bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studies on the viscosity of solutions of bovine liver glutamate dehydrogenase and on related hydrodynamic models; effect of toluene on enzyme association
Authors: Reisler E. , Eisenberg H. 
Published: December 2004

AbstractThe viscosity of bovine liver glutamate dehydrogenase solutions was studied at 10 and 20° C in 0.2.M sodium phosphate buffer at pH 7, in the concentration range 0.1–8 mg/ml. A method for the study of the viscosity of very dilute solutions of associating enzymes is described. It was found that the reduced specific viscosity ηsp/c of glutamate dehydrogenase continuously increases with increasing enzyme concentration, from about 4 ml/g at the lowest concentrations to about 16 ml/g at 8 mg/ml. In the presence of 10−3M GTP and 10−3M NADH the viscosity increase is much smaller and the results can be extrapolated to zero enzyme concentration to yield an intrinsic viscosity [η] = 3.2. The values of ηsp/c in phosphate buffer alone apparently extrapolate to the same value of [η], or to a value close to it. We also observe that, in the presence of toluene ηsp/c increases very much more with enzyme concentration: ηsp/c already equals 16 ml/g at a concentration of 0.75 mg/ml. These observations are in good agreement with the hypothesis that the active oligomer of glutamate dehydrogenase (MW = 312,000) associates with increasing enzyme concentration to form linear rodlike polymers of indefinite length. This association is strongly diminished by the addition of 10−3M GTP, 10−3M NADH. Toluene, on the other hand, promotes reversible association to linear polymers of very high molecular weight. The transverse and axial rotary frictional coefficients of macroscopic bodies, similar to a physical model for the structure of glutamate dehydrogenase recently advanced, were determined. Assuming that the viscosity of the model is equal to that of an ellipsoid of rotation with identical frictional coefficients, we calculate [η] = 3.26 ml/g according to Kuhn and 3.20 ml/g according to Simha, for the glutamate dehydrogenase oligomer, in good agreement with the result derived from the study of enzyme solutions.
Surface chemistry of poly(β‐beiizyl L‐aspartate)
Authors: Malcolm B. R. 
Published: December 2004

AbstractMolecular monolaycrs of poly(β‐benzyl L‐aspartate) spread at. an air‐water interface have been studied. The results obtained both by direct observations on the monlayer and from examination of collapsed films with polarized infrared spectroscopy and electron diffraction are consistent with the presence of right handed α‐helices in the mono‐layer when the molecular weight is high. When 1% (v/v) isopropanol is present in the subphase the right‐handed helix prevails, provided that the monolayer is first spread on water. Monolayers of low molecular weight polymer appear to form the crossed‐β structure. Orientated collapsed films of high molecular weight polymer can be converted to the left‐handed α‐helical and to the ω‐conformation, and the mechanisms are discussed. The surface chemistry of this polymer is compared with that of related polymers and a consistent pattern of behavior emerges.
Electric dichroism studies: Interaction of trifluoroacetic acid with poly(gamma;‐benzyl L‐glutamate)
Authors: Milstien Julie B. , Charney Elliot 
Published: December 2004

AbstractElectric dichroism studies on poly(γ‐benxyl L‐glutamate) show that the addition of small amounts (up to 5%) of trifluoroacetic acid causes complete disappearance of dichroism in contrast to the electric birefringence, which drops to an observable plateau at 20% of its initial value. This loss of dichroism cannot be explained simply by a decrease in the effective dipole moment of the benzyl ester side chains, and the nature of this interaction is explored by nuclear magnetic resonance and infrared spectral studies. Theories of the helix‐coil transition which require an initial protonation of the helix backbone to form a more flexible rod consisting of helical segments interrupted by regions of random coil are shown to be inadequate to describe the changes in poly(γ‐benzyl L‐glutamate) effected by small amounts of trifluoroacetic acid. Rather, trifluoroacetic acid in small amounts interacts with the ester carbonyl oxygen in the side chain, either by hydrogen bonding or protonation, before there is evidence of any effect on the backbone or of loss of helix content.
Kinetics for the transition between cis‐ and trans‐helices in poly‐L‐proline
Authors: Rifkind Joseph M. 
Published: December 2004

AbstractThe kinetics for the cis‐trans isomerization of long‐chain poly‐L‐proline has been studied as a function of pressure, temperature, and solvent composition in the acetic acid + n‐propanol solvent system. Our complete kinetic curves were fitted by Monte Carlo techniques, and rate constants for nucleation, growth, and termination were estimated. It was found that for the formation of a cis‐helix, high pressure, low temperature, and increased acetic acid content of the solvent, lowered the rate of nucleation relative to growth. The inverse seems to be t rue for the formation of a trans‐helix. Molecular models suggest that this behavior of the kinetic constants can be due to the exposure of peptide units to solvent in the transition state for trans nucleation, and the burying of peptide units in the transition state for cis nucleation. It is further suggested from our analysis of complete kinetic curves that at least one of the assumptions usually made in the analysis of relaxation kinetics is invalid for poly‐L‐proline.
Electrophoretic charge of a cylindrical macroion in aqueous 1 : 1 electrolyte
Authors: Mills R. A. 
Published: December 2004

AbstractThe potential problem is formulated for rodlike macroions and reduced to a single dimensionless equation with appropriate boundary conditions. A method of solution based on piecewise linearization of the potential equation is detailed and compared with two other approaches. It is suggested that the present method yields improved estimates of macroion charges. Some numerical results are included, and the relation between electrophoretic charge and macroion charge is considered.
Heats of water vapor sorption in swelling biopolymers
Authors: Bettelheim Frederick A. , Block Allan , Kaufman Leslie J. 
Published: December 2004

AbstractHeats of water vapor sorption by three biopolymers, polygalacturonic acid, sodium hyaluronate, and calcium salt of bovine submaxillary mucin, were determined calorimetrically. These calorimetric heats of sorption were compared with the isosteric heats of sorption as a function of water uptake. Maxima in both of these functions occur at “monolayer” coverage. The differences between the calorimetric and isosteric heats are explained in terms of the irreversibility of the sorption process, especially in terms of the structural changes that occur in the biopolymers during swelling.
An obligatory α‐helical amino acid residue
Authors: Burgess Antony W. , Leach Sydney J. 
Published: December 2004

AbstractStereochemical studies predict that α‐amino isobutyric acid, one of the amino acids found in antibiotics, can fold only into left‐ or righthanded α‐helical conformations. Such residues will direct chain folding and should be useful in synthetic analogs of protein sequences to increase helix stability.
Analysis of the 1H‐NMR spectra of ferrichrome peptides. I. The non‐amide protons
Authors: Demarco Antonio , Llinás Miguel , Wüthrich Kurt 
Published: December 2004

AbstractThe thus far unexplored aliphatic region of the proton magnetic resonance spectra of ferrichrome peptides was investigated at 360 MHz. Six isomorphic diamagnetic analogues of the ferric cyclohexapeptide differing in the coordinated cation (AL3+ or Ga3+) and the amino acid composition were studied in d6‐DMSO solution. By use of a novel resolution enhancement technique which applies a sinusoidal half‐wave window to the free induction decay combined with multiplication by an increasing exponential, the proton chemical shifts and spin‐spin couplings were accurately measured. Homonuclear decoupling combined with Fourier difference spectroscopy was used to selectively extract resonances out of crowded spectral regions. The spectra revealed unique features of fine structure in the proton resonance lines. Thus, the conformation‐dependent geminal coupling constants of glycyl α‐protons were found to be constant throughout the suite of analogue peptides. A similar invariance was observed for the vicinal coupling constants between α‐, β‐, γ‐, and δ‐protons in the ornithyl side chains. Comparison of the proton spin–spin coupling constants with the crstallographic dihedral angles led to a unique stereochemical assignment of the side‐chain resonances. The combined data sets of x‐ray atomic coordinates and 1H‐nmr spin‐spin coupling parameters have been used to calibrate the coefficients for a Karplus curve related to the torsional x angles in amino acid side chains:

Structurial information was also obtained for the seryl residues, where the multiplet structures of the OH resonances indicate preferred spatial arrangements of the side chains.
The effects of aqueous neutral‐salt solutions on the melting temperatures of deoxyribonucleic acids
Authors: Gruenwedel Dieter W. , Hsu Chi‐Hsia , Lu Don S. 
Published: December 2004

AbstractThe helical stability of a variety of DNA samples, ranging in base composition from 0 to 72 mole‐% GC, has been studied by heat denaturation at neutral pH in increasing concentrations of LiCl, NaCl, KCl, CsCl, Li2SO4, and K2SO4. The variation of melting temperature with average base composition, dTm/dXGC, was found to decrease drastically in the concentrated salt media, e.g., from 41°C in 0.006M LiCl to 29°C in 3.2M LiCl, and from 39°C in 0.003M Li2SO4 to 18°C in 1.6M Li2SO4. At the same time, the thermal transition is much more cooperative in the concentrated salt solutions than at low ionic strength. Indeed, at limiting salt concentrations, the transition breadth seems to reach a minimum value irrespective of the compositional heterogeneity of the DNA samples. Attempts to correlate the observed decrease of dTm/dXGC with predicted changes in the enthalpy of melting, deduced from a simple theoretical treatment, experimental data on the binding of counterions and water to DNA, and experimental data on thermal denaturation, were unsuccessful. However, the strongly reduced composition dependence of the melting temperature can be understood in terms of a destabilizing effect of the concentrated salt media on GC‐base pairs. It is suggested, though not proven, that the destabilization involves the displacement of water molecules from the DNA helix.
Stereochemistry of nucleic acids and their constituents. X. solid‐slate base‐slacking patterns in nucleic acid constituents and polynucleotides
Authors: Bugg C. E. , Thomas J. M. , Sundaralingam M. , Rao S. T. 
Published: December 2004

AbstractThe base‐stacking patterns in over 70 published crystal structures of nucleic acid constituents and polynucleotides were examined. Several recurring stacking patterns were found. Base stacking in the solid state apparently is very specific, with particular modes of interaction persisting in various crystalline environments. The vertical stacking of purities and pyrimidines in polynucleotides is similar to that observed in crystals of nucleic acid constituents. Only partial base overlap was found in the majority of the structures examined. Usually, the base overlap is accomplished by positioning polar substituents over the ring system of an adjacent base. The stacking interactions are similar to those found in the crystal structures of other polar aromatic compounds, but are considerably different from the ring–ring interactions in nonpolar aromatic compounds. Apparently, dipole‐induced dipole forces are largely responsible for solid‐state base stacking. It is found that halogen substituents affect base‐stacking patterns. In general, the presence of a halogen substituent results in a stacking pattern which permits intimate contact between the halogen atom and adjacent purine or pyrimidine rings. Considering differences in the stacking patterns found for halogenated and nonhalogenated pyrimidines, a model is proposed to account for the mutagenic effects of halogenated pyrimidines.
Characteristic parameters and polydispersity elimination factors for hydrodynamic quantities of semirigid polymers, especially of DNA
Authors: Reinert K. E. 
Published: December 2004

AbstractRelations are given allowing the calculation of intrinsic viscosity, diffusion constant, and related molecular weights of monodisperse subfractions of polydisperse samples from the measured averages of the hydrodynamic quantities and the individual (reduced) sedimentation constant distribution. The peculiarities resulting from the special behavior of semirigid polymers like DNA are treated. Expressions are derived which describe the dependence of the exponents as(aηs = aη/as), and aη of the relations so = ksMas [η] = kηs(so)aηs, and [η] = kηMaη on so and [η], respectively, and which are useful for practical and theoretical discussions of the wormlike chain. Furthermore, a generalized exponent rule for aη and as has been suggested, considering the dependence of the Mandelkern‐Flory‐Scheraga parameter β(≙Φ1/3P−1) on molecular weight. The results of this paper are applied extensively in the following paper to molecular weight and hydrodynamic properties of homogeneous DNA.
Helix–coil transition in copolypeptides. I. Poly (γ‐benzyl‐co‐γ‐methyl L‐glutamate)
Authors: Roig A. , Cortijo M. 
Published: December 2004

AbstractThe helix–coil transition in poly(γ‐benzyl L‐glutamate‐co‐γ‐methyl L‐glutamate) copolypeptides was studied experimentally in nonaqueous solvents and the results compared with theory. It is found that the transition can be described by the same theory as for the homopolypeptides, but the corresponding parameters are not related in the expected way to those of the homopolymers, due to the effect of the side chains on the stability of the helix, which is not taken into account explicitly by the theory.
Interaction of proflavine and 9‐aminoacridine with DNA at temperatures below and above the melting temperature
Authors: Jordan D. O. , Sansom L. N. 
Published: December 2004

AbstractThe influence of temperature on the binding of 9‐aminoacridine and of proflavine to E. coli DNA in 10−3M NaCl solution has been determined by a spectrophotometric technique. The inadequacy of the expression normally used for the determination of the extent of binding is discussed with reference to measurements at temperatures above which dissociation of the double helix occurs. A method of determining the relative extents of binding to native and denatured DNA at elevated temperatures is described.
Studies on the conformation of amino acids. IX. Conformations of butyl, seryl, threonyl, cysteinyl, and valyl residues in a dipeptide unit
Authors: Ponnuswamy P. K. , Sasisekharan V. 
Published: December 2004

AbstractPotential energies of conformation of a dipeptide unit with butyl, seryl, threonyl, eysteinyl, and valyl side groups have been computed by using classical energy expressions. The presence of a γ‐atom introduces characteristic restrictions on the backbone rotational angles ϕ and ψ the γ‐atom itself is restricted to three staggered positions about the Cα—Cβ bond. The important results are that a γ‐carbon in position I (χ1 ≃ 60°) cannot be accommodated in the standard right‐and left‐handed α‐helices, whereas a γ‐oxygen or sulfur could easily be accommodated in the right‐handed α‐helix. Further, a γ‐carbon or a heteroatom in position II (χ1 ≃ 180°) does not favor a conformation ψ ≃ 180°, compared to two other positions. The valyl side group significantly reduces the allowed ϕ and ψ values and energetically prefers a β‐conformation compared to right‐or left‐handed α‐helical conformations. The less favorable α‐helical conformation is possible only for γ (III, II) combination of the valyl residue. The observed ϕ, ψ, and χ1 values of all the amino acid residues in the three protein molecules, lysozyme, myoglobin, and chymotrypsin are compared with the theoretical predictions and the agreement is excellent. The results bring out the important fact that even in large molecules, the conformation of local segments are predominantly governed by the short‐range intramolecular interactions.
Simple methods for the orientation of DNA molecules in films suitable for optical studies
Authors: Kurucsev T. , Zdysiewicz J. R. 
Published: December 2004

AbstractThree methods are described for the preparation of oriented samples of DNA molecules in films. The methods involve simple equipment and produce films of good optical qualities, suitable for the determinations of dichroic spectra, for example. To illustrate the quality of the films the dichroism of DNA and of acridine orange–DNA complex are described. Evidence is given that native DNA structure is stabilized by poly‐(vinyl alcohol).
Thermal conformational transformations of tropocollagen. II. Viscometric and light‐scattering studies
Authors: Privalov P. L. , Serdyuk I. N. , Tiktopulo E. I. 
Published: December 2004

AbstractIt was shown by viscometric measurements that a tropocollagen solution at low shear gradients manifests elastic features which can be connected only with the existence of a labile spatial structure which develops in time in the solution. To judge by the concentration dependence of the rate of formation of this structure, it does not represent a molecular net formed by direct contact of macromolecules. Most likely this structure is a result of stabilization of macromolecules at a certain distance from each other. The study of light scattering by tropocollagen solutions demonstrated that it does not correspond with the scattering by rigid rod‐shaped units. Anomalies in the character of light scattering are probably the result of intermolecular interference produced by a spatial supermolecular structure and, in turn, indicate that this structure is to some extent regular. In the presence of salts the elastic features in the tropocollagen solution and anomalies in light scattering disappear in a narrow range of temperatures immediately before the process of denaturation which makes it possible to conclude that the supermolecular regular structure is disrupted in this temperature range.
The circular dichroism in the ultraviolet of aminoacridines and ethidium bromide bound to DNA
Authors: Dalglkish D. G. , Peacocke A. R. , Fey G. , Harvey C. 
Published: December 2004

AbstractThe circular dicrosim (CD) spectra of complexes of DNA with ethidiun bromnide, profiavine, 9‐aminoacridine and 4‐etliyl‐9‐amino‐acridine have been determined between 220 and 450 nm, the range lieing extended to 600 nm for ethidiufm bromide. The variation of the magnitude of the visible and near—ultraviolet CD spectra of ethidium bromide—DNA complexes with the amount of ligand bound (r) suggests a common binding position with profiavine. On the other hand, 4‐ethyl‐9‐aminoacndine complexed to DNA shows CD spectra not distinguishable from those of 9‐aminnoacnidmc in both the visible and ultraviolet. The interpretation of these results with respect to the stereochemistry of the DNA‐ligand complexes is discussed.
Consistent force field calculations on 2,5‐diketopiperazine and its 3.6‐dimethyl derivatives
Authors: Karplus Susan , Lifson Shneior 
Published: December 2004

AbstractThe minimum energy conformations are calculated for 2, 5‐diketopiperazine (DKP) and its 3,6‐dimethyl derivatives (DL‐DMDKP and LL‐DMDKP), using a consistent force field approach developed previously. The energy function parameters that were not required in earlier calculations on alkanes, amides, mid lactams are fitted to spectral and conformational data on the diketopiperazines. Vibrational assignments are suggested for DKP.Conformational energies are also determined over a range of selected values for ring dihedral angles, and the shape of the potential energy functions is examined over deviations from planarity. DKP and LL‐DMDKP are found to have non‐planar minimum energy conformations, separated from planar by less than a kcal/mole. DL‐DMKP exhibits a nearly flat trough about the planar conformation. Calculations of minimum energies with one dihedral angle coordinate constrainted show a coupling between bond angles and dihedral angles in agreement with recent suggestions of Benedetti.
Molecular motion in poly(β‐benzyl‐L‐aspartate)
Authors: Happey F. , Jones D. W. , Watsox B. M. 
Published: December 2004

AbstractAs the temperature of solid poly(β‐benzyl‐L‐aspartate) (PBLA), (CO.NH.CH.‐CH2COOCH2C6H5)n, in the α‐helieal form is raised from −150 °C, tlie line width and second moment of the proton magnetic resonance (PMR) signal decrease in stages until the conformational transition to the ω‐helix occurs at about 90 °C. A similar temperature dependence of the PMR parameters is observed as the transformed polymer is cooled. Below −100°C (where the lattice is presumed to be rigid), the measured second moments are 9.5 Oe2 and 10.7 Oe2 for the α and ω forms, respectively. Second moments, calculated from the Van Vleck formula for the rigid lattice and also estimated for possible motional cases in which the polymer is taken to be in the ω form, are compared with the PMH data. By combination with the results of X‐ray diffraction and infrared spectroscopic measurements, a tentative explanation can be made of the types of motion occurring in PBLA.
Temperature dependence of the aminoacylation of tRNA by bacillus stearothermophilus aminoacyl‐tRNA synthetases
Authors: Johnson Lee , Söll Dieter 
Published: December 2004

AbstractValine specific transfer RNA (tRNAVal) was isolated from Bacillus stearothermophilus and Escherichia coli by chromatography on benzoylated DEAE–cellulose (BD–cellulose). Likewise isoleucine specific transfer RNA (tRNAIle) was isolated from B. stearothermophilus and from Mycoplasma sp. Kid. The thermal denaturation profiles (melting curves) of the two tRNAVal species in the presence of Mg+ + were nearly identical. However, the Tm for the Kid tRNAIle was about 10°C lower than that for the B. stearothermophilus tRNAIle. A nuclease and tRNA‐free aminoacyl‐tRNA synthetase (AA‐tRNA synthetase) preparation from B. stearothermophilus was able to function efficiently at temperatures up to 80°C in the aminoacylation of all four tRNA species. Determination of the amino acid‐acceptor activity of each tRNA species as a function of temperature of the aminoacylation reaction showed in each case a strong correlation between the loss of acceptor activity and the thermal denaturation profile of the tRNA. Evidence is presented that the loss in acceptor activity is most likely due to a change in structure of the tRNA as opposed to denaturation of the enzyme. These results further support the idea that correct secondary and/or tertiary structure must be maintained for tRNA to be active as a substrate for the AA‐tRNA synthetase.
Cis–Trans isomerism of the peptide bond
Authors: Andrews P. R. 
Published: December 2004

AbstractThe molecular orbital method PCILO is applied to eight. N‐monsubstituted amides. Experimentally known geometric properties are reasonably predicted by minimization of total energy with respect to molecular geometry. The same procedure shows that molecular deformations during rotation around the peptide bond significantly lower calculated barriers. Experimental heats of activation and the free‐energy changes associated with cis–trans isomerism are in good agreement with those calculated, which include qualitative estimates of configurational entropy contributions to the isomerism energies. Both the calculations and revised infrared data indicate that N‐phenylurethane, which has been used as a model for the cis peptide bond, should be predominantly trans. However the variations in rotational barriers and cis–trans isomerism energies among the N‐monosubstituted amides provide no reason to suppose that the cis peptide bond should be excluded from stable protein conformations.