Each torsion appears confined to a surprisingly narrow range, comprising about 4°–8° in most cases. In all, the proline ring is far less “floppy” than hitherto assumed.
Optical second‐harmonic scattering in rat‐tail tendon
Authors: Roth Shmuel , Freund Isaac 
Published: December 2004

AbstractThe angular dependence of optical second‐harmonic generation by native, wet, rat‐tail tendon is found to display a sharp, intense, forward peak superimposed on a broad background. The sharp peak is shown to imply long‐range polar order, while the broad background corresponds to that predicted for the random “up”/“down” array of collagen fibrils seen with the electron microscope. The degree of polar order is determined, and the dependence of the fibril diameter distribution on age and state of hydration is measured. The coherence length of tendon for harmonic generation and the absolute magnitude of the nonlinear susceptibility of the collagen fibril are also determined. The biological significance of these various findings is discussed.
Conformation of amylose–iodine–iodide complex in aqueous solution
Authors: Handa Takashi , Yajima Hirofumi 
Published: December 2004

AbstractThe conformational characteristics of the amylose–iodine–iodide complex in aqueous solution, particularly for a rapidly mixed system, were studied by resonance polarized scattering measurements using a He‐Ne laser at low concentrations of the complex and by viscosity measurements at high concentrations of the complex. For the scattering measurements, the following results were obtained: the depolarization ratios ρu and ρv showed a pronounced increase with the degree of saturation of the bound iodine (q) in amylose, depending on KI concentration. At q ≃ 0.7, the increase in these values appeared to be suppressed. However, the ρh value was approximately 1, irrespective of q. Additionally, the dissymmetry Z decreased appreciably with increasing q. The conformational change of the complex with q was characterized by the changes in the contour and persistence lengths of the chain and in the optical anisotropy of the scattering segments, which were obtained from numerical computations based on the polarized scattering equation for a wormlike‐chain model with a restriction by the entropy force of the chain. The viscosity of the complex solution decreased with increasing q; above q ≃ 0.7 it increased strikingly. The conformational change of the complex with q was characterized by the change in exponent α in the Houwink‐Mark‐Sakurada equation [η] = KMα. It was concluded that the iodine‐saturated complex has the characteristics of a rod, regardless of the complex concentration.
The equivalent conductivity of aqueous salt‐free solutions of DNA: Influence of univalent counterions
Authors: Kuznetsov I. A. , Apolonnik N. V. 
Published: December 2004

AbstractThe equivalent conductivity of salt‐free solutions of deoxyribonucleates of alkali metals and ammonium obtained by filtering an isoionic DNA solution through a cation exchanger in the corresponding form has been investigated in the concentrations range of 1 × 10−4 to 4 × 10−3M. For all counterions investigated there is a linear dependence of the equivalent conductivity on \documentclass{article}\pagestyle{empty}\begin{document}$ \sqrt {C_p} $\end{document}, where Cp is the nucleic phosphorus concentration. The limiting equivalent conductivity of deoxyribonucleates increases linearly with the limiting mobility of a counterion. By extrapolation to the zero mobility of the counterion, we have obtained the limiting mobility of a macroion, which is equal to 19 × 10−4 Sm m2 equiv.−1, which is in good agreement with the literature data for denatured DNA obtained by the method of a moving boundary. It is shown that the degree of binding of counterions calculated from the conductometric data in diluted DTA solutions in independent of the nature of the univalent counterion. The degree of dissociation of H+‐DNA in the isoionic solution calculated with allowance for the fraction of unprotonated bases practically coincides with this value for salts of DNA. The parameter of Manning's theory calculated from the experimental data corresponds to the distance between phosphates along the chain of the macroion, which is equal to 6.7 Å. We attribute the smaller value of this distance as compared with the theoretical one for denatured DNA to the aggregation of macroions.