bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of chemical structures of acridine and triphenylmethane dyes on the induced optical activity of DNA–dye complexes
Authors: Yamaoka Kiwamu 
Published: December 2004

AbstractFifteen symmetrically substituted acridine dyes, all of which are interrelated by their chemical structures, each belonging to a C2v symmetry, and three triphenylmethane dyes with amino or dimethylamino substituents are utilized to study necessary conditions for the appearance of extrinsic Cotton effects upon their binding to native and heat‐denatured deoxyribonucleic acid (DNA). Three different kinds of the DNA–dye complexes, i.e., (1) dye added to native DNA, (2) heat‐denatured DNA–dye complex, and (3) dye added to preheated DNA, were examined for each dye at a fixed P/D value of about 4. Optical activity was always observed for the compelexes of type (1) in each absorption band of the dyes in the visible and near‐ultraviolet region. Two exceptions are 9‐acetamido‐ and 9‐hydroxyacridine, both being nonionic in aqueous solution at a pH range of 6. Acridinium chloride was unable to exhibit any definite extrinsic Cotton effect for complexes (2) and (3). Thus, the monocationic form of a dye due to the protonation or quaternization of the ring nitrogen in acridines or exonuclear amino nitrogen in triphenylmethane dyes is concluded to be an essential factor for extrinsic Cotton effect to appear. Changes in the absorption spectra upon complex formation are also related to the structure of dyes. Hypochromism and bathochromism are associated with the induced optical activity in all cases in the presence of native and denatured DNA.
Hydrodynamic shear breakage of DNA
Authors: Bowman Ray D. , Davidson Norman 
Published: December 2004

AbstractThe rate of breakage of duplex DNA molecules by laminar flow through a capillary has been studied. For λb2b5c DNA (molecular wt., M = 25 × 106) the point at which breakage occurs is normally distributed around the center of the molecule with a standard deviation of 12.5% of the molecular length. At constant shear stress or shear rate, the breakage rate is independent of ionic strength. Thus, shear induced local denaturation is not a rate limiting, preliminary step in breakage. In experiments at constant temperature with varying solvent viscosity (controlled by added sucrose) the breakage rate is a function of shear rate, not of shear stress. The rate of opening of hydrogenbonded circles into linear molecules by hydrodynamic shear is also shown to be a function of shear rate and not of shear stress. The breakage rate at constant shear rate is not greatly dependent on temperature. The shear rate required to achieve breakage is inversely proportional to M1,2. The breakage rate constant, k varies as a very high power of the shear rate; at 25°C, d In k/d In Gm ∼ 15; at 10°C, d In k/d In Gm ∼ 26, where Gm is the maximum shear rate at the capillary wall. The unexpected result that breakage rate is mainly dependent on shear rate, not shear stress, supports a model in which the DNA molecule is distorted with a driving force which depends on the hydrodynamic shear stress, ηG, but the rate limiting step is segment diffusion into a highly extended configuration. The characteristic time to achieve this configuration is proportional to solvent viscosity, η, hence the breakage rate is dependent on ηG/η or G, the shear rate.
Intramolecular conformational transitions “random coil–helix–folded structure” in polypeptides
Authors: Adonts V. G. , Birshtein T. M. , Elyashevich A. M. , Skvortsov A. M. 
Published: December 2004

AbstractA general theory has been developed for conformational intramolecular transitions in a single macromolecule with a high degree of polymerization (an infinite length model) capable of forming two types of ordered structures: the α‐helix and the folded β‐structure, as well as acquiring the random coil conformation. The phase diagram analysis of this system has shown that the regular β‐structure state is separated from all other states of the chain by the phase boundary line. Any intersection of the phase boundary is a phase transition which can be either of the first order or second order, depending on values of the energy parameters of the system. Mechanisms of intramolecular rearrangements: β‐structure–random coil and α‐helix–β‐structure have been discussed. It has been shown that there exist two different mechanisms for each of these rearrangements, and the regions of parameter variation corresponding to each mechanism have been specified.
Calculation of the molecular parameters of the α‐helix–coil and β‐structure–coil transitions
Authors: Birshtein T. M. , Skvortsov A. M. , Alexanyan V. I. 
Published: December 2004

AbstractMonte‐Carlo calculations of geometric and thermodynamic characteristics of the α‐helix and the β‐structure of polypeptides have been carried out. To describe a hydrogen bond both the Lippincott–Schroeder and Morse potentials were used. The internal rotation angles φ and ψ in the α‐helix have been shown to fluctuate in the range of ±7°. The distribution functions on angles φ and ψ and on hydrogen bond lengths and angles in the α‐helix have been computed and compared with those in myoglobin and lysozyme. Thermodynamic characteristics of the α‐helix calculated in different approximations with the two forms of the hydrogen bond potentials have also been compared. The data obtained are close to the experimental values for polypeptides in neutral solution.Some geometric and thermodynamic characteristics of the regular parallel and antiparallel and irregular antiparallel β‐structure have been found. In the β‐structure the internal rotation angles vary within the interval ±15–20°. An increase in the cross and longitudinal dimensions of the β‐structure only slightly influence both the geometric and thermodynamic characteristics.
The use of moment index displacement in analyzing fluorescence time‐decay data
Authors: Small Enoch W. , Isenberg Irvin 
Published: December 2004

AbstractMoment index displacement automatically corrects a number of significant nonrandom instrumental errors in fluorescence time‐decay measurements. Three‐component data, obtained by measuring the fluorescence decay of three different species mixed in the same solution, were used as a test sample. It was shown, as predicted by theory, that moment index displacement corrects three nonrandom instrumental errors: (1) the presence of scatter in the data; (2) time origin shifts between lamp and fluorescence data; and (3) lamp drift, or time‐dependent changes in the shape of the excitation curve. The data clearly show that the use of the method of moments with moment index displacement to analyze fluorescence decay data is not a curve‐fitting procedure. This procedure will accurately obtain decay parameters for multiple‐exponential decays from certain badly distorted data, yielding a calculated curve very different from the actual data.
Catalysis by polymer complexes. I. Enhanced esterolytic reactivity of hydroxamate–polymer complexes
Authors: Kunitake Toyoki , Shinkai Seiji , Hirotsu Sumio 
Published: December 2004

AbstractN‐methylmyristohydroxamic acid (1) bound to polymer micelles of laurylated poly(2‐ and 4‐vinylpyridines) (lauryl group contet: 2VP‐L, 30 mol%; 4VP‐L, 33 mol%) quantitatively reacted with p‐nitrophenyl acetate (NpAc) within a few seconds at 30°C, pH 8.95. Second order rate constants ka were 34,000 M−1 sec−1 for 1–2VP‐L and 11,400 M−1 sec−1 for 1–4VP‐L at μ = 0.5, and they were pronouncedly improved by a decrease in ionic strength (ka = 27,500–80,200 M−1 sec−1 at μ = 0.08). In contrast, poly(N‐ethyl‐4‐vinylpyridinium bromide) hardly affected the nucleophilicity of the hydroxamate ion. Therefore, the enhancement was considered to be associated with some micellar characteristics. Typical saturation phenomena of the reaction rate were observed for p‐nitrophenyl hexanoate (NpOCOPe) and 3‐nitro‐4‐acetoxybenzoic acid (NpAcCOOH). It was suggested that binding of NpOCOPe is caused by the hydrophobic interaction, while that of NpAcCOOH is probably induced by the electrostatic interaction. It is demonstrated that the cationic polymer micelle enormously activates the bound hydroxamate anion, and these complexes would be of much interest as a biomimetic system for enzyme catalysis.
Spatial electron distribution and population analysis of amides, carboxylic acid, and peptides, and their relation to empirical potential functions
Authors: Hagler A. T. , Lapiccirella A. 
Published: December 2004

AbstractThe properties of the electron distribution in amides, peptides, and carboxylic acids, obtained from ab‐initio molecular orbital calculations using both minimal and extended basis sets have been studied. These properties are discussed in terms of some of the common assumptions made in empirical conformational calculations of biomolecules. In particular, population analyses of 15 compounds in these families were carried out with both the minimal and extended basis sets, and compared with results of CNDO/2 calculations. It is suggested that population analysis is a useful tool for recognizing patterns of charge distributions, and investigating the transferability of parameters of different functional groups. However, its use for providing partial charges for conformational analysis is a questionable procedure.A more detailed analysis of the charge distribution was carried out by calculating the spatial electron distribution in the four compounds, N‐methylacetamide, acetic acid, diketopiperazine, and N‐acetyl‐N′‐methylalanine. Both total electron‐density maps and differencedensity maps are presented. The properties of the overall shape of the molecule and the atoms in the molecule, are discussed in terms of the former along with three‐dimensional shape plots of the total density. The distortion accompanying molecular formation, resulting in such features as the lone pair orbital and “bonding deensities” is discussed in terms of the difference maps. Semiquantitative estimates of the bonding and orbital densities resulting from the integration of the densities are also presented. Finally, one of the novel features of the study is the presentation of three‐dimensional surfaces of constant difference densities from which the shapes of the orbitals and bonding densities emerge.
Spectroscopic properties of complexes of acridine orange with glycosaminoglycans. I. Soluble complexes
Authors: Salter Mary K. , Rippon W. Barton , Abrahamson E. William 
Published: December 2004

AbstractThe interaction of acridine orange with dermatan and chondrotin sulfates results in the formation of complexes containing bound dye molecules ordered into dissymmetric arrays. Complexes containing an excess of available disaccharide residues compared to dye are completely soluble, and exhibit biphasic circular dichroism bands. Analysis of the dependence of the extrinsic circular dichrosim on dye aggregation indicates the presence of extended dye stacks bound to the glycosaminoglycan. Complexes formed in solutions containing an excess of dye are only partially soluble, and exhibit circular dichroism spectra having band shifts and intensity changes relative to the soluble complexes. The latter complexes show a sharp drop in induced circular dichroism with temperature, due to a cooperative change in the structure of the complex. The structural order of the dye–glycosaminoglycan complex may differ from the intrinsic structure of the glycosaminoglycan itself in dilute solution.
Conformational properties of the sequential polyproline analogs poly(Pro‐Aze‐Pro) and poly(Aze‐Pro‐Aze)
Authors: Boni R. , Di Blasi R. , Farina A. , Verdini A. S. 
Published: December 2004

AbstractThe lack of the positive band at around 226 nm in the CD spectra of poly(prolyl‐azetidine‐2‐carbonyl‐proline) in trifluoroethanol and of poly(azetidine‐2‐carbonyl‐prolyl‐azetidine‐2‐carboxylic) acid in F3EtOH and water, the hyperchromism of the absorption maximum at about 202 nm, and the extremely small intensity of the Cβ‐Pro, Cγ‐Pro, and Cβ‐Aze signals for the cis peptide bonds in the 13C nmr spectrum of poly(Pro‐Aze‐Pro) in F3EtOH indicate that both polyproline analogs exist as disordered chains in this solvent, the trans peptide group being maintained. The disordering of the chains is attributed to an increase in the accessible range of ψ due to the reduced dimensions of the square ring of L‐azetidine‐2‐carboxylic acid residue relative to the pyrrolidine ring of proline and to strong interactions of the haloalcohol with the peptide groups of the chains.
Frictional properties of nonspherical multisubunit structures. Application to tubules and cylinders
Authors: McCammon J. A. , Deutch J. M. 
Published: December 2004

AbstractMethods are described for numerical calculation of the anisotropic components of the translational and rotational friction coefficient tensors and of the intrinsic viscosity for rigid multisubunit structures in dilute solution. The methods apply to assemblies of any shape, provided that translation–rotation coupling is negligible.Application is made to short cylindrical and tubular structures. Anomalous results arise when the Oseen tensor is used to describe the hydrodynamic interaction of the subunits, but these are corrected by use of a modified tensor. Transport coefficients for hollow tubules with typical supramolecular dimensions are found to be nearly the same as those for the corresponding solid cylinders. The Scheraga–Mandelkern equation is found to be useful for the determination of the molecular weights of such structures. For long hollow structures such as microtubules, use of the corresponding solid cylinder or wormlike chain equations should be adequate for interpreting hydrodynamic studies.
Vibrational spectrum of the unordered polypeptide chain: A Raman study of feather keratin
Authors: Hsu S. L. , Moore W. H. , Krimm S. 
Published: December 2004

AbstractRaman spectra of native and solubilized feather keratin have been obtained, and the amide I and amide III regions have been analyzed by band resolution techniques. The amide I region of the native form indicates that at least 64% of the protein has an antiparallel chain pleated sheet structure, the remainder being unordered. For the solubilized keratin all of the protein is in an unordered state. The amide III region is not as easily analyzed into component contributions. Normal vibration analyses on N‐acetyl‐L‐alanine‐N‐methylamide support the conclusion that the amide III region is not as satisfactory as the amide I region in characterizing unordered structures. Even in the latter case caution must be used, since the observed amide I band is an average over the conformational distribution in the particular unordered system.
Studies on cyclic peptides. IV. Conformation of cyclo(Sar‐Sar‐Gly)2, cyclo(Sar)6 and cyclo(Sar‐Gly‐Gly)2 and their conformational change induced by alkali thiocyanates
Authors: Sugihara Toshiharu , Imanishi Yukio , Higashimura Toshinobu 
Published: December 2004

AbstractConformation of cyclo (Sar‐Sar‐Gly)2, cyclo(Sar)6, and cyclo(Sar‐Gly‐Gly)2 was investigated by nmr spectroscopy. cyclo(Sar‐Sar‐Gly)2, were shown to assume various conformations in dimethysulfoxide. It was attributed to the distribution of cis as well as trans Gly‐Sar or Sar‐Sar amide links along the peptide backbone. In particular, cyclo(Sar‐Sar‐Gly)2 took five or six different conformations: one or three C2‐symmetric conformations and four or three asymmetric conformations, respectively. Three of nine NH resonance signals were ascribed to the internally hydrogen‐bonded glycine residues. cyclo(Sar‐Sar‐Gly)2 and cyclo(Sar)6 showed a spectral change on the addition of alkali thiocyanates, indicating a conformational change induced by a complex formation with the alkali cations. The complex nmr spectrum due to a hybridization of different conformations changed with the salt addition into a simple nmr spectrum, suggesting a preponderence of a new, single conformation. On the basis of the spectral change, the strength for the cations binding the cyclic peptides was found to be in the order of K+ > Na+ > Rb+ > Cs+ for cyclo(Sar‐Gly‐Gly)2 and K+ > Rb+ > Cs+ for cyclo(Sar)6. On the other hand, cyclo(Sar‐Gly‐Gly)2 in dimethylsulfoxide assumed a single C2 conformation having two glycyl peptide protons shielded from solvent and the other two exposed to solvent. This conformation did not change with the salt addition. Finally, the conformations of several cyclic peptides containing the sarcosine residue such as cyclo(Sar)6 cyclo(Sar‐Sar‐Gly)2 cyclo(Pro‐Sar‐Gly)2, and cyclo (Sar‐Gly‐Gly)2 were compared. It appeared that proline and glycine residues reduced the conformational multiplicity of the cyclic peptide backbone, and the ability to bind alkali metal cations decreased in the above order.
Binding of water and electrolytes to proteins. An equilibrium dialysis study
Authors: Bull Henry B. , Breese Keith 
Published: December 2004

AbstractThe technique of equilibrium dialysis has been used to study water and salt binding to egg albumin, to human carbon monoxide hemoglobin, and to bovine serum albumin. The salts used were CsCl, KCl, NaCl, LiCl, Gu·HCl, NaBr, Cs2SO4, K2SO4, Na2SO4, Li2SO4, and Gu2SO4. The amount of water bound by proteins depends on the probe being used. Sulfates tend to bind to proteins and they also increase the water binding. At saturation, about 41 and 140 mol Gu·HCl bind to 1 mol egg albumin and to 1 mol carbon monoxide hemoglobin, respectively. Both proteins are dehydrated by Gu·HCl.The hydrodynamic hydration of egg albumin as determined by viscosity appers to increase as the relative viscosity of the medium increases.
N‐methylleucine gramicidin‐S and (di‐N‐methylleucine) gramicidin‐S conformations with cisL‐Orn‐L‐N‐MeLeu peptide bonds
Authors: Patel Dinshaw J. , Tonelli Alan E. 
Published: December 2004

AbstractConformations containing all trans peptide bonds have previously been proposed for N‐methylleucine gramicidin‐S and (di‐N‐methylleucine) gramicidin‐S based on an evaluation of proton nuclear magnetic resonance parameters in a series of solvents. These gramicidin‐S derivatives exhibit full biological activity despite the fact that the proposed solution conformations differ in backbone topology and relative orientation of the Phe and Orn side chains compared to gramicidin‐S. The present authors discuss conformations for N‐methylleucine gramicidin‐S and (di‐N‐methylleucine) gramicidin‐S which incorporate cis peptide bonds at L‐Orn‐L‐N‐MeLeu, where the gramicidin‐S backbone is essentially retained, and the relative orientation of the Pro, Orn, Val, and Phe side chains correspond to those observed for gramicidin‐S. A novel hydrogen‐bond arrangement involving one carbonyl group interacting with two peptide protons (1 ←4 and 1 ←5 types) is proposed to stabilize the backbone conformation in the gramicidin‐S derivatives. A recent report on the cyclic heptapeptide antibiotic, Ilamycin B1, shows the presence of cis peptide bonds at N‐CH3 amino acids, as well as the novel hydrogen‐bond arrangement presented above.
Synthetic peptides as probes for conformational preferences of domains of membrane receptors
Authors: Naider Fred , Khare Sanjay , Arshava Boris , Severino Beatrice , Russo Joe , Becker Jeffrey M. 
Published: December 2004

AbstractPeptide models have been widely used to investigate conformational aspects of domains of proteins since the early 1950s. A pioneer in this field was Dr. Murray Goodman, who applied a battery of methodologies to study the onset of structure in homooligopeptides. This article reviews some of Dr. Goodman's contributions, and reports recent studies using linear and constrained peptides corresponding to the first extracellular loop and linear peptides corresponding to the sixth transmembrane domain of a G‐protein coupled receptor from the yeast Saccharomyces cerevisiae. Peptides containing 30–40 residues were synthesized using solid‐phase methods and purified to near homogeneity by reversed phase high performance liquid chromatography. CD and NMR analyses indicated that the first extracellular loop peptides were mostly flexible in water, and assumed some helical structure near the N‐terminus in trifluoroethanol and in the presence of micelles. Comparison of oligolysines with native loop residues revealed that three lysines at each terminus of a peptide corresponding to the sixth transmembrane domain of the α‐factor receptor resulted in better aqueous solubility and greater helicity than the native loop residues. © 2004 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2005
Conformational aspects of polypeptide structure XVI. Rotatory constants, cotton effects, and ultraviolet absorption data for glutamate oligomers and co‐oligomers
Authors: Goodman Murray , Rosen Ira G. 
Published: December 2004

AbstractWe have reinvestigated the stereochemistry of a series of L‐glutamate oligomers, preparing the peptides mainly via the azide route rather than the p‐nitrophenyl ester method. Our results are in agreement with our previously published studies. Both investigations relied on derived rotatory dispersion constants b0 and λc, ultraviolet spectra in the 190 mμ range, and molar rotation data. Our measurements have now been extended to include the 233 mμ Cotton effect region. This paper also includes a study of the solvents, 2,2,2‐trifluoroethanol and hexafluoroacetone “trihydrate.” Both solvents are transparent in the far ultraviolet region. The former is a solvent supporting helical structures in glutamate oligomers above the heptamer. The latter solvent does not support secondary structure for any of the oligomers studied. We have treated our data for b0 and Cotton effect rotations in terms of molar quantities. We use the additivity principle and plot molar b0 or 233 mμ molar rotations against the number of residues in the oligomer chain. We are able to relate the changes in the slopes of the straight lines to the onset of helicity and the actual magnitudes of the slopes to the high polymer residue values. Co‐oligomers of glutamic‐aspartic acid form secondary structures of the glutamate type while glutamic acid‐glycine co‐oligomers show very little secondary structure. Finally, hexafluoroacetone “trihydrate” supports stable helices for several high polymers but denotes weak helices in polymer systems.
Energy levels of almost‐periodic polymers
Authors: Herzenberg A. , Modinos A. 
Published: December 2004

AbstractNumerical calculations have been done on the exciton spectrum of a schematic model of a linear polymer. The model consists of a random sequence of two kinds of subunit whose energy levels and transition moments are almost, but not quite, the same. The orders of magnitude of parameters are taken from DNA, but the full helical geometry has not been considered. Results are given for the density of energy levels, the dipole transition strength per unit energy, and the distribution of excitation energy along the polymer in individual states. A number of localized exciton states were found.