bluuebunny/crossref_metadata_2025_split huggingface dataset:
The structure of triple‐stranded G·2C polynucleotide helices
Authors: Hattori Masao , Frazier Joe , Miles H. Todd 
Published: December 2004

AbstractThe thermal stability of a new polynucleotide complex has been used to establish the hydrogen‐bonding structure of three‐stranded C‐G·CH+ helices. In the Hoogsteen structure, the 8NH2 group of 8NH2GMP can form a third hydrogen bond to the CH+ strand, but in the alternative structure, the 8NH2 group can form no interbase hydrogen bonds. For the new complex, 8NH2GMP·2 poly(C), a transition temperature of 80°C is observed under conditions in which the corresponding complex formed with 5′‐GMP has a Tm of 20°C. We conclude from this 60° elevation of transition temperature that a third hydrogen bond is formed by the 8NH2 group and that the structure must have Hoogsteen bonding. In order to be compatible with this structure in regular helices formed by U,C copolymers, A·2U bonding would also have to have a Hoogsteen structure.
Intermediates in the strand‐separation transition of T7 DNA
Authors: Wensley C. Glen , Record M. Thomas 
Published: December 2004

AbstractSedimentation velocity runs as a function of temperature in the region of the alkaline helix‐coil transition have enabled us to demonstrate the existence of stable two‐stranded intermediates in the strand‐separation process for T7 DNA. The strand‐separation transition under these conditions has an intrinsic breadth of ∼1°C, and within this temperature range (Tm + 2°C < T < Tm + 3°C) the intermediate forms are progressively converted (as a function of temperature) to single‐stranded DNA. Parallel characterizations of the strand‐separation transition by viscosity and absorbance–renaturation studies in the alkaline solvent are entirely consistent with the sedimentation experiments. Comparison of the experimental mean sedimentation coefficient of the intermediate forms with theoretical predictions for branched structures suggests that in these molecules the two strands are connected at a single point, not centrally located with respect to the ends of the molecule.
Thermal properties of collagen in helical and random coiled states in the temperature range from 4° to 300°K
Authors: Andronikashvili E. L. , Mrevlishvili G. M. , Sh. Japaridze G. , Sokhadze V. M. , Kvavadze K. A. 
Published: December 2004

AbstractThe low‐temperature heat capacity of collagen (in the hydrated and dehydrated states) and the large entropy of collagen in the coiled state relative to the same protein in the helical state were investigated. The heat capacity for collagen in the solid state in the temperature range 4°–50° K changes proportionally to the square of temperature (Cp ∼ T2). Above 50°K there is a linear dependence (Cp ∼ T). The differences in the character of temperature dependence of heat capacity for the hydrated and dehydrated collagen show the importance of the specific interaction of water molecules with polypeptide chains of this protein. The peculiarities of the temperature dependence of the heat capacity difference (ΔCp) of hydrated denatured (random coiled) and hydrated native (helical) collagen are observed at 15°, 120°, and 240°K. These differences are caused by the varying degree of ordering of the hydrate water molecules in native and denatured collagen macromolecules. At all temperatures (4°–300°K) the entropy of the random coiled state is higher than that of collagen in the native state and at 298°K ΔS = ∫ (ΔCp/T)dT = 0.8 cal/100 g °K.
Electronic energy transfer between tyrosine and tryptophan in the peptides trp‐(pro)n‐Tyr
Authors: Chiu H. C. , Bersohn R. 
Published: December 2004

AbstractA series of peptides, Trp‐(Pro)n‐Tyr, n = 0,…,5 were synthesized. Details of the synthetic method using the Merrifield method are given. The initial objective was to determine the characteristic distance R0 for energy transfer from tyrosine to tryptophan. This objective became submerged in the question of the structure of the chain of prolyl spacers. The efficiency of the energy transfer diminishes as the number of intervening prolines increases. Quantitatively the fit is much better if we assume that the peptides have a polyproline I structure (cis) than if we assume a trans polyproline II structure. Proton nmr spectra on the other hand suggest that the n = 1,3,5 peptides are mixtures of rotamers. Our conclusions are similar to those of previous workers, i.e., that in water there is a transition from a mixture of structures for small n to an all‐trans structure at some n > 5. This means that in water, at least, proline is a dubious spacer for energy‐transfer studies.
Influence of local interactions on protein structure. I. Conformational energy studies of N‐acetyl‐N′‐methylamides of pro‐X and X‐pro dipeptides
Authors: Zimmerman S. Scott , Scheraga Harold A. 
Published: December 2004

AbstractConformational energy calculations using an Empirical Conformational Energy Program for Peptides (ECEPP) were carried out on the N‐acetyl‐N′‐methylamides of Pro‐X, where X = Ala, Asn, Asp, Gly, Leu, Phe, Ser, and Val, and of X‐Pro, where X = Ala, Asn, Gly, and Pro. The conformational energy was minimized from starting conformations which included all combinations of low‐energy single‐residue minima and several standard bend structures. It was found that almost all resulting minima are combinations of low‐energy single‐residue minima, suggesting that intra residue interactions predominate in determining conformation. The calculations also indicate, however, that inter residue interactions can be important. In addition, librational entropy was found to influence the relative stabilities of some minima. Because of the existence of 10–100 low‐energy minima for each dipeptide, the normalized statistical weight of an individual minimum rarely exceeds 0.3, suggesting that these dipeptides have considerable conformational flexibility and exist as statistical ensembles of low‐energy structures. The propensity of each dipeptide to form bend conformations was calculated, and the results were compared with available experimental data. It was found that bends are favored in Pro‐X dipeptides because ϕPro is fixed by the pyrrolidine ring in a conformation which is frequently found in bends, but that bends are not favored in X‐Pro dipeptides because interactions between the X residue and the pyrrolidine ring restrict the X residue to conformations which are not usually found in bends.
A nuclear magnetic resonance study of the helix–coil transition of poly(L‐glutamic acid)
Authors: Lader H. J. , Komoroski R. A. , Mandelkern L. 
Published: December 2004

AbstractThere have been many reports that the nuclear magnetic resonance (nmr) spectra of a large number of polypeptides exhibit peak doubling of the α‐carbon and the α‐carbon proton in the helix–coil transition region. One apparent exception to this generalization has been polypeptides with ionizable side chains, where the helix–coil transition is induced by changes in pH in aqueous solution. Because it is important to establish the proper theoretical reason for the peak doubling and its relation to the rate of conformational change of amino acid residues, we have reexamined the proton and carbon‐13 nmr spectra, at high field, for two polydisperse samples of poly(L‐glutamic acid). Doubling of the α‐carbon proton resonance as well as those of the α‐ and β‐carbon, and backbone carbonyl are observed for a low‐molecular‐weight sample (DP = 54), while a higher molecular weight sample (DP = 309), exhibits only single resonances. Thus, polydispersity by itself is not sufficient to observe peak doubling; low‐molecular weight is also required.
Architecture of chitin gel as examined by scanning electron microscopy
Authors: Hirano Shigehiro , Yamaguchi Ryuji , Matsuda Noriaki 
Published: December 2004

AbstractAn architecture of the solid phase of chitin gel was examined by scanning electron microscopy. The ultrastructure of the xerogel was microporous with parallel channels surrounded with membranous walls. The pore shapes at cross section were polyhedral with three walls at the junctions. The pore was 30–50 μm in diameter and 80–300 μm in length, and the thickness of the walls was less than 1.5 μm. The gel is considered to be a polyphasic gel, consisting of small droplets of water held up in these pores.
The concentration dependence of transport processes: A general description applicable to the sedimentation, translational diffusion, and viscosity coefficients of macromolecular solutes
Authors: Rowe A. J. 
Published: December 2004

AbstractThe transport coefficients of macromolecular solutes are normally extrapolated to “infinite dilution” to remove the effects of concentration‐dependence terms, for which no satisfactory general treatment has been available. It is shown that a simple general treatment for the concentration‐dependence effect can be derived, applicable to limiting concentrations in the absence of charge effects or other forms of specific interactions between the solute particles. The relationships derived are of considerable practical significance for the characterization of the size and conformation of natural and synthetic polymers.
Scattering correction to the absorbance, wavelength dependence of the refractive index increment, and molecular weight of the bovine liver glutamate dehydrogenase oligomer and subunits
Authors: Eisenberg Henryk , Josephs Robert , Reisler Emil , Schellman John A. 
Published: December 2004

AbstractThe wavelength dependence of the refractive index increments of bovine serum albumin and bovine liver glutamate dehydrogenase solutions was determined in the range 650–300 nm. It was shown, by measuring the extinction coefficients of glutamate dehydrogenase under conditions of widely differing molecular weights, that a significant scattering correction need not be applied to correct extinction measurements in the absorbtion band. The molecular weight of glutamate dehydrogenase oligomer determined by light scattering and sedimentation equilibrium agrees with the value calculated from the primary structure, if a recently reported value of the extinction coefficient is used.
Light‐scattering and depolarization in biopolymers: Distinction between flexible chain models
Authors: Shkorbatov A. G. , Verkin B. I. , Kulik I. O. 
Published: December 2004

AbstractThe general formulas describing the low‐angular dependence of polarized (Vv) and depolarized (Hv) light‐scattering intensity by a chain macromolecule of arbitrary form with anisotropic polarizability are derived. It is shown that the value dHv/dtHvo (where t = [〈R2〉S/L]2, S being the scattering vector) is an indication of the chain‐flexibility mechanism. This permits one to distinguish between the models of a wormlike chain, regular zigzag, or statistical zigzag. The results of numerical calculations useful for the interpretation of experimental data are presented.
The analysis of circular dichroism spectra of natural DNAs using spectral components from synthetic DNAs
Authors: Gray Donald M. , Hamilton Frederick D. , Vaughan Marilyn R. 
Published: December 2004

AbstractWe have tested 21 different basis sets of synthetic DNA circular dichroism spectra and have slected one for use in spectral analyses of natural DNAs. This “standard” set consists of spectra of eight polymers: poly[d(A‐A‐T)·d(A‐T‐T)], poly[d(A‐G‐G)·d(C‐C‐T)], poly[d(A‐T)·d(A‐T)], poly[d(G‐C)·d(G‐C)], poly[d(A‐G)·d(C‐T)], poly[d(A‐C)·d(G‐T)], poly[d(A‐T‐C)·d(G‐A‐T)], and poly[d(A‐G‐C)·d(G‐C‐T)]. This basis set, applied according to the first‐neighbor polymer procedure of Gray and Tinoco, allows a more uniformly accurate spectral analysis of six natural complex DNAs and eight (A+T)‐rich satellite DNAs for base composition and first‐neighbor frequencies than was previously possible. We find that spectra of poly[d(A)·d(T)] and/or poly[d(A‐C‐T‐)·d(A‐G‐T)] are not generally required for good analysis results but we show in this and the following paper that these spectra are needed for the most accurate analyses of some satellite DNAs.
Cooligopeptides containing aromatic residues spaced by glycyl residues. IX. Fluorescence properties of tryptophan‐containing peptides
Authors: Wiget Peter , Luisi Pier Luigi 
Published: December 2004

AbstractThe fluorescence properties of several cooligopeptides of glycine, phenylalanine, and tryptophan, containing one or two aromatic residues, are investigated. In particular, a detailed analysis is made of the influence of pH upon the quantum yield and the position of the emission maximum (λmax) in H‐Trp‐Trp‐OH, H‐Trp‐Gly‐OH, H‐Gly‐Trp‐OH, H‐Gly‐Trp‐Gly‐OH, H‐Trp‐Trp‐OH, H‐Trp‐Trp‐Gly‐OH, H‐Gly‐Trp‐Trp‐OH, H‐Phe‐Trp‐OH, H‐Phe‐Trp‐Gly‐OH, H‐Gly‐Phe‐Trp‐OH, and H‐Gly‐X‐(Gly)n‐Trp‐Gly‐OH, with X = Phe or Trp, and n = 0,1,2. It is shown that raising the pH from ca. 2 to 11 results in a red shift of λmax, and an increase in the quantum yield. These changes, mostly structure dependent, are in most cases attributable to electronic perturbations acting directly upon the λmax of the fluorophore(s) and upon the quenching efficiency of the free amino and carbonyl groups. For the compounds having two adjacent tryptophyl residues, it is shown that the two fluorophores do not appear to have the same emission properties and the quantum yield is lower than expected. The causes of this behavior are discussed in terms of conformational effects, stacking interactions, and radiationless energy transfer. Finally, an attempt is made to correlate fluorescence data with previous circular dichroism data which had indicated the occurrence of a conformationally rigid structure for some of the compounds having two adjacent aromatic residues.
Conformational studies on Cu(II) polycomplexes of pyridoxal Schiff bases of polypeptides
Authors: Dentini M. , Savino M. , De Santis P. , Verdini A. S. 
Published: December 2004

AbstractStructures of Cu(II) complexes of pyridoxal Schiff bases with poly(L‐lysine), poly(L‐ornithine), and poly(L‐α,γ‐diaminobutyric acid) were investigated by absorption spectra, CD, and conformational analysis.Although the polypeptides retain their typical right‐handed α‐helical conformation, opposite Cotton effects were found for the poly(L‐lysine) and poly(L‐ornithine) polycomplexes in the whole range of wavelengths from 600 to 250 nm. As in the analogous derivatives of salicyladehyde, this effect seems to be due to a stereospecific binding of the square planar Cu(II)‐bis‐pyridoxylideneimine group to the α‐helical matrix. Circular dichroism spectrum of poly(L‐α,γ‐diaminobutyric acid) polycomplex is similar to that found for poly(L‐lysine) derivative, but indicates large tetrahedral distortion of the square‐planar coordination of copper ion.
Vectorial interpretation of spectra for the study of associations
Authors: Marck Ch. , Schneider Ch. , Brehamet L. 
Published: December 2004

AbstractIf one considers CD spectra as vectors, then a CD spectrum may be treated as a single parameter, every wavelength entering with the same weight. The representation of a set of spectra as a vector space and the problem of the linear independence of the concentrations are discussed. Three examples of vectorial interpretation are given: determination of the number of independent molecular species; determination of the stoichiometry of a complex; and graphical representation of the overall variation of a spectrum as a function of an external parameter.
Theory of ligand binding to heterogeneous receptor populations: Characterization of the free‐energy distribution function
Authors: Thakur Ajit K. , Delisi Charles 
Published: December 2004

AbstractWe present a method for characterizing the free‐energy and affinity distributions of a heterogeneous population of molecules interacting with a homogeneous population of ligands, by driving expressions for the moments as functions of experimental binding curve characteristics, and then constructing the distribution as an expansion over a Gaussian basis set. Although the method provides the complete distribution in principle, in practice it is restricted by experimental noise, inaccuracies in data fitting, and the severity with which the distribution deviates from a Gaussian. Limitations imposed by experimental inaccuracies and the requirement of an appropriate analytic function for data fitting were evaluated by Monte Carlo simulations of binding experiments with various degrees of error in the data. Thus a distribution was assumed, binding curves with random errors were generated, and the technique was applied in order to determine the extent to which the characteristics of the assumed distribution could be recovered. Typical inaccuracies in the first two moments fell within experimental error, whereas inaccuracies in the third and fourth were generally larger than standard deviations in the data. The accuracy of these higher‐order moments was invarient for experimental errors ranging from 2 to 10% and may thus be limited, within this range, primarily by the curve fitting procedure. The other aspect of the problem, accurate inference of the distribution, is limited in part by inaccuracies in the moments but more importantly by the extent to which the distribution deviates from a Gaussian. The extensive statistical literature on the problem of inference enables the delineation of specific criteria for estimating the efficiency of construction, as well as for deciding whether certain features of the inferred distribution, such as bimodality, are artifacts of the procedure. In spite of the limitations of the method, the results indicate that the mean and standard deviation are obtainable with greater accuracy than by a Sipsian analysis. This difference is particularly important when the distribution is narrow and width detection is beyond the sensitivity of the Sips plot. The method should be more accurate than the latter as an assay for homogeneity as well as for characterizing the moments, though equally easy to apply.
Lysinonorleucine cross‐link formation in alpha amino heptenoic acid‐substituted peptide derivatives
Authors: Karwoski Gene , Galione Michael , Starcher Barry 
Published: December 2004

AbstractStudies on the cross‐linking of a tripeptide (t‐butyloxycarbonyl‐L‐alanyl‐D,L‐2‐amino‐6‐heptenoyl‐L‐alanine methyl ester) have shown that it is possible to form specific cross‐links in good yields through Schiff base formation of the ε amino group of lysine. The heptenoic acid residue has been ozonized to an aldehyde and condensed with the ε amino of lysine in the compounds alpha‐t‐butyloxycarbonyl‐L‐alanyl‐L‐lysine methyl ester and alpha‐t‐butyloxycarbonyl‐L‐lysine methyl ester to form the cross‐link, lysinonorleucine. This compound has been stabilized by reduction with sodium borohydride and quantitated on the amino acid analyzer. This technique converts from 60 to 98% of the available aldehyde to lysinonorleucine.
The flow linear dichroism of DNA: Comparison with the bead‐spring theory
Authors: Wilson Robert W. , Schellman John A. 
Published: December 2004

AbstractThe flow linear dichroism if T7 bacteriophage DNA has been obtained as a function of velocity gradient in neutral aqueous solutions containing 0.15M Na+ or K+. The data are compared with the hydrodynamic bead‐spring theory of Rouse and Zimm using currently available spectroscopy, structural, and hydrodynamic parameters. Good agreement between theoretical and experimental isocline angle behavior is found. The magnitude of the measured linear dichroism is not in exact agreement with theory when presently accepted stiffness and optical parameters are used. Agreement is improved either by assuming a shorter persistence length or a less negative value for the limiting dichroism of DNA.
Solvent denaturation
Authors: Schellman John A. 
Published: December 2004

AbstractSolvent denaturation is developed along thermodynamic lines rather than from multiple‐binding theory. Almost all the relations derivable from site‐binding theory have their counterparts in the thermodynamic formulation showing that the details of binding models may be sufficient but are not necessary for the general description of solvent denaturation. Equations are derived for the effect of denaturant concentration on stability at constant temperature and on tm. It is recommended that the thermodynamic treatment be used instead of binding models unless stoichiometric interactions are demonstrable experimentally.
Competition between native and monoacetylated polymyxin for charged adsorption sites
Authors: Miller I. R. , Teuber M. , Accad Y. 
Published: December 2004

AbstractThe native antibiotic polymyxin B, carrying five positive charges, displaces the monoacetylated on from its adsorbed state at the interface between negatively charged lipid layers ans water. A simulation model for asdorption, governed by electrostatic forces, is presented. The model adequently representes the competitive adsorption kinetics and equilibria.
Effects of solvent viscosity and different guanidine salts on the kinetics of ribonuclease A chain folding
Authors: Tsong Tian Y. , Baldwin Robert L. 
Published: December 2004

AbstractThe kinetics of folding of the two forms of unfolded ribonuclease A have been measured as a function of solvent viscosity by adding either glycerol or sucrose. The aim is to find out if either reaction is rate limited by segmental motion whose rate depends on external friction. The fast folding reaction (U2 ⇄ N) is known to be the direct folding process, and the slow folding reaction (U1 ⇌ N) is known to be rate limited by an interconversion between two forms (U1 ⇌ U2) which are present after unfolding in strongly denaturing conditions. No dependence on solvent viscosity is found, either for the direct folding reaction or for the interconversion reaction. Each folding reaction has also been tested to see if its rate depends on the concentration of one or more partly folded intermediates, by adding denaturants destabilize any partly folded structures. Different guanidine salts are used as denaturants to vary the denaturing effectiveness of the salt while holding the guanidinium ion concentration constant. The rates both of the direct folding reaction and of the interconversion reaction decrease in relation to the denaturing effectiveness of the salt. However, there is a basic difference between the responses of the fast and slow folding reactions to low concentrations of denaturants. Although each folding reaction produces native protein, there is an 800‐fold decrease in the rate of the fast folding reaction in 1M guanidine thiocyanate and only a 13‐fold decrease in the rate of the slow folding reaction. This is consistent with the fast reaction being the direct folding process and the slow reaction being rate limited by the initial conversion of the slowrefolding to the fast‐refolding form. Both the lack of viscosity dependence and the effects of denaturants indicate that the formation of structure is rate limiting in the direct folding reaction, U2 ⇌ N. The failure to find a viscosity dependence for the interconversion reaction, U1 ⇌ U2, indicates that in this reaction also friction‐limited segmental motion is not the rate‐limiting process. Since the U1 ⇌ U2 interconversion still occurs when the polypeptide chain is completely unfolded, the surprising result is that its rate in refolding conditions depends significantly on a reaction intermediate which is “denatured” by guanidine salts.