bluuebunny/crossref_metadata_2025_split huggingface dataset:
Influence of D and L amino‐acid residues on the conformation of peptides in solution: A carbon‐13 nuclear magnetic resonance study of cyclo(prolyl‐leucyl)
Authors: Deslauriers Roxanne , Grzonka Z. , Walter Roderich 
Published: May 2005

AbstractThe 13C chemical shifts and spin‐lattice relaxation times are reported for cyclo(L‐Pro‐L‐Leu) and cyclo(L‐Pro‐D‐Leu). The chemical shifts of the D and L leucyl residues in the cyclic peptides differ from each other by 1.8 and 3.6 parts per million for the α and β carbons, respectively. The α‐carbons of the prolyl residues differ by 1.0 ppm as a consequence of proximity to a D or an L leucyl residue. The 13C spin‐lattic relaxation time(T1) of the prolyl residues, but not the leucyl residues, in both compounds are indicative of difference in conformational equilibria within the pyrrolidine ring in the L‐L isomer as compared to the L‐D isomer. Anisotropic overall molecular reorientation is not responsible for the differences observed in the T1 values. The differences in T1 values and chemical shifts between cyclo(L‐Pro‐L‐Leu) and cyclo(L‐Pro‐D‐Leu) appear to result from a difference in conformations of the two diketopiperazine rings.
Dinucleoside monophosphates. I. Optical properties and conformation in solution with one base charged
Authors: Topal Michael D. , Warshaw Myron M. 
Published: May 2005

AbstractA least squares analysis of the titration properties of several dinucleoside monophosphates enables calculation of the pK's for protonation. These pK's are used to resolve the spectral properties of dinucleoside monophosphates with one base charged from the apparent spectral properties of a dinucleoside monophosphate in aqueous solution. This method is applied to dinucleoside monophosphates containing adenosine and/or cytidine. Results of CD, nmr, and CD‐temperature dependence measurements are presented. The results indicate that singly protonated dimers of these nucleosides stack as do their unprotonated analogs. It is suggested that this is true for all dimers with one base charged.
Calorimetric measurement of enthalpy change in the isothermal helix–coil transition of poly(L‐ornithine) in aqueous solution
Authors: Fu Yi‐Chang , Van Wart Harold E. , Scheraga Harold A. 
Published: May 2005

AbstractThe enthalpy change associated with the isothermal pH‐induced uncharged coil‐to‐helix transition ΔHh° in poly(L‐ornithine) in 0.1 N KCl has been determnined calorimetrically to be −1530 ± 210 and −1270 ± 530 cal/mol at 10° and 25°C, respectively. Titration data provided information about the state of charge of the polymer in the calorimetric experiments, and optical rotatory dispersion data about its conformation. In order to compute ΔHh°, the observed calorimetric heat was corrected for the heat of breaking the sample cell, the heat of dilution of HCl, the heat of neutralization of the OH− ion, and the heat of ionization of the δ‐amino group in the random coil. The latter was obtained from similar calorimetric measurements on poly(D,L‐ornithine). Since it was discovered that poly(L‐ornithine) undergoes chain cleavage at high pH, the calorimetric measurements were carried out under conditions where no degradation occurred. From the thermally induced uncharged helix–coil transition curve for poly(L‐ornithine) at pH 11.68 in 0.1 N KCl in the 0°–40°C region, the transition temperature Ttr and the quantity (∂θh/∂T)Ttr have been obtained. From these values, together with the measured values of ΔHh°, the changes in the standard free energy ΔGh° and entropy ΔGh°, associated with the uncharged coil‐to‐helix transition at 10°C have been calculated to be −33 cal/mol and −5.3 cal/mol deg, respectively. The value of the Zimm–Bragg helix–coil stability constant σ has been calculated to be 1.4 × 10−2 and the value of s calculated to be 1.06 at 10°C, and between 0.60 and 0.92 at 25°C.
[4‐Amino‐D‐phenylalanine6]luliberin. A biologically active abalog of the luteinizing hormone‐releasing factor suitable for affinity labeling
Authors: Sakarellos Constantinos , Donzel Bernard , Goodman Murray 
Published: May 2005

AbstractThe syntheis of [4‐amino‐D‐phenylalanine6]luliberin by the solid‐phase method is described. The analog was found to be ten times more potent than luliberin. Some possibilities for the easy derivatization of the 4‐amino‐phenylalanyl residue into addinity labels suitable for the study of hormone‐receptor interations are considered. The preparation of Nα‐t‐butyloxycarbonyl‐4‐(benzyloxycarbonylamino)‐D‐phenylalanine, one of the key intermediates used in the synthesis of this luliberin analog, is also reported.
The application of polyelectrolyte limiting laws to the helix–coil transition of DNA. VI. The numerical value of the axial phosphate spacing for the coil form
Authors: Manning Gerald S. 
Published: May 2005

AbstractIt is concluded on the basis of comparison of polyelectrolyte theory with published data that the mean phosphate spacing b along the contour axis of an unfolded polynucleotide single strand is in the range 3–4 Å (polyelectrolyte parameter ξ ≈ 2), regardless of temperature, base composition, or extent of stacking. This result is consistent with the low‐angle X‐ray scattering measurements of Gulik, Inoue, and Luzzati on poly(C). No conclusion may be drawn from this value of b concerning the structure of the chain skeleton or the spatial arrangement of the bases other than that the chain is far from an all‐trans local conformation (for which b would be about 6–7 Å, the length of a nucleotide unit). The structural implications, or lack thereof, are discussed in detail in the following paper.
Polymerization of optical isomers of phenylalanine N‐carboxyanhydride by various secondary amines
Authors: Hashimoto Yutaka , Aoyama Akimasa , Imanishi Yukio , Higashimura Toshinobu 
Published: May 2005

AbstractIn the polymerization of phenylalanine NCA initiated by some secondary amines, the two enatimorphs of phenylalanine NCA were polymerized with the same rate, which was almost twice as high, as that found for the racemic mixture. This stereoselectivity was observed only when the polymerization was initiated by secondary amines which are sterically crowded and reluctant to undergo a nucleophilic addition to NCA. Poly(DL‐phenylalanine) produced in the stereoselective polymerization had a higher molecular weight than that produced in nonstereoselective polymerization. These findings point to the possibility that the stereoselectivity arises only in those polymerizations which are propagated by the activated monomers and not in the propagation involving the terminal amine of the growing polymer. A possible mechanism for the stereoselective polymerization is proposed and examined.
Circular dichroism calculations for double‐stranded polynucleotides of repeating sequence
Authors: Cech Carol L. , Tinoco Ignacio 
Published: May 2005

AbstractOptical property calculations are presented for poly(A·U), poly[(A‐U)·(A‐U)], poly(G·C), and poly[(G‐C)·(G‐C)] in RNA, B‐DNA, and C‐DNA conformations. An all‐order classical coupled oscillator polarizability theory was used, and an effective dielectric constant of 2 was assumed. The calculated CD spectra were found to be sensitive to both geometry and sequence. Agreement with the measured CD spectra of poly(A·U), poly(G·C), and poly(dG·dC) is very good. Calculations for other sequences and geometries are less satisfactory and are particularly poor for poly[(G‐C)·(G‐C)] in RNA geometry and poly(A·T) in B‐DNA geometry. Attempts to improve agreement with measured spectra by varying monomer properties have been only partially successful for these calculations, but they illustrate the types of changes that may prove to be necessary. Calculations using other published X‐ray coordinates for certain deoxypolynucleotides of simple sequence, some of which are quite different from B‐DNA coordinates, did not result in better agreement with measured spectra. Finally, the dependence of the calculated CD on chain length is examined. Results show that non‐nearest neighbor interactions can be important when runs of 3 or more identical base pairs appear in a given sequence.
Inapplicability of “Scatchard‐type” analysis to highly cooperative binding systems
Authors: Schmitz Kenneth S. 
Published: May 2005

AbstractThere are several studies of small molecule binding by biopolymers which use “Scatchard‐type” plots to determine the intrinsic binding constant (k) and pairwise interaction energy between bound sites (S). “Scatchard‐type” refers to the plot ln (r/m(n – r)) versus r in this text whereas “Scatchard plot” conventionally refers to the plot r/m versus r. The quantities r, n, and m are, respectively, the average bound ligand/site, ligand/site at saturation, and concentration of free ligand. Although these plots result from approximate solutions to the problem of binding small molecules on a general three‐dimensional lattice, they are often used to represent binding isotherms in linear systems for which the solutions are known exactly. A critical examination regarding the applicability of “Scatchard‐type” analysis to systems with a large number of binding sites is presented herein.Both experimental and simulated binding data are analyzed by “Scatchard‐type” and exact nearest neighbor plots (θ versus ln m, where θ = r/n). Numerical determination of k and S for the two theoretical approaches differ greatly in highly cooperative systems although their theoretical equivalence (interconversion) is demonstrated. A modified Scatchard theory, which correctly counts the degenerate energy states, is presented which reconciles this discrepancy. The “Scatchard‐type” plot for the modified theory in the highly cooperative limit is mathematically equivalent to the form ln (r/n – r) + p, where p contains all the molecular information and locates the r/n = 1/2 point. Contrary to the original theory, the r dependence in the “Scatchard‐type” representation is devoid of molecular interpretation and is characterized by curvature in the low and high‐binding regions with a (maximum) slope of 4 at r/n = 1/2. The modified theory is shown to reproduce accurately the poly(cytidylic acid)‐guanosine data of Sarocchi et al. and to account for the maxima exhibited in the conventional Scatchard plots.
Quantitative electron microscope observations of the collagen fibrils in rat‐tail tendon
Authors: Parry D. A. D. , Craig A. S. 
Published: May 2005

AbstractAn electron microscope study of collagen fibrils from fixed tail tendons of rats has revealed that from some time shortly after birth until maturity, the fibril diameters have a bimodal distribution. The “two” types of fibril are indistinguishable in both transverse and longitudinal section. Unfixed specimens of eight‐week‐old‐tail tendon showed a similar bimodal distribution of diameters though the positions of the peak values compared to fixed specimens of an eight‐week‐old‐tail tendon were shifted upwards by about 30%. It has also been shown quantitatively that the polar collagen fibrils are directed randomly “up” and “down” with respect to their neighbors. Whilst it has been suggested by others that anastomosis is a feature of collagen structure, the results presented here do not support this hypothesis. Fibrillar units ∼ 140 Å in diameter have been observed and the possibilities that these are elastic fibers or the breakdown products of collagen fibrils have been considered.
The organization and repair of DNA in the mammalian chromosome. III. Determination of the molecular weight of a mammalian native DNA
Authors: Lange Christopher S. , Liberman Daniel F. , Clark Roger W. , Ferguson Pamm , Sheck Lorraine E. 
Published: May 2005

AbstractThe necessary conditions for a unique solution of the sedimentation vs DNA molecular weight equations are considered and applied to the native DNA of the L5178Y mouse leukemia cell. A brief review and critique of the literature of sedimentation anomalies is given to demonstrate that such anomalies are not present in the data reported here. It is shown that the chromosomal DNA of L5178Y cells comes in uniform packages of 1.0 (0.5–2.0) × 1010 daltons. All pieces are of an identical size which corresponds to the DNA content of about 1/13 the average chromatid. Both the size estimate and the number of such molecules/cell are confirmed by viscoelastometry. This DNA is shown to be free of radioactively demonstrable protein and/or lipid contaminants and of the same isopycnic density as T4 DNA. Variance analysis is applied to determine the precision of all measurements and to pinpoint major sources of error. A relationship between [η] and M is derived for native DNA in 1.0M NaCl. A necessary conclusion from these data is that mammalian chromosome models requiring degrees of polynemy greater than 16‐neme (in G1) are incorrect (to the extent that the L5178Y cell is typical of mammalian cells).
Synthesis and characterization of four sequential glycyl/glutamate polypeptides
Authors: Rippon W. B. , Lowbridge J. , Walton A. G. 
Published: May 2005

AbstractPoly(Glu(OBzl)‐Gly)n, poly(Glu‐Gly)n, poly(Gly)‐(Glu(OBzl)‐Gly), and poly(Gly‐Glu‐Gly) were synthesized from the pentachlorophenyl esters of the sequential monomer. Both of the polymers containing free glumatic‐acid residues are soluble in water, as is the lower molecular weight fraction of the polytripeptides with the benzyl ester in place. Circular dichroism studies and infrared dichroism studies suggest that the 21 helix is favored for the polydipeptide with removal of the benzyl ester reducing the conformational integrity. The polytripeptide showed evidence of 31 helix in addition to the 21 form, depending on solvent. A rationale for the conformations observed is developed based on the bulkiness of the side‐chain residues and conformational stabilization, in certain cases, by hydrophobic interactions between the benzyl ester groups.
Elastin as a rubber
Authors: Dorrington K. L. , McCrum N. G. 
Published: May 2005

AbstractThe thermoelastic behavior of water solvated elastin has been investigated in simple tension, in the temperature range 0–70°C. Specimens purified from both the ox ligamentum nuchae and pig thoracic aorta have been studied. Force data obtained by cycling the temperature for various constant specimen lengths display a separated variable dependence of the form f = A(T)B(α), where T is absolute temperature and α the extension ratio. For ligament elastin B(α) is a linear function whereas for aortic elastin it is a nonlinear function. The applicability of the rubber elasticity theory to elastin has been tested by setting A(T) equal to the temperature‐dependent front factor for simple tension of a homogeneous rubber whilst B(α) is left undefined. In this way it has been possible to take into account the fibrous nonhomogeneity of the polymer, and also to avoid any inconsistency within the theory of attributing a dependence of the variable fe/f upon extension ratio. The behavior of both ligament and aortic elastin agrees well with the conclusion that the dominant deformation mechanism is entropy elastic, fe/f ≪ 1. The linearity of the load isotherm for ligament elastin permits a particularly simple experimental procedure using a single force‐temperature plot for one value of interclamp length. Using this procedure high precision has been obtainble, and the data shows a close adherence to the theory with fe/f = 0.1. The relationship between this result and current controversy over the molecular conformation of elastin is discussed.
The viscometric behavior of native and relaxed closed circular PM2 DNAs at intermediate and high ethidium bromide concentrations
Authors: Watson Robert , Bauer William R. 
Published: May 2005

AbstractWe have measured the specific viscosity of closed circular PM2 DNA in the presence of concentrations of ethidium bromide ranging up to 5 mg/ml. Both native viral PM2 DNA I and enzymatically prepared relaxed, closed circular PM2 DNA I0 exhibit a complex dependence of the specific viscosity upon the extent of supercoiling. As the number of superhelical turns is increased in the positive sense from zero, the viscosity first decreases to a minimum, then passes through a secondary maximum, and eventually again increases as the dye‐induced duplex unwinding proceeds. In the case of DNA I, a corresponding behavior is mirrored in the negative sense as dye is removed from the principal viscometric maximum (complete relaxation of the DNA by dye). The shape of the curve relating specific viscosity to extent to supercoiling is similar for superhelical DNAs of either handedness, a result which we interpret to mean that the influence of any regions of special secondary structure (such as denatured loops) upon the viscosity is minimal. At very high dye concentrations the specific viscosity decreases dramatically. This effect might arise either from intermolecular aggregation or from a dye‐induced collapse in the DNA secondary structure.
Interactions of highly charged colloidal cylinders with applications to double‐stranded DNA
Authors: Stigter Dirk 
Published: May 2005

AbstractThis paper presents new applications of the McMillan‐Mayer solution theory to dispersions of highly charged colloidal cylinders in monovalent salt solutions. The thermodynamic solution properties are given in terms of the virial expansions relating to a Donnan membrane equilibrium. General expressions are derived for the second Donnan pressure virial coefficient B2 and for the first two salt distribution coefficients A1 and A2. The effect of electric interactions is represented as an increased effective diameter dB or dA of the colloidal cylinder. This yields the simple excluded volume expressions B2 = πdBL2/4 and A1 = πdA2L/4 for hard cylinders of length L and diameter dB and dA, respectively. The coefficient A2 is derived from the dependence of B2 on the salt concentration.Computations are made for double‐stranded DNA in sodium chloride solutions with the DNA model developed in the preceding paper: a uniformly charged cylinder, with size and charge consistent with transport experiments, and surrounded by a Gouy double layer. In 1–0.005M sodium chloride solutions dB is found to vary from 29 Å to about 220 Å, and dA from 30 Å to about 170 Å, with little sensitivity to the uncertainties in the kinetic diameter d ≈ 24 Å and the experimental ζ potentials of DNA. Corresponding results predicted by the classical Donnan theory are 6–167 times too high for B2.Values of A2 are relatively small, in line with the expected rapid convergence of the virial expansion for the salt distribution. This is consistent with a phase transition from random to parallel orientation of the cylinders predicted first by Onsager for hard cylinders on the basis of B2, but not yet observed for DNA in simple salt solutions.
The interaction of 8‐anilino‐1‐naphthalenesulfonate with polylysine and polyarginine
Authors: Ichimura Sachiko , Zama Mitsuo 
Published: May 2005

AbstractComparative studies on the interaction of 8‐anilino‐1‐naphthalenesulfonate (ANS) with polylysine and polyarginine have been made by equilibrium dialysis and fluorescence or circular dichroism measurements, to investigate the structural characteristics of the polypeptides. The results are summarized as follows: (i) ANS binds to either of the polypeptides primarily by electrostatic interaction while hydrophobic interaction partially facilitates the dye binding; both interactions are stronger in the polyarginine‐dye binding than the polylysine‐dye binding. (ii) The fluorescence of ANS is more intensified when the dye binds to polyarginine than to polylysine regardless of the value of r (number of bound dye per amino‐acid residue) of polypeptide‐dye complexes, although the intensification depends on the r value and becomes maximum at r = 0.25–0.35 for both cases. (iii) The binding of ANS to each polypeptide is cooperative at r < 0.4. (iv) The circular dichroism is more efficiently induced in the spectral region of ANS by binding to polyarginine than to polylysine.From these results, it was concluded that, compared to polylysine, polyarginine suffers some structural change by ANS binding into a more compact molecular configuration having some regularity with a lower dielectric environment.
Measurement of diffusion coefficient and electrophoretic mobility with a quasielastic light‐scattering–band‐electrophoresis apparatus
Authors: Lim Tong K. , Baran George J. , Bloomfield Victor A. 
Published: May 2005

AbstractWe have constructed an apparatus for the simultaneous measurement of electrophoretic mobility, μ, and diffusion coefficient, D, of macromolecules and cells. It combines band electrophoresis in a vertical, sucrose‐gradient stabilized column, with quasielastic laser light‐scattering determination of the diffusion coefficient of the species within the band. The entire electrophoresis cell is scanned through the laser beam of the quasielastic laser light‐scattering apparatus by a vertical translation stage. Total intensity light‐scattering measurement at each point in the cell gives the macromolecular concentration at that point. Solvent viscosity and electrical potential are measured at each point in the cell. Application of this apparatus to resealed red blood cell ghosts and to bovine hemoglobin indicates that measurements of field, viscosity, and migration distance are reliable, and that electroosmosis is insignificant. Application to T4D bacteriophage gives μ20,w = (−1.05 ± 0.05) × 10−4 cm2/V sec and D20,w = (3.35 ± 0.10) × 10−8 cm2/sec for fiberless particles, and μ20,w = −(0.59 ± 0.03) × 10−4 cm2/V sec and D20,w = (2.86 ± 0.09) × 10−8 cm2/sec for whole phage with 6 fibers. Approximate analysis of these results with the Henry electrophoresis theory for spheres in dicates that each fiber contributes about 193 positive charges to the phage particle, compared with 327 from amino‐acid analysis. The advantages and disadvantages of this apparatus, relative to conventional electrophoresis and to electrophoretic light scattering, are discussed.
Helix‐coil stability constants for the naturally occurring amino acids in water. XII. Asparagine parameters from random poly(hydroxybutylglutamine‐co‐L‐asparagine)
Authors: Matheson R. R. , Nemenoff R. A. , Cardinaux F. , Scheraga H. A. 
Published: May 2005

AbstractThe synthesis and characterization of water‐soluble random copolymers containing L‐asparagine with N5‐(4‐hydroxybutyl)‐L‐glutamine, and the thermally induced helix‐coil transitions of these copolymers in water, are described. The incorporation of L‐asparagine was found to decrease the helix content of the polymers in water at all temperatures. The Zimm‐Bragg parameters σ and s for the helix‐coil transition in poly(L‐asparagine) in water were deduced from an analysis of the copolymer melting curves in the manner described in earlier papers. The computed values of s indicate that asparagine destabilizes helical sequences at all temperatures in the range 0–60°C.
Helix‐coil stability constants for the naturally occurring amino acids in water. XIII. The presence of by‐products in amino‐acid analysis of copolymers and their effect on the guest parameters; recomputed values of σ and s for L‐serine
Authors: Van Nispen J. W. , Hill D. J. , Scheraga H. A. 
Published: May 2005

AbstractPreviously used procedures for processing the amino acids from 6N hydrochloric acid hydrolysis of poly[N5‐(4‐hydroxybutyl)‐L‐glutamine], poly[N5‐(3‐hydroxypropyl)‐L‐glutamine], and several random copolymers derived from these, led to the formation of spurious products. These have been isolated and characterized as the γ‐ester of glutamic acid and the hydroxyalkyl amine, and chloro‐alkyl amine hydrochloride. The former reduces the observed values for glutamic acid, but the latter has no effect on them. A method is used to avoid formation of these artifacts in the amino‐acid analysis. Of all the copolymers studied previously in this series, the compositions of only those containing L‐serine are in error as a result of the formation of the γ‐ester. A redetermination of the amino‐acid compositions of the copolymer fractions studied earlier leads to slightly revised values for the Zimm‐Bragg parameters σ and s of serine.