bluuebunny/crossref_metadata_2025_split huggingface dataset:
The buoyant and potentiometric titrations of human immuno‐gamma globulin
Authors: Ruark John E. , Ifft James B. 
Published: December 2004

AbstractThe buoyant density and potentiometric hydrogen ion titration curves of human immuno‐gamma globulin in 3M cesium chloride have been recorded. In addition, the amino acid analysis of the IgG employed has been completed. The hydration of the protein and the variation of the hydration with pH have been calculated from the buoyant density data. The potentiomtric hydrogen ion titration curve has been employed to estimate the intrinsic pK′s of the acidic and histidyl residues of the molecule, and to confirm the hypothesis that it does in fact conform to the oil drop model of protein conformation. Correlations have been drawn between the three sets of data in the following manner. The results of the potentiometric hydrogen ion titration have been checked against the amino acid analysis to determine whether the numbers of groups observed to titrate and the numbers of groups observed in the amino acid analysis do correspond. Second, previous hypotheses as to the direct correlation between potentiometric hydrogen ion titration behaviour and buoyant density titration behaviour have been investigated and substantially confirmed.
The effects of cooperativity, finite chain length, and field‐induced changes of the conformational equilibrium on the electric birefringence of polypeptides in the range of the helix–coil transition
Authors: Schwarz Gerhard , Schrader Uwe 
Published: December 2004

AbstractAn electric birefringence apparatus with an He–Ne laser is described, which permits a high sensitivity of measurement for field strengths up to 20 kV/cm and pulse durations between 10−5 to 1 sec. It is applied to poly(γ‐benzyl‐L‐glutamate) and poly(β‐benzyl‐L‐aspartate) in a nonaqueous solvent mixture, especially under the conditions of the helix‐coil equilibrium. A theoretical treatment of the problem shows that the usual neglect of end effects is only justified for comparatively long chains. On the basis of a computational procedure taking into account the finite chain lengths, the experimental data for 15 kV/cm reveal an obvious enhancement of the coil‐to‐helix transition caused by the electric field. This effect is quantitatively confirmed by a pertinent theory. The cooperative parameter σ may be best determined from the initial linear increase of the bire‐fringence versus the square of the field strength where the conformational equilibrium is not affected.
An X‐ray diffraction study of poly‐L‐homoarginine hydrochloride
Authors: Suwalsky M. , Bunster M. , Wagner K. G. 
Published: December 2004

AbstractAn X‐ray study of the synthetic polypeptide poly(L‐homoarginine hydrochloride) has been made to investigate whether, like the chemically related polypeptides poly(L‐lysine hydrochloride), poly(L‐arginine hydrochloride), and poly(L‐ornithine hydrobromide), it can undergo conformational transitions merely from variations in its degree of hydration. X‐ray photographs of powder and oriented specimens containing one to 15 molecules of water per L‐homoarginine hydrochloride residue showed that this polymer forms only a β‐pleated‐sheet structure. The pleated sheets, formed by antiparallel polypeptide chains hydrogen‐bonded to each other, are piled up along the b axis in an alternating sequence (“sandwich structure”). This structure did not appreciably change with variations of the degree of hydration, and the observed reflections at 56% relative humidity (1.8 molecules of water per residue) could be indexed satisfactorily in terms of a monoclinic unit cell, of space group P21, with a = 9.34 Å, b = 40.07 Å, c = 6.94 Å, and γ = 106°. These dimensions are shown by models to be compatible with the proposed structure, and the calculated density of 1.27 g/cm3 agrees well with the experimental value of 1.29 g/cm3. Removal of the last molecule of water results in a very diffuse pattern, while specimens containing 20 molecules of water per residue show only reflections due to water.
Characterization of the A ⇄ B transition of DNA in fibers and gels by laser Raman spectroscopy
Authors: Erfurth Stephen C. , Bond Peter J. , Peticolas Warner L. 
Published: December 2004

AbstractBoth Raman spectra and X‐ray diffraction patterns have been obtained from oriented fibers of sodium deoxyribonucleic acid (Na‐DNA) as a function of salt content and relative humidity. We have confirmed the previously reported X‐ray results that, for oriented fibers, the A‐form always exists between 75 and 92% relative humidity and that the conformation will change to the B‐form at 92% relative humidity only if an excess (3–5%) of added salt is present. Oriented fibers containing low amounts of added salt remain in the A‐type conformation at 92% relative humidity and higher. An exact correlation has been found between the familiar A‐ and B‐type X‐ray diffraction patterns of DNA fibers and the Raman spectra previously reported without X‐ray verification from this laboratory for the A‐ and B‐forms. In particular, a band at 807 cm−1 was always present when a fiber showed the A‐type diffraction pattern, and this band shifts to 790 cm−1 in the B‐form. Using the Raman spectrum to determine the specific conformation of DNA in samples less amenable to X‐ray analysis, we have studied the A ⇄ Btransformation in unoriented fibrous masses of DNA and in concentrated, oriented gels. We find that in unoriented fibrous masses, the A ⇄ B transition always occurs at 92% relative humidity even at very low salt concentration (0–4%). However, in oriented DNA gels at low salt, the A‐form can persist as a metastable state to concentration as low as 20% DNA. The origin of the bands at 807 and 790 cm−1 and the possible biological implications of these findings are discussed.
Analysis of the effects of chloride and 2,3‐diphosphoglycerate on the cooperative binding of oxygen to hemoglobin
Authors: Deal Walter J. 
Published: December 2004

AbstractAnalysis of experimental equilibrium constants for the oxygenation of hemoglobin leads to a plausible mechanism for the effect of pH and of chloride ions on cooperativity in hemoglobin. According to this mechanism, the structural changes responsible for cooperativity in chloride‐ and 2,3‐diphosphoglycerate‐free hemoglobin are affected only slightly by changes in pH, and the effect of chloride can be accounted for by sequential binding and release of chloride ions during oxygenation.
Magnetic susceptibility of various ferrihemoglobin species
Authors: Anusiem A. C. I. 
Published: December 2004

AbstractMeasurements of the magnetic susceptibility of guinea pig, human A, and pigeon ferrihemoglobins as a function of pH at 30°C demonstrate maxima very near the extrema found for the standard enthalpies and standard entropies of ligand binding, i.e., at the so‐called “characteristic pH” values, which are very different for these three species. Ligand binding is dependent on spin state, at least through the characteristic pH behavior, which is not yet understood.
Nature of amino acid side chain and α‐helix stability
Authors: Arfmann H.‐A. , Labitzke R. , Wagner K. G. 
Published: December 2004

AbstractIn order to investigate the ability of neutral amino acids to support the α‐helix conformation, the coil–helix transition of poly(L‐lysine) and of lysine copolymers with these amino acids was studied in water/methanol using circular dichroism. The transtions were recorded at constant pH adding buffer to the methanol/water mixtures. With poly(L‐lysine), experiments were performed at several constant pH's; the transition midpoint on the water (methanol) concentration scale was found to depend strongly upon pH; the helix stability region is shifted towards higher water concentrations, when the pH is increased. Copolymers of lysine and several neutral amino acids revealed the same effect in that increasing amounts of, for example, norleucine also shifted the transition midpoint to higher water concentrations. A series of copolymers containing L‐lysine as the host and different hydrophobic amino acids were synthesized and the helix–coil transition in water/methanol was observed at constant pH. Different copolymers of equal composition showed significant differences with respect to the nature of the amino acid incorporated into polylysine. From these studies an α‐helix‐philic scale (in decreasing order): Leu, Nle, Ile, Ala, Phe, Val, Gly is deduced and discussed; the results obtained were compared with those of different procedures.
Electron microscopy of ribosomal RNA mounted by adsorption in the absence of protein
Authors: Johnson Thomas R. , Caston J. Douglas 
Published: December 2004

AbstractA method is described for visualizing ribosomal RNA in the electron microscope by an adsorption technique. The visual configuration of the molecules is sensitive to the composition of the medium from which they are adsorbed, and is reproducible under a given set of conditions. Regular structural features occur in the larger rRNA species similar to those observed with protein monolayer techniques. The dimensions of adsorbed molecules, however, are more consistent with current models of ribosomal RNA as it exists in solution.
Potentiometric titrations involving the β‐coil transition
Authors: Maeda Hiroshi , Ikeda Shoichi 
Published: December 2004

AbstractPotentiometric titrations of poly(S‐carboxymethyl‐L‐cysteine) and poly(S‐carboxy‐ethyl‐L‐cysteine) were carried out in aqueous sodium chloride solutions and in water. For samples of both polymers of high molecular weight, a new pattern was observed concerning the change of titration curve with time; the β‐coil transition became sharper and the transition free energy increased by about 100 cal mole−1 as the equilibrium was approached. This suggests that equilibrium data were not obtained in most previous studies on the titration involving the β‐coil transition. It also shows that the reversbility is not necessarily sufficient to confirm the equilibrium. Another pattern, which was previously observed, was also confirmed with a low molecular weight sample of poly(S‐carboxymethytl‐L‐cysteine). The titration curves were shown to be insensitive to polymer concentration, even when aggregation or phase separation was present. The validity of the Gouy model to describe the titration curve of the β‐structure was found to depend on molecular weight as well as on the nature of the side chain.
Conformation of a rare nucleoside in the anti‐codon loop of tRNAs: Potential energy calculations for 2′‐O‐methyl cytidine
Authors: Stellman S. D. , Hingerty B. , Broyde S. , Langridge R. 
Published: December 2004

AbstractThe classical potential energy of 2′‐O‐methyl cytidine was calculated using contributions from van der Waals', electrostatic, and torsional terms. All five conformational angles, namely χ, Ψ, the methoxy angles m1 and m2 which are unique to O′‐methylated nucleosides, and the sugar pucker P were varied simultaneously, and the energy was minimized with respect to these parameters. An extensive search of conformation space was made, particularly with respect to the sugar pucker. At the predicted global minimum, χ and Ψ are anti‐gg, P is C(2′)‐endo‐C(3′)‐exo, and the methyl group is staggered with respect to the sugar. This calculated minimum agrees very well with the recently determined crystal structure of 2′‐O‐methyl cytidine. Thus, 2′‐O‐methylation still permits the conformational regions of the common nucleosides to be adopted. However, we infer that the predicted C(2′)‐endo sugar pucker results from the added methyl group, since cytidine is C(3′)‐endo in the crystal, and the common ribopyrimidine nucleosides generally favor C(3′)‐endo.
The interaction between two oppositely charged polyelectrolytes
Authors: Polderman A. 
Published: December 2004

AbstractMixtures of a weak polybase (polyethylenimine) and a weak polyacid acrylamide‐acrylic acid copolymer in aqueous solutions at several ionic strengths and polymer concentrations are studied potentiometrically. When the concentrations of the polyethylenimine and acrylamide‐acrylic acid copolymer charges are not too different, phase separation into two liquid phases (“complex coacervation”) is observed. In the pH region where no phase separation occurs, potentiometric titrations are performed on mixtures of both polymers. From the titrations of polyethylenimine solutions, acrylamide‐acrylic acid copolymer solutions, and the mixtures, the free energy of interaction has been evaluated according to the theory of Litan. The dependence of the free energy of interaction on pH, polymer concentrations, and ionic strength is explained quantitatively with a model of cooperative electrostatic physical association.
Synthesis of sequential polypeptides containing L‐azetidine‐2‐carboxylic acid residues
Authors: Boni R. , De Gregoriis E. , Di Blasi R. , Verdini A. S. 
Published: December 2004

AbstractThe synthesis and characterization of a series of sequential polypeptides with the repeating sequences Aze‐Pro‐Aze, Pro‐Aze‐Pro, Pro‐Aze‐Gly, Aze‐Pro‐Gly, Ala‐Aze‐Gly, Aze‐Ala‐Gly, and Pro‐Pro‐Gly are reported. The polymers were prepared by the active ester method, using the p‐nitrophenyl, pentachlorophenyl, and N‐hydroxysuccinimide esters as the polymerizable tripeptide derivatives. Except for poly(Ala‐Aze‐Gly) obtained via the N‐hydroxysuccinimide ester, all polymers were isolated in good yields and have weight‐average molecular weights in the range 10,000–30,000. The molecular weights have been determined by applying the calibrated gel chromatography system described by Fairweather et al. [J. Chromatogr. (1972) 67, 157] and by viscometry. All di‐ and tripeptide intermediates were chemically and optically pure.
Frictional properties of multisubunit structures
Authors: McCammon J. A. , Deutch J. M. , Felderhof B. U. 
Published: December 2004

AbstractThe translational drag, rotational drag, and intrinsic viscosity of spherical multisubunit structures have been calculated analytically using the Felderhof–Deutch theory of polymer frictional properties. The structures considered were hollow shells, spheres with uniform subunit density, and spheres covered with a subunit layer of different density. Changes in the transport coefficients resulting from the random removal of subunits and from the variation of subunit size are calculated. For the case of the shell, the results agree with the numerical computations of Bloomfield, Dalton, and Van Holde [Biopolymers 5, 135, 149 (1967)].
Competitive cooperative bindings of a small ligand to a linear polymer. II. Investigations on the mechanisms of proflavine binding to poly(A) and DNA
Authors: Dourlent M. , Hogrel J. F. 
Published: December 2004

AbstractExperimental binding isotherms relative to the interactions between proflavine and poly(A) or DNA are analyzed by comparison with theoretical models dealing with competitive cooperative bindings.In the case of poly(A), there are apparently no specific binding sites for the positive co‐operative binding (complex I) leading to dye aggregation along the polyanionic chain. The second complex (complex II) seems to involve specific base‐dye interactions, but it cannot be said whether this binding displays negative cooperativity or noncooperativity. None of the two simpler theoretical models agree quantitatively with all experimental data. A plausible interpretation can be given if it is assumed that (i) the electrostatic binding of one isolated bound dye molecule (nucleus of complex I) involves a definite interaction between a phosphate group and the positive charge of the dye; (ii) the structure of complex II is such that a dye–phosphate ionic interaction is maintained.In the case of DNA, our model of monoexclusive interactions fits the data more closely than does the model of biexclusive interactions. This gives experimental support for structural models in which the intercalated molecule interacts preferentially with one strand of the double helix and blocks only one phosphate for electrostatic binding. In order to propose a mechanism consistent with equilibrium and relaxation kinetic data, a modified reaction scheme is considered which takes account of the cooperativity effects in external binding and extends previous models.
Kinetic study of cooperative binding reaction of toluidine blue to poly(α,L‐glutamic acid) by means of the electric‐field pulse method
Authors: Ushio Hidetoshi , Yasunaga Tatsuy , Sano Takayuki , Tsuji Yoshikuni 
Published: December 2004

AbstractInteraction of toluidine blue with helical and randomly coiled poly(α,L‐glutamic acid) was studied with absorption spectra, titration, and electric‐field pulse measurements. The obtained values of various parameters for the helical form of poly(α,L‐glutamic acid)differed from those for its coiled form. The difference of parameters in these two forms of poly(α,L‐glutamic acid) was attributed to differences of the binding mechanism in both forms. Furthermore, the binding of toluidine blue to poly(α,L‐glutamic acid) was considered to be due to hydrogen binding in the helical conformation and ionic interaction in the coiled conformation of the polymer.
An analysis of the association of collagen based on structural models
Authors: Cunningham Leon W. , Davies Hugh A. , Hammonds R. Glenn 
Published: December 2004

AbstractThe existence and distribution of vertical, interacting edges on cylindrical surfaces, which were derived from the basic structural features of the collagen molecule, have been examined as a function of the angle θ of the superhelix. Over the range θ = 26°–33° and near θ = 36°, the strongest intermolecular association was detected at 29.95°. This model exhibited three similar, self‐interacting edges, separated by approximately 120°. The potential for three similar but nonidentical edges lies in the geometry of the collagen molecule, but the existence of such edges and their ability to self‐associate is dependent upon the unique amino acid sequence. The relative strengths of association of each edge with itself and with the other edges are not identical, but the present analysis does not permit a judgment as to whether this variation could result in functional specificity in such interactions. All three chains participate in each edge though their contribution to the relative interaction strength is not identical.These edges showed distinct maxima when displaced past one another by integral intervals of D, where D = 233 residue positions (quarter‐stagger). The strongest relative interaction occurs at a displacement of 1D.
An interpretation of the depolarization of the fluorescence of diphenylanthracene in solutions of polymers
Authors: Mazo Robert M. 
Published: December 2004

AbstractIt is argued that the decrease of fluorescence depolarization observed when diphenylanthracene is dissolved in poly(γ‐benzyl‐L‐glutamate) or polystyrene solution is due to short‐range interactions, and not to long‐range hydrodynamic interactions. Estimates of the hydrodynamic effect are given. Rough estimates of the effect to be expected on the short‐range hypothesis are in qualitative agreement with experiment.
Circular dichroism of collagen, gelatin, and poly(proline) II in the vacuum ultraviolet
Authors: Jenness Duane D. , Sprecher Cindy , Johnson W. Curtis 
Published: December 2004

AbstractCircular dichroism spectra for acid‐soluble calfskin collagen, gelatin, and poly(proline) II in solution have been extended into the vacuum ultraviolet region. The extended spectrum of gelatin reveals that the circular dichroism of this unordered polymer is more closely related to the spectrum of charged polypeptides than might be evident from near ultraviolet work. A short‐wavelength band is found at about 172 nm, which corresponds in position, magnitude, and sign to a band recorded earlier for poly(L‐glutamic acid) at pH 8.0. This band is observed in a helical structure for the first time in the vacuum ultraviolet circular dichroism and absorption spectra of poly(proline) II. Both circular dichroism and absorption spectra point to the assignement of this band as the nσ*. Neither the nσ* nor the expected positive lobe of the ππ* helix band is observed in the extended circular dichroism spectrum of collagen. We postulate that these two bands cancel here in analogy to the case of α‐helical poly(L‐glutamic acid).
The importance of coulombic interactions for the induction of β structure in lysine oligomers by sodium dodecyl sulfate
Authors: Mattice Wayne L. , Harrison William H. 
Published: December 2004

AbstractCircular dichroism spectra have been obtained for tri(L‐lysine), tetra(L‐lysine), and penta(L‐lysine) in aqueous sodium dodecyl sulfate at 25°C. None of the oligomers are affected significantly by sodium dodecyl sulfate at detergent concentrations exceeding 0.01 M. Literature results show that the high‐molecular‐weight polymer forms a β strucure under these conditions. At detergent concentrations near 3.5 × 10−4 M the penta(L‐lysine), but not the smaller oligomers, undergoes a conformational change. Its circular dichroism under these conditions is essentially identical to that observed with poly(L‐lysine) when it forms a β structure in sodium dodecyl sulfate. Solutions of the penta(L‐lysine), which exhibit this modified circular dichroism, are also turbid, leading to the conclusion that the oligomer has formed an intermolecular β structure. When these experiments are conducted in the presence of 0.1 M sodium hydroxide, the sodium dodecyl sulfate produces neither turbidity nor a modified circular dichroism spectrum. These observations provide compelling evidence that Coulombic interaction between the anionic detergent head and the cationic lysyl amino groups is essential for the conformational change induced in penta(L‐lysine) by sodium dodecyl sulfate.
Hyperfine structure in melting profile of bacteriophage lambda DNA
Authors: Gotoh Osamu , Husimi Yuzuru , Yabuki Sadato , Wada Akiyoshi 
Published: December 2004

AbstractA high‐resolution plotter of differential melting profiles of DNA, RNA, or related biopolymers with an on‐line mini‐computer is described. With this device, more than 15 transition steps were identified in the thermal melting profile of DNA from bacteriophage lambda. These fine structures were found to be reproducible, and some of them disappear in the deletion mutant.To Examine the melting profile, computer simulations for several hypothetical polynucleotide sequences were performed, and compared with experimental data. The sharp peaks that appeared in the differential melting profile of λ DNA may come from some homogeneous sequences of 500 bases or longer.
Structural investigations on DNA·protamine complexes
Authors: Herskovits T. T. , Brahms J. 
Published: December 2004

AbstractProtamine·DNA complexes in film and in solution have been investigated by means of infrared linear dichroism, ultraviolet circular dichroism, and laser Raman spectroscopy. At high relative humidity and in solution both infrared linear dichroism and ultraviolet circular dichroism indicate the presence of a modified B form of DNA (designated as B* in our other papers27,28,46). This modified B form is characterized by a change of the orientation of the \documentclass{article}\pagestyle{empty}\begin{document}$ \widehat{OPO} $\end{document} bisector angle by about 4° with respect to the helical axis when compared to the B form of DNA. At decreasing relative humidities the same modified B form is maintained and no structural transitions B → A (or B → C) normally occurring in free DNA were observed. The absence of the A form in these complexes was also confirmed by laser Raman scattering studies of protamine·DNA complexes. On the basis of these results, a model of the protamine·DNA complex is proposed, which suggests that the presence of apolar amino‐acid residues, and probably the folding of the polypeptide chain, is responsible for preventing the B‐to‐A transition; this occurs either by protecting the high‐humidity modified B form against dehydration or by steric interference of this protein probably located in one of the DNA grooves.