bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theory of boundary spreading in velocity ultracentrifugation of polydisperse solutes
Authors: Fujita Hiroshi 
Published: December 2004

AbstractUnder the assumptions that the rectangular approximation to the sector‐shaped cell is valid and that both the sedimentation coefficient s and the diffusion coefficient D are independent of concentration, asymptotic solutions to the boundary spreading equation for velocity ultracentrifugation of polydisperse solutes have been derived for three cases: case A, D = constant for all s; case B, sD = constant; case C, \documentclass{article}\pagestyle{empty}\begin{document}$ \sqrt {sD} = {\rm constant} $\end{document}. Case A is the situation treated by all of the previous authors but supposed to be unrealistic for ordinary macromolecular solutes. Cases B and C may be associated with synthetic polymers under theta conditions and globular proteins in aqueous media, respectively. The solutions obtained have been used to explore the theoretical background of the empirical Gralén method for evaluating the distribution of s from sedimentation boundary curves, with special interest in the behavior of a plot for Sversus 1/t. Here S is the value of s for a fixed value of the apparent integral distribution of s and t is the time of centrifugation. It was found that when the distribution of s is Gaussian‐like and fairly narrow, this plot becomes linear over a more extended range of t in the order case B > case C > case A.
Interchain packing energies of multistranded α‐helical ropes
Authors: Parry D. A. D. , Suzuki E. 
Published: December 2004

AbstractThe interchain packing energy of two‐, three‐, and four‐stranded α‐helical ropes has been investigated. Poly‐L‐alanine was chosen as a model, and the interchain energies were calculated for various combinations of chain sense as a function of interchain distance, axial orientation and displacement. For comparison, the packing energies of the analogous assemblies of straight α‐helices were also computed. Only those systems in which the chains were equivalent, i.e., related by line symmetry, were considered. The results indicate that for structures in which all the chains are equivalent the interchain packing energy favors the coiled coil arrangements.
Counterion fluctuation and dielectric dispersion in linear polyelectrolytes
Authors: Oosawa Fumio 
Published: December 2004

AbstractThe thermal fluctuation in the concentration of counterions bound to a rodlike polyion was analyzed by expanding the fluctuation in a Fourier series along the rod. The amplitude and the relaxation time of fluctuations of various wave lengths were obtained as functions of the charge density and the length of the polyion. From these results the real and imaginary parts of the dielectric constant of the polyelectrolyte solution were derived as the sum of contributions of fluctuations of different modes. The dielectric dispersion curve or the Cole‐Cole plot obtained was found to be in good agreement with experimental data.
Testing of A size criterion for DNA–hydrocarbon binding
Authors: Craig Morrie , Isenberg Irvin 
Published: December 2004

AbstractThe intercalation model of DNA–hydrocarbon binding appears reasonable, but rests on indirect evidence only. To test the model, a size criterion for binding has been proposed. The size criterion is based on the assumption that hydrophobic forces play a major role in the binding of hydrocarbons to DNA. It states that hydrocarbons which are small enough to intercalate into DNA and be well protected from contact with the medium, will be found to bind to DNA; those that are too large will not. We report results on the binding of fourteen polycyclic aromatic hydrocarbons to DNA. Predictions based on the size criterion were found to be valid in all cases tested.
Investigation of fibrous structures. I. Computations for collagen
Authors: Tumanyan V. G. 
Published: December 2004

AbstractThe structure of collagen is investigated by means of an energy minimization procedure. There is a rather broad trough of potential energy which involves a variety of structures (all collagen II type). It is seen that the unit height and the unit twist can strongly deviate from 2.86 Å, 36° values. Some of the good conformations are presented.
The Role of ions in the acid melting of DNA
Authors: Dore E. , Frontali C. , Gratton E. 
Published: December 2004

AbstractThe use of a simple chemical equilibrium and of the law of mass action leads to correct prediction when applied to the study of the role of the counterions in the process of acid melting of the DNA molecule. This approach allows an estimate to be given of the enthalpy variation per base pair associated with this process. Experiments have been carried out to test (a) the linearity of the dependence of pHm vs. 1/T; (b) the stabilizing effect of Na+ concentration. The enthalphy variation per base pair, deduced from the slope of the pHm vs. 1/T plot, and from the number of H+ bound per base pair, is in agreement with direct measurement.6,8
The net hydration of phage lambda
Authors: Costello R. C. , Baldwin R. L. 
Published: December 2004

AbstractThe banding density of phage lambda varies with the activity of water when the phage particles are banded in a series of different cesium salts. The results are comparable to those Hearst and Vinograd for free DNA. Lambda phage ghosts show less net hydration than the phage particles and band in a fairly narrow range of densities in these cesium salts. The phage banding density may be predicted to a first approximation by a simple additive approximation: the total net hydration of the phage is approximately equal to the net hydrations of free λ DNA λ hosts, all measured at the same water activity. The simple additive approximation is not adequate, however, to explain the banding density differences between a deletion mutant and phage lambda in the different cesium salts. The density differences evidently are sensitive to second‐order effects: they apparently are affected by a restriction of DNA hydration inside the phage head, which depends both on water activity and on DNA length (or free volume inside the phage head). This becomes a striking effect in Cs2SO4 solutions where the net DNA hydration is large. Changing the phage banding density by substituting 5‐bromouracil for thymine, which increases the DNA mass while leaving the DNA volume relatively unchanged, gives results consistent with a restriction of the net DNA hydration that depends on the DNA volume. Data on the sedimentation velocity behavior that λ and λb2 in diferrent salts are presented and discussed. It appears possible to estimate the size of a DNA deletion from the phage sedimentation coefficient.
Salt bonding in proteins. A model for the abnormal hydrogen ion titration and the strong anion binding of serum albumin
Authors: Arvidsson E. O. 
Published: December 2004

AbstractSerum albumin undergoes a conformational change at pH 4, known as the N–F transition. In the customary Linderstrøm‐Lang treatment of hydrogen ion titration, the carboxyl groups in serum albumin either have an abnormally low pK, or are buried in charged form, and the Linderstrøm‐Lang charging parameter ω decreases dramatically at the N–F isomerization. In the present paper partition functions are derived and distribution functions are calculated for a model permitting salt bonding between the positively and negatively charged sites on a macromolecule. The N‐form has an abnormally high salt bonding constant whereas that of the F‐form corresponds to that of small ions. The result obtained is consistent with a “normal” intrinsic pK of the carboxyl groups of serum albumin without burying of any charges and with an unchanged ω. The nature of the postulated salt bonding is discussed.Further, it is shown that the “abnormal salt bonding” of serum albumin can explain its unusual ability to bind anions. Theoretical binding curves are calculated and compared with literature data of the Cl− binding of serum albumin. The relation of the present model to other models of hydrogen ion and anion binding to proteins is discussed. Some additional consequences of the present model are pointed out; a transition in the alkaline range, analogous to the acid transition, seems probable. Literature data support the existence of such a transition but do not allow detailed calculations at present.A general, thermodynamic treatment of the interactions between small ligands and macromolecules is outlined. Important points are the choice of the statistical‐me‐ chanical ensemble and considerations of the fluctuations about the mean bonding, if (i) there are not only a ligand‐locus interaction but also interligand interactions (in par‐ ticular intdigand attraction), or (ii) there is a conformational change in themacromole‐ cule depending on the ligand binding. In these cases, the binding isotherms obtained from thermodynamically closed systems (canonical ensemble) may erroneously indicate a distribution about a single probability maximum, i.e., the statistical mean binding N̄, and fluctuations about this value. The description of a phase change in a bound phase or a change in the “internal” self‐interactions of a macromolecule requires a bind‐ ing equation permitting distributions about two maxima, i.e., (i) N1* < N̄ (“thin” phase) and N2* > N̄ (“condensed” phase) or (ii) two macromolecular conformations P′, and P″, having occupancy numbers N̄, and N̄2, respectively. The N–F transition is an example illustrating the relation between the complete distribution functions and the two‐state approximation.
Far from equilibrium synthesis of “prebiotic” polymers
Authors: Babloyantz Agnessa 
Published: December 2004

AbstractThe existing experimental data on prebiotic nonenzymic biopolymer synthesis is used to construct a model which shows autocatalysis and highly nonlinear behavior. It is shown that far from thermodynamic equilibrium such systems may exhibit multiple steady states favoring the enhancement of the polymer population in the medium. The role of step by step chain propagation and template directed autocatalysis are studied and contrasted.
Helix–coil transition in nucleoprotein—theory and applications
Authors: Li Hsueh Jei 
Published: December 2004

AbstractA general theory of helix–coil transition of irreversibly complexed nucleoproteins is presented. The equations are tested by experimental results in basic polypeptide–DNA complexes, nucleohistone I and pea bud nucleohistones. They show good agreement between theory and experiments. The theory provides direct measurement of a fraction of DNA base pairs covered by proteins, yielding a value of about 75% histone‐covered base pairs in pea bud nucleohistone. It also provides a measurement of an average number of amino acid residues per nucleotide in protein‐bound regions. This number varies from 1.0 to 1.4 in DNA–polylysine or DNA–polyarginine and from 2.9 to 3.3 in nucleohistone Ia, Ib, f1, and pea bud nucleohistone.
Investigation of DNA structural changes by infrared spectroscopy
Authors: Pilet J. , Brahms J. 
Published: December 2004

AbstractDNA‐oriented samples of various origins were studied under different conditions of humidiity and sodium chloride content by means of infrared spectroscopy.(1) Oriented DNA (M. Lysodeikticus, E. coli, calf thymus and salmon sperm) films at 3–4% sodium chloride yield polarized spectra which show drastic changes at relative humidities (r.h.) between 94% and 0% indicative of conformational changes:
B form → a form → disordered form
The measurements of the infrared dichroism at frequencies of about 1230 cm−1 and at about 1090 cm−1 allow one to determine the orientation of the phosphate group, whereas the measurements at 1710 cm−1 characterize the base orientation. At humidities higher than 90% r.h. (B form) the bisector of OPO forms an angle of 70° relative to the helix axis, whereas at lower humidities, between 75% and 50% r.h. (A form) a rotation to about 45° is observed. Simultaneously, the 0—0 line of phosphate group changes its orientation from 55° to 65° to the helix when B → A transition takes place. The results are in general agreement with that of X‐ray diffraction and allow one to determine the orientation of the phosphate group with greater precision.(2) The B–A conformational change is not observed for satellite DNA, isolated from Cancer pagurus, of which the guanine + cytosine content is below 5%. As a function of decreasing humidities, one observes the transition:
B form → disordered form
A diagram of conformational changes of DNA's as a function of base composition and of r.h., suggests that B–A transition will occur for DNA of relatively higher G + C content, whereas for high (A + T) content, base sequence may be of importance.The B–A transition is prevented in DNA at a relatively high or very low sodium chloride content.
Packing analysis of carbohydrates and polysaccharides. II. B‐amylose
Authors: Zugenmaier P. , Sarko A. 
Published: December 2004

AbstractA procedure is described for the simultaneous optimization of the bond lenglths and angles of the glucose residue and the chain conformation of the B‐amylose helix, while performing a packing analysis of the chains into a crystalline array. The results show that care must be exercised in selecting monomer residue coordinates for the packing analyis and optimum coordinates are given for the α‐D‐glucopyranose residue suitable for B‐amylose. The packing analysis shows that of the four proposed unit cells for B‐amylose the Rundle‐Daasch‐French, the Schieltz and the hexagonal unit cell of Blackwell et al. are not suitable, while the larger cell of Blackwell et al. is suitable. The most probable packing of B‐amylose chains in that cells is antiparallel, which the chains in a lefthanded sixfold helical conformation and with the O(6) atoms in the gt rotational position.
Studies on cytochrome c. Part II. Synthesis of the protected heptapeptide (sequence 17–23) of Baker's yeast iso‐1‐cytochrome c
Authors: Moroder Luis , Marchiori Fernando , Borin Gianfranco , Scoffone Ernesto 
Published: December 2004

AbstractSynthesis is described for the N‐o‐nitrophenylsulfenylheptapeptide tert‐butoxycarbonylhydrazide corresponding to positions 17–23 of the amino acid sequence of baker's yeast iso‐1‐cytochrome c. Moreover a new method of selective removal of the S‐acetamidomethyl group for analytical and preparative purpose is reported.
Studies on cytochrome c. Part III. Synthesis of the protected heneicosapeptide (sequence 24–44) of Baker's yeast iso‐1‐cytochrome c
Authors: Moroder Luis , Borin Gianfranco , Marchiori Fernando , Scoffone Ernesto 
Published: December 2004

AbstractSyntheses are described for two N‐benzyloxycarbonylpeptide tert‐butoxycarbonylhydrazides which correspond to positions 24–34 and 35–44, respectively, of the primary structure of baker's yeast iso‐1‐cytochrome c. The two peptide derivatives were coupled via the azide procedure to form the N‐benzyloxycarbonylheneicosapeptide tert‐butoxycarbonylhydrazide (sequence 24–44).
Interactions between chondroitin‐6‐sulfate and poly‐L‐lysine in aqueous solution: Circular dichroism studies
Authors: Gelman R. A. , Rippon W. B. , Blackwell J. 
Published: December 2004

AbstractThe interactions between chondroitin‐6‐sulfate (chondroitin sulfate C) and poly‐L‐lysine have been studied as models for investigation of possible complex formation between fibrous proteins and mucopolysaccharides. Results obtained using circular dichroism spectroscopy show that poly‐L‐lysine adopts the α‐helical conformation in dilute aqueous salt solution at pH 7 when mixed with chondroitin‐6‐sulfate, rather than the “charged‐coil” observed in the absence of this mucopolysaccharide. This conformation‐directing interaction is at a maximum when the ratio of lysine to disaccharide residues is 1 : 1. Changes in the CD spectrum of a 1 : 1 mixture following increase in the salt concentration, or addition of non‐polar solvents, indicate that the interaction is ionic in nature. No such effects are observed for non‐sulfated mucopolysaccharides mixed with poly‐L‐lysine, suggesting that, for chondroitin‐6‐sulfate, it is the sulfate groups rather than the carboxyls which interact with the amine groups of the polypeptide.Elevation of the temperature leads to disruption of the interactions between the polypeptide and polysaccharide species. A sharp melting transition occurs at 47.0 ± 1.0°C, when the poly‐L‐lysine reverts to the “charged‐coil” conformation. The sharp transition suggests that regular ionic bonds are formed between the polypeptide and polysaccharide. These results suggest that a conformation‐directing interaction may occur between sulfated mucopolysaccharides and the polar regions of collagen and other fibrous proteins.
Studies on cytochrome c. Part V. Synthesis of the protected decapeptide (sequence 57–66) of Baker's yeast iso‐I‐cytochrome c
Authors: Borin Gianfranco , Moroder Luis , Marchiori Fernando , Scoffone Ernesto 
Published: December 2004

AbstractThe synthesis is described of the N‐benzyloxycarbonyldecapeptide tert‐butoxycarbonylhydrazide, which corresponds to the sequence 57–66 of baker's yeast iso‐1‐cytochrome c. The peptide derivative was synthesized coupling two smaller subunits via the Rudinger modified azide procedure.
Interaction of poly‐α,L‐glutamic acid with acridine orange
Authors: Hatano M. , Yoneyama M. , Sato Y. 
Published: December 2004

AbstractInteraction of poly‐α,L‐glutamic acid (PGLA) with acridine orange (AO) was studied with circular dichroism and absorption spectra measurements. The following results were observed: (1) the addition of a comparable amount of AO with the glutamyl residue to the PLGA solution at pH of 4.5 reduced the fraction of helix of the polymer; (2) when AO was added to the PGLA solution, the pH range of the helix‐coil transition of the polymer shifted toward higher pH regions; and (3) when the mixture of the same amount of AO and the glutamyl residue was brought to the neutral and alkaline pH region, some induced circular dichroism bands were observed. In this case, it was assumed that PLGA in the system takes a helical form due to the neutralization of the anionized side chains by the cationic species of AO. We concluded that AO molecules bound to the carboxylate groups of the side chains of PLGA arrange to from a righthanded super‐helix which surrounds the core of the righthanded α‐helix of PLGA.
Dielectric behavior of DNA–Proflavine complex
Authors: Goswami D. N. , Das Jyotirmoy , Gupta N. N. Das 
Published: December 2004

AbstractThe dielectric relaxation of namtive DNA and DNA–proflavine complexes at different DNA phosphate (P) to dye (D) ratios, were investigated in the frequency range 100 c/sec to 100 Kc/sec. The proflavine molecules were found to have a profound effect on the static dielectric constant and the relaxation time of the polymers. The static dielectric constant was oberserved to decrese with increasing level of added proflavine. At P/D = 1, the variation of dielectric constant with frequency was small. Relaxation time (τ) was greater for the DNA–proflavine complexes compared to that for free DNA, Maximum value of the relaxation time was obtained at P/D = 10. The increase in the relaxation time and decrease in the static dielectric constant were attributed to the increase in length and meutralization of surface charges of the DNA molecules, respectively, as aresult of proflavine binding.
The effect of ions on the superstructures of reconstituted collagen
Authors: Chang E. P. , Chien James C. W. 
Published: December 2004

AbstractThe effect of a variety of electrolytes on the stabilization and destabilization of the rod‐like superstructures in reconstituted collagen membranes have been studied by small‐angle light scattering (SALE). Structural orders at two levels are effected: association–disassociation at the micron level and the helix‐coil transitions at the mollecular level. In addition to lyotropic salts, several transition metal ions were also studied. They act to disassociate collagen aggregates by the formation of stable complexes.
Histone IV binding of 3,4‐benzpyrene, pyrene, anthracene, and 9‐methylanthracene
Authors: Small Enoch W. , Craig A. Morrie , Isenberg I. 
Published: December 2004

AbstractUltraviolet absorption, fluorescence excitation and emission, and fluorescence anisotropy demonstrate that the polycyclic aromatic hydrocarbone 3,4‐benzpyrene, Pyrene, anthracene, and 9‐methylanthracene bind to histone IV after the sow conformational change in the presence of divalent phosphate anion. These hydrocarbons do not bind, within our limits of detection, to histone IV in the diosorderde form at low pH or to the form produced by the fast conformational change when the slow change is prevented. High anisotropy values for the bound hydrocarbon indicate a high degree of aggregation for the histone IV.
Conformation of malformin A: A proton magnetic resonance and a circular dichroism study
Authors: Ptak Marius 
Published: December 2004

AbstractMalformin A is a cyclic pentapeptide with an intramolecular disulfide bridge. The conformation in solution of this molecule has been studied by NMR and CD. The 270 MHz Proton spectrum in dimethyl sulfoxide is well resolved and the peaks corresponding to the five residues have been assigned.From the temperature dependence of chemical shifts of the peptide protons and from the exchange rate of these protons, it is concluded that the NH proton of one Cys is shielded from the solvent. This observation and HNαCH angles, estimated from the corresponding coupling constants, a proposed conformation of the peptide backbone. From the HβCαCH coupling constants, a P chirality for the disulfide bridge is proposed. Such a conformation is confirmed by the circular dichroism spectrum which shows a negative band at λ > 250 nm.It is concluded that the conformation of malformin A is rigid and that the disulfide bridge is exposed to interact with biological receptors.
Influence of telopeptide on the morphology and physicomechanical properties of reconstituted collagens
Authors: Chien James C. W. , Chang E. P. 
Published: December 2004

AbstractThe morphology and physicomechanical properties of two types of collagen membranes, one of which does not have telopeptides, were compared with small‐angle light scattering, rheo‐optical, dynamic mechanical, and dynamic rheo‐optical techniques. The presence of telopeptides in native collagen allows the formation of larger rod‐like superstructures; it renders the membrane more resistant to irreversible deformation yet more responsive to dynamic mechanical perturbation. Telopeptides are also responsible for relaxation at room temperature, and impart more linearly elastic properties to the material as compared to membranes derived from enzyme‐treated collagens.
Buoyant and potentiometric titrations of synthetic polypeptides. I. Six ionizable homopolypeptides in CsCl solutions
Authors: Almassy Robert , Zil John S. V. , Lum Lawrence G. , Ifft James B. 
Published: December 2004

AbstractThe buoyant density and potentiometric titrations of six ionizable homopolypeptides in concentrated CsCI solutions have been studied. These six homopolypeptides were chosen as models of the behavior of ionizable residues in proteins. Their buoyant and potentiometric results will be of value in interpreting the buoyant and potentiometric results observed for proteins.The buoyant densities for all six homopolypeptides were found to increase sigmoidally as the pH is increased. These density changes are interpreted in terms of changes in the hydrations and ion binding which are associated with the titration of the residues. Preferential hydrations for the homopolypeptides are calculated. The buoyant density titrations are combined with the potentiometric titrations to determine the relationship between the buoyant density and the degree of ionization.A better method of computing buoyant densities of proteins is described. The slope of β(ρ) has been computed for CsCl using least‐squares curve fitting and this is used in calculating the isoconcentration position. This method has been found to be more accurate than calculating the isoconcentration position from the normalized isoconcentration ratio, which is known only under limited conditions.