bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time‐dependent model for hemoglobin and allosteric enzymes. I. General formulation
Authors: Bush Robert Ter , Thompson Colin J. 
Published: May 2005

AbstractA previous equilibrium model is generalized to study time‐dependent behavior of hemoglobin and allosteric enzymes. An exact solution for two interacting subunits (e.g., diheme) is given, and a general method for solving the resulting set of differential equations is outlined. At half saturation (equilibrium) concentration, the model takes a particularly simple form which suggests an experiment to determine the number of subunits of an allosteric enzyme, or in particular to distinguish diheme from ordinary hemoglobin. The relation between the present model and other kinetic models is also discussed.
Microscopic model for the study of fluctuations and the kinetics of conformational changes of polypeptides. I. Diglycine
Authors: Simon Eliot M. 
Published: May 2005

AbstractIn this paper a microscopic model is developed which considers conformational changes in polypeptides. The model applied here to diglycine involves calculation of torques due to pairwise interatomic forces acting about the two single bonds (NC and CC′) of the peptide unit. Account is taken of Brownian motion and rotational frictional resistance in addition to a van der Waals 6–12 potential, a classical electrostatic potential and a torsional potential. The rates of the conformational transition from an initial α‐helical position are computed. The mechanism of Conformational change is a random walk within the minimum well followed by a jump out of the minimum into another portion of the energy surface. The latter process occurs when a fluctuation carries the dipeptide into a high energy region of the potential surface. Correlation times for the process are computed. Estimates are made for the relaxation times for the process. A first passage‐time treatment is developed and used to compute internal diffusion coefficients for the relaxation process.
Sedimentation studies of DNA in concentrated solutions of magnesium salts
Authors: Vijayendran B. R. , Vold R. D. 
Published: May 2005

AbstractThe sedimentation coefficient of calf thymus and of T7 DNA was determined at several concentrations up to saturation in solutions of each of the following salts: MgCl2, MgBr2, and MgSO4. Under certain conditions, a plot of the product of the relative viscosity and sedimentation coefficient against the density of the solution has been found to be linear and to extrapolate to zero at a density corresponding to that of the solvated molecule. This behavior was realized in MgSO4 solutions, the zero intercept occurring at a density of 1.41 g/cc, corresponding to a wafer activity of 0.89. The preferential solvation of DNA in MgSO4 solutions calculated for this value is 10.5 moles water/mole of nucleotide, in good agreement with published values of solvation of DNA at the same water activity in univalent salt solutions. Since linear plots were not obtained in MgCl2 and MgBr2 solutions, buoyant densities could not be determined in these cases. The nonlinear behavior observed in MgCl2 and MgBr2 solutions may be due to a change in shape of the DNA molecule at the lower water activities reached in these solutions. The possibility of increased DNA–solute interactions in MgBr2 and MgCl2 solutions is also considered as an explanation for the difference in behavior between MgSO4 and the two magnesium halides.
Distorted α‐helix for poly (γ‐benzyl L‐glutamate) in the nematic solid stale
Authors: Samulski E. T. , Tobolsky A. V. 
Published: May 2005

AbstractA strong magnetic field has been utilized to orient the liquid crystalline phase of concentrated polypeptide solutions enabeling the preparation of nematic solid films. The uniaxially oriented nematic films are suitable for x‐ray studies of the polypeptide backbone chain conformation. A distorted α‐helix with 3.5 residues per turn is observed in nematic films of the L‐isomer of poly (benzyl glutamate) when the film is cast from chloroform. The normal α‐helix (3.6 residues per turn) is found in similarly prepared films cast from dichloromethane.
Size and shape determination of apotransferrin and transferrin monomers
Authors: Rosseneu‐motreff M. Y. , Soetewey F. , Lamote R. , Peeters H. 
Published: May 2005

AbstractDielectric dispersion and viscosity measurement, s were performed on apotransferrin and transferrin monomers in aqueous solutions so as to check the influence of iron binding on the overall conformation of the molecule. Iron saturation by two iron atoms per transferrin molecule modifies the parameters of the equivalent ellipsoid. The molecule becomes more spherical while its hydration value remains high.
Representation of a protein molecule as a tree and application to modular computer programs which calculate and modify atomic coordinates
Authors: Hermans Jan , Ferro Dino 
Published: May 2005

AbstractThe concept and representation of a logical tree as defined in computer science is applied to obtain a suitable representation of protein molecules in computer programs which handle or calculate atomic coordinates of protein molecules. On the basis of this analysis and of the analysis of the calculation and modification of the structure of a protein from bond lengths, bond angles, and dihedral angles, which is reproduced in an appendix, program modules which accomplish the various required computations are described. Three such modules are given in Iverson notation; in fact, it is hoped that this article will serve as a reasonably complete basis for the preparation of machine programs by moderately proficient programmers.
Physicochemical studies of oligodextran. I. Molecular weight dependence of intrinsic viscosity, partial specific compressibility and hydrated water
Authors: Gekko Kunihiko , Noguchi Hajime 
Published: May 2005

AbstractThe number average molecular weight, Mn, of low molecular weight dextran was determined through endgroup analysis, and the intrinsic, viscosities of these materials in aqueous solution were determined at 25°C. The ultrasonic velocities in their aqueous solutions were also measured at 25 and 45°C. As concerns the molecular weight dependence of the intrinsic viscosity, partial specific compressibility of solute and the hound water around the solute, the following results were obtained. (1) log [η]‐log Mn and [η]/Mn0.5 – Mn0.5 plots were in accord with the Mark‐Houwink and Stockmayer‐Fix‐man equations respectively for Mn > 2, 000, but these plots deviated from the equations for Mn < 2, 000. (2)The partial specific compressibility, β1°, of dextran is expressed by following equation for Mn < 2,000: β1° = 10−12 × (13.6 log Mn ‐ 51.7) (cm2/dyne). In contrast, it, becomes the constant value, ‐‐ 7.3 × 10−12 cm2/dyne, for Mn > 2,000. (3) The amount of bound water of dextran calculated from the sound velocity measurement lakes constant value of 0.17 ml g for Mn > 2, 000, but the amount of hydration increase with decreasing molecular weight for Mn < 2,000. From these results, a dextran molecule in aqueous solution is expected to change its conformation from random coiling to uncoiling stretched form at the molecular weight of around 2, 000 or about 12 glucose units.
Elude dielectrique de la transconformation thermique du Na DNA en solution
Authors: Grassi Hexri , Vasilescu Dane 
Published: May 2005

AbstractA dielectric method is presented to measure the ejection of counterion during the thermal fusion of Na DNA solutions. The dielectric conductivity behavior at fixed frequency versus temperature is a measure of the molar concentration of counterfoils formed from the macromolecules. A linear dependence between Na+ cations released and DNA concentration was verified. We consider the variation of sodium activity coefficient Δ during thermal transconformation to be in good agreement with other experimental data.
Conformational energy calculations on alginic acid. II. Conformational statistics of the copolymers
Authors: Whittincjton S. G. 
Published: May 2005

AbstractConformational energy maps have been calculated for α‐D‐mannuronic acid (1–4) α‐L‐guluronic acid and for α‐L‐guluronic acid (1–4) β‐D‐mannuronic acid. These have been used, together with maps previously calculated for the homomonomeric dimers, to estimate the characteristic ratios and Kuhn lengths of the alternating copolymer and of a stochastic copolymer similar in composition to that extracted from L. digitata.The results show that the alternating copolymer is less extended than either homopolymer. Kuhn lengths calculated for the stochastic copolymer agree well with experimental results on high ionic strength solutions of alginate isolated from L digitata.
Conformational Changes in the Reassembly of MS2 Protein Subunits
Authors: Oriel P. J. , Lindsey Pamela , Schueneman Cheryl 
Published: May 2005

AbstractConformatioiial changes during the reassembly of bacteriophage MS2 coat proteiii from guanidiiie hydrochloride have been investigated by optical rotatory dispersion. Optical rotatory dispersion aid circular dichroism data of the reassembled particles are interpreted as those of β structure. Refolding of the subunit with increasing temperature demonstrated in 2 M guauidine hydrochloride. The stabilization of this structure by hydrophobic bonds and its role in reassembly is discussed.
Polyelectrolyte complexes of glycol chitosan with some polysaccharides. II. Electrical conductivity
Authors: Srinivasan R. , Kamalam R. 
Published: May 2005

AbstractThe dc electrical conductivity of films of the polyelectrolyte complexes of glycol chitosan (GlChi) with the sodium salts of dextran sulfate (DS), carboxymethyl cellulose (CMC), polygalacturonic acid (GalUA)n, and alginic acid (AlgA) was measured at temperatures above and below room temperature. The maximum field strength in the thinnest film used amounted to 3 × 104 V/cm. A plot of normalized current against the reciprocal of the absolute temperature revealed two regions with different slopes, and activation energies in these two regions have been obtained for all the complexes. The activation energies in the high‐temperature region vary from 0.85 to 1.18 eV and in the low‐temperature region from 0 to 0.22 eV. Reasons are given to show that the conductivity is probably ionic. Near room temperature, the current–voltage relation is almost linear in the GlChi–DS complex, while in the other three complexes the current varies as a power n of the voltage with the value of n ranging from 1.7 to 2.5. A rise in temperatures causes an increase in the slope of the log I vs log V plot in GlChi–DS and GlChi–CMC complexes. The nonlinear current–voltage relation is ascribed to a space‐charge‐limited conductivity.
15N‐nmr spectroscopy. 33. Assignments of isotactic and syndiotactic sequences in poly(D,L‐amino acids)
Authors: Kricheldorf Hans R. , Hull William E. 
Published: May 2005

Abstract15N‐enriched (D,L‐Leu)n, (γ‐OMe‐D,L‐Glu)n, (D,L‐Val)n, and (D,L‐Phe)n were prepared, 40.55‐MHz 15N‐nmr spectra were measured in various solvents. The signal patterns depend strongly on the nature of the solvent, yet in most cases at least four signals are resolved, representing the four enantiomeric pairs of triads L‐L‐L (D‐D‐D), L‐D‐L (D‐L‐D), L‐L‐D (D‐D‐L), and D‐L‐L (L‐D‐D). Numerous copolypeptides of the general structure (A)n‐B*‐(A)m (the asterisk denotes 40–50% 15N enrichment) were synthesized and measured as models for syndiotactic sequences in the spectra of poly(D,L‐amino acids). In this way unambiguous assignments for both isotactic and syndiotactic trials were obtained. A spectroscopic rule was established: “isotactic sequences absorb downfield of syndiotactic ones.” Furthermore, the spectra of various types of stereocopolypeptides such as (L‐Leu/L‐Val)n and (L‐Leu/D‐Val)n were investigated, including the ternary systems (L‐Leu/L‐Ala/D‐Ala)n (L‐Leu/L‐Ala/Gly)n, (L‐Leu/D‐Ala/Gly)n, (L‐Val/L‐Ala/Gly)n, and (L‐Val/D‐Ala/Gly)n. All copolymerization of D‐ and L‐amino acid NCAs investigated in this work showed a low degree of stereoselectivity.
Spin‐label studies of the pH‐induced random coil to α‐helix conformational transition in poly(L‐lysine)
Authors: Skinner James F. , Calkins Hugh H. , Liles W. Conrad , Kaplan Lawrence J. 
Published: May 2005

AbstractPoly(L‐lysine) of various molecular weights between 2700 and 475,000 was spin‐labeled. From the electron spin resonance spectra, the degree of freedom of the nitroxide was determined by calculation of the rotational correlation time as the poly(L‐lysine) underwent the pH‐induced random coil to α‐helix conformational transition. In general, the rotational correlation time of the nitroxide increased as the pH was increased, indicating a more restricted environment for the spin label when poly(L‐lysine) is deprotonated. For the high‐molecular‐weight poly(L‐lysine) this corresponds to the formation of the α‐helix and indicates that the side chain–side chain interaction and decreased segmental motion of the backbone (slightly) restricts the motion of the spin label. For the 2700‐molecular‐weight poly(L‐lysine), previously shown not to assume a helical conformation at high pH, the increase in the rotational correlation time of the spin label indicates that the side chain–side chain interaction takes place after deprotonation but without helix formation. This may indicate that helix formation per se is not needed to produce the observed effect even with the high‐molecular‐weight polymers. The rotational correlation time of the spin label at a particular pH did not depend on the molecular weight of the poly(L‐lysine) over the 200‐fold range of molecular weights. This indicates that the rotational correlation time reflects the rotational mobility of the spin label in a localized environment and not the rotational diffusion of the entire macromolecule.
Circular dichroism study of modified nucleosides
Authors: Gałat Andrzej , Jankowski Aleksander 
Published: May 2005

AbstractCD study of four modified nucleosides, constituents of tRNA molecules, revealed that 2‐thio‐5‐methyluridine and 5‐methyluridine in aqueous solution, 0.1N HCl, and organic solvents essentially occur in an anti‐conformation. 5‐Methylcytidine also occurs in an anti‐conformation similar to cytidine in aqueous solution and organic solvents, while 2‐thiocytidine dihydrate appears to occur in an anti‐conformation. It is stressed that the CD data of thionucleosides might be applied to the successfully conformational analysis of tRNA molecules.
Calculated compression, bending, shearing, torsion, and base‐tilting force constants of B‐ and A‐form poly(dG)·poly(dC)
Authors: Putnam B. F. , Prohofsky E. W. , Zandt L. L. Van 
Published: May 2005

AbstractForce constants associated with large‐scale motions of the DNA double‐helical homopolymer poly(dG)·poly(dC) are projected out of a long‐range atom–atom Coulomb force field. Force constants for both B‐ and A‐conformations have been calculated. Using the Coulomb interaction as previously incorporated into our DNA normal mode calculations, we obtain the forces determined by this long‐range interaction. These include compression, bending, shearing, torsion, and base tilting. We show, quantitatively, how the shearing and torsional transverse interactions fall off with intercell distance more rapidly than the compressional (longitudinal) interactions. Reasonable values for the elastic moduli of B‐ and A‐DNA are calculated. An important prediction of the present interaction theory is that although the single adjustable strength parameter in the Coulomb force field was chosen so as to reproduce an experimental value for the longitudinal sound velocity, the transverse torsional potential resulting from this fitted force field is in excellent agreement with results reported from supercoiling data and fluorescence measurements.
Cooperative binding of n‐mers with steric hindrance to finite and infinite one‐dimensional lattices
Authors: Tsuchiya Takashi , Szabo Attila 
Published: May 2005

AbstractThe cooperative binding of n‐mers to a finite ring, a finite open chain, and an infinite chain is treated in a unified way using the matrix method. For an infinite chain, the implicit closed‐form expression (“Scatchard formula”) for the fraction of bound sites obtained by McGhee and von Hippel, is simply rederived using a procedure involving implicit differentiation of the characteristic equation. A variety of models for n‐mer binding that incorporate steric hindrance for formulated, and corresponding Scatchard formulas are derived using our procedure.
Energy embedding of trypsin inhibitor
Authors: Crippen Gordon M. 
Published: May 2005

AbstractEnergy embedding has been shown recently to be a useful extension of the distance geometry approach to conformational calculations in the case of very small molecules and simple energy functions. This paper tests the ability of energy embedding to locate low energy conformations satisfying both weak and strong geometric constraints when the molecule is the small protein, bovine pancreatic trypsin inhibitor, and the energy function is the complicated Oobatake‐Crippen residue–residue potential. Using the potential function alone, the algorithm reaches a structure with energy lower than that of the native conformation, but with little resemblance to it. Aided by numerous geometric constraints, such as preformed secondary structure segments, the algorithm again finds a local minimum with energy better than that of the native, and with only 3.3 Å rms deviation from it. This is significantly closer to the native value than can be obtained using standard distance geometry and the geometric constraints alone. Thus, energy embedding using the Oobatake‐Crippen potential function is a significant help in finding native conformations of proteins. However, additional trials on a hairpin bend fragment of trypsin inhibitor demonstrate the potential's shortcomings in encouraging proper secondary structure.
Molecular‐mechanical studies of Z‐DNA: A comparison of the structural and energetic properties of Z‐ and B‐DNA
Authors: Kollman Peter , Weiner Paul , Quigley Gary , Wang Andrew 
Published: May 2005

AbstractMolecular‐mechanical studies of the left‐handed Z‐DNA polymers have been carried out and the results compared with similar calculations on B‐DNA polymers. We have studied d(CGCGCG)2, d(GCGCGC)2 (and their 5‐methyl cytosine analogs), dG6·dC6, d(ATATAT)2, and d(TATATA)2 in both B‐ and Z‐forms. For the left‐handed Z helices, we considered the ZI and ZII model of Quigley and co‐workers [Wang, A. H., Quigley, G. J., Kolpak, F. J., Crawford, J. L., van Boom, J. H., van der Marel, G. & Rich, A. (1979) Nature (London) 282, 680–686], the actual “Z spermidine” and “Z spermine” structures of Quigley and the model‐built structure of Chandresekharan et al. [Arnott, S., Chandresekharan, R., Bindsall, D. L., Leslie, A. G. W. & Ratliff, R. L. (1980) Nature 283, 743–745]. The major conclusions of this study are as follows. (1) The stabilization of Z‐DNA relative to B‐DNA occurs as one increases the “effective” dielectric constant or adds counterions, consistent with observations of Z‐DNA only under high salt conditions. (2) The ZII polymer is calculated to be more stable than the ZI polymer. It is not yet clear whether the greater stability of ZII than ZI is a real effect or an artifact caused by the lack of inclusion of specific solvation effects in these calculations. (3) The greater tendency of the 5‐methyl cytosine analog of poly(dG‐dC)·poly(dG‐dC) to undergo the B → Z transition is found in our calculations and is due to destabilizing base–base and base–phosphate interactions, which are greater in the B‐ than in the Z‐form of the 5‐methyl cytosine polymer. (4) There are no large sequence‐dependent effects on the relative stabilities, and the AT polymers are calculated to be as likely to form Z‐helices as the GC polymers. In addition, the relative stability of a nonalternating sequence in the conformation is only slightly less than that found for alternating sequences.
Crystal structure and solution conformation of 1‐N‐acetyl‐β‐D‐glucopyranosyl amine: A model for the glycopeptide linkage
Authors: Bush C. Allen , Blumberg Karl , Brown Joe N. 
Published: May 2005

AbstractThe crystal structure of the title compound, a model for the glycosyl linkage between the asparagine side chain and N‐acetyl glucosamine in glycoproteins, has been determined and compared to other model structures. The pyranose ring in the crystal is in the 4C1 chair conformation and the amide functions at C1 and at C2 are both oriented such that the amide protons are nearly trans to their respective sugar‐ring protons. Coupling constants determined from the fully assigned proton nmr spectrum in aqueous solution are consistent with the conformation in the crystal.
Flow dichroism of capsid DNA phages. II. Effect of DNA deletions and intercalating dyes
Authors: Hall Stephen B. , Schellman John A. 
Published: May 2005

AbstractThe flow linear dichroism of bacteriophage λ and its deletion mutants, λ b2 and λ b221, was determined. The hydrodynamic behavior of the three phages differed slightly, but the magnitude of the dichroism was substantially the same with 〈cos2θμp〉 = 0.364, 0.368, and 0.372, respectively. The dichroism of intercalating dyes combined with bacteriophage was used as a further probe of phage structure. The reduced dichroism from proflavin with T4 showed no change with time during the reaction, but the interpretation of the ligand dichroism is complicated by an alteration of the hydrodynamic behavior of the phage–dye complex relative to the phage alone. Ethidium with λ also produced a stable reduced dichroism, but the signal indicated an average orientation of intercalated dye that is different from the average base orientation. The reduced dichroism of ethidium changes with time as it penetrates λ b2, eventually approaching the dichroism of the nucleotide bases. The implication of these findings on the plausibility of various simple DNA packing models is discussed.
Pulsed field gradient nmr determination of the temperature dependence of the tracer diffusion coefficient of hemoglobin
Authors: Everhart Cherie H. , Johnson Charles S. 
Published: May 2005

AbstractWe have studied the temperature dependence of the tracer diffusion coefficient of carbonmonoxy hemoglobin A (HbA‐CO) by means of pulsed‐field gradient nmr (PFG‐nmr). Measurements were made over the temperature range from 15 to 35°C for samples having concentrations 7.4 and 16.7 g/dL. No significant deviations were found from the predictions of the Stokes‐Einstein relation. Thus, this work does not corroborate the recently proposed conformational change in hemoglobin at 22°C. The advantages of PFG‐nmr for the study of hemoglobin are discussed.
Effect of water on piezoelectric, dielectric, and elastic properties of bone
Authors: Maeda Hideatsu , Fukada Eiich 
Published: May 2005

AbstractThe complex piezoelectric constant (d = d′ − id″), elastic constant (c = c′ + ic″), and dielectric constant (ε = ε′ − iε″) were measured at a frequency of 10 Hz over the temperature range from −150 to 50°C and for a range of hydration up to 0.26 g/g for decalcified bone and up to 0.084 g/g for bone. For decalcified bone, ε′ and ε″ increased with increasing hydration with a deflection at the critical hydration hc = 0.08 g/g;d′ at −150°C increased below hc but decreased above hc with increasing hydration; c′ increased below −60°C but decreased above −60°C with increasing hydration; and the peak temperatures of ε″, d″, and c″ below −50°C agree with each other and decreased with increasing hydration with a deflection at hc. For bone, similar hydration and temperature dependences were observed for ε and c. However, the dependence of d on hydration and temperature was different from that of decalcified bone, reflecting a two‐phase structure consisting of collagen fibers and mineral hydroxyapatite. The critical hydration for bone was 0.04 g/g.