bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oligonucleotide conformations. III. Comparative optical and thermodynamic studies of uridylyl‐3′‐5′‐nucleosides containing ribose, deoxyribose, or 2′‐deoxy‐2′‐fluororibose in the uridine moiety
Authors: Catlin Joseph C. , Guschlbauer Wilhelm 
Published: May 2005

AbstractThe synthesis of uridylyl‐3′‐5′‐nucleosides containing ribose, deoxyribose, or 2′‐fluoro‐2′‐deoxyribose in the uridine‐3′‐bound moiety and adenosine, guanosine, cytidine or uridine in the 5′‐nucleoside is reported. The temperature dependence of the circular dichroism of these dinucleoside phosphates in 0.06 M phosphate buffer at pH 7 was analyzed by the two‐state model and the oscillating dimer model. From the former, apparent thermodynamic parameters were determined by means of an iterative computer method. The comparison between the three different dinucleoside phosphates in each series indicated that the fluororiboside and the riboside resembled each other and were more stacked than the analogue containing deoxyribose. It further appeared that the similarity between the fluororiboside and the riboside is influenced by the nature of the neighboring 5′‐bound base. The interaction between the 3′‐bound sugar moiety and the 5′‐bound base is evoked as a possible stabilization mechanism.
The structure of the anticodon loop of tRNAPhe from yeast as deduced from spectroscopic studies on oligonucleotides
Authors: Maelicke Alfred , Von Der Haar Friedrich , Sprinzl Mathias , Cramer Friedrich 
Published: May 2005

AbstractThe hexanucleotide Gm‐A‐A‐Y‐A‐ψp excised from the anticodon loop of yeast tRNAPhe and its constituent oligonucleotides have been studied by ultraviolet absorption spectroscopy, static fluorescence, and circular dichroism. Gm‐Ap has a melting point of 45°C and a high melting enthalpy when compared with G‐Ap; hence 2′‐O‐methylation seems to stabilize stacking interactions. The nucleobase Y adjacent to the 3′‐side of the anticodon triplet interacts stronger with its 3′‐neighboring A than with its 5′‐neighboring A. It is concluded that the base Y disconnects the stack of the anticodon itself from the stack of the anticodon stem, thereby setting a reading frame for the mRNA in the course of protein biosynthesis. From the opposite signs of the short‐wavelength Cotton effects in the spectra of Gm‐A‐A‐Y‐Ap and Gm‐A‐A‐Y, it is concluded that Y after removal of its 3′ neighbor undergoes a dramatic change in its conformation. The fluorescence of the nucleobase Y upon addition of Mg2+ is enhanced in oligonucleotides longer than two. An identical enhancement is observed for tRNAPhe, indicating that this Mg2+ effect is a property of an oligonucleotide segment and does not reflect conformational changes of the whole tRNA. The data presented here reveal that the basic structural features of the anticodon loop are already present in the hexanucleotide Gm‐A‐A‐Y‐A‐ψp and are not determined by the overall structure of tRNA.
Electric birefringence in concentrated solutions of tobacco mosaic virus
Authors: Asai Hiroshi , Watanabe Nozomu 
Published: May 2005

AbstractA tentative and phenomenological analysis of negative electric birefringence, which has often been observed as an anomalous birefringence phenomenon in a concentrated solution of rodlike macromolecules, is presented. Tobacco mosaic virus (TMV) was used as a typical example for the investigation. It was found that if the applied electric field is sufficiently high, the steady‐state birefringence becomes becomes positive even at a very high concentration of TMV. From this finding and analysis of the time course of birefringence transients, it was suggested that the TMV (common strain, OM type), which originally has no inherent permanent dipole, behaves as if it possesses a permanent dipole perpendicular to its long axis. Supporting evidence was also obtained from birefringence experiments on concentrated solutions of the HR strain of TMV, which has an inherent permanent dipole along its long axis. Other possibilities, for example, the effects of the walls of electrodes or of polymerization of TMV molecules, were excluded.
Na+ effects on transitions of DNA and polynucleotides of variable linear charge density
Authors: Record M. Thomas , Woodbury Charles P. , Lohman Timothy M. 
Published: May 2005

AbstractA range of linear charge densities of the ordered and disordered forms of DNA or polynucleotides can be obtained experimentally by acid or alkaline titration, or by the investigation of unusual complexes involving protonated bases or three‐stranded helices. The variation of melting temperatures with Na+ concentration for various of these systems is known and in some cases is complemented by structural and thermodynamic information. We have extended the condensation–screening theory of Manning [Biopolymers, 11, 937–955 (1972)] to these systems. The stabilizing and destabilizing effects of Na+ (condensation and screening, respectively) and be independently varied, and the theory is successful in predicting the qualitative (in some cases, quanittative) behaviour that is observed. Comparison of theory and experiment indicates that the axial phosphate distance b for single‐stranded polynucleotides increases with increasing pH. Values of the critical parameter ξ are obtained for the various polynucleotide structures. These values are essential for an understanding of ionic effects on charged ligand–polynucleotide interactions.
Interaction between collagen and adenosine 5′‐triphosphate
Authors: Fung B. M. , Hillson Randall A. , Lee Garland G. , Nunnery Arthur W. , Bradford Reagen H. 
Published: May 2005

AbstractA quantitative study was made of the adsorption of adenosine 5′‐triphosphate (ATP) on collagen by following the change in the absorbance at 258 nm of ATP in the soaking solution. The amount of ATP adsorbed decreased exponentially with the increase of pH up to pH 8 and fell off more rapidly at higher pH values. At a given pH, when the concentration of ATP was increased, the amount of ATP adsorbed increased following the pattern of a Langmuir isotherm. The adsorption was independent of the cation present. The adsorption of adenosine 5′‐diphosphate was essentially the same as that for ATP. For tendons deposited with calcium phosphate, the amount of ATP adsorbed decreased compared to natural tendons.The adsorption of ATP on collagen fibers inhibited the contraction caused by calcium chloride, calcium bromide, and lithium bromide. In solution, ATP had very little effect on the denaturation of acid‐soluble collagen caused by calcium chloride.
Nmr studies of aqueous solutions of tetra and branched peptides. I. Sequence determination of amino‐acid residues and the assignment of peptide hydrogen signals
Authors: Sheinblatt M. , Rahamim Y. 
Published: May 2005

AbstractSequential determination of glycyl residues (and in several cases different amino‐acid residues) in tetra and branched peptides using the nmr technique is reported. The method is based on changes in the nmr spectra of (1) the peptide hydrogens of the different residues and (2) the methylene groups of the glycyl residues, as a result of increasing the rate of the base‐catalyzed exchange reaction of the peptide hydrogens. Hence, the spectral changes are pH dependent. However, the exact pH dependence is a function of the location of the residue in the peptide molecule. Thus, it is possible to determine the sequence of the amino‐acid residues by studying the changes in the spectra with pH.For peptide molecules of known sequences, the above method can be used for unequivocal assignment of the peptide hydrogen signals.
Circular dichroism and structure of the complex of acridine orange with poly(L‐glutamic acid)
Authors: Imae Toyoko , Ikeda Shoichi 
Published: May 2005

AbstractCircular dichroism and absorption spectra have been measured on solutions of acridine orange and poly(L‐glutamic acid) mixed at two molar ratios of carboxyl group‐to‐dye, P/D 25 and 0.8, and at different pH's. Characteristic circular dichroism is induced at the absorption bands of acridine orange when the P/D is 25 and the solution is acidic. Another type of circular dichroism is manifest at neutral and alkaline pH when P/D is 0.8. For the induction of the former type of circular dichroism, a helical array of acridine‐orange dimers bound to the α‐helix is postulated, in which the dye molecular planes are almost perpendicular to the helical axis. Assuming the helical geometry and optical parameters, combined with the observed magnitude of transition electric moment, the rotatory strength of the complex is calculated to the zeroth order approximation, and the observed circular dichroism spectra have been reproduced.
Moments of the probability distribution of moving molecules undergoing reversible isomerization, with applications to experiments
Authors: Mitchell R. M. 
Published: May 2005

AbstractExact expressions are obtained for the mean position and the variance about the mean of macromolecules which are moving in an electrostatic or centrifugal field and which, at the same time, are switching back and forth between two isomeric states. Comparison with experiment then yields the forward and backward switching rates. The following special cases are considered: (a) only one species present initially; (b) both species present initially but not in their equilibrium proportions; (c) both species present initially in their equilibrium proportions. It is shown that in the first two cases we need only measure the mean position of all the molecules in order to measure the absolute switching rates k1 and k2. In the third case, however, we must measure the variance (mean‐square deviation) of the position in order to obtain k1 and k2. The first two situations arise when “jumps” (e.g., in temperature or pressure) are made, while the third situation is obtained if the experiment is conducted with the species in chemical equilibrium throughout the experiment.
Dinucleoside monophosphates. II. Nearest neighbor interactions
Authors: Topal Michael D. , Warshaw Myron M. 
Published: May 2005

AbstractA method has been developed which enables calculation and unambiguous comparison of the thermodynamics for the stacking process of dinucleoside monophosphates (dimers) from a study of their titration properties. This method has been applied to dimers containing adenosine and/or cytidine with the result that the dimers studied can be ordered with respect to their tendency to stack as ApA > ApC > CpA ≃ C – containing homodimers. This dependence of the relative magnitude of ΔFstacking on composition is consistent with hydrophobic interactions, as manifested by the solubility of the bases, being the main driving force toward stacking. The sequence dependence of ΔFstacking as well as of the optical properties of the dimers is related to van der Waals interaction between the bases. The lack of variation in ΔFstacking of the C‐containing isomers indicates that the role of the 2′‐OH in RNA versus DNA structure is not H‐bonding.
Synthesis of sequential oligopeptides and polypeptide having the sequence of L‐alanyl‐L‐leucylglycine
Authors: Katakai Ryoichi 
Published: May 2005

AbstractA series of sequential oligopeptides having simple nonpolar side chains, Nps‐(L‐Ala‐L‐Leu‐Gly)n‐ OEt has been prepared by a stepwise fragment‐condensation method using Nps‐L‐alanyl‐L‐leucylglycine N‐hydroxysuccinimide ester, which was prepared by the Nps‐N‐carboxy α‐amino‐acid‐anhydride method. The success of the synthesis of the peptide having a high‐molecular weight, such as octadecapeptide, results from the highest solubility of the tripeptide unit, L‐alanyl‐L‐leucylglycine. The sequential polypeptide having the same tripeptide sequence was also prepared by polycondensation of the tripeptide N‐hydroxy‐succinimide ester.
Conformational studies of peptides. The crystal structures of N‐acetyl‐L‐prolinamide and N‐acetyl‐(S)‐thiazolidine‐4‐carboxamide
Authors: Benedetti E. , Christensen A. , Gilon C. , Fuller W. , Goodman M. 
Published: May 2005

AbstractThe crystal structure of N′‐acetyl‐L‐prolinamide and its isomorphous alalog N′‐acetyl‐(S)‐thiazolidine‐4‐carboxamide was determined using highly accurate parameters obtained by room‐ and low‐temperature data‐collecting systems. Both crystals are orthorhombic, space group P212121, with four molecules per unit cell held together by a hydrogen‐bond system that extends in all directions.Both molecules exhibit the following conformational features: the acetyl group is in the trans configuration in respect to the tertiary amide. The primary amide is almost at right angles with respect to the mean plane of the ring and the –NH2 group is over the ring. The pyrrolidine and thiazolidine rings were found to be rather flexible with Cβ puckering in the former and sulfur in the latter.
Mass–length ratio of fibrin fibers from gel permeation and light scattering
Authors: Carr Marcus E. , Shen Linus L. , Hermans Jan 
Published: May 2005

AbstractMass–length ratios of fibers in fibrin gels were obtained from measurements of the angular dependence of the intensity of light scattered by dilute gels and from the permeability of more concentrated gels. The permeability was determined by measuring the forced flow of buffer through a short column of gel held in a glass tube. The results obtained with the two methods are consistent. At high pH and high ionic strength the mass–length ratio is found to be that calculated for a protofibril, i.e., a double strand of fibrin molecules laid end to end at a separation of 450 Å. This same value is found under conditions where the polymerized fibrin is not gelled (pH 10.25) and where it is just gelled (pH 10.0). At pH 7.4, ionic strength 0.35, the fibers are found to have a higher mass–length ratio, the average fiber consisting of some three protofibrils associated laterally. At pH 7.4 and low ionic strength (0.10 M) the fibers are up to a hundred times more massive.
Circular dichroism of the complex between N‐N′‐diethylpseudoisocyanine and sodium poly(L‐glutamate) in aqueous solutions
Authors: Pal M. K. , Mandel M. 
Published: May 2005

AbstractIn the presence of sodium poly(L‐glutamate) at pH = 7.5 the dye pseudoisocyanine in dilute aqueous solution (Cd = 1.10 × 10−5 M) and low P/D values exhibits an absorption spectrum with a very sharp red‐shifted J‐band. Under the same conditions circular dichroism (CD) in the visible region is observed with an extremely sharp peak at the position of the J‐band. At pH = 4.6, where the polypeptide is in the α‐helix conformation, no such J‐band is observed and no CD spectrum can be detected at the same P/D values. CD spectra in the uv range demonstrate that the occurrence of the dye–polypeptide complex which gives rise to the J‐band at slightly alkaline pH is not accompanied by a conformational transition of the polypeptide towards the α‐helical form.
Effect of the fluctuations in electron density within a globular protein on the excess small‐angle X‐ray scattering
Authors: Mattice Wayne L. , Carpenter Dewey K. 
Published: May 2005

AbstractExcess small angle X‐ray scattering in solvents of differing electron density has been calculated from the crystal structures obtained for rubredoxin, trypsin inhibitor, myogen, ferricytochrome c2, ribonuclease S, lysozyme, nuclease, myoglobin, α‐chymotrypsin, elastase, subtilisin, carboxypeptidase A, thermolysin, methemoglobin, deoxyhemoglobin, and a single polypeptide chain of M4 lactate dehydrogenase. The scattering curves for each protein can be reproduced by the sum of three curves, with the weighting of the three curves depending on the electron density of the solvent. The radius of gyration obtained from the small angle X‐ray scattering by globular proteins in aqueous solution will usually exceed the values defined by the shape of the macromolecule. Deviations for certain of the proteins cited are calculated to be as large as 6%. These deviations arise from the tendency for the amino acid residues with low electron density to be situated closer to the center of the protein than the amino acid residues of high electron density. An upper limit of 19% is obtained for the discrepancy between the radius of gyration defined by the shape of a spherical globular protein of typical amino acid composition and the apparent radius of gyration measured for that protein in water by small angle X‐ray scattering.
Ion complexation in nonactin, monactin, and dinactin: A Raman spectroscopic study
Authors: Asher Irvin M. , Phillies George D. J. , Kim B. J. , Stanley H. E. 
Published: May 2005

AbstractThe ability of the macrotetrolide nactins to complex selectivity with a wide variety of cations makes these ionophorous antibiotics important model systems for the study of biologic ionic transport. We report a Raman spectroscopic investigation of the Na+, K+, Rb+, Cs+, Tl+, NH4+, NH3OH+, C(NH2)3+, and Ba++ complexes of nonactin, monactin, and dinactin in 4:1 (v/v) CH3OH/CHCl3 and in the solid state. The nactins display characteristic spectral changes upon complexation, some of which are specific for a given cation. In the K+, Rb+, Cs+, NH3OH+, and C(NH2)3+ complexes, which are apparently isosteric, the ester carbonyl stretch frequency is found to be linearly proportional to the cation–carbonyl electrostatic interaction energy, as calculated from a simplified model. Deviations for the Na+, NH4+, Tl+, and Ba++ complexes are interpreted as arising from additional nonelectrostatic interactions. Additional information is obtained from other spectral regions and from measurements of depolarization ratios. Spectra of the nactin complexes differ from each other more in the solid state than in solution, reflecting the effects of crystalline contact forces.
Polymerization of N‐carboxyanhydrides of various α‐amino acids using secondary amines as initiator
Authors: Imanishi Yukio , Aoyama Akimasa , Hashimoto Yutaka , Higashimura Toshinobu 
Published: May 2005

AbstractIn the polymerizations of alanine, γ‐ethyl glutamate, and leucine N‐carboxyanhydrides (NCA's) initiated by tertiary amines and some secondary amines such as N‐methyl‐L‐alanine dialkylamide, a stereoselectivity was observed: the polymerization rates of L‐ and D‐NCA's were identical to each other and larger than that of DL‐NCA. However, this selectivity was not observed in the polymerizations of valine and isoleucine NCA's initiated by N‐methyl‐L‐alanine dialkylamide. The stereoselective polymerizations of valine and isoleucine NCA's were induced only with tetriary amines such as tri‐n‐butylamine. N‐Methyl‐L‐alanine di‐alkylamide has been shown to initiate the polymerization of usual α‐amino acid NCA according to the activated‐NCA mechanism, but it initiated the polymerizations of valine and isoleucine NCA's according to the primary amine‐type mechanism. This is because in the latter NCA's the N–H group is masked by the adjacent Cβ‐branched alkyl substituent against the approach of the secondary amine. Poly(DL‐alanine)s produced in the stereoselective polymerization had higher viscosities and were more stereoblock‐like than those produced without the stereoselectivity. These experimental results indicate that the stereoselective polymerization is possible only when the polymerization proceeds through the activated‐NCA mechanism.
ESR investigation of the binding of some neutral polyamino acids to synthetic apatite
Authors: Peckauskas R. A. , Pullman I. , Termine J. D. 
Published: May 2005

AbstractInteraction between synthetic crystalline apatitic calcium phosphate and neutral polypeptides [poly(DL‐alanine), poly(L‐proline), poly(L‐hydroxyproline)] was investigated by elecron‐spin‐resonance spectroscopy of mineral‐macromolecule complexes doped with vanadyl ion (VO++) as a paramagnetic probe. Changes in magnetic parameters were interpreted in terms of polypeptide‐induced axial interactions with VO++ ions that have mineral surface phosphate oxygens as their primary ligands. This implies very close proximity between mineral surface and macromolecular peptide bond dipolar substituents.
Characterization of meningococcal polysaccharides by optical mixing spectroscopy. II. Effects of temperature, EDTA, and ionic strength on aggregation of group C polysaccharides in solution
Authors: Fujime S. , Chen F. C. , Chu B. , Liu T. Y. 
Published: May 2005

AbstractWe have studied the effects of temperature, EDTA, and ionic strength on C‐polysaccharides in solution by examining the details of the time‐correlation function using a 96‐channel single‐clipped photon correlation spectrometer. Our linewidth results have shown that the C‐polysaccharides in buffer solution form aggregates of very broad distributions. Thus, fractionation by gel‐filtration chromatography is only mildly effective. Although the aggregate sizes seem to remain relatively constant from 4 to 25°C, a fraction of those aggregates break up to form smaller fragments or monomers at higher temperatures. However, the dissolution‐association process is quite slow and takes days even at room temperatures before the equilibrium is reached. We have also shown that by adding an excess amoutn of EDTA, the aggregates can be broken up. Again the dramatic changes occur only at short delay times suggesting that a protion of the larger aggregates remains. Finally, the amount and size of aggregates depend upon the ionic strength which exhibit a maximum ΓT/sin2 (θ/2) around 0.1–0.2 M KCl.If the activities of polysaccharides in solution depend upon molecular size, the standard techniques such as gel‐permeation chromatography and ultracentrifugation cannot properly characterize the detailed size distribution. Quasielastic laser light scattering can provide us with a qualitative model. The quantitative details must necessarily await more extensive investigations using a combination of the techniques and better fractionation procedures in an appropriate buffer solution.
The interaction of carboxymethylamylose and diethylaminoethylamylose with iodine
Authors: Cesàro Attilio , Brant David A. 
Published: May 2005

AbstractSpectrophotometric titrations of slightly substituted carboxymethylamylose (CM‐Amy) and diethylaminoethylamylose (DEAE‐Amy) with iodine in the presence of iodide (I2/I−) were carried out as a function of iodide concentration, temperature, and polymeric charge. Binding isotherms for the polymer‐I2/I− complex are reported in terms of an apparent binding constant (Ka) plotted versus degree of saturation of the complex (θ). The dependence of Ka upon polymeric charge is interpreted as evidence for the negatively charged character of the bound species. The cooperative nature of the binding process is evident in the positive slope of Ka vs (θ). Whereas the apparent binding constants and binding cooperativities for the derivatives are smaller than for the amylose‐I2/I− complex, the binding enthalpies deduced from the temperature dependence of Ka at θ = 0.5 appear to be the same for amylose and CM‐Amy. A viscometric titration of fully charged CM‐Amy with I2/I−, conducted at dialysis equilibrium between the CM‐Amy‐I2/I− solution and the polymer‐free solvent phase, disclosed a maximum in the plot of intrinsic viscosity ([η]) vs θ. The increase in [η] at small θ was interpreted as a reflection of polyelectrolyte expansion provoked by absorption of the negatively charged bound species; the subsequent decline in [η] is attributed to stabilization by I2/I− of compact helical sequences or to the formation at higher θ of intermolecular aggregates.