bluuebunny/crossref_metadata_2025_split huggingface dataset:
tRNA structure and binding sites for cations
Authors: Danchin Antoine 
Published: December 2004

AbstractEquilibrium dialysis and electronic and nuclear resonance spectroscopy show that tRNA cooperatively binds divalent metal ions at very low concentrations (free metal concentration 3 × 10 −6 M). The first two methods show that different purified tRNAs have a very similar behavior, including initiator tRNAFmet. tRNAs with an extra arm in the clover‐leaf model, however, appear to have a slightly different behavior.The binding can be described in terms of two classes of sites. The cooperative association of divalent ions binding first does not parallel a cooperative change in the hyperchromism of the tRNA, while the non‐cooperative association of the second class of divalent ions corresponds to the concentrations needed to obtain a cooperative melting of the tRNA.The temperature dependence of the number of binding sites and of their binding constants is also presented.The nature of the divalent ion gives the following efficiency: for the cooperativity Co++>Mg++>Mn++ for the weak binding sites Mn++>Co++>Mg++
Structure of β,D(1–>4′)‐xylan hydrate
Authors: Nieduszynski I. A. , Marchessault R. H. 
Published: December 2004

AbstractA structure is proposed for xylan hydrate as a result of investigations by x‐ray fiber diffraction and computer‐aided chain‐packing methods. The unit‐cell dimensions are a = b = 9.16 Å, c (fiber axis) = 14.85Å, γ = 120° and the proposed anti‐parallel chain arrangement corresponds to a space group symmetry of P3221. Left‐handed threefold screw helices are stabilized in this conformation by their interaction with chains of water molecules, so that a satisfactory hydrogen‐bonding scheme is achieved. The proposed structure provides an explanation of the changes in the x‐ray diagram with relative humidity and yields a very good structure factors agreement. An x‐ray fiber diagram corresponding to a higher hydrate (xylan dihydrate) is presented. Comments are made on the possible role of xylan in nature and in technological processes.
An analysis of the results for the binding of formaldehyde to polyuridylic acid
Authors: Aylward N. N. 
Published: December 2004

AbstractSpectrophotometric measurements were made on the extent of binding of formaldehyde to polyuridylic acid under conditions of varying temperature and formaldehyde concentration. The data is interpreted in terms of a temperature‐dependent stacking of the bases in poly U at 20°, but not at 40°C. A theory of cooperative stacking is developed which considers the base residues to be either non‐bonded, non‐bonded and methylolated, or stacked. The results indicate essentially non‐cooperative base stacking under these conditions with an equilibrium constant for base stacking of 0.92 at 20°C.
Studies on spin‐labeled polyriboadenylic acid
Authors: Bobst Albert M. 
Published: December 2004

AbstractSpin‐labeled samples of poly rA, poly rU, and poly rG have been prepared, and physicochemical properties primarily of labeled poly rA are reported. The nitroxide radical, 4‐(2‐iodoacetamido)‐2,2,6,6‐tetramethylpiperidinooxyl, is incorporated to a greater extent in poly rA and poly rU, as compared to poly rG. No incorporation is observed in the case of poly rC. Special attention has been paid to the separation of the covalently attached labels from the free labels, and to the preservation of the integrity of the chain length of the labeled polymers. The determination of molar extinction coefficients of the three labeled polymers indicates virtually no difference from those known for the chemically unpertubed polyribonucleotides. The correlation times for the spin‐labeled single stranded poly rA and poly rU have been calculated. More mobile building blocks are found in poly rU as compared to poly rA. Conformational properties of labeled poly rA in aqueous solutions have been investigated using electron spin resonance, circular dichroism, and absorption spectroscopy. The objective of the study of labeled poly rA was to examine its conformational transitions upon the uptake of protons by the adenine bases. Based on electron spin resonance data there is strong evidence that the single strand‐double strand transition can take place in three steps. In addition to the already known two forms of double‐stranded poly rA in acidic solution, called A and B, it is suggested that a third phase, consisting possibly of large aggregates, is involved in the transition of the less protonated double strands to those of complete protonation.
Simple sequential model for the kinetics of conformational transitions of oligomeric helices and proteins
Authors: Elson Elliot L. 
Published: December 2004

AbstractA simple sequential model is developed which is applicable to the kinetics of melting of some types of oligomeric helices and as an idealization to the kinetics of unfolding of some protein molecules. A procedure is presented for calculating the concentrations of all conformational species as functions of time. The time course of experimentally observable quantities which depend on these concentrations may then be computed.One of the most characteristic features of the model is the distinction between a transient and a steady‐state phase. During the latter all molecular parameters change at the same rate, which depends strongly on the difficulty of nucleation and the length of the sequence. Simple approximations to the steady‐state rate are discussed in terms of the exact solution. Rates of transient processes dependless strongly on the rate of nucleation and the number of steps and are a more direct reflection of the rates of the rates of the elementary process of propagation. The value of experimental observation of transient process is emphasized.
Electrophoretic behavior of poly‐L‐glutamic acid and poly‐L‐lysine
Authors: Prokopová E. , Ciferri A. 
Published: December 2004

AbstractTwo electrophoretic components have been detected on the ascending boundary in unbuffered solutions of polyglutamic acid and polylysine under certain experimental conditions. If the conditions are favorable to aggregation, another maximum, the third in order, is formed on this boundary. We attribute this maximum to the formation of aggregates. The behavior of both boundaries and all components at various pH, concentrations, and temperature of solutions and at different molecular weights of polymers was described.
Electric and hydrodynamic properties of polypeptides in solution. III. Aggregation of poly(L‐glutamic acid) in aqueous methanol solvents studied by electric birefringence
Authors: Matsumoto Mitsuhiro , Watanabe Hiroshi , Yoshioka Koshiro 
Published: December 2004

AbstractThe rise and decay of electric birefringence for poly(L‐glutamic acid) (PLGA) in aqueous solvents containing 20 and 10 vol % methanol have been found to be unusual. The decay curves have been analyzed on the assumption that there exist two kinds of particles, namely, one (component I) with a shorter relaxation time exhibiting positive birefringence and the other (component II) with a longer relaxation time exhibiting negative birefringence at low fields. From the field strength dependence of the steadystate birefringence the permanent dipole moment, the anisotropy of electric polarizability, and the saturation value of birefringence have been determined for each component. Furthermore, from the relaxation time the length of component I and the diameter of component II have been computed on the models of cylindrical rod and oblate ellipsoid, respectively. The dipole moment, the anisotropy of electric polarizability, and the relaxation time of component II are much larger than those of component I. Both the anisotropy of electric polarizability and the optical anisotropy factor are positive in sign for component I and negative for component II. It is concluded that component I is the helical PLGA molecule itself and component II is the side‐by‐side (antiparallel) aggregate composed of many helical PLGA molecules. The optical anisotropy factor of each component has been discussed on the basis of Peterlin‐Stuart theory.
The absence of an isotope effect on the stability of the poly‐β‐benzyl‐L‐aspartate α‐helix in aprotic solvents
Authors: Dubin P. , Karasz F. E. 
Published: December 2004

AbstractOptical rotatory dispersion measurements were used to follow the transition from the helical to the random coil conformation of poly‐β‐benzyl‐L‐aspartate as induced by changes in temperature and solvent composition in mixtures of dioxane and dimethylsulfoxide. Within experimental error, there is no difference in the stability of the helical state as measured in this way for the protonated and deuterated forms of the polypeptide. This result is considered in terms of previous attempts to study the isotope effect on conformational transitions of helical biological macromolecules and polypeptides. The conclusion is drawn that the apparent changes in conformational stability observed in these previous systems arise from alteration of the properties of the solvent. Speculations are advanced regarding the contribution of the interpeptide bond to the stability of the helical state.
Conformational aspects of polypeptide structure. XLI. Crystal structure of S‐thiazolidine‐4‐carboxylic acid and helical structure of poly[(S)‐thiazolidine‐4‐carboxylic acid]
Authors: Goodman Murray , Chen Vera , Benedetti Ettore , Pedone Carlo , Corradini Paolo 
Published: December 2004

AbstractThe helical structures of poly[(S)‐thiazolidine‐4‐carboxylic acid], in the cis and trans forms, were redetermined by using the new sets of bond angles and bond lengths established by X‐ray diffraction analysis of L‐thioproline. Calculations of the helical structures of poly‐L‐proline and poly[(S)‐oxazolidine‐4‐carboxylic acid] were also repeated. As a result of these energy calculations, it is suggested that, in contrast to poly‐L‐proline and poly[(S)‐oxazolidine‐4‐carboxylic acid], poly[(S)‐thiazolidine‐4‐carboxylic acid] should not mutarotate from the trans to the cis form. This result is due to the fact that the energy barrier for the conversion is most likely too high. Previous experimental work is consistent with this finding.
Normal vibrations of crystalline polyglycine I
Authors: Abe Yasuaki , Krimm S. 
Published: December 2004

AbstractA valence force field has been refined for crystalline polyglycine I using its known antiparallel chain pleated‐sheet structure and without replacing the CH2 group by a point mass. Polyglycine I and four of its isotopic derivatives were used in the refinement. The calculated frequencies are in good agreement with the observed, except for the amide I modes. It is shown that this is a consequence of the fact that no reasonable force field predicts a large D10 term of the Miyazawa perturbation treatment. The amide I splittings can, however, be satisfactorily accounted for by introducing a direct interaction force constant between adjacent CO groups in neighboring chains. This can reasonably arise from transition dipole coupling and corresponds to the heretofore neglected D11 term.
The conformation of polycytidylic acid, polyguanylic acid, polyinosinic acid, and their helical complexes in aqueous solution from laser Raman scattering
Authors: Brown Kenneth G. , Kiser Ernest J. , Peticolas Warner L. 
Published: December 2004

AbstractThe Raman spectra of the double helical complexes of poly C–poly G and poly I–poly C at neutral pH are presented and compared with the spectra of the constituent homopolymers.When a completely double‐helical structure is formed in solution a strong sharp band at 810–814 cm−1 appears which has previously been shown to be due to the A‐type conformation of the sugar–phosphate backbone chain. By taking the ratio of the intensity of the 810–814 cm−1 band to the intensity of the 1090–1100 cm−1 phosphate vibration, one can obtain an estimate of the fraction of the backbone chain in the A‐type conformation for both double‐stranded helices and self‐stacked single chains. This type of information can apparently only be obtained by Raman spectroscopy.In addition, other significant changes in Raman intensities and frequencies have been observed and tabulated: (1) the Raman intensity of certain of the ring vibrations of guanine and hypoxanthine bases decrease as these bases become increasingly stacked (Raman hypochromism), (2) the Raman band at 1464 cm−1 in poly I is asigned to the amide II band of the cis‐amide group of the hypoxanthine base. It shifts in frequency upon base pairing to 1484 cm−1, thus permitting the determination of the fraction of I–C pairs formed.
Potentiometric titration studies on globular proteins
Authors: Nitta Katsutoshi , Sugai Shintaro 
Published: December 2004

AbstractA power series method was applied to solve the Poisson‐Boltzmann equation for the spherical polyelectrolyte model and numerical calculation with an electronic computer was performed to obtain surface electric potential on rigid globular proteins. Deviation from the ideal linear relationship in Linderstrom‐Lang's plot was found to become noticeable as the surface charge density and the radius of protein increases and ionic strength decreases. The calculated surface potential was compared with potentiometric titration data of several proteins whose radii have been analyzed. Assuming the radius of the counterions to be equal to about 1.0 Å, the data for phenolic groups in ribonuclease and for carboxyl groups in conalbumin were interpreted. Reversible intramolecular transformation was found for α‐lactalbumin by comparing the present results with the potentiometric titration data for carboxyl groups. The molecular size of each protein was discussed.
Theoretical calculation of the circular dichroism of unordered polypeptide chains
Authors: Ronish E. W. , Krimm S. 
Published: December 2004

AbstractA calculation has been done of the circular dichroism (CD) spectrum of an unordered polypeptide chain. This has been based on a Boltzmann averaging over a dipeptide conformational CD map. This is shown to be valid by comparing the CD spectra of 28‐mer oligopeptides with those generated by summing dipeptide CD spectra. The calculated CD spectrum of an unordered polypeptide chain is found to agree with the assignment proposed by Tiffany and Krimm from experimental studies.
An ordered precipitate of polyadenylic acid formed by freezing at acidic pH: Comparison of X‐ray diffraction and other properties of the precipitate with those of fibers or direct acid‐precipitates
Authors: Zimmerman Steven B. , Coleman Norma F. 
Published: December 2004

AbstractPoly A was found to precipitate upon freezing acidic solutions at pH values where it is normally soluble; this precipitate tends to have the form of small thin plates of irregular outline (“plates”). The X‐ray diffraction pattern and solubility properties of the “plates” were compared with those of poly A precipitated solely by exposure to lower pH values, and with fibers drawn from acidic solution. There is considerable molecular order in each of these three types of preparation. In all cases, the diffraction patterns are consistent with the presence of the double‐stranded helical structure proposed by Rich, Davies, Crick, and Watson (J. Mol. Biol., 3, 71 (1961)) based on fiber diffraction data. The diffraction pattern from the “plates” is compared in detail with that of the fibers, and is shown to be in accord with a packing scheme having the chain axis of the molecular structure confined to the plane of the “plate,” but oriented randomly in that plane.
The thermodynamic effects of exposing nucleic acid bases to water: Solubility measurements in water and organic solvents
Authors: Scruggs Robert L. , Achter Eugene K. , Ross Philip D. 
Published: December 2004

AbstractIn order to examine the thermodynamic effects of exposing nucleic acid bases to water, we have measured the solubility of adenine, cytosine, and uracil in water and in organic solvents as a function of temperature. Transfer of a nucleic acid base from an organic environment into water is characterized by positive values for ΔH and for ΔS. We conclude from this result that the overall interaction between nucleic acid bases and water cannot be hydrophobic. If the effect we observe represents structure breaking in water by nucleic acid bases, this process would account for a major portion of the large, positive melting entropy of DNA, and would also contribute substantially to the melting enthalpy.
Ultrasonic absorption and relaxation spectra in aqueous bovine hemoglobin
Authors: White R. D. , Slutsky L. J. 
Published: December 2004

AbstractMeasurements of the frequency and pH dependence of acoustic absorption at 0°C in aqueous solutions of freshly prepared bovine oxyhemoglobin are reported. The role of ionization and possible direct proton‐transfer between proximal pairs in determining the characteristic times for the relaxation of the internal charge distribution is discussed. It is concluded that treatments which consider various classes of residues as ionizing independently will not give approximately correct relaxation spectra. A model which takes into account the coupling between the degrees of ionization of the various residues is found to give rough agreement with the observed acoustic absorption in the pH range in which the native conformation is stable.
Effect of organic solvents on the properties of the complexes of DNA with proflavine and similar compounds
Authors: Löber G. , Schütz H. , Kleinwächter V. 
Published: December 2004

AbstractIn order to obtain information on the binding forces involved in the formation of the complex proflavine–DNA by the stronger process I, the stability of the complexes was investigated in the presence of various organic solvents, methanol, ethanol, n‐propanol, isopropanol, formamide, dimethyl sulfoxide, p‐dioxane, glycerol, and ethylene glycol. Quantitative data on binding in terms of K/n and r were obtained by means of absorption and fluorescence spectra, as well as by a thermal denaturation technique.All organic solvents used decrease the binding ability of the dye. The effectiveness of the solvents increases with their hydrocarbon content, but can hardly be related to their dielectric constant. The complex formation is effectively suppressed by organic solvent concentrations, in which DNA still preserves its double‐helical conformation. These results demonstrate the importance of hydrophobic forces in the formation of the complex proflavine–DNA in aqueous solution.The similarity in spectroscopic properties of proflavine bound to DNA by process I and the same dye dissolved in an organic solvent make it possible to interpret the observed red shift of the long‐wavelength absorption peak as being due to the interaction of the dye molecules with the less polar environment.The same behavior was found for other dyes capable of intercalation like purified trypaflavine, phenosafranine and ethidium bromide. However, intercalation is not a necessary condition, as it was shown in the case of pinacyanol, which binds only at the surface of DNA.
Synthesis and conformation of poly(L‐lysyl‐L‐alanyl), a sequence‐ordered water‐soluble copolymer
Authors: Yaron A. , Tal (Turkeltaub) N. , Berger A. 
Published: December 2004

AbstractThe sequence‐ordered copolymer poly‐(Lys‐Ala‐Ala) was synthesized by polycondensation of the N‐hydroxysuccinimide ester of ε,Z‐Lys‐Ala‐Ala and deprotection of the polymerization product. A fraction of molecular weight 13,000 obtained by ion‐exchange chromatography was investigated. The polymer is freely soluble in water at all pH values, and is completely digested by trypsin and elastase. From CD and ORD data it was concluded that in water at 1°C the ionized form (at pH 6.5) of the polymer is helical. On heating, helix‐coil transition curves were obtained with a midpoint, Tm, depending on salt concentration. In salt‐free water Tm = 12.3°C and in 0.2M NaCl Tm = 28.5°C. Adding MeOH, causes an increase in the helical content of the polymer (half helicity at 20% MeOH, without salt, at 29°C). Guanidine·HCl was shown to decrease the helicity. At 1°C half helicity. The nonionized polymer helix is more stable (Tm∼90°C). At the high pH, at 60°C, when concentration of the polymer is higher than 1.9 × 10‐2M, a precipitate is formed which redissolves on cooling with the original helicity. This does not occur in the presence of 50% MeOH. By comparison with polylysine it was concluded that replacing two‐thirds of the lysine residues in polylysine by alanine leads to a polymer forming a more stable α‐helix, when fully ionized. This is essentially due to the diminished coulombic repulsion. Uncharged lysine residues are comparable to alanine residues in their helix‐forming tendency since the sequential polymer as well as one‐third ionized polylysine are helical to approximately the same extent at room temperature.
Raman scattering of chymotrypsinogen A, ribonuclease, and ovalbumin in the aqueous solution and solid state
Authors: Koenig J. L. , Frushour B. G. 
Published: December 2004

AbstractThe Raman spectra of three globular proteins, beef pancreas chymotrypsinogen A, beef pancreas ribonuclease, and hen egg white ovalbumin have been obtained in the solid state and aqueous solution. X‐ray diffraction and circular dichroism evidence have indicated that these proteins have a low α‐helical content and a large fraction of the residues in the unordered and β‐sheet conformation. The frequencies and intensities of the amide I and amide III lines are consistent with assignments based on the Raman spectra of polypeptides. The intense amide III lines observed in all the spectra would be expected for proteins with a low fraction of the residues in the α‐helical conformation. Several spectra changes occur upon dissolution of the proteins in water and may be associated with further hydration of the proteins. The spectrum of thermally denatured chymotrypsinogen is presented. A 3 cm–1 decrease in the frequency of the amide I line of the protein dissolved in D2O upon heating was observed. This observation is consistent with a denaturation mechanism allowing only slight changes in the secondary structure but an increase in solvent penetration upon going from the native to the reversibly denatured state.
Thermal transitions in gelatin: Optical rotation and enthalpy changes
Authors: Macsuga D. D. 
Published: December 2004

AbstractEnthalpy changes [as determined by differential scanning calorimetry (DSC)] and optical rotation changes over the helix → coil transition were measured for various gelatin solutions and films. From these studies it has been concluded that: (1) a linear correlation between ΔH and Δ[α] exists for gelatin solutions, independent of the temperature at which gelation occurred; (2) the amount of triple helical structure regained when a melted gelatin solution is quenched can be calculated from DSC data, but the values obtained will be dependent on assumptions about the number and strength of hydrogen bonds; (3) the anomalously high levorotation values found for cold‐dried films of gelatin do not reflect the presence of an extraordinarily large amount of triple helical structure; rather, the large rotations appear to be the result of orientation of helices in the plane of the film.