bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved technique for calculating X‐ray scattering intensity of biopolymers in solution: Evaluation of the form, volume, and surface of a particle
Authors: Pavlov M. Yu. , Fedorov B. A. 
Published: May 2005

AbstractAn improved cube method has been developed for calculating the intensity of diffuse x‐ray scattering of macromolecules in solution using a certain set of their atomic coordinates. The technique is based on the ideas of B. Lee and F. M. Richards [(1971) J. Mol. Biol. 55, 374–400] and Richards [(1977) Annu. Rev. Biophys. Bioeng. 6, 151–176] on the possibility of estimating the molecular and accessible surface of a particle by “rolling” a sphere, simulating a water molecule, on its molecular surface. It is shown that this technique is more advantageous than earlier versions of the cube methods. The improved technique for calculating scattering curves was utilized for several globular proteins, and for the first time, reliable scattering curves were obtained for protein‐“bound” water complexes. In the case of globular proteins and tRNA, this technique has permitted a strict evaluation of their accessible surfaces, their volumes, and, apparently for the first time, their complete molecular surfaces.
Model for the irreversible dissociation kinetics of cooperatively bound protein–nucleic acid complexes
Authors: Lohman Timothy M. 
Published: May 2005

AbstractWe present a quantitative model for the irreversible dissociation kinetics of cooperatively bound nonspecific protein–nucleic acid complexes. The model assumes that the major pathway of dissociation is via singly contiguously bound protein that “peels” off the ends of clusters of bound protein. It should therefore be most applicable for proteins that bind nucleic acids with high cooperativity (w > 103). Furthermore, the model assumes that no redistribution of bound protein occurs during the time course of the dissociation. Solutions to the rate equations are presented for the entire time course of the dissociation. Under initial conditions such that the nucleic acid is less than fully saturated with protein, a single‐exponential decay is predicted (if w is large). However, when the nucleic acid lattice is initially fully saturated, zero‐order kinetics, corresponding to a constant rate of protein dissociation, is predicted. The experimental observation of zero‐order dissociation kinetics in a cooperative protein–nucleic acid system is a good qualitative indicator for the dissociation mechanism discussed here. A discussion of the analysis of experimental data that enables one to extract molecular rate constants is presented. Furthermore, comparisons are made between the nonredistributing model presented here and Epstein's model [Epstein, I. R. (1979) Biopolymers 18, 2037–2050] in which protein can translocate infinitely quickly while bound to the nucleic acid, and hence protein clusters redistribute during dissociation and maintain an equilibrium distribution on the nucleic acid at all times.
Linear dichroism studies of nucleic acids. III. Reduced dichoism curves of DNA in ethanol–water and in poly(vinyl alcohol) films
Authors: Matsuoka Yukio , Nordén Bengt 
Published: May 2005

AbstractThe uv linear dichroism of calf thylus DNA has been studied at different degrees of orientation both in flow‐oriented ethanol–water solutions and in a stretched aqueous host of poly(vinyl alcohol) (PVA). The reduced dichroism (LDR) curves in the region 250–290 nm for DNA in PVA films at 75 and 100% relative humidity (r.h.) are in fair agreement with the curves calculated for the A‐ and B‐forms of DNA, based on the fiber structures and the π‐π* transitions of the free bases. This suggests that DNA adopts its A and B conformations in PVA at 75 and 100% r.h. In ethanol, on the other hand, a deviation from the A‐form spectrum shows that the conformation of DNA in the solution can differ from the fiber structure. At shorter wavelenghts, a positive contribution to LDR is explained in terms of an out‐of‐plane polarized n‐π* transition.
Localized vibrational modes at a double‐helix‐single‐strand junction
Authors: Putnam B. F. , Prohofsky E. W. 
Published: May 2005

AbstractA vibrational analysis has been performed for a double‐helix–single‐strand junction. A Green's function technique has been used in treating the junction as a defect on an otherwise perfect system of infinite chain homopolymers. We calculate that the hydrogen‐bond stretching at the junction is amplified by a factor of two relative to the interior of the double helix, B poly(dG)–poly(dC). Breathing modes localized near the junction have also been predicted at 77 and 94 wave numbers. The calculated results are shown to be consistent with predictions from recent nmr studies.
Nmr studies of a free and protected tetrapeptide glycyl‐L‐prolylglycylglycine in β‐turn‐supporting environment
Authors: Perly B. , Helbecque N. , Forchioni A. , Loucheux‐Lefebvre M. H. 
Published: May 2005

AbstractNmr studies of the protected and free tetrapeptide Gly‐Pro‐Gly‐Gly were carried out in β‐turn‐supporting solvents, that is, in CDCl3 for Z‐Gly‐Pro‐Gly‐Gly‐OMe and in Me2SO‐d6 for H‐Gly‐Pro‐Gly‐Gly‐OH. Comparisons with specifically α‐deuterated analogs gave complete assignments of the NH and methylene regions. Analysis of chemical shifts, coupling constants, and the temperature dependence of chemical shifts show that the peptide adopts a type II β‐turn conformation. This turn is stabilized for the protected tetrapeptide by two hydrogen bonds between (i) CO (Gly1) and NH(Gly4), and (ii) urethane function NH and methyl ester CO.
Fluorescence correlation spectroscopy and photobleaching recovery of multiple binding reactions. II. FPR and FCS measurements at low and high DNA concentrations
Authors: Icenogle R. D. , Elson E. L. 
Published: May 2005

AbstractThe preceding paper develops the theory for the interpretation of fluorescence photobleaching recovery (FPR) measurements of multiple binding of a ligand to a multivalent substrate molecule. Based on a reasonable assumption about the mechanism of the photobleaching process, this analysis shows that the observed behavior of a multivalent system should be practically identical to that of a univalent binding system. This is in contrast to the expected and observed behavior of fluorescence correlation spectroscopy (FCS) measurments. Experimental FPR measurements of multivalent binding of ethidium bromide to DNA confirm these conclusions. The FCS and FPR measurements also reveal an apparently enhanced diffusion of ethidium at high DNA concentration. This enhancement might result from direct transfer of ethidium among DNA molecules.
New plot showing the existence of cooperativity, anticooperativity, and an arbitrary value of the neighbor‐exclusion parameter in systems of ligand binding to linear biopolymers
Authors: Tsuchiya Takashi 
Published: May 2005

AbstractA new way of plotting the isotherm for ligand binding to linear biopolymers is presented. In this plot the isotherm for noncooperative binding of ligands of length n (n‐mers) becomes a straight line and the existence of cooperativity and anticooperativity between bound ligands is detected by appearance of opposite convexity of the curved isotherm. It is also usable for cases of fractional n values. Usefulness of the new plot in determining precise mechanisms of binding is shown using experimental data.
Correlation of Tm and sequence of DNA duplexes with ΔH computed by an improved empirical potential method
Authors: Ornstein Rick L. , Fresco Jacques R. 
Published: May 2005

AbstractTm values for 20 DNA duplexes with different repeating base sequences provided the data base for developing a rational and relatively simple methodology for computing apparent enthalpies for the helix → coil transitions of DNA helices, ΔHcalc. The computational variables and their range of acceptable values were selected on the basis of physically plausible arguments. Over 350,000 different combinations of the variables were tested for degree of fit. It was therby possible to find a combination giving a high degree of linear fit between Tm and ΔHcalc (correlation coefficient, 0.99), with Tm values deviating (on average) from the regression line by only ±2.17°C. Most of this uncertainty is attributed to experimental limitations, although computational approximations also contribute. With ΔHcalc for the melting of each of the unique complementary dinucleotide fragments computed by the method developed, it is possible to estimate Tm and (relative) ΔHcalc reliable for the melting of any particular DNA [with base pairs G(I)·C and A·T] given only its base sequence. The ΔHcalc values for the complementary dinucleotide fragments, together with statistical considerations, make it apparent that Tm of DNAs with repeating base sequence show only an approximate linear dependence on G·C content because A·T and G·G pairs do not contribute to helix stability independently of the base‐pair sequence in which they occur. In fact, the nearestneighbor stacking interactions are so significant that certain complementary dinucleotide fragment sequences with 0,50, and 100% G·C content have the same stability.
Possible observation of a defect resonance in DNA
Authors: Lindsay S. M. , Powell J. 
Published: May 2005

AbstractA sharp feature is observed at about 600 MHz in the inelastic scattered light spectrum of fibers of calf thymus DNA. It broadens so as to be no longer distinctly resolved when the ordering of a fiber is disrupted by convection caused by laser heating. To within experimental uncertainties the frequency of this feature is wavevector independent. A possible origin of the feature lies in a defect resonance such as that associated with the chain terminus.
The heminucleotide scheme: An effective probe in the analysis and description of ordered polynucleotide structures
Authors: Malathi R. , Yathindra N. 
Published: May 2005

AbstractThe heminucleotide scheme formulated recently permits treatments of the repeating nucleotide backbone in terms of two conformationally similar moieties of constant magnitude spanning its 5′ and 3′ halves. The scheme is utilized in describing the conformational features of the ordered poly(mononucleotide) helices of A‐, B‐, and D‐DNA, polyadenylic acid, and poly(dinucleotide) helices of ZI and ZII types through distance diagonal plots. The unique feature of these diagonal plots lies in the fact that the variations in the observed patterns can be directly correlated with pairs of backbone bond rotations ψ,ψ′ (C5′—C4′ and C4′—C3′), of the sugar residue and ω′,ω (P—O3′ and P—O5′) of the phosphodiester, which determine the relative orientations of the heminucleotides and, therefore, the variety in the secondary structures. Thus, the heminucleotide scheme through its constant P˙C4′ and C4′˙P separations provides common premises for characterization and comparison of the observed secondary structures. It is not feasible otherwise through a distance plot of nucleotide P˙P separations or between any other atoms, since they vary depending on the backbone torsions, especially (ψ,ψ′) of the sugar residue. The plots afford identification at a glance of the secondary structural features such as the differences in the widths of the major and minor grooves, regions of closer separation, the parallel and antiparallel nature of the helical strand, and even the characteristic of the repeating motif, whether mono‐ or dinucleotide. A simple description such as the above may aid in better understanding the binding of metals, salts, solvents, etc., and hence of the conformational transitions among the different secondary structures.
Comparative study of GuHCl denaturation of globular proteins. I. Spectroscopic and chromatographic analysis of the denaturation curves of ribonuclease A, cytochrome c, and pepsinogen
Authors: Saito Yoshio , Wada Akiyoshi 
Published: May 2005

AbstractNovel devices for the spectroscopic and chromatographic analysis of the denaturation curves of the protein are described. A multidimensional spectroscopic measuring system makes it possible to carry out simultaneous and continuous acquisition of a set of data of different spectroscopic dimensions at several wavelengths in the course of increasing or decreasing denaturational perturbation. GuHCl‐gradient chromatography can provide information about the progressive change of the protein volume in the course of increasing GuHCl concentration. Thus, denaturation curves with a high data‐point density can be obtained. The data‐storing function by a magnetic disk memory provides enough precision for a rigorous investigation of the correlation among the curves that probe different aspects of denaturation. The GuHCl denaturation of RNase A, cytochrome c, and pepsinogen are studied to demonstrate the high performance of these devices. Three types of transitions are found in these three proteins and the multiphasic nature of the transitions is clearly detected in the last two proteins.
Comparative study of GuHCl denaturation of globular proteins. II. A phenomenological classification of denaturation profiles of 17 proteins
Authors: Saito Yoshio , Wada Akiyoshi 
Published: May 2005

AbstractGuHCl denaturation profiles of 17 proteins were studied by the spectroscopic and chromatographic methods described in the preceding report. The profiles are broadly classified into three types according to their multiphasic characteristics. It seems likely that more complex processes than those previously accepted take place in the denaturational conformation change of proteins.
Slow relaxational processes in the melting of linear biopolymers: A theory and its application to nucleic acids
Authors: Anshelevich V. V. , Vologodskii A. V. , Lukashin A. V. , Frank‐Kamenetskii M. D. 
Published: May 2005

AbstractWe treat the problem of the mean time of complete separation of complementary chains of a duplex containing N base pairs. A combination of analytical and computer methods is used to obtain the exact solution in the form of a compact expression. This expression is used to analyze the limits of application of the equilibrium theory of helix–coil transition in oligo‐ and polynucleotides. It also allows the melting behavior of a biopolymer to be predicted when its melting is nonequilibrium. In the case of oligonucleotides for which the equilibrium melting takes place at a high value of the stability constant s, the general expression turns into the equation of Craig, Crothers, and Doty, used by them to determine the rate constant kf of the growth of a helical region from temperature‐jump experiments. For the case of fragmented DNA with N ∼ 102, the melting process is shown to be completely nonequilibrium, and as a result, the observed melting temperature should be higher than that for the equilibrium. A simple equation is obtained that makes possible calculation of the real, “kinetic” melting temperature Tk. As N increases, the observed melting temperature should approach the equilibrium value, Tm. This analysis has explained quantitatively the peculiar chain‐length dependence of the experimentally observed shift in the DNA melting temperature during fragmentation. A thorough analysis is given of the nonequilibrium effects in the melting process of long DNA molecules (N ≳ 103). The main conclusion is that even in the presence of profound hysteresis phenomena, the melting profile observed on heating may differ only slightly from the equilibrium profile.
Reversing‐pulse electric birefringence of poly (γ‐benzyl‐L‐glutamate). II. Field‐strength dependence of steady‐state and decay signals of well‐fractionated samples
Authors: Ueda Kazuyoshi , Mimura Masaharu , Yamaoka Kiwamu 
Published: May 2005

AbstractThe electric field dependence (up to 21 kV/cm) of the steady‐state and decay signals has been examined on the four well‐fractionated samples of poly(γ‐benzyl‐L‐glutamate), [Glu(OBzl)]n, in N,N‐dimethylformamide at 535 nm and 20°C. Together with the data previously obtained from the reversing‐pulse electric birefringence [Ueda, K., Nomura, M. & Yamaoka, K. (1983) Biopolymers 22, 2077–2090], the steady‐state birefringence and field‐free relaxation time were analyzed by a method that takes into account the polydispersity of the chain length. The weight‐average chain length, (lw), permanent dipole moment, (μw), electric polarizability anisotropy, (Δαw), and the length‐independent optical anisotropy factor were evaluated. The axial translation per residue was calculated for the [Glu(OBzl)]n helix, but the uncertainly involved in the weight‐average molecular weights, determined from light scattering by different investigators, makes the determination of the exact conformation of [Glu(OBzl)]n difficult. The contribution of Δαw to electric field orientation was found to be significant, since Δαw was approximately proportional to lw. A linear relationship also exists between μw and lw, when the [Glu(OBzl)]n helix is shorter than about 1200 Å.
Matrix formulation of the transition from a statistical coil to an intramolecular antiparallel β sheet
Authors: Mattice Wayne L. , Scheraga Harold A. 
Published: May 2005

AbstractA tractible matrix formulation is developed for the formation of intramolecular antiparallel β sheets in a homopolymer chain molecule. The formulation is applicable to chains with a finite degree of polymerization. It can readily be extended to treat specific‐sequence heteropolymers. Individual sheets may contain any number of strands, the number of residues per strand can range upward from two, and there is no artificial constraint linking the numbers of residues in adjacent strands. The weighting scheme utilizes two end‐effect parameters, denoted by τ and δ. The first parameter is associated with each residue that does not have a partner in a proceding strand, and the latter is associated with each β bend. A third parameter, t, is associated with every residue in the sheet. Conditions are described which lead to the formation of different types of sheets: (1) “sheets” comprised of isolated extended strands; (2) cross‐β fibers in which a sheet contains a large number of very short strands; (3) fibers in which a few very long strands run parallel to the fiber axis; (4) sheets comprised of several strands in which the average strand contains five residues. The fourth type of sheet resembles those found in globular proteins. It is formed when τ and δ are both small, with the ratio, τ/δ, being slightly less than one.
Dielectric properties of slightly hydrated collagen: Time–water content superposition analysis
Authors: Sasaki Naoki 
Published: May 2005

AbstractThe frequency dependences of the dielectric constant, ε′, and the loss factor, ε″, in collagen were measured at several water contents from 0.1 to 0.3 g/g collagen over a frequency range of 30 Hz to 100 kHz and at a temperature of 20°C. Remarkable dispersion was observed at the lower frequencies for higher water contents. According to accumulated results on the thermodynamic and structural investigations, the dispersion has some analogy to the surface conduction proposed by B. V. Hamon [(1953) Aust. J. Phys. 6, 304–315]. An empirical relation bewteen ε″ and frequency, f, ε″ ∝︁ fn, where 0 < n < 1, suggests that the dielectric and conductive properties of hydrated collagen are related to carrier jumps between neighboring sites. For the polarization mechanism of this dispersion, we supposed a model of the transfer of protons between absorbed water molecules, and found that the time–water content superposition procedure is applicable to slightly hydrated collagen. The results derived from the superposition procedure show that the water content, ϕ, is related to the conductivity, σ, or the dielectric loss factor by the following equations: σ (ϕ, f) = const. × ϕnm−1f1−n and ε″ (ϕ, f) = const. ϕnmf−n, respectively, where m is a constant independent of ϕ and f. These results agree with that derived by another treatment of the same data. The role of water molecules in the conduction and polarization in slightly hydrated collagen is considered to be not far from that assumed in the model.
Mathematical models of depolymerization of amylose by α‐amylases
Authors: Mazur A. K. 
Published: May 2005

AbstractFor a long time the action pattern of depolymerizing enzymes was explored by examining the distribution of products. Some attempts to interpret the data on the action of α‐amylases on amylose quantitatively have led to conflicting results. In the present work, new mathematical models are developed based on the properties of the most‐probable distribution and on the recently established fact of its partial stability at enzyme depolymerization. Published data for several α‐amylases are reexamined in light of this theoretical analysis. The theory proposed permits us to resolve a controversy concerning the interpretation of experimental data in this field.
Calculation of the thermodynamic quantities of solvation for lysozyme and β‐lactoglobulin a in guanidinium chloride
Authors: Lapanje Savo 
Published: May 2005

AbstractThe thermodynamic quantities of solvation, that is, Gibbs free energy, enthalpy, and entropy for the transfer of lysozyme and β‐lactoglobulin A from water to 6M guanidinium chloride solution, were calculated from the respective contributions of constituent groups. Comparison of the calculated values with the experimental ones reveals satisfactory agreement for lysozyme, whereas for β‐lactoglobulin A, it is semiquantitative. Thus the method of calculation appears to be fundamentally sound. The reasons for the differences in calculated and experimental value are briefly discussed.
Theoretical studies on protein–nucleic acid interactions. II. Hydrogen bonding of amino acid side chains with bases and base pairs of nucleic acids
Authors: Kumar N. Vasant , Govil Girjesh 
Published: May 2005

AbstractWith a view to understanding the role of hydrogen bonds in the recognition of nucleic acids by proteins, hydrogen bonding between the bases and base pairs of nucleic acids and the amino acids (Asn, Gln, Asp and Glu, and charged residues Arg+, Glu−, and Asp−) has been studied by a second‐order perturbation theory. Binding energies have been calculated for all possible configurations involving a pair of hydrogen bonds between the base (or base pair) and the amino acid residue. Our results show that the hydrogen bonding in these cases has a large contribution from electrostatic interaction. In general, the charged amino acids, compared to the uncharged ones, form more stable complexes with bases or base pairs. The hydrogen‐bond energies are an order of magnitude smaller than the Coulombic interaction energies between basic amino acids (Lys+, Arg+, and His+) and the phosphate groups of nucleic acids. The stabilities of the complexes of amino acids Asn, Gln, Asp, and Glu with bases are in the order: G–X > C–X > A–X U–X or T–X, and G · C–X > A · T(U)–X, where X is one of these amino acid residues. It has been shown that Glu− and Asp− can recognize guanine in single‐stranded nucleic acids; Arg+ can recognize G · C base pairs from A · T base pairs in double‐stranded structures.