bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concentration distribution and spatial moments of moving macromolecules undergoing isomerization
Authors: Killalea M. K. , McCoy B. J. 
Published: December 2004

AbstractExpressions for zeroth, first, and second spatial moments are obtained for diffusing macromolecules A and B that move due to an external field and undergo reversible isomerization, switching back and forth according to first‐order kinetics. In addition, expressions for third and fourth moments are derived for the special case of equal diffusion coefficients, equal rate constants, and equal but opposite velocities. The initial conditions are arbitrary amounts of A or B concentrated in an infinitesimally narrow region. The moments are computed from derivatives of the Fourier‐transformed concentration profiles of A and B. The moments are used in an expansion in term of Hermite polynomials, the Gram‐Charlier expansion, to construct the concentration profiles of A or B or A and B together. The examples presented show that a few terms of the expansion, for which explicit expressions are given, can give tolerable accuracy if the velocity is not too large and the rate constants and diffusion coefficient are not too small. The expansion can be used to determine when the profiles are unimodal.
Circular dichroism of N‐phenylnaphthylamine derivatives complexed with the β‐form of poly(L‐lysine)
Authors: Sato Yukio , Woody Robert W. 
Published: December 2004

AbstractComplex formation of 1‐anilinonaphthalene‐8‐sulfonate (ANS) and 2‐p‐toluidinonaphthalene‐6‐sulfonate (TNS) with the β‐form of poly(L‐lysine) [(β‐Lys)n] has been studied by circular dichroism (CD) and absorption spectra measurements. Not only hydrophobic interactions but also hydrogen‐bonding and electrostatic interactions contribute to complex formation. The relative importance of these stabilizing factors depends on the relative position of the arylamino group and the sulfonate. For example, ionic interactions play a significant role in the binding of 1,8‐ANS and 1,8‐TNS, but not in the case of 2,6‐TNS. The induced CD of the complexes of (β‐Lys)n with 1,8‐ANS and 1,8‐TNS is consistent with theoretical calculations for nonplanar conformations of these dyes, twisted in a left‐handed sense. As expected for steric reasons, the dominant isomer is one in which the arylamino group is oriented away from the 8‐sulfonate (α1). The induced CD of complexes with 2,6‐TNS can be accounted for by an equimolar mixture of left‐handed isomers in which the arylamino group is oriented toward the 1‐position (β2) and toward the 3‐position (β1). Our results demonstrate that (β‐Lys)n is capable of chiral discrimination and suggest its general utility for CD studies of racemic anionic dyes.
New synthesis of somatostatin according to the S‐tert‐butylthiocysteine procedure
Authors: Moroder L. , Gemeiner M. , Goehring W. , Jaeger E. , Thamm P. , Wünsch E. 
Published: December 2004

AbstractTo exemplify the usefulness of the S‐tert‐butylthio group for a reversible blocking of the cysteine thiol function in peptide synthesis, fully protected dihydrosomatostatin was prepared by the fragment‐condensation procedure. The experimental results confirm the excellent stability of the asymmetric disulfide under the normal conditions of peptide synthesis and prove that the selective, acid‐catalyzed nucleophil removal—as well as by mercaptans—of the 2‐nitrophenylsulfenyl group proceeds smoothly in the presence of this thiol protection. Thus, the strategy of overall acid‐labile side‐chain protection in combination with the Nα‐2‐nitrophenylsulfenyl group for the chain‐elongation steps can be successfully applied to the synthesis of cysteine‐containing peptides using their S‐tert‐butylthio derivatives. Removal of the acid‐labile groups, followed by reductive cleavage of the asymmetric disulfides and successive air oxidation, allowed a clean conversion of protected dihydrosomatostatin into somatostatin at a high degree of purity and in good yields.
Laser light‐scattering analysis of the dimerization of transfer ribonucleic acids with complementary anticodons
Authors: Wang Chun‐Chen , Ford Norman C. , Fournier Maurille J. 
Published: December 2004

AbstractPhoton‐correlation spectroscopy is a powerful technique for measuring the translational diffusion coefficient of particles and macromolecules in solution. In the study described here, this technique was used to analyze a specific dimerization process involving the association of two tRNA molecules through complementary anticodons. The tRNAs used in the analysis were E. coli tRNA and yeast tRNAPhe. The experimental data on the concentration dependence of the observed diffusion constants are shown to agree well with theoretical predictions. From these data, the equilibrium constant of the association reaction was determined for dimers formed over a wide range of temperatures and in several different solution conditions. In solutions of 0.1M ionic strength at 22°C, the equilibrium constants vary from 1 × 105M−1 in the absence of magnesium to 1.5 × 106M−1 in 10 mM Mg+2. The enthalpy and entropy changes for dimer formation in the absence and presence, 5 and 10 mM, of magnesium have been obtained from the temperature dependence of the equilibrium constant. The results show that both ΔH and ΔS contribute to the free energy of binding and that their relative contributions are similar for each solution condition evaluated.
Interaction of the antimalarial drug fluoroquine with DNA, tRNA, and poly(A): 19F‐NMR chemical‐shift and relaxation, optical absorption, and fluorescence studies
Authors: Bolton Philip H. , Mirau Peter A. , Shafer Richard H. , James Thomas L. 
Published: December 2004

AbstractThe interaction of the fluorinated antimalarial drug fluoroquine [7‐fluoro‐4‐(diethyl‐amino‐1‐methylbutylamino)quinoline] with DNA, tRNA, and poly(A) has been investigated by optical absorption, fluorescence, and 19F‐nmr chemical‐shift and relaxation methods. Optical absorption and fluorescence experiments indicate that fluoroquine binds to nucleic acids in a similar manner to that of its well‐known analog chloroquine. At low drug‐to‐base pair ratios, binding of both drugs appears to be random. Fluoroquine and chloroquine also elevate the melting temperature (Tm) of DNA to a comparable extent. Binding of fluoroquine to DNA, tRNA, or poly(A) results in a downfield shift of about 1.5 ppm for the 19F‐nmr resonance. The chemical shift of free fluoroquine depends on the isotopic composition of the solvent (D2O vs H2O). The solvent isotope shift is virtually eliminated by fluoroquine binding to any one of the nucleic acids. 19F‐nmr relaxation experiments were carried out to measure the spin‐lattice relaxation time (T1), 19F{1H} nuclear Overhauser effect (NOE), off‐resonance intensity ratio (R), off‐resonance rotating‐frame spin‐lattice relaxation time (T), and linewidth for fluoroquine in the nucleic acid complexes. By accounting for intramolecular proton‐fluorine dipolar and chemical‐shift anisotropy contributions to the fluorine relaxation, all of the relaxation parameters for the fluoroquine–DNA complex can be well described by a motional model incorporating long‐range DNA bending on the order of a microsecond and an internal motion of the drug on the order of a nanosecond. Selective NOE experiments indicate that the fluorine in the drug is near the ribose protons in the RNA complexes, but not in the DNA complex. Details of the binding evidently differ for the two types of nucleic acids. This study provides the foundation for an investigation of fluoroquine in intact cells.
A theory of aggregation in the thermal denaturation region of multistrand biopolymers
Authors: Shibata John H. , Schurr J. Michael 
Published: December 2004

AbstractA theory explicitly allowing the possibility of aggregation of multistrand biopolymers is proposed. It is found that the same secondary bonds responsible for stabilizing the native structure at low temperature will promote aggregation in the thermal denaturation region for sufficiently long chains. A requirement for both open and zippered regions dictates that the aggregation region does not extend far below Tm. However, its width, or extension on the high‐temperature side of Tm, is a strongly increasing function of chain length and also of the cooperativity parameter. The present theoretical results obtained for DNA and collagen with almost no adjustable parameters are in good qualitative agreement with a number of previously poorly understood experimental observations. The significance of such a spontaneous aggregation phenomenon for genetic recombination is noted.
Calculated microwave absorption of double‐helical B‐conformation poly(dG)·poly(dC)
Authors: Kohli M. , Mei W. N. , Prohofsky E. W. , Van Zandt L. L. 
Published: December 2004

AbstractWe have estimated the absorption of microwave radiation by the four acoustic modes of poly(dG)·poly(dC) in B conformation. The eigenvectors used in this calculation are those obtained from a refined normal coordinate analysis by fitting the velocity of the longitudinal acoustic mode to that observed by Brillouin scattering. The acoustic modes couple to the radiation field when translational invariance is broken such as for finite segments of helix and as may be the case in vivo. Calculations for various helix lengths show that the estimated absorption is greater than that of water by at least two to three orders of magnitude in some cases.
Stabilities of nearest‐neighbor doublets in double‐helical DNA determined by fitting calculated melting profiles to observed profiles
Authors: Gotoh Osamu , Tagashira Yusaku 
Published: December 2004

AbstractMelting profiles were calculated for restriction fragments of ϕX174 and fd phage DNAs and compared with experimental profiles. The algorithm of Fixman and Freire was slightly modified so that a stability parameter was assigned not to a base pair but to each nearest‐neighbor doublet. Stabilities of the 10 kinds of nearest‐neighbor doublets were estimated by fitting the calculated profiles to the observed ones. Agreement of the calculated and observed profiles was much improved by this modification. The most interesting finding was that purine (3′‐5′) pyrimidine stackings are much more stable than their respective reverses. The order of nearest‐neighbor stabilities is in excellent agreement with that of negative stacking energies calculated by Rein and coworkers by a quantum‐chemical method.
Thermodynamics and equilibrium sedimentation analysis of the close approach of DNA molecules and a molecular ordering transition
Authors: Brian A. A. , Frisch H. L. , Lerman L. S. 
Published: December 2004

AbstractMeasurement of the equilibrium distribution of persistence length fragments of DNA in high concentration in the ultracentrifuge shows that the reduced osmotic pressure rises much faster than linearly. From analysis of the data in terms of the Zimm cluster integral we infer that the net interactions between helices are purely repulsive at all distances. A theoretical equation of state derived from scaled particle theory with one adjustable parameter is in excellent agreement with the experimental data so long as the salt concentration is not excessively low. The parameter represents the hard‐core radius in a simplified approximation to the potential function for the electrostatic repulsion between helices. Its value depends on the salt concentration, and it shrinks at high salt to a radius in close agreement with direct structural estimates. At a particular value of the osmotic pressure that is only slightly salt dependent, the solution undergoes a reversible transition to a denser, turbid, optically anisotropic phase. The relation between DNA volume fraction, including the electrostatic radius, at the transition point and the effective asymmetry of the molecules as a function of salt is in approximate correspondence with various theoretical treatments. However, the experimental function extrapolates to the correct limit for spherical particles. The work needed to bring DNA to a high concentration is estimated. The results suggest that the phase transition is first order.
Early stages of fibrinogen to fibrin conversion studied by static and dynamic light scattering
Authors: Wiltzius P. , Känzig W. , Hofmann V. , Straub P. W. 
Published: December 2004

AbstractThe early steps of fibrin aggregation induced by low Reptilase concentrations were studied by means of static and dynamic light scattering. In order to obtain information on the size and shape of the first oligomers, the angular dependence of the scattered intensity and the mean Rayleigh line width were measured. Under physiological pH and ionic strength, oligomer formation was detectable immediately after enzymatic activation. Comparison of the calculated data for different models with experimental results shows that the early fibrin polymerization proceeds as an end‐to‐end aggregation of elongated and possibly flexible molecules approximately 75 nm long.
Influence of the telopeptides on type I collagen fibrillogenesis
Authors: Brennan Maureen , Davison Peter F. 
Published: December 2004

AbstractPreparations have been made of acid‐soluble collagens whose telopeptides have suffered different levels of proteolytic attack. The collagens with more intact telopeptides form fibrils more rapidly than those with degraded telopeptides. In addition, we have shown that a high molecular weight aggregate rich in the carboxyterminal CNBr peptide, α1CB6, can be found in cyanogen bromide digests of fibrils formed from intact collagen. A similar aggregate is found in CNBr digests of native tendons. The aggregate formed in fibrils assembled in vitro can be stabilized by reduction, and its generation is strongly dependent on the presence of intact telopeptides. The latter point is the most objective evidence that to reproduce the characteristics of native fibrils in vitro, the collagen telopeptides must be preserved from proteolysis.
Influence of water structure and of hydrophobic interactions on the strength of side‐chain hydrogen bonds in proteins
Authors: Némethy George , Steinberg Izchak Z. , Scheraga Harold A. 
Published: December 2004

AbstractThe thermodynamic properties derived earlier for the formation of side‐chain hydrogen bonds were re‐evaluated, taking into account medium effects and interactions of the side chains with nearby nonpolar groups. In determining the enthalpy of formation of the hydrogen bond, competitive hydrogen bonding with water has to be considered, except for “buried” groups, i.e., groups surrounded entirely by nonpolar groups. For such buried groups, the earlier estimate of ΔH = −6 kcal./mole is still valid, but for groups exposed to water, a lower value has to be used, estimated to be −1.5 kcal./mole. The internal bond rotations of side chains involved in hydrogen bonding are not restricted completely; therefore, ΔS is only −2 to −5 e.u. per side chain, instead of the much higher values estimated earlier. As a result, the new estimated value of ΔF is 0 to −0.5 kcal./mole, not much different from the earlier estimate. The ease of hydrogen bond formation may be changed by cooperative or competitive hydrophobic bonding of the nonpolar portions of the polar side chains with the backbone or nearby nonpolar side chains. Various cases of such interactions are discussed, including the burying of polar groups and the formation of hydrogen bonds between buried groups. It is shown that, in aqueous environment, the polar groups form more than one hydrogen bond with water, an effect to be taken into account when considering buried groups. Medium effects due to the presence of nonpolar groups and the effects of changes in the water structure on the ease of formation of the α‐helix are mentioned. Estimates for the thermodynamic parameters of the various hydrogen‐bonding and hydrophobic interactions are given. It is shown that hydrophobic interactions will, in general, enhance the strength of hydrogen bonds. The net free energy of formation of a simple structure involving both interactions may range from about −0.5 to −2.4 kcal./mole. It may reach much more highly negative values for large structures. The corresponding ranges of the net enthalpy and entropy of formation are −1.5 to −0.5 kcal./mole and −3 to +7 e.u., respectively.
Absorption spectra of nucleotides, polynucleotides, and nucleic acids in the far ultraviolet
Authors: Voet D. , Gratzer W. B. , Cox R. A. , Doty Paul 
Published: December 2004

AbstractUltaviolet absorption spectra down to 185 mμ are presented for a number of nucleic acids and synthetic polynucleotides in the helical and random forms, and of their constituent mononucleotides, as well as the corresponding nucleosides and free bases. A short wavelength absorption band is in all cases observed with a maximum varying between about 187 and 201 mμ. These bands are more intense than those near 260 mμ. The helical polymers show a hypochromic effect in this region of a somewhat similar magnitude to that in the 260 mμ region. Other spectral phenomena accompanying denaturation and degradation are described.
Infrared spectra and molecular conformations of D,L‐copoly‐γ‐benzylglutamates
Authors: Tsuboi Masamichi , Mitsui Yukio , Wada Akiyoshi , Miyazawa Tatsuo , Nagashima Nobuya 
Published: December 2004

AbstractInfrared absorption and x‐ray diffraction measurements have been made of D,L‐copoly‐γ‐benzylglutamate fibers (cast from dioxane solutions) with various D/L ratios and with various degrees of polymerization. It was found that each chain of these copolymers consists of a random coil portion and an α‐helix portion and that the conformation of the latter is similar to the α‐helix of pure poly‐γ‐benzyl‐L‐glutamate. It was also found that the fraction of the α‐helix portion increases with the degree of polymerization of the copolymer. A simplified polymerization mechanism has been proposed for mixtures of D‐ and L‐amino acid N‐carboxyanhydrides. A model of the molecular conformation of the D,L‐copolypeptide chains derived from this proposed polymerization mechanism is in good agreement with infrared, x‐ray, and other measurements. Based on the results of these observations, we discuss the number of L‐ or D‐residues linked in succession that is required for initiating the formation of an α‐helix during the course of polymerization.
Sedimentation and diffusion of polyelectrolytes. Part I. Theoretical description
Authors: Alexandrowicz Z. , Daniel Ezra 
Published: December 2004

AbstractThe effect of charges on sedimentation and diffusion of macroions is treated along the lines adopted by Svedberg‐Pedersen for the description of sedimentation, with the difference that the virtual electrophoretic motion of the macroions which gives rise to the charge effect is not equated to the real electrophoretic mobility. Furthermore the activity correction is introduced through the recently established representation, according to which a constant fraction of the counter‐ions may be considered to be permanently immobilized. Lastly, for the sake of simplicity, it is assumed that the frictional coefficient of the macroions does not depend on the ionic strength. On this basis a relatively simple description in terms of readily accessible parameters is obtained. The charge effects in sedimentation and diffusion are closely related, one to another, and to other polyelectrolyte properties. The physical significance of the results is discussed. The description is compared to experimental data in the literature and also to the second experimental part of this work: it is found that the main features of the charge effect are satisfactorily described under widely differing conditions, although some deviations indicate the limitations of the approximate treatment.
Sedimentation and diffusion of polyelectrolytes. Part II. Experimental studies with poly‐L‐lysine hydrohalides
Authors: Daniel Ezra , Alexandrowicz Z. 
Published: December 2004

AbstractThe sedimentation, diffusion, and osmotic behavior of poly‐L‐lysine hydrochloride is examined over a wide range of ionic strengths and in solutions which range in relative composition from a swamping excess of added salt (suppression of charge effect) to salt‐free solutions (maximum effect). The charge effect is found to essentially obey the theoretical treatment proposed in Part I of this work. The frictional coefficient of the macroion in salt‐free solutions is comparable to that of the fully stretched chain. In excess of salt the friction is appreciably smaller, its magnitude not varying greatly with ionic strength. The molecular weight is determined osmotically and also from diffusion‐sedimentation, with the charge effect suppressed by addition of salt or eliminated through the use of non‐ionized forms of the polymer; a reasonable agreement is obtained between the methods. The influence of small ions on sedimentation is also examined. The secondary salt effect is found to be much smaller than that predicted theoretically; on the other hand, the substitution of different counterions in the absence of secondary salt effect gives rise to changes of the expected magnitude.
Synthesis of poly‐L‐lysine and poly‐L‐lysyl albumin via ϵ,N‐trifluoroacetyl‐α,N‐carboxy‐L‐lysine anhydride
Authors: Sela Michael , Arnon Ruth , Jacobson Israel 
Published: December 2004

AbstractFree poly‐L‐lysine base has been synthesized from ϵ,N‐trifluoroacetyl‐α,N‐carboxy‐L‐lysine anhydride via poly‐ϵ,N‐trifluoroacetyl‐L‐lysine (IV). No racemization occurred during the removal of trifluoroacetyl groups from IV with 1M piperidine. Measurements of optical rotatory dispersion suggest that IV exists in methanol in a helical form. The synthesis of poly‐L‐lysyl rabbit serum albumin is also described.
Properties of poly‐β‐hydroxybutyrate. I. General considerations concerning the naturally occurring polymer
Authors: Alper R. , Lundgren D. G. , Marchessault R. H. , Cote W. A. 
Published: December 2004

AbstractPoly‐β‐hydroxybutyric acid has been isolated from two bacterial sources by two different procedures. Molecular weight and intrinsic viscosity for the two samples were vastly different. This was blamed on degradation occurring during polymer isolation. An optical rotatory dispersion curve for the high molecular weight sample showed a sharp increase in specific rotation at wavelengths less than 450mμ. From this fact and the reported optical activity of the monomer it is concluded that the polymer is stereo‐regular. X‐ray examination of the “native” and “regenerated” polymer yielded the same crystalline pattern. Electron diffraction and x‐ray data on single crystals of the polymer indicate a fiber repeat of 5.9 A. The value can only be reconciled with some kind of helical conformation in the solid state.
Reduced sedimentation equilibrium time by two‐step initial loading
Authors: Todd G. Peter , Haschemeyer Rudy H. 
Published: December 2004

AbstractComputer simulation shows that the time required to attain near sedimentation equilbrium is dramatically reduced by a two‐step initial loading in which a macromolecular solution at low or zero concentration is layered above one at a higher concentration. To achieve the minimum time requires a good estimate of the molecular weight, but at least a 50% reduction in time can be achieved if the molecular weight of the macromolecule is known only within a factor of 2. Numerical solutions to the differential equation of the ultracentrifuge are calculated using the finite element method. An efficient Gaussian elimination algorithm can be used to minimize calculation time and computer storage requirements.