bluuebunny/crossref_metadata_2025_split huggingface dataset:
The conformation and aggregation of bovine β‐casein A. II. Thermodynamics of thermal association and the effects of changes in polar and apolar interactions on micellization
Authors: Evans M. T. A. , Phillips M. C. , Jones M. N. 
Published: December 2004

AbstractA sedimentation analysis has been used to determine the proportion of protein present as monomer and aggregate in 0.5 and 1.0 g/dl solutions of β‐casein A in pH 7 phosphate buffer over the temperature range 10–40°C. The amount and molecular weight of the aggregate increase with temperature; under the conditions used, the aggregation number (n) of β‐casein is given approximately by n = 0.6t + 2 with t in degrees centigrade. The concentration of β‐casein in monomeric and aggregated states at different temperatures is used to calculate the standard enthalpy of aggregation ΔH° (Van't Hoff) by assuming that β‐casein undergoes a cooperative, two‐state, micellization process; aggregation is an endothermic process and ΔH° = 66.0 ± 2.6 kJ mol−1. Combination of this ΔH° with the amount of protein calculated to dissociate when 1 g/dl solutions are diluted isothermally to 0.5 g/dl gives the heat of dilution at various temperatures. These calculated heats of dilution are compared with the experimental values obtained by carrying out the same dilutions in a microcalorimeter. The heat of dilution decreases linearly with β‐casein concentration, but the extrapolated zero‐concentration values of 65.8 ± 1.6 kJ mol−1 is the same as the Van't Hoff enthalpy. This agreement in the enthalpy values indicates that the micellization of β‐casein occurs cooperatively. The effect of modifying the hydrophobic/hydrophilic balance of the system on the micellization of β‐casein A has been investigated. The hydrophobic interaction between the protein molecules is decreased by removing the three C‐terminal residues (Ileu Ileu Val) with carboxypeptidase‐A. This modification drastically reduces the ability of the β‐casein molecule to form micelles. Substitution of 2H2O for H2O at constant temperature perturbs the monomer–micelle equilibrium in favor of micelles because of enhanced hydrophobic interactions in the former solvent. The results are consistent with β‐casein micellization involving a delicate balance of the hydrophobic forces favoring aggregation and electrostatic forces opposing it.
Experimental investigations on the backbone folding of proline‐containing model tripeptides
Authors: Boussard Guy , Marraud Michel , Aubry André 
Published: December 2004

AbstractSome proline‐containing tripeptides with the general formulas R0CO‐L‐Pro‐X‐NHR3 (X = Gly,Sar,L‐Ala,D‐Ala) and R0CO‐X‐L‐Pro‐NHR3 (X = Gly,L‐Ala,D‐Ala) have been investigated in solution by ir and 1H‐nmr spectroscopies. Their favored conformational states depend mainly on both the primary structure and the chiral sequence of the molecules. In inert solvents the βII‐folding mode is the most favored conformation for the L‐Pro‐D‐Ala and L‐Pro‐Gly tripeptides, while the βII′‐turn is largely preferred by D‐Ala‐L‐Pro derivatives. Under the same conditions only about one‐third of the whole conformers of L‐Pro‐L‐Ala molecules adopts the βI‐folding mode. Semiopened C7C5 and C5C7 conformations are appreciably populated in the L‐Pro‐L‐Ala sequence, on the one hand, and in the Gly‐L‐Pro and L‐Ala‐L‐Pro derivatives, on the other hand. In L‐Pro‐Sar and X‐L‐Pro models, the cis–trans isomerism around the middle tertiary amide function is observed. Thus cis L‐Pro‐Sar and L‐Ala‐L‐Pro conformers are folded by an intramolecular i + 3 → i hydrogen bond, whereas cis D‐Ala‐L‐Pro and Gly‐L‐Pro molecules accommodate an open conformation. In dimethylsulfoxide the βII‐ and βII′‐folding modes are not essentially destabilized, as contrasted with the βI conformation, which is less populated. In water solution all the above‐mentioned conformations, with the possible exception of the βII′‐folding mode for D‐Ala‐L‐Pro molecules, seem to vanish. Solute conformations are also compared with the crystal structures of four proline‐containing tripeptides.
Dynamic light scattering from collagen solutions. II. Photon correlation study of the depolarized light
Authors: Thomas John C. , Fletcher Guy C. 
Published: December 2004

AbstractThe depolarized forward‐scattered light from solutions of rat tail collagen has been studied by photon correlation spectroscopy. The measured autocorrelation function is seen to decay on two widely different time scales. The decay time for the fast component is consistent with the rotational diffusion of rodlike collagen monomers. The slowly decaying autocorrelation component is attributed to large nonspecific aggregates of collagen. A substantial fraction of the collagen is in this aggregated form. Extrapolation of the faster decay times to zero concentration yields a value of θ = 1082 ± 30 sec−1 for the rotational diffusion coefficient of the collagen monomer.
Mechanism for unwinding of double‐helical polynucleotides by formaldehyde
Authors: Chay Teresa Ree 
Published: December 2004

AbstractWe have formulated a mathematical model for the unwinding process of polynucleotides induced by formaldehyde by making use of the master equation approach. Our model assumes that the formaldehyde kinetics follows the helix–coil theory of Zimm and Bragg. The model incorporates experimental features such as the interplay between pH‐dependent and ‐independent reactions and the dependence of the initial and final helix stability on the unwinding. That is, our model incorporates the existence of the critical point such that if the pH of the system is high enough (i.e., pH ≳ 7), the unwinding of polynucleotides occurs by means of two separate chemical reactions, either by the HCHO–imino reaction alone or by the HCHO–amino reaction alone. The critical point depends on the ionic strength, temperature, and the formaldehyde concentration satisfying the relations= 1 +KUλ, wheresis the helix stability parameter,KUis the binding constant for the HCHO–imino reaction, and λ is the formaldehyde concentration. Thus above the critical point, i.e.,s< (1 +KUλ), the unwinding is due to the reaction of imino groups with formaldehyde, and below the critical point, i.e.,s> (1 +KUλ), the unwinding is due to the reaction of amino groups with formaldehyde. Although, below the critical point, the imino group does not participate directly in the rate‐determining step, it participates indirectly in such a manner that it reduces the initial helix stability parameterstos/(1 +KUλ) by forming a complex. The kinetic constants in the master equation have been determined by making use of the principle of detailed balance and the breathing mechanism proposed in the past. With this model we have quantitatively explained the anomalous temperature dependence observed in the kinetics of formaldehyde‐induced poly[d(A‐T)] and the salt dependence observed in poly(A·U).
Difference in substrate binding processes between intact and iodine‐inactivated lysozyme
Authors: Segawa Shin‐Ichi , Nakayama Masaaki 
Published: December 2004

AbstractThe binding of glycol chitin to intact and iodine‐inactivated lysozyme was studied by measuring the absorbance of the complex with N‐methylnicotinamide chloride, which binds to the subsite C in lysozyme as a competitive inhibitor. The association constant of glycol chitin to inactivated lysozyme was determined from static experiments to be 1.7 × 104M−1. The kinetics of the substrate binding to intact and iodine‐inactivated lysozyme were measured by the stopped‐flow method at 23°C and pH 5.6. The binding to inactivated lysozyme was clearly monophasic, whereas in intact lysozyme it consisted of multiple phases. In the substrate binding to intact lysozyme, a fast bimolecular process and two subsequent slow unimolecular processes were observed besides the hydrolysis process of polymer substrate. These slow phases were missing completely in inactivated lysozyme. It results from the alteration in the local structure occurring at the subsite D in inactivated lysozyme. These results mean that the slow phases are important for catalytic action of lysozyme. The rate constants of association and dissociation in the fast bimolecular process were determined in this paper. Furthermore, the association constant of the substrate to intact lysozyme was also determined kinetically to be 6.5 × 103M−1.
7‐Amino‐actinomycin D complexes with deoxynucleotides as models for the binding of the drug to DNA
Authors: Chiao Yu‐Chih Chen , Rao K. Gurudath , Hook John W. , Krugh Thomas R. , Sengupta Sisir K. 
Published: December 2004

AbstractFluorescence, CD, absorption, and 1H‐nmr studies are reported for complexes of 7‐amino‐actinomycin D with deoxydinucleotides, deoxytetranucleotides, and poly(dG‐dC)· poly(dG‐dC). The optical spectra for the 7‐amino‐actinomycin D complex with pdG‐dC, pdG‐dC‐dG‐dC and pdC‐dG‐dC‐dG are similar in shape to the 7‐amino‐actinomycin D complex with either DNA or poly(dG‐dC). The changes in the 1H chemical shifts of the 7‐amino‐actinomycin D and the pdG‐dC resonances that accompany complex formation show that 7‐amino‐actinomycin D forms a minature intercalated complex with two pdG‐dC molecules. The magnitudes of the induced chemical shifts for the 7‐amino‐actinomycin D complex formation with pdG‐dC are similar to, but slightly different from, the induced chemical shifts which are obtained when actinomycin D forms a minature intercalated complex with two pdG‐dC molecules. The pdN‐dG dinucleotides (N = C, A, or T) form stacked complexes with 7‐amino‐actinomycin D. The presence of the 7‐amino‐group results in a larger dimerization constant (in aqueous solution) for 7‐amino‐actinomycin D [KD(6°C) = 4.4 × 103M−1], as compared to actinomycin D [KD(6°C) = 1.7 × 103M−1]; the chemical shifts which accompany dimer formation indicate that the chromophores stack in an inverted manner. Intercalation of 7‐amino‐actinomycin D into minature double helices, as well as into calf thymus DNA, poly(dG‐dC)·poly(dG‐dC), and poly(dA‐dC)·poly(dG‐dT), results in an enhancement of the relative fluorescence intensity and a shift in both the absorbance and corrected emission spectra.
Bromophenol red as a probe of lysozyme‐active site environment: A temperature‐jump study
Authors: Krishnamoorthy G. , Prabhananda B. S. , Gurnani S. 
Published: December 2004

AbstractSpectrophotometric techniques have been employed to study the binding of bromophenol red (BPR) to hen egg white lysozyme and the consequent inhibition of enzyme activity. Experimental evidence is given from the dye binding studies in the presence of hexasaccharide and from the studies on activity that BPR binds at a site outside the proposed cleft region (A–F) in such a way that it inhibits the lytic activity towards cell walls but does not inhibit the activity towards hexasaccharide. These observations are consistent with the kinetics of binding [studied using temperature‐jump (T‐jump)] in the presence of Co++ or chitotriose in large concentrations and the experiments with acetylated lysozyme which suggest that the binding site of BPR is closer to a lysine residue near the cleft. It is suggested that the binding site of BPR could be important in positioning the peptide segment of the cell walls, which are cleaved in the cleft.Evidence for the statement that this binding takes place at least by a two‐step process, in which the bimolecular step is followed by a slower monomolecular step, is given from the observations of two types of 1:1 complexes at 24°C in equilibrium studies and from the concentration dependence of the relaxation observed at 605 nm in the T‐jump experiments. The binding process is examined by analyzing the T‐jump data obtained between 18 and 33°C in the pH range 5.2–9.2 and ionic strength 0.01–01. The ionic strength and pH dependences of the equilibrium constant associated with the bimolecular step k2/k1 and the forward rate constant associated with monomolecular step k3 have been given as evidence for the suggestion that a Coulombic interaction is involved in the first step of binding. However, the final state of binding is hydrophobic in nature. The enthalpy of activation ΔH and the entropy of activation ΔS associated with kf[= k3(k1/k2)] showed compensation behavior with pH variation, with maxima around pH ∼ 7.5 in H2O. This has been interpreted as a maximal disordering of water structure in a region of the enzyme at this pH during the monomolecular step. However, the binding of chitotriose or Co++ in the cleft reduces the ΔH and ΔS associated with the monomolecular step of BPR binding, probably by disordering the structured water during their binding in the cleft. The differences in the kinetic parameters obtained in H2O and in D2O probably arise due to subtle differences in the conformation of the enzyme in the two solvents and apart from isotope effects.The correlation between the pH (or pD) dependence of the “intrinsic activity” towards cell walls and ΔH or ΔS indicates that ordered water structure could be playing a role in controlling the catalytic activity. It is also suggested that this factor is associated with the rate constant k3s of the monomolecular step leading to the formation of the final bound state of the substrate in cell lysis, which is also a factor controlling kcat.
Circular dichroism study on polyelectrolytic properties of carboxymethyldextran
Authors: Gekko Kunihiko 
Published: December 2004

AbstractThe effects of neutralization, charge density, concentration, counterion, and added salts on CD spectra of carboxymethyldextran (Cm‐dextran) were systematically investigated in order to understand the polyelectrolytic effects of ionic polysaccharides on CD spectra. CD curves of sodium Cm‐dextran showed a negative band near 214 nm due to the carboxyl n – π* transition, but the acid spectrum indicated an additional positive band near 225–228 nm, depending on the charge density. The increase in charge density caused the increase in the magnitude of ellipticity and the red shift of the band. The magnitude of the CD band showed a remarkable concentration dependence in water without any change of position and shape but was independent of concentration in the presence of salt. CD spectra of Cm‐dextran were drastically influenced by the kind of counterion and added salts. These variations of CD spectra under different conditions are discussed from the viewpoint of ion binding and the intermolecular and intramolecular electrostatic interactions of this polysaccharide.
Intensity fluctuation spectroscopy and transfer RNA conformation. III. Influence of NaCl concentration on the size and shape of the initially salt‐free tRNA in solution
Authors: Patkowski A. , Chu B. 
Published: December 2004

AbstractThe influence of sodium ion concentration in solution on the initially salt‐free conformation of bulk tRNA from baker's yeast has been investigated by means of photon correlation spectroscopy. From the measured values of translational (DT) and rotational (DR) diffusion coefficients, the semiaxes of an ellipsoid of revolution, which are hydrodynamically equivalent to the tRNA molecule, were calculated for tRNA solutions in pure H2O as well as in 0.005, 0.1, 0.5M NaCl and 0.01M MgCl2 solutions at pH 4.2 and 7.5. These data, combined with our previous studies, suggested a model which describes the formation of an ordered tRNA structure due to increasing NaCl concentrations. Furthermore, we have obtained information concerning intermolecular interactions between tRNA molecules in solution. In low‐salt or salt‐free tRNA solutions, we detected in the linewidth distribution function an extra‐fast component which can be attributed as possibly due to charge fluctuations related to the reaction of ionization of organic bases. In our light‐scattering linewidth measurements, we do not see fluctuations of charged and uncharged states directly as concentration fluctuations. Rather, we postulate a modulation of long‐range intermolecular electrostatic interactions between the tRNA molecules due to such charge fluctuations. It is this modulation which is related to the fast component of the time correlation function at finite concentrations. A quantitative theory is needed to provide a more definitive explanation of the dynamical behavior of tRNA in salt‐free or low‐salt solutions.
Conformations of a monodisperse homohexapeptide, Nps‐[Glu(OBzl)]6‐NHEt, and its critical concentration of β‐form formation in solution
Authors: Okahashi Kenji , Ikeda Shoichi 
Published: December 2004

AbstractNps‐[Glu(OBzl)]6‐NHEt has been prepared by coupling Nps‐[Glu(OBzl)]2‐OH with HCl,H‐[Glu(OBzl)]4‐NHEt by means of dicyclohexylcarbodiimide. The ir spectra of its nujol mull show that the hexapeptide has the β‐structure of antiparallel chains. When it is dissolved in dioxane or ethylene dichloride, the hexapeptide consists of a mixture of the β‐form and the solvated σ‐form, but the β‐form can exist only above a certain critical concentration. The critical concentration is about 0.4g dl−1 in dioxane and 0.08g dl−1 in ethylene dichloride, and the content of β‐form increases with increasing concentration above it. The CD of the dioxane and ethylene dichloride solutions shows concentration dependence in visible and uv regions.
Vibrational approach to the dynamics of an α‐helix
Authors: Levy Ronald M. , Karplus Martin 
Published: December 2004

AbstractThe dynamics of a finite α‐helix have been studied in the harmonic approximation by a vibrational analysis of the atomic motions about their equilibrium positions. The system were represented by an empirical potential energy function, and all degrees of freedom (bond lengths, bond angles, and torsional angles) were allowed to vary. The complete results were compared with a more restrictive model in which the peptide dihedral angle was kept rigid; also, a model potential excluding hydrogen bonds was examined. Thermal fluctuations in the backbone dihedral angles ϕ and ψ are 12° to 15°. The fluctuations of adjacent dihedral angles are highly correlated, and the correlation pattern is affected by the flexibility of the peptide dihedral angle. Time‐dependent autocorrelations in the motion of ϕ and ψ appear to decay due to dephasing in less than 1 psec, while the motions of the carbonyl oxygen and amide hydrogens out of the peptide plane are more harmonic. Length fluctuations have been evaluated and exhibit a strong end effect; the calculated elastic modulus is in agreement with other values. Rigid and adiabatic total energy surfaces corresponding to dihedral angle rotations in the middle of the helix have been obtained and compared with the quadratic approximation to those surfaces. The magnitudes and correlations between the fluctuations obtained by averaging over the adiabatic energy surface most closely resemble the vibrational results. Of particular interest is the fact that hydrogen bonds play a relatively small role in the local dihedral angle fluctuations, though the hydrogen bonds are important in the energy of overall length changes.
Infrared spectra of the N‐acetyl‐N′‐methylamides of glycine, L‐alanine, and L‐leucine in dilute solutions of chloroform and carbon tetrachloride
Authors: Maxfield F. R. , Leach S. J. , Stimson E. R. , Powers S. P. , Scheraga H. A. 
Published: December 2004

AbstractWe have examined the NH stretching frequencies of N‐acetyl‐N′‐methyl‐L‐alanineamide (blocked Ala), N‐acetyl‐N′‐methylglycineamide (block Gly), and N‐acetyl‐N′‐methyl‐L‐leucineamide (blocked Leu) in chloroform using irspectroscopy. Their spectrum of blocked Leu in carbon tetrachloride was also obtained. A major absorption band at 3450 cm−1 is attributed to the unperturbed NH stretching frequency. Another major band at 3437 cm−1 (for Ala) or 3432 cm−1 (for Leu) is attributed to conformations in which the NH stretching frequency is perturbed by the spatial proximity of the Cβ atom. An absorption band between 3300 and 3370 cm−1, which has in the past been assigned to the intramolecular hydrogen‐bonded NH in the C conformation, was found to be concentration dependent and could not be observed below 5 × 10−4M in chloroform; thus we find no evidence for a strongly hydrogen‐bonded NH in the C conformation in chloroform. An absorption band at 3416 cm−1 was observed in chloroform solutions of blocked Gly, and a similar absorption appeared as a shoulder on the 3437‐ and 3432‐cm−1 bands of blocked Ala and blocked Leu, respectively, in the same solvent. These bands, occurring near 3416 cm−1, may be assigned to extended (C5) conformations [Avignon et al., Biopolymers 8, 69 (1969)]. In CCl4 the spectrum of blocked Leu remained concentration dependent below 2.8 × 10−4M, with the 3300–3370‐cm−1 band progressively weakening and shifting to higher frequencies on dilution from higher concentrations. Analysis of the spectra indicates that there is considerable flexibility in the blocked single residues, in agreement with the results of conformational energy calculations.
Origin of multipeak behavior in the NMR spectra of poly(L‐glutamic acid)
Authors: Lader H. J. , Mandelkern L. 
Published: December 2004

AbstractThe previous report that poly(L‐glutamic acid) exhibits doubled resonances in the helix–coil transition region by either proton or carbon‐13 nmr resolves the question of whether or not this behavior is limited to uncharged polypeptides in organic solvents, as had been previously thought. In the present work, we show that the underlying principle causing this anomalous double‐peak behavior is due to molecular‐weight polydispersity of the sample. The molecular‐weight range in which this phenomenon is observed is largely dependent on the values of σ, the nucleation or cooperativity factor. The principles developed are shown to encompass all classes of polypeptides in a very natural way and to explain the key experimental data in the literature.
Ionic strength‐dependent conformational transitions of chromatin. Circular dichroism and thermal denaturation studies
Authors: Fulmer Andrew W. , Fasman Gerald D. 
Published: December 2004

AbstractHigh‐molecular‐weight chicken erythrocyte chromatin was prepared by mild digestion of nuclei with micrococcal nuclease. Samples of chromatin containing both core (H3, H4, H2A, H2B) and lysine‐rich (H1, H5) histone proteins (whole chromatin) or only core histone proteins (core chromatin) were examined by CD and thermal denaturation as a function of ionic strength between 0.75 and 7.0 × 10−3M Na+. CD studies at 21°C revealed a conformational transition over this range of ionic strengths in core chromatin, which indicated a partial unfolding of a segment of the core particle DNA at the lowest ionic strength studied. This transition is prevented by the presence of the lysine‐rich histones in whole chromatin. Thermal‐denaturation profiles of both whole and core chromatins, recorded by hyperchromicity at 260 nm, reproducibly and systematically varied with the ionic strength of the medium. Both materials displayed three resolvable thermal transitions, which represented the total DNA hyperchromicity on denaturation. The fractions of the total DNA which melted in each of these transitions were extremely sensitive to ionic strength. These effects are considered to result from intra‐ and/or internucleosomal electrostatic repulsions in chromatin studied at very low ionic strengths. Comparison of the whole and core chromatin melting profiles indicated substantial stabilization of the core‐particle DNA by binding sites between the H1/H5 histones and the 140‐base‐pair core particle.
Poly(ε‐L‐lysine): Synthesis and conformation
Authors: Kushwaha D. R. S. , Mathur K. B. , Balasubramanian D. 
Published: December 2004

AbstractThe synthesis of poly(ε‐L‐lysine) is described. This is a poly(ε‐amino acid) in which the ε‐amino group of lysine is condensed with the α‐carboxyl group to produce a chain backbone that is a variant of the usual one seen in proteins and the side chain is the α‐amino group. Conformational studies of poly(ε‐L‐lysine) and its t‐butyloxycarbonyl derivative suggest the likelihood of a chain order that is formally similar to the antiparallel pleated‐sheet conformation of proteins.