bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theory of H1‐mediated control of higher orders of structure in chromatin
Authors: Manning Gerald S. 
Published: December 2004

AbstractIt is known that the lysine‐rich histone H1 induces both higher orders of folding in chromatin and donut shapes in DNA. However, these phenomena occur only on the high‐salt side of a narrow transition range located at about 0.02M salt. Previous theoretical analyses of the ionic‐strength dependencies of DNA persistence length and denaturation rate have provided the information that the basic rigid‐rod unit in high‐molecular‐weight DNA is a segment 60 base pairs in length and that if the phosphate charge is neutralized, this segment will spontaneously adopt a bent conformation with radius of curvature 170 Å. On the assumption that an H1 molecule does not completely neutralize the DNA charge in its vicinity, the theory has been extended here to determine the onset of spontaneous bending as a function of salt concentration and extent of phosphate neutralization. A salt transition of the kind observed has been found for the realistic value of 82% charge neutralization, with the actual value likely to be in the neighborhood of 90%, as suggested by the measurements of Wilson and Bloomfield.1 It is recalled that the spacer DNA length in chromatin is of about the same length as the DNA rigid‐rod unit. If binding of H1 to the spacer induces, as predicted, a bent conformation of radius about 170 Å, then the observed value of about 150 Å for the outer radius of the solenoid presently thought to be the basic mode of folding for a nucleosome chain can be understood as a reflection of the inherent maximum curvature of DNA in aqueous salt solution.
Flexibility of the pyranose ring in α‐ and β‐D‐glucoses
Authors: Joshi N. V. , Rao V. S. R. 
Published: December 2004

AbstractConformational energies of α‐ and β‐D‐glucopyranoses were computed by varying all the ring bond angles and torsional angles using semiempirical potential functions. Solvent accessibility calculations were also performed to obtain a measure of solvent interaction.The results indicate that the 4C1 (D) chair is the most favored conformation, both by potential energy and solvent accessibility criteria. The 4C1 (D) chair conformation is also found to be somewhat flexible, being able to accommodate variations up to 10° in the ring torsional angles without appreciable change in energy. Observed solid‐state conformations of these sugars and their derivatives lie in the minimum‐energy region, suggesting that the substituents and crystal field forces play a minor role in influencing the pyranose ring conformation. Theory also predicts the variations in the ring torsional angles, i.e., CCCC < CCCO < CCOC, in agreement with the experimental results. The boat and twist‐boat conformations are found to be at least 5 kcal mol−1 higher in energy compared to the 4C1 (D) chair, suggesting that these forms are unlikely to be present in a polysaccharide chain. The 1C4 (D) chair has energy intermediate between that of the 4C1 (D) chair and that of the twist‐boat conformation. The calculated energy barrier between 4C1 (D) and 1C4 (D) conformations is high—about 11 kcal mol−1.
Relaxational contributions to protein compressibility from ultrasonic data
Authors: Sarvazyan A. P. , Hemmes Paul 
Published: December 2004

AbstractThe ultrasonic absorption spectra of proteins in solution generally show relaxational behaviour. There will be a corresponding dispersion of sound velocities accompanying each relaxation. The compressibility of the protein as measured by sound velocity techniques will therefore include a relaxational contribution. We have evaluated this contribution for a number of proteins and found that in some cases the relaxational contribution is a significant fraction of the total compressibility. The relaxational contribution will be large only if the molecule has a large number of degrees of freedom with low force constants. However, such motions are likely to be those involved in the biological functioning of the molecule. Care is needed in interpreting the relaxation spectrum since proton transfer processes give large apparent relaxational compressibilities.
Temperature dependence of macromolecular interactions in dilute and concentrated hemoglobin solutions
Authors: Veldkamp Wilfrid B. , Votano Joseph R. 
Published: December 2004

AbstractWe studied the temperature‐dependent effects of intramolecular interactions on the mutual diffusion coefficient of normal human oxygenated hemoglobin in salt solution. We used photon correlation spectroscopy to observe this temperature dependence of the mutual diffusion coefficient of two protein concentrations (1.25 and 17.0 g %) between 13 and 37°C. This coefficient was our probe for monitoring temperature‐dependent structural changes of hydrated hemoglobin in solution. Comparison of our measured diffusion coefficient with that predicted by the Stokes‐Einstein relationship in terms of solvent or solution viscosity showed a clear transition in the conformation of hemoglobin at approximately 22°C, independent of the hemoglobin concentration. We postulated that at this physiological temperature, a considerable quaternary rearrangement of the hemoglobin chains takes place. We believe this rearrangement changes the effective volume and the hydration sphere of the hemoglobin macromolecule.
Conformation of sequential and random lysine–phenylalanine copolypeptides
Authors: Seipke Gerhard , Arfmann Hans‐Adolf , Wagner Karl G. 
Published: December 2004

AbstractThe sequential copolypeptides (Lys‐Phe‐Lys)n and (Lys2‐Phe‐Lys)n and a series of related random copolypeptides were investigated with respect of their ability to adopt the α‐helix or β‐conformation. Conformational transitions were induced by increasing the pH or by addition of NaClO4 or methanol and were observed by recording the CD spectra. In contrast to the respective alternating copolypeptide (Phe‐Lys)n with its strong tendency for the β‐structure reported previously, (Lys‐Phe‐Lys)n can adopt either secondary structure, whereas (Lys2‐Phe‐Lys)n strongly favors the α‐helix. Together with the random copolypeptides, whose composition varied from 20 to 50 mol % phenylalanine and whose average molecular weights ranged from 10,000 to 90,000, the influence of the phenylalanine content and of the chain length on conformational stability and the rotatory strength of the respective secondary structures were elaborated.
DNA bis‐intercalation: Application of theory to the binding of echinomycin to DNA
Authors: Shafer Richard H. , Waring Michael J. 
Published: December 2004

AbstractThe statistical mechanical model for the binding of bifunctional intercalating ligands to duplex DNA described in the preceding paper is applied to the example of echinomycin–DNA interactions. This is the only system for which binding curves have been obtained under conditions leading to binding by both bis‐intercalation and mono‐intercalation simultaneously. Binding parameters and Scatchard plots are calculated for a variety of conditions. A detailed comparison of these calculations with the results from the previous analysis of the same binding data in terms of the McGhee‐Von Hippel theory, assuming only one mode of binding, is presented. The results of our calculations are consistent with the model of bis‐intercalation requiring the two bound chromophores of a bifunctional ligand to be separated by two base pairs. It is not necessary to assume violation of the nearest‐neighbor exclusion principle, as occurred in the original analysis.
Conformational flexibility of peptides containing α,β‐unsaturated amino acid residues. I. Conformational analysis of N‐acetyl‐N′‐methylamides of dehydroalanine and N‐methyldehydroalanine
Authors: Ajò David , Granozzi Gaetano , Tondello Eugenio , Del Prà Antonio 
Published: December 2004

AbstractConformational energy calculations on the N‐acetyl‐N′‐methylamides of dehydroalanine and N‐methyldehydroalanine indicate that their conformational behavior is very different from that of the corresponding saturated compounds. The conformational data in the literature from x‐ray and nmr investigations on peptides containing α,β‐unsaturated residues are discussed on the basis of these theoretical results.
Spectroscopic and equilibrium dialysis studies of poly(α‐L‐glutamic acid)–Cu(II) complexes in the pH range 4–7
Authors: Masujima Tsutomu , Yamaoka Kiwamu 
Published: December 2004

AbstractThe formation of complex between the Cu2+ ion and poly(α‐L‐glutamic acid) [poly(Glu)] in 150 mM NaCl solutions was studied by uv–visible absorption and equilibrium dialysis methods at the mixing ratios of Glu residues to Cu2+, R, of 32, 16, and 8 and in the pH range 4–7. The results showed that more than 90% of Cu2+ ions bind to the poly(Glu) at pH > 4.9, but the bound Cu(II) begins to dissociate with a decrease in pH. The absorption spectra of bound Cu(II) varied with pH and R in a complicated manner. Three different component spectra were disclosed from the analysis of the pH dependence of the bound spectra. We concluded that poly(Glu)–Cu(II) complexes fall into three classes in the pH range 4–7, with the proportions of these complexes varying with both pH and R. The three complexes predominate either in the helix or extended‐coil region, in the helix–coil transition region, or in the helix‐aggregate region. The stability constant and binding mode of each Cu(II)–Glu complex were estimated from the dialysis data. With these results, the possible structure of each complex is discussed.
NMR relaxation processes of 31P in macromolecules
Authors: Shindo Heisaburo 
Published: December 2004

Abstract31P‐Nmr relaxation parameters (spin‐lattice relaxation time, linewidth, and nuclear Overhauser effect) were obtained at three different frequencies for poly(U) and a well‐defined (145 ± 3 base‐pair) fragment of DNA in solution. Data sets for the two samples were analyzed by theories which included relaxation by the mechanisms of 31P chemical shift anisotropy as well as by 1H‐31P dipole–dipole interaction. Neither data set could be satisfactorily described by a single correlation time. A model of a rigid rotor most nearly fits the data for the DNA molecule. Parameters obtained from the least‐square fit indicate (1) that the DNA undergoes anisotropic reorientation with a correlation time τ0 = 6.5 × 10−7 sec for the end‐to‐end motion, (2) the ratio of diffusion constants D∥/D⊥ is 91, and (3) that the linewidth is due to chemical shift dispersion to the extent of 0.5 ppm. Some deviations of the calculated from the observed values suggested that significant torsional and bending motions may also take place for this DNA. Another model which contains isotropic motion but with a broad distribution of correlation times was required to fit the data for poly(U). A log − χ2 distribution function of correlation times [Scheafer, J. (1973) Macromolecules 6, 881–888] described well the motion of poly(U) with the average correlation time τ = 3.3 × 10−9 sec and a distribution parameter p = 14.
Adsorption of polypeptides on the solid surface. II. Effect of secondary chain structure and helix–coil transition
Authors: Zhulina E. B. , Birshtein T. M. , Skvortsov A. M. 
Published: December 2004

AbstractThe theory of adsorption of semistiff chains on a planar surface developed by the authors previously has been used to consider the helix–coil transition in single‐stranded macromolecule interacting with an adsorbent plane. The cases of nonselective interaction when the adsorption energy is independent of the unit conformation (a) and selective interaction with only helical (b) or coiled (c) sequences active in adsorption were investigated. In case (b) the existence of secondary structure favors chain bonding to the surface. This leads to the increase in the stability of the helical state and complete polypeptide chain spiralization. The profile of the conformational helix–coil transition acquires an asymmetrical shape inherent to the second‐order phase transition.In case (c) the bonding of a partially helical chain to the surface is similar to the adsorption of Gaussian coils and is accompanied by the destruction of secondary structure, this destruction being appreciable even if the helical state in space was favorable.
Dielectric relaxation of DNA solutions. IV. Effects of salts and dyes
Authors: Sakamoto Masanori , Hayakawa Reinosuke , Wada Yasaku 
Published: December 2004

AbstractThe effects of salts (NaCl, LiCl, Me4NCl, AgNO3, MgCl2, CuCl2 and MnCl2) and dyes (acridine orange and methylene blue) on the low‐frequency dielectric relaxation (0.1 Hz–30 kHz) of dilute aqueous solutions of DNA were investigated with varying salt or dye concentrations. Both the dielectric relaxation time τD and the rotational relaxation time τ estimated from the reduced viscosity decrease in quite parallel ways with increasing M/P (M/P being the normality ratio of cation to phosphate residue), reflecting the contraction of DNA molecule due to electrostatic shielding and cation binding. The agreement between τD and τ through the whole range of M/P supports our previous conclusion that the low‐frequency relaxation of DNA arises from rotation of the molecule. The dielectric increment Δε also decreases with increasing M/P on account of both the contraction of DNA and the decrease in effective degree of dissociation of DNA. Δε as a function of M/P is interpreted in terms of a quasi‐permanent dipole due to counterion fluctuation. These effects of cations are the strongest for divalent cations and rather weak for Na+, Li+, and Me4N+. Effects of dye on τD and Δε are also well explained by the rotation of DNA molecule with a quasi‐permanent dipole due to counterion fluctuation on the basis of intercalation of dye at D/P < 0.2 (D/P being the molarity ratio of dye to phosphate residue) and external binding at 0.2 < D/P < 1.0.
Characterization of multiple bends in proteins
Authors: Isogai Y. , Némethy G. , Rackovsky S. , Leach S. J. , Scheraga H. A. 
Published: December 2004

AbstractThe concept of bends or chain reversals [nonhelical dipeptide sequences in which the distance R3 (i,i+3) between the Cα atoms of residues i and i+3 is ≦ 7.0 Å] has been extended to define double bends as tripeptide sequences, not in an α‐helix, in which two successive distances R3(i,i+3) and R3 (i+1, i+4) are both ≦7.0 Å, with analogous definitions for higher‐order multiple bends. A sample of 23 proteins, consisting of 4050 residues, contains 235 single, 58 double, and 11 higher‐order multiple bends. Multiple bends may occur as combinations of the “standard” type I, II, and III chain reversals (as well as their mirror images), but usually they require distortions from these well‐defined conformations. The frequency of occurrence of amino acids often differs significantly between single and multiple bends. The probability distribution of R3 distances does not differ in single and multiple bends. However, R4 (the distance between the Cα atoms of residues i and i+4) in multiple bends is generally shorter than in tripeptide sequences containing single bends. The value of R4 in many multiple bends is near those for α‐helices. In some other multiple bends, R4 is even shorter, indicating that these structures are very compact. The signs of the dihedral angles about the virtual bonds connecting Cα atoms and the values of curvature and torsion, as defined by means of differential geometry, indicate that there is a preference for single and multiple bends to be right‐handed (like an α‐helical sequence, for example) and that there is a strong tendency to conserve the handedness in both single‐bend components of many multiple bends. These often have a strong resemblance to distorted single turns of an α‐helix and do not constitute chain reversals. Double bends, in which the signs of two successive virtual‐bond dihedral angles differ, have conformations that are very different from an α‐helix. They act as chain reversals occuring over three residues. These chain reversals have not been described previously. Multiple bends may play an important role in protein folding because they occur fairly frequently in proteins and cause major changes in the direction of the polypeptide chain.
Heavy‐atom effects associated with methylmercury (II) binding to rabbit glyceraldehyde‐3‐phosphate dehydrogenase
Authors: Hershberger Martin V. , Maki August H. 
Published: December 2004

AbstractThe complex of CH3Hg(II) with the accessible cysteines of glyceraldehyde‐3‐phosphate dehydrogenase (GAPD, EC 1.2.1.12) from rabbit muscle has been studied by phosphorescence and optically detected magnetic resonance (ODMR) spectroscopy. The wavelength dependence of the phosphorescence decay kinetics has also been measured. Comparison of CH3Hg(II)–GAPD with GAPD by these methods shows that a specific optically resolved tryptophan site of GAPD is perturbed by the interaction with a nearby mercury atom. The perturbation on the luminescence and ODMR properties is typical of an external heavy‐atom effect. Based on the x‐ray diffraction structure of the lobster enzyme, it is proposed that the heavy‐atom effect results from the interaction of tryptophan‐310 with CH3Hg(II) bound to cysteine‐281 in the rabbit muscle enzyme.
Interaction of spermine with different forms of DNA. A conformational study
Authors: Zhurkin Victor B. , Lysov Yury P. , Ivanov Valery I. 
Published: December 2004

AbstractThe energy of interaction of a spermine molecule with the A‐ and B‐forms of DNA has been calculated, assuming that the molecule of spermine is fixed in the narrow groove of the DNA helix with the formation of hydrogen bonds between the amino groups of spermine and the phosphate groups of DNA. The atom–atom potentials method was used. Optimal structures for the A‐DNA–spermine and B‐DNA–spermine complexes are suggested. It is shown that, in agreement with the experimental data, the interaction of the spermine molecule with the A‐DNA is energetically more favorable than that with the B‐DNA. Two main factors are responsible for this: (1) the distance between neighboring phosphates of the chain in A‐DNA (which is about 1 Å less than that in B‐DNA) corresponds better to the distance between the amino groups of the propyl part of spermine; and (2) the orientation of phosphate groups in A‐DNA inside the groove is preferable for complex formation with spermine to the outside groove arrangement of the phosphates in B‐DNA. These conclusions are further confirmed by the calculations for DNA–propane diamine complexes.
The translational friction of toroids
Authors: Allison Stuart A. , Easterly Russell A. , Teller David C. 
Published: December 2004

AbstractAn approximate analytic expression for the translational friction coefficient of a toroid modeled as a continuous shell of frictional elements is derived using the Kirkwood approximation. The accuracy of this expression was determined by comparing the friction coefficients predicted by it to those predicted by extrapolated shell‐model calculations using the modified Oseen tensor. To show that these calculations do indeed yield the correct friction coefficients, actual translational friction coefficients were determined by observing settling rates of macroscopic model rings or toroids in a high‐viscosity silicone fluid. Our conclusion is that the approximate expression yields friction coefficients that are about 1.5–3% low for finite rings. For thin rings, a comparison is also made with the exact result of Yamakawa and Yamaki [J. Chem. Phys. 57, 1572 (1972); 58, 2049 (1973)] for the translational friction of plane polygonal rings. This comparison shows that the approximate expression yields results which are low by 2–3% unless the rings are extremely thin, in which case the error is larger. In the limit of an infinitely thin ring the approximate expression reduces to the Kirkwood result [J. Polym. Sci. 12, 1 (1954)], which is low by 8.3%. We discuss briefly how this work may be useful in determining the structure of DNA compacted by various solvent–electrolyte systems and polyamines.
Conformational analysis of the milk oligosaccharides
Authors: Biswas Margaret , Rao V. S. R. 
Published: December 2004

AbstractPossible conformations of lacto‐N‐tetraose, lacto‐N‐neotetraose, related disaccharides, and other milk oligosaccharides have been studied by an energy‐minimization procedure using empirical potential functions. Lacto‐N‐tetraose favors a “curved” conformation, while lacto‐N‐neotetraose favors an approximately “straight” conformation. These two conformations differ mainly in the position of the terminal galactose residue with respect to the rest of the molecule. This difference explains the greater strength of lacto‐N‐neotetraose compared with lacto‐N‐tetraose in its ability to inhibit the cross‐reaction of blood group P1 fractions with Type XIV pneumococcal antipolysaccharide. Although the favored conformation of lacto‐N‐tetraose (inactive) agrees with the model proposed by the earlier workers, that for lacto‐N‐neotetraose (active) differs. The favored conformations for the disaccharides galactose‐β(1‐4)‐N‐acetylglucosamine, galactose‐β(1‐3)‐N‐acetylglucosamine, and lactose are similar in overall shape, differing only in the nature and orientation of the side groups. This explains their nearly equal inhibitory activity. These theoretical models also explain the increased activity of lacto‐N‐fucopentaose I over that of lacto‐N‐tetraose and the relative activities of the substituted lactoses. The present studies suggest that it is the overall shape of the molecule which is important for activity, rather than the terminal β(1‐4)‐linked galactose residue alone.
Toroidal elastic supercoiling of DNA
Authors: Calladine C. R. 
Published: December 2004

AbstractCovalently closed circular DNA can exist in different configurations known as circular, toroidal, and interwound. Changes among these forms can be made in several ways, including the insertion of dye molecules between adjacent base pairs, which tends to untwist the double‐helical structure. The aim of this paper is to discuss these configurations, and the changes among them, in the context of classical elastomechanics. The concepts of twisting, linkage and writhing are explained. Simple experiments on a twisted linear‐elastic rod are described, and it is shown that although the circular and interwound forms may be modeled in this way, the toroidal form does not occur, being mechanically unstable. Theoretical energy calculations by Levitt on bent and twisted DNA show that DNA exhibits a particular kind of nonlinear elasticity in which there is an unusual coupling between bending and twisting. The aim of the paper is to show qualitatively that this special kind of elasticity can stabilize the toroidal form of closed circular DNA.
Fluorine nmr studies of poly(N‐acryloyl‐β‐alanine)–α‐chymotrypsin conjugates
Authors: Gerig J. T. , Loehr D. T. 
Published: December 2004

AbstractFluorine nmr experiments carried out at 51.0 and 94.1 MHz have been used to explore the interaction of the probe molecule p‐fluorocinnamate with conjugates formed from α‐chymotrypsin and poly(N‐acryloyl‐β‐alanine). The data obtained include enzyme‐induced chemical‐shift effects, spin‐lattice (R1) and transverse (R2) relaxation rates, and the rate constant for dissociation of the fluorocinnamate–enzyme complexes. Analysis of the results indicates that while overall molecular tumbling of the enzyme molecule is not greatly changed by attachment of polymers of various sizes, conjugated polymer can appreciably affect the structure of the p‐fluorocinnamate binding site. The important variable involved in such structural changes appears to be the amount of polymer present per mole of protein.