bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐resolution thermal denaturation of DNA. I. Theoretical and practical considerations for the resolution of thermal subtransitions
Authors: Ansevin Allen T. , Vizard Douglas L. , Brown Barry W. , McConathy Judy 
Published: December 2004

AbstractThe fidelity achieved in first derivative profiles of DNA thermal denaturation is shown to depend on a number of factors including the thermal increment of data gathering, the precision of absorbance readings, and the manner in which data are smoothed prior to calculating the derivative of hyperchromicity. The closeness with which thermal denaturation data can be fitted by a cubic polynomial is carefully considered, and a derivation is presented for the estimated error in calculated values of the derivative of hyperchromicity with respect to temperature. After reviewing both theoretical and experimental evidence for the expected minimum width of a thermal transition in DNA, we conclude that thermal increments of 0.05°C or less are required for an adequate representation of transitions in naturally occurring DNA's.Data gathered under conditions meeting the requirements suggested here for quantitative recording of thermal denaturation profiles (Vizard and Ansevin, submitted for publication) show that virtually all of the high‐resolution thermal denaturation profile of a simple, naturally occuring DNA may consist of small subtransitions, which we call thermalites. The finding of substransitions is consistent with current theories of DNA melting. A particularly well‐resolved thermalite of λ bacteriophage DNA has a breadth of only 0.30°C (2σ width), and thus is narrower than previously reported thermal transitions for DNA. For this thermalite, the combination of width, shape, and position in the profile suggests that the substransitions observed in accurately recorded DNA thermal denaturation profiles are not described satisfactorily by existing theories.Knowledge of the requirements for the quantitative recording of thermal denaturation profiles should greatly favor the usefulness of denaturation experiments for physical genomic analysis.
Comparison of four proteoglycans in terms of their interactions with poly(L‐arginine)
Authors: Schodt K. P. , Blackwell J. 
Published: December 2004

AbstractConnective tissue proteoglycans undergo interaction with poly(L‐arginine) when mixed in dilute neutral aqueous solution. Circular dichroism spectroscopy indicates that the polypeptide adopts the α‐helical conformation rather than the extended coil form normally observed at neutral pH. The interactions of a series of proteoglycans with different protein and glycosaminoglycan contents have been compared. The arginine/disaccharide residue ratio at maximum interaction appears to be constant with varying protein content of the proteoglycans that contain chondroitin 4‐sulfate. The thermal stability of the proteoglycan interaction is the same as for the component polysaccharide. Thus in terms of the strength of interaction with homopolypeptides, the properties of proteoglycan and the component glycosaminoglycans are the same, and this is likely also to be the case for collagen–proteoglycan systems.The interactions of keratan sulfate‐2 have also been investigated. These are similar but have much lower thermal stability than corneal keratan sulfate‐1. The results are consistent with the weak interaction of the keratan sulfate‐2 component of bovine nasal septum proteoglycan.
Infrared spectra and resonance interaction of amide‐I vibration of the antiparallel‐chain pleated sheet
Authors: Chirgadze Yu. N. , Nevskaya N. A. 
Published: December 2004

AbstractTheoretical treatment of resonance interaction of amide‐I vibration has been done in a dipole–dipole approximation on the basis of perturbation theory. A single infinite antiparallel‐chain pleated sheet as well as different kinds of its finite fragments have been considered. A good agreement has been obtained between calculated spectral parameters of amide I of the infinite sheet and observed ones in infrared and Raman spectra of synthetic polypeptides and fibrous proteins. A theoretical dependence of the resonance frequency shift of the main component and frequency splitting of two components active in the infrared spectra on the number of polypeptide chains in the finite sheet has been found.
Peptide synthesis using o‐nitrophenylsulfenyl N‐carboxy α‐amino acid anhydrides. Sequential oligopeptides having alternate γ‐methyl L‐glutamyl and L‐phenylalanyl residues
Authors: Katakai Ryoichi , Nakayama Yohko 
Published: December 2004

AbstractA series of sequential oligopeptides having the sequence alternating γ‐methyl L‐glutamyl and L‐phenylalanyl residues have been successfully prepared by a rapid method involving the reaction of o‐nitrophenylsulfenyl N‐carboxy α‐amino acid anhydrides with amino acid and peptide esters. The sequential oligopeptides, which are interesting from a conformational aspect, were obtained in optical pure forms above 74% yields. This result demonstrates that the o‐nitrophenylsulfenyl N‐carboxy α‐amino acid anhydride method is especially useful for easy synthesis of protected oligopeptides with o‐nitrophenylsulfenyl group.
Ultrasonic absorption in aqueous solution of lysozyme
Authors: Kanda Hiroshi , Ookubo Norio , Nakajima Haruhiko , Suzuki Yasuko , Minato Michio , Ihara Takuro , Wada Yasaku 
Published: December 2004

AbstractThe titration curve of ultrasonic absorption at 2.82 MHz in aqueous solutions of lysozyme measured by Zana and Lang [J. Phys. Chem., 74, 2734 (1970)] is theoretically analyzed. The maxima at pH 3 and pH 11 are describable with proton‐transfer reactions of dissociable carboxyl and amino groups by assuming that volume changes due to the reactions are 2.3 and 5.2 cm3/mole, respectively, which are appreciably smaller than those of simple amino acids. The remaining, pH‐independent excess absorption over solvent is measured at frequencies ranging from 3 to 150 MHz. The absorption is ascribed to the internal loss of protein. The complex compressibility β′p − iβ″p of lysozyme molecule is evaluated as β′p = 7.2 × 10−12 cm2/dyne and β″P = 4.3 × 10−14 cm2/dyne from the increments over solvent in absorption as well as in sound velocity.
Conformational studies in aqueous solution on random copolymers of L‐glutamic acid and ortho‐nitrobenzyl‐L‐glutamate. Circular dichroism and potentiometric titration studies
Authors: Estevez Jacky , Loucheux‐Lefebvre Marie H. 
Published: December 2004

AbstractRandom copolymers of L‐glutamic acid and ortho‐nitrobenzyl‐L‐glutamate were synthesized with different percentages of nitrobenzyl‐L‐glutamate, from 3 to 22%. These copolymers were studied by circular dichroism (CD) and potentiometric titrations in aqueous solutions in order to determine the variation of the stability of the secondary structure when the concentration of nitrobenzylglutamate varies in the copolymer. We observed that the stability increases with the concentration of glutamate. Such a stabilization could be due to either side‐chain interactions or interactions between the aromatic side chain with the backbone. An intermolecular aggregation was observed when the percentage of nitrobenzylglutamate was sufficently important, but such an aggregation may be avoided if a dioxane/water mixture is used as a solvent.
A potentiometric and CD investigation on the conformational properties of poly (L‐p‐aminophenylalanine) in aqueous solution
Authors: Peggion E. , Cosani A. , Palumbo M. , Terbojevich M. , Goodman M. 
Published: December 2004

AbstractThe conformational properties of poly(L‐p‐aminophenylalanine) have been investigated by potentiometric and circular dichroism (CD) techniques. It has been found that the polymer in the charge‐free state can assume two ordered conformations, depending upon temperature conditions. At room temperature the polymer assumes the right‐handed helical form by described Goodman and Peggion.1 At temperatures higher than 40°C a new ordered conformation has been found, whose slow rate of formation and ir absorption properties are typical of the β‐structure. The thermodynamic parameters relative to the coil‐β transition, determined by potentiometric titration techniques, revealed that the thermodynamic stability of the β‐structure is mainly due to enthalpic factors. The formation of this structure is unfavored on a kinetic basis.
Ferric complexes of acetoacetyl derivatives of poly(L‐lysine), poly(L‐ornithine), and poly(L‐diaminobutyric acid). II. Conformational properties in solution. Evidence for a stereospecific complex formation
Authors: Palumbo M. , Cosani A. , Terbojevich M. , Peggion E. 
Published: December 2004

AbstractThe conformational properties of ferric complexes of poly(Nε‐acetoacetyl‐L‐lysine), poly(Nδ‐acetoacetyl‐L‐ornithine), and poly(Nγ‐acetoacetyl‐L‐diaminobutyric acid) were investigated in 1:1 water/dioxane by CD techniques. Optical activity was found in the visible and in the uv absorption region of the polymeric complexes. The conformation of the peptide backbone was always that of a right‐handed α‐helix, and was found independent of the degree of complexation, at least up to a degree of binding of 20%. In the absorption region of the side‐chain chromophores the optical activity is substantially affected by complex formation. In all three cases a splitting of the ligand π → π* transition centered at 257 nm is observed. These data suggest a stereospecific complex formation. From the signs of the splitting it also appears that the chirality of the poly(Nδ‐acetoacetyl‐L‐ornithine) complex is opposite that of the other two polymers.
Interaction of sodium decyl sulfate with poly(L‐ornithine) and poly(L‐lysine) in aqueous solution
Authors: Satake Iwao , Yang Jen Tsi 
Published: December 2004

AbstractThe binding isotherms of sodium decyl sulfate to poly(L‐ornithine), poly(D,L‐ornithine), and poly(L‐lysine) at neutral pH were determined potentiometrically. The nature of a highly cooperative binding in all three cases suggests a micelle‐like clustering of the surfactant ions onto the polypeptide side groups. The hydrophobic interaction between the nonpolar groups overshadows the coulombic interaction between the charged groups. The titration curves can be interpreted well by the Zimm–Bragg theory. The average cluster size of bound surfactant ions is sufficiently large to promote the β‐structure of (L‐Lys)n even at a very low binding ratio of surfactant to polypeptide residue, whereas the onset of the helical structure for (L‐Orn)n begins after about 7 surfactant ions are bound to two turns of the helix. The CD results are consistent with this explanation.
Interaction of water with native collagen
Authors: Nomura S. , Hiltner A. , Lando J. B. , Baer E. 
Published: December 2004

AbstractThe interaction of water with collagenous tissue was investigated using dynamic mechanical spectroscopy and cryogenic X‐ray techniques. The loss spectrum was found to be very sensitive to water which is highly associated with the macromolecule. Two water‐sensitive loss peaks were observed below 0°C: the β2 or “water dispersion” at 150°K and the β1 at 200°K which is attributed to motion of polar side chains. Changes in peak temperature and intensity were not continuous with water content, but exhibited regimes in behavior which were associated with two types of nonfreezable water, structural and bound water. In cryogenic X‐ray experiments, specimens which contained some freezable water exhibited reflections identified with the cubic form of ice. These ice crystals underwent an irreversible transition to the more common hexagonal form when warmed above 200°K. On the basis of these experiments, a model for the hydration of native collagenous tissue was proposed.
Intensity fluctuation spectroscopy of deoxyribonucleic acid (DNA). II. Temperature profile of bacteriophage ϕ29‐DNA
Authors: Schmidt R. L. , Whitehorn M. A. , Mayo John A. 
Published: December 2004

AbstractIntensity‐fluctuation laser‐scattering spectroscopy measurements have been reported for the DNA isolated from bacteriophage ϕ29. The cumulant method of data analysis gives well‐defined weighted average decay frequencies. Available theoretical models are shown to yield good values for the diffusion coefficient and longest intramolecular relaxation time for low‐molecular‐weight DNA's but not for higher molecular weight species. The temperature dependence of the apparent diffusion coefficient exhibits drastic oscillations in the helix–coil transition region. The number of these oscillations is consistent with independent measurements of uv hyperchromicity measurements and suggests that ϕ29‐DNA is composed of at least three regions of differing G + C content.
Spectral analysis on the melting fine structure of λ DNA and T2 DNA
Authors: Akiyama Chuji , Gotoh Osamu , Wada Akiyoshi 
Published: December 2004

AbstractThe fine structure of the thermal denaturation of viral DNA's was analyzed with the spectral method established by Felsenfeld and Hirschman, and Fresco et al. A fully automated system measuring melting curves at four wavelengths at the same time was developed for this purpose. With this device, (G + C)‐contents of melting components of λ DNA's were determined. The correlation between the (G + C)‐content and the melting temperature of each melting component is found to be well described by the linear relationship given by Marmur and Doty. The denaturation of each component is regarded as cooperative. The Marmur–Doty relation also stands for the local denaturation of T2 DNA, which has a narrow melting range.
Interpretation of energy‐transfer experiments by theoretical studies of model compounds using semiempirical potential functions. II. Monte Carlo calculations on oligopeptides
Authors: Leclerc Marc , Premilat Samuel , Guillard Roger , Renneboog‐Squilbin Claire , Englert Anne 
Published: December 2004

AbstractThe properties relevant to nonradiative energy transfer have been computed in the unperturbed chain model for oligopeptides composed of from 4 to 21 residues of the formula Tyr‐(Ala)n‐Tyr and Trp‐(X)n‐Tyr, X being either Ala or Gly. A Monte Carlo method has been used for the generation of the chains.The relation between the distribution functions of the distances between the luminophores and the various properties in energy transfer has been examined for chains of different lengths and compositions.The averge of the orientation factor κ2 has been computed as a functions of chain length both for molecules in a randomly coiled state and for molecules with backbones in a well‐defined three‐dimensional structure.The various averaging regimes of energy‐transfer efficiency and of fluorescence decay are compared. Theoretical curves relating experimental efficiencies to the mean distance between the luminophores are proposed.
Translational diffusion coefficient of α‐chymotrypsinogen A by laser‐light‐scattering spectroscopy
Authors: Raj T. , Flygare W. H. 
Published: December 2004

AbstractThe translational diffusion coefficient of a pure sample of α‐chymotrypsinogen A is measured by laser light scattering to give a value of D20,w0 = (8.40 ± 0.15) × 10−7 cm2/sec.
Transient electric birefringence of the bacteriophages T3 and T7
Authors: De Groot G. , Greve J. , Block Joh. 
Published: December 2004

AbstractElectric birefringence measurements of suspensions of T3 and T7 bacteriophages in 10−2 M phosphate buffer, pH 6.9, show that there is a difference in their rotational diffusion coefficient. The values corrected to 25°C and water viscosity are D25,w = 4630 ± 130 sec−1 and D25,w = 5290 ± 260 sec−1 for T3 and T7, respectively. The value obtained from shell model calculations (according to Filson and Bloomfield) is D25,w = 4500 ± 600 sec−1. The apparent permanent dipole moments are 4.5 × 10−26 C·m and 1.7 × 10−26 C·m for T3 and T7, respectively. For both phage particles the intrinsic optical anisotropy is +7.2 × 10−3. It is shown that this anisotropy is mainly due to the DNA molecule inside the head of the phage. Its positive value means that there exists an excess orientation of the DNA helix perpendicular to the symmetry axis of the particle. For T7 an unexpectedly large increase of Δns and Ksp occurs at a glycerol concentration of about 30% (v/v). This increase is interpreted as being caused by a change of the shape of the particle and/or a change in the secondary structure of the DNA inside the head of the bacteriophage.
Thermodynamics of mucopolysaccharide–dye binding. II. Binding constant and cooperativity parameters of acridine orange–dermatan sulfate system
Authors: Menter Julian M. , Hurst Robert E. , West Seymour S. 
Published: December 2004

AbstractIn the acridine orange–dermatan sulfate system, free and bound dye can be distinguished from each other spectroscopically. This permits the use of fluorometric methods to study the binding of acridine orange to the acid mucopolysaccharide dermatan sulfate. Experiments were conducted at 24°C in 10−3 M citrate/phosphate buffer at pH = 7.0. The binding of the dye is highly cooperative, as evidenced by considerable interaction between adjacent bound dye molecules. Analysis of the data indicates that dermatan sulfate binds 2.3 ± 0.3 mol of acridine orange per dermatan sulfate uronic acid residue with a cooperative binding constant, Kq ranging from 4.9 to 6.0 × 105 M−1 which corresponds to a free energy of 7.74 ⩽ ΔG° ⩽ 7.86. The cooperativity parameter q apparently increases with increasing polymer‐to‐dye ratio.
Kinetic analysis of the reversible folding reactions of small proteins: Application to the folding of lysozyme and cytochrome c
Authors: Hagerman Paul J. 
Published: December 2004

AbstractA general kinetic analysis for unimolecular three‐species models is presented. Criteria are established for each model in order to allow selection among alternative models on the basis of their amplitude behavior. These criteria are applied to the previously reported kinetic data for the folding transitions of lysozyme and cytochrome c in guanidine hydrochloride. The degree of success in applying these criteria is found to depend on the extent to which the apparent rate constants, λ1 and λ2, approach each other in certain conditions. Ikai and Tanford have presented a similar kinetic analysis, although these authors considered only the case where no intermediate kinetic species was populated initially. For one protein system, namely, ribonuclease A (RNase A), at least one stable intermediate exists after unfolding outside of the equilibrium transition zone. The criteria developed by Ikai and Tanford cannot be applied to RNase A kinetics and, therefore, a more general analysis is presented. Previously published studies of the reversible folding kinetics of lysozyme and cytochrome c are reexamined using the current amplitude analysis, and it is found that both of these folding transitions can be described by the three‐species model,

used previously to describe the folding kinetics of RNase A (U1 and U2 are two forms of unfolded enzyme and N is the native species). These results suggest that this three‐species model may provide a fairly general description of the reversible folding kinetics of small proteins. As an outgrowth of the current analysis, several suggestions for experimental design in studying protein folding will be presented and discussed.
Investigation of molecular motion in collagen using the spin‐probe technique
Authors: Nagamura T. , Woodward A. E. 
Published: December 2004

AbstractThe spin‐probe technique was employed to study molecular motion in collagen and modified collagen samples in the −160° to +200°C region. The effect of water content in the 0–30‐wt. % range, relative to vacuum dried samples, on the electron spin resonance spectrum of the probe was also investigated. The spectra at the lowest temperatures consisted of a broad asymmetric triplet. Narrowing of this triplet above −40° to −70°C and the appearance of additional lines in the spectrum, interpreted as due to a narrow triplet, at a temperature dependent on the water content were observed. For samples with low water contents [(0–0.4)%] the broad triplet was that expected for a glassy system up to 150–190°C; for these samples the narrow triplet appears at a temperature above 50°C, its intensity increasing with increasing temperature up to 70–100°C, then decreasing with a further temperature increase. For samples with water contents near 30%, the narrow triplet first completely appears at about 0°C, and reaches relative intensities of 35% at 30°C. The motion taking place in collagen and related samples is discussed in terms of these results.
A study of the growth of normal and iodinated collagen fibrils in vitro using electron microscope autoradiography
Authors: Haworth R. A. , Chapman J. A. 
Published: December 2004

AbstractElectron microscopic autoradiographic observations on collagen fibrils grown in vitro allow growth rates in the N‐ and C‐terminal directions to be measured on individual fibrils. Such observations, made on normal and iodinated collagen, show that normal fibrils grow at both ends (although rather more rapidly at the N‐terminal end), whereas fully‐iodinated collagen fibrils grow only at the N‐terminal end.Measurements of growth rates at different temperatures provide estimates of the activation enthalpy (ΔH≠) and entropy (ΔS≠) of precipitation for the two types of collagen. Solubility measurements have also yielded values for the thermodynamic enthalpy (ΔH) and entropy (ΔS) of precipitation. Results show that the activated (rate‐limiting) state is characterized by a large positive ΔH≠ and ΔS≠ similar in magnitude to the ΔH and ΔS of transition from solution to fibril. It is also concluded that the different rates of precipitation of normal and iodinated collagen cannot be explained in terms of fibril formation requiring ionization of the tyrosine residues.
Hydrodynamic properties of a rigid molecule: Rotational and linear diffusion and fluorescence anisotropy
Authors: Small Enoch W. , Isenberg Irvin 
Published: December 2004

AbstractThe fluorescence anisotropy of a general rigid body is formally the sum of five exponentials. We show that, to a high degree of approximation, there are relationships between the five time constants. As we define the time constants here, τ1 ≅ τ5, τ2 ≅ τ3, and τ1−1 + 3τ4−1 ≅ 4τ2−1. In practical cases, at most only three exponentials will be observed, and, of these, only two are independent.Using a numerical integration procedure, Perrin's equations for the rotational and translational diffusion of a general ellipsoid are solved. Rotational friction coefficients, frictional ratio, rotational relaxation times, and the five exponential terms in the fluorescence anisotropy are tabulated as functions of the axial ratios of the ellipsoid.In principle, the three axes of a general ellipsoid may be determined by a simultaneous measurement of the anisotropy and the linear diffusion constant. We examine, and illustrate, the effect of experimental error on such a determination.
Theoretical conformational analysis of Asn1, Val5 angiotensin II
Authors: De Coen Jean‐Louis , Ralston Evelyn 
Published: December 2004

AbstractA theoretical analysis of the conformation of the octapeptide hormone Asn1, Val5 angiotensin II has been carried out by semiempirical potential energy calculations. A preliminary study of the Ala6‐Pro‐Ala molecule, which mimics the angiotensin backbone, provided us with likely backbone structures on which the effect of the full side chains of the hormone could be assessed. For angiotensin II, the calculations show that only a small number of folded, compact conformations have a high probability of existence. This is the consequence of favorable packing and of the presence of proline in position 7. These results are consistent with various experimental data, both structural and biological. This method is readily applicable to the study of analogs of the hormone or to other peptides of comparable size.