bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catalyses by polymer complexes. VII. Enhanced esterolytic reactivity of polymer‐coenzyme A, glutathione complexes
Authors: Shinkai Seiji , Kunitake Toyoki 
Published: May 2005

AbstractThe association of coenzyme A(CoASH) and glutathione (GSH) with the water‐soluble polymers and their esterolytic reactivities were evaluated through the reaction with p‐nitrophenyl acetate in the presence of cationic polymer micelles: partially laurylated poly(2‐ethyl‐1‐vinylimidazole) and poly(4‐vinylpyridine). The polymer micelles with high lauryl‐group content (more than 12 mol%) markedly accelerated the reaction at very low concentrations of the polymer. Other polymers with no or small lauryl‐group content only slightly enhanced the association and the reaction rate. From the rate‐polymer concentration profiles, the association constants (K) and the rate constants for thiol coenzymes bound to the polymer (k′a,bound) were determined: for polymers with more than 12 mol % lauryl‐group content, KCoASH = 1110–2270 M−1, KGSH = 170–503M−1, k′a,bound at pH 8.65 = 142–341M−1 sec−1. k′a,bound were 20–340 times larger than that observed in the absence of the polymer. The logarithm of k′a,bound was found to be correlated well with the polymer hydrophobicity, indicating that the hydrophobic environment of the polymer activated the bound thiol anions. On the other hand, the polymer hydrophobicity did not correlate with the association constant.
Electrostatic effects in divalent ion binding to tRNA
Authors: Leroy J. L. , Guéron M. 
Published: May 2005

AbstractThe binding of Mn2+ to yeast tRNAPhe at 25°C is measured by esr, and found to depend strongly on the concentration of monovalent cations, showing the importance of electrostatic effects. In low sodium (<15mM/l.), the affinity is high and the Scatchard plots are distinctly curved. In high sodium (>50mM/l.), the affinity and the curvature are reduced. In a limited range of sodium concentrations (15–30mM/l.), the folding of tRNA which is induced by the divalent ions results in cooperative binding, leading to upwards convexity of the Scatchard plot. An electrostatic model is developed, based on a single type of binding site which we take to be the phosphates, with a binding constant for Mn2+ in the range of that found for ApA, 10 l./M. We compute the change in the binding constant due to the electrostatic potential of the distant charges (other phosphates and counterions), using a single set of parameters for all sodium concentrations. The model predicts that the plots in low sodium are curved, and a good fit to the experimental results is obtained: it is therefore not legitimate or necessary to interpret these results in terms of two types of binding sites. In high salt, the model gives plots that are only slightly curved, corresponding to weaker electrostatic effects. This shows that a search for sites with a special binding mode should be done in high salt. The computed plots are in good agreement with the data, except for slight differences concerning the first bound ions, which give a possible indication in favor of special binding. Given the observation of one special site for Mg2+ at 4°C in high sodium [Stein, A. & Crothers, D. M. (1976) Biochemistry 15, 157–160] in E. coli tRNAfMet, we have measured the binding of Mn2+ at lower temperature. At 12°C, in both yeast tRNAPhe and E. coli tRNAfMet, the plots clearly indicate special binding. A site found in high sodium is on a very different footing from the four to six so‐called strong sites unduly derived from low‐salt binding plots.
Vibrational modes of A‐DNA, B‐DNA, and A‐RNA backbones: An application of a green‐function refinement procedure
Authors: Lu K. C. , Prohofsky E. W. , Van Zandt L. L. 
Published: May 2005

AbstractNormal vibrational analysis was carried out for DNA molecules in both A and B conformations as well as for A‐RNA. A simplified backbone model was examined and expanded to include the backbone phosphate‐group and the ribose ring. We applied the new force‐constant refinement procedure discussed in the preceeding paper [Van Zandt, L. L., Lu, K.‐C. & Prohofsky, E. W. (1977) Biopolymers, 16, 2481–90] to fit some observed frequencies in the Raman spectra for all three nucleic acids with the same set of force constants. The results indicate that the observed frequency shift can be attributed to the conformational change solely. We ignored the second‐order differences in force constants for the different geometries. The agreement between the observed and calculated frequencies derived from the final refined set of force constants is good and apparently justifies this assumption. Two modes previously assigned to the symmetric diester O‐P‐O stretch and the symmetric dioxy O‥P‥O stretch are actually fitted. They are mainly backbone phosphate‐group modes. The refined ribose‐ring force‐constants were transferred to the calculation of the vibrational spectrum of tetrahydrofuran. The overall agreement is again good. We discuss these calculations and the resulting normal modes. We also discuss the application of the Green‐function refinement scheme and several strategies adopted to bias the convergence of the procedure.
The use of light‐scattering and turbidity measurements to study the kinetics of extensively aggregating proteins: αs‐Casein
Authors: Parker T. G. , Dalgleish D. G. 
Published: May 2005

AbstractThe Ca2+‐induced association of αs‐casein has been studied using the methods of stopped‐flow light‐scattering and stopped‐flow turbidity. The methods used are described, and the analysis of the results to give plots of Mw against time in the time‐scale 0–15 sec is demonstrated. The validity of the method is discussed, and it is shown to be applicable to the association kinetics of aggregating proteins whose molecular‐weight averages lie between 107 and 109. The method was used to study the association of bovine αs‐casein in the presence of Ca2+, and results obtained are briefly discussed in terms of possible association mechanisms, and a mechanism for the overall reaction of αs‐casein with Ca2+, and the subsequent precipitation of the caseinate is proposed.
Calculation and use of protein‐derived conformation‐related spectra for the estimate of the secondary structure of proteins from their infrared spectra
Authors: Eckert K. , Grosse R. , Malur J. , Repke K. R. H. 
Published: May 2005

AbstractThis paper probes the calculation of conformation‐related basis spectra from infrared spectra (amide I′band) of reference proteins of known conformational composition and, with their aid, the computation of conformations from the amide I′ band of globular proteins using in both approaches a least‐squares, curve‐fitting computer program for the analysis of the spectra. The following results were obtained. The infrared basis spectra for the α‐helix conformation, the β‐(antiparallel‐chain pleated sheet) conformation and the ρ‐conformation were calculated and their physical reality was substantiated. The basis spectra were shown to be similar when the absorption contributions of the side chains of amino acids were either neglected or taken into account (uncorrected or corrected basis spectra). The mutual correlation of the basis spectra, quantified by the roots of the diagonal elements of the inverse matrix, was found to be low enough only for the β‐conformation to allow a statistically reliable estimate of the β‐conformation content of proteins. The comparison of the percentages of the β‐conformation derived from x‐ray structural analysis or calculated from infrared spectra showed the suitability of the basis spectra for the rough estimate of the β‐conformation percentages of proteins. The results were not significantly different when using the uncorrected or corrected basis spectra.
Investigation of the flexibility of DNA using transient electric birefringence
Authors: Hagerman Paul J. 
Published: May 2005

AbstractIn the preceding article, a Monte Carlo analysis was presented which provides a quantitative numerical relationship between the rotational diffusion coefficients, as measured by the decay of optical anisotropy following an electric field pulse, and the flexibility (persistence length) of short, wormlike chains. In the present article, the results of the foregoing analysis are applied to the observed rates of decay of birefringence for a series of sequenced DNA fragments ranging in size from 104 to 910 base pairs. Under the conditions used in this study, the DNA fragments exist as native, duplex molecules. Furthermore, conditions are defined in which the observed relaxation times are not dependent on DNA concentration, field strength, or the duration of the pulse. It is pointed out that the ionic atmosphere associated with a wormlike polyion does not exert any significant (direct) influence on the rotational diffusion of the polyion and, therefore, that the rotational relaxation times are a true measure of the configurations of the DNA molecules in solution. Moreover, excluded‐volume effects are shown not to be significant for the moderately short molecules employed in this study. The major conclusion of this study is that there is no strong ionic strength dependence of the persistence length for ionic strengths above 1 mM and that the persistence length, under conditions where electrostatic contributions are negligible, is approximately 500 Å. For ionic strengths significantly lower than 1 mM, electrostatic contributions to the stiffness of DNA become significant.
Rates of structural fluctuations of lysozyme in the range of thermal unfolding transition
Authors: Segawa Shin‐Ichi , Nakayama Masaaki , Sakane Masamichi 
Published: May 2005

AbstractThe hydrogen–deuterium exchange reaction for the tryptophan residues in lysozyme have been followed in 4.5M LiBr at pH 7.2 in the temperature range of the unfolding transition by measuring the transmittance change at 293 nm. The exchange reaction proceeded in three phases at low temperature for native protein. The first and the second phases were ascribed to the H‐D exchange reactions of three relatively exposed tryptophan residues on the molecular surface. The third phase corresponded to the H‐D exchange reaction of the three tryptophan residues buried in the interior of the molecule. The H‐D exchange reaction proceeded in two phases near the melting temperature and in a single phase at high temperature, where almost all molecules are unfolded. The H‐D exchange of three tryptophan residues buried in folded molecules was caused by fluctuation between the folded and unfolded structure of the protein molecule. The rates of such a fluctuation were determined from the rates of the exchange reaction at various temperatures. These rates agreed very well with those determined from the temperature‐jump method. This means that a protein molecule in solution fluctuates between the N‐ and D‐states at every temperature within the transition region, where the N‐form is the tightly folded native structure and the D‐form the randomly coiled chain. From measurements of thermal unfolding of ester‐108‐lysozyme and the binding constant of (NAG)3 to ester‐108‐lysozyme, it was found that almost all cross‐linked molecules are in the folded state near 50°C and pH 7.2 in 4.5M LiBr, where intact molecules are unfolded. We also studied the H‐D exchange reaction of ester‐108‐lysozyme. In the temperature region of 43–50°C, about 70% of the exchangeable tryptophan residues of ester‐108‐lysozyme were exchanged within 1 s immediately after the mixing of D2O, in spite of the fact that almost all molecules are in the folded state. This was considered the premelting of the surface of a corss‐linked molecule.
Totally synthetic crystalline ribonuclease A
Authors: Yajima Haruaki , Fujii Nobutaka 
Published: May 2005

AbstractImproved chemical synthesis of bovine pancreatic ribonuclease (RNase) A was achieved by applying a new deprotecting procedure with trifluoromethanesulfonic acid–thioanisole in combination with a modified air‐oxidation procedure with glutathione for the disulfide formation. After purifications by affinity chromatography, followed by ion‐exchange chromatography, a protein with the full enzymatic activity was obtained and subsequently crystallized from aqueous ethanol according to Kunitz. A totally synthetic enzyme with full RNase A activity was thus obtained in a crystalline form for the first time.
On the location of β‐turns
Authors: Kopple Kenneth D. 
Published: May 2005

Abstractβ‐Turns are a common feature of cyclic peptides, but judging from recent x‐ray and solution studies of cyclic hexapeptides it is not always possible to predict in advance the type of turn and the position of the turns in the sequence. Two or more backbone conformations containing β‐turns may be of comparable energy and in rapid solvent‐ and temperature‐dependent equilibrium in solution. The use of differential relaxation effects produced by a nitroxyl radical to locate β‐turns with only minor perturbation of such equilibria is noted. Examination of the effect of a nitroxyl on the N‐H resonances of the decapeptide hormone luteinizing hormone releasing hormone supports a dominant conformation with a β‐turn at Gly6‐Leu7. Although this turn is probably part of the biologically active conformation, it is not obvious in the more active [D‐Ala6] analog.
Nmr analyses of conformations of linear peptides in solution
Authors: Miyazawa Tatsuo , Higashijima Tsutomu 
Published: May 2005

AbstractImportant aspects in detailed nmr analyses of the conformations of linear peptides are discussed using enkephalin and the α‐mating factor of Saccharomyces cerevisiae as examples. The cationic, dipolar, and anionic forms in dimethyl sulfoxide solution may be identified by ir analyses. Because of the electrostatic interaction between the N‐ and C‐terminal groups, the dipolar form of enkephalin takes the folded conformation, as well as extended conformation(s), in dimethyl sulfoxide solution. Such conformational equilibrium is responsible for anomalous temperature dependences and solvent‐composition dependences of the amide and Cα proton chemical shifts. Active analogs, enkephalinamide and enkephalinol, take extended conformation(s) in solution. These opioid peptides probably take a specific active conformation upon binding with a receptor. For the α‐mating factor and active peptide analogs in aqueous solution, a folded conformation with two βturn structures is responsible for the biological activity.
Conformation and activity in angiotensin II peptides
Authors: Fermandjian Serge , Piriou François , Sakarellos Constantin , Lintner Karl , Khosla Mahesh C. , Smeby Robert R. , Bumpus F. Merlin 
Published: May 2005

AbstractAngiotensin II and its competitive inhibitor [Sar1, Ile8]‐angiotensin II, as well as several analogs of these two compounds specifically chosen for their well‐defined pharmacological properties, were studied by circular dichroism and nuclear magnetic resonance methods at various pH values in aqueous solution and in d6‐dimethylsulfoxide. The results were compared with their biological activities. This allowed us to establish relationships between conformation and pressor activity, explaining most of the properties of angiotensin II, its inhibitor, and the analogs successively substituted in positions 3 and 5.
Excluded volume effects on the rate of renaturation of DNA
Authors: Wetmur James G. 
Published: May 2005

AbstractThe rate of renaturation of T2 DNA hits been investigated by using complementary DNA strands of different length. The length of the shorter strand ranged from 0.02 to 1.0 times the length of the longer strand. An excluded volume theory is developed to include this type of reaction as well as the DNA–RNA hybridization reaction. Experimental and theoretical rates of renaturation of DNA are found to be in agreement. For the cases studied, the rate was never greater than twice that observed for short strands of the same length renaturing with themselves. The products of renaturation reactions are also considered.
Calorimetric measurement of enthalpy change in the isothermal helix–coil transition of poly‐L‐lysine in aqueous solution
Authors: Chou Peter Y. , Scheraga Harold A. 
Published: May 2005

AbstractThe heat ΔH° for converting an uncharged lysine residue from a coil to an α‐helical state in poly‐L‐lysine in 0.1N KCl has been determined calorimetrically to be −1200 cal/mole at both 15°C and 25°C. Essentially the same value has been obtained for the conversion of an uncharged residue from a coil to a β‐pleated sheet state. Titration data provided information about the state of charge of the polymer in the calorimetric experiments, and optical rotatory dispersion data about its conformation. In order to compute ΔH°, the observed Calorimetric heat was corrected for the heat of breaking the sample cell, the heal of dilution of HCl, the heat of neutralization of OH− ion, and the heat of ionization of the ε‐amino group in the random coil. The latter was obtained from similar Calorimetric measurements on poly‐D,L‐lysine, which was shown to be a good model for the random coil form of poly‐L‐lysine. The measured transition heat was ∼0.7 cal., which is only 7% of the total heat liberated when a 40 ml solution of 0.25% w/v poly‐L‐lysine is brought, from pH 11 to pH 7; nevertheless it could be determined with a precision of ±8%. The conformation of poly‐L‐lysine at pH 11 appears to be completely helical at 15°C, but a mixture of 90% α‐helix, 5% β form, and 5% coil at 25°C. Since ΔH° ∼ 0 for the α ⇌ β conversion, the polymer behaves like one of 95% α‐helix and 5% coil in the calorimeter at 25°C. At neutral pH, poly‐L‐lysine is an extended coil, like poly‐D,L‐lysine.
Infrared spectra of transfer ribonucleic acids. III. Fragments of formyl‐methionine tRNA from Escherichia Coli
Authors: Katsura Tatsuo , Morikawa Kosuke , Tsuboi Masamichi , Kyogoku Yoshimasa , Seno Takeshi , Nishimura Susumu 
Published: May 2005

AbstractFour fragments (named K, L, M, and N) of Escherichia coli formylmethionine transfer RNA have been prepared by a partial digestion with ribonuclease T1 followed by a chromatographic separation with a DEAE–Sphadex (A‐25) column and then a DEAE–cellulose column. The fragment K is the anticodon fragment with 19 nucleotides (previously reported). L is a fragment with 57 nucleotides involving the 3′‐terminal (CCA). M is a fragment with 51 nucleotides which is equal to L except that M lacks 6 nucleotides at the 3′‐terminal. N is a fragment with 20 nucleotides which involved the 5′‐terminal and corresponds to the complementary half to L. The infrared absorption spectrum has been observed of each of these fragments and two equimolar mixtures L + N and M + N in D2O solutions at several temperatures. The results indicate that at 37°C, K has about 4 hydrogen‐bonded base‐pairs, L about 11, and M about 13. On the other hand, fragment N is found to have only three weak G‐C pairs. For both L + N and M + N, 15–17 strong base pairs are found. The observations give direct support to the clover‐leaf structure and at the same time provide information on the stability of each of the four arms in the structure.
Infrared investigation of poly‐L‐histidine structure dependent on protonation
Authors: Muehlinghaus J. , Zundel G. 
Published: May 2005

AbstractPoly‐L‐histidine (PLH) films at different degrees of protonation were produced mid subjected to infrared spectroscopic investigation (range 4000‐650 cm−1). In addition, the N‐deuterated film spectra were plotted. The amide II and III bands show that the peptide group is present in the trans form. The amide I and II bands show that at 0% and 50% protonation the PLH occurs as an α‐helix and at 100% protonation as a random coil with some ranges in β structure. At 0% and 50% protonation, no hydration water is bound to the backbone. At 0% protonation all NH groups are linked to each other or to water molecules via hydrogen bonds. At 50% protonation NH+ċN bonds form between the imidazole rings. These protons are present in continuous energy level distribution. Such bonds with tunneling protons are extremely polarizable and between these bonds may act proton dispersion forces. The Cl− ions are bonded to the NH groups of the imidazole groups. The hydration water is bonded to the Cl−− ions and to the NH groups. At 100% protonation, hydration water is bonded also to the CO groups of the backbone. The NH groups of the backbone, like those of the rings, endeavor especially in the dry state to bond to the Cl− ions. This leads to a strong steric constraint of the random coil.
X‐Ray diffraction by amorphous polymers: Models for biological systems
Authors: Balyuzi H. H. M. , Burge R. E. 
Published: May 2005

AbstractThe x‐ray scattering method has been used to investigate the structure in two amorphous crosslinked polymers which are regarded as test systems to establish the power of the method as applied to amorphous biologically significant polymer associations. It is shown that structural information can be determined about the rigid regions within the polymer systems, i.e., those regions held in particular configuration by stereochemical effects. Models of such regions extending over distances with dimensions of ca 18 Å are proposed for an Araldite polymer and for crosslinked poly (methyl/butyl methacrylate). The results allow some general statements about the usefulness and limitations of the amorphous x‐ray method.
Optical Rotatory Dispersion of Polypeptides in the Near‐Infrared Region
Authors: Chirgadze Yu. N. , Venyaminov S. Yu. , Lobachev V. M. 
Published: May 2005

AbstractFor the first time ORD measurements in the near‐infrared region from 0.7 to 2.0 μ for well‐known polypeptides, namely, poly(γ‐benzyl L‐glutamate), poly(L‐glutamic acid), poly‐L‐lysine·HCl, poly‐S‐carbobenzoxymethyl‐L‐cysteine, and Bombyx mori silk fibroin, were carried out. It was found that the value of the optical activity infrared term, which is proportional to the sum of rotational strengths of vibrational transitions, depends on polypeptide conformation. The optical activity infrared term value is equal to zero for the random‐coil conformation, it is small but exceeds the measurement error for the α‐helical state, and finally, for the β conformation it is an order of magnitude higher than for the α‐helical state. The obtained results permit one to hope that on the basis of ORD measurement in the near‐infrared region it will be possible to suggest a method of determining the β‐form content in polypeptides and proteins
Sedimentation analysis of the ionic strength dependence of the tertiary structure of native DNA in solution
Authors: Triebel H. , Reinert K. E. 
Published: May 2005

AbstractSedimentation experiments have been performed on a polydisperse bacterial DNA sample over a wide range of ionic strength (8 × 10−4M to 2M Na+), at very low DNA concentrations (5–30 μg ml). True sedimentation constant distributions were obtained by careful analysis of experimental data and extrapolation to infinite dilution. In order to give a quantitative description of macromolecular shape, the changes of the exponent as in the general equation, s0 = ksM, have been determined by comparing sedimentation constant distributions obtained at different ionic strengths. as has been found to vary from 0.419 at 2M Na+ to 0.200 at 8 × 10−4M Na+. As well as the decrease of the mean sedimentation constant, this result indicates a pronounced expansion of DNA molecules with decreasing ionic strength. A discussion of the distinct mechanism responsible for the expansion behavior of DNA is given. Furthermore, the dependence of the Mandelkern‐Flory parameter β on ionic strength has been calculated by combining the s0 data with the corresponding [η] values of the sample.
Tautomerism in cytidine
Authors: Johnson W. C. , Vipond P. M. , Girod J. C. 
Published: May 2005

AbstractThe large change in the electronic absorption spectrum of cytidine on going from an aqueous to an aprotic medium is attributed to the existence of a hydrogen bonded solvent‐solute complex in solvents capable of donating a proton. The spectrum of cytidine in a variety of solvents and the spectra of a number of nontautomerising model compounds are presented. The tautomerisin of cytidine and its biological implications are discussed.