bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circular dichroism of histone‐bound regions in chromatin
Authors: Li Hsueh Jei , Chang Catherine , Evagelinou Zoi , Weiskopf Manuel 
Published: May 2005

AbstractNative, NaCl‐treated, trypsin‐treated, and polylysine‐bound nucleohistones were studied in 2.5 × 10−4 M EDTA, pH 8.0, using circular dichroism (CD) and thermal denaturation. Removal of histone I by 0.6 M NaCl has a much smaller effect on both Δε220 and Δε278 than the removal of other histones. This indicates that histone I has less helical content and less conformational effect on the DNA in nucleohistone. By extrapolating to 100% binding by histones other than I, the positive CD band near 275 nm is close to zero. Comparison is also made between the effects of binding by the more basic and the less basic halves of histones by trypsin‐digestion and polylysine‐binding experiments. Trypsin digestion of nucleohistone reduces melting band IV at 82°C much more than melting band III at 72°C. However, the CD changes of Δε278 and Δε220 induced by trypsin digestion are small, unless melting band III is also reduced by the use of a higher trypsin level. This implies that the less basic halves of histones, which stabilize DNA to 72°C (melting band III), have more helical structure and are more responsible for conformational change in DNA than are the more basic halves, which stabilize DNA to 82°C (melting band IV). Polylysine binding to nucleohistone diminishes melting band III but has no effect on melting band IV. This binding affects only slightly the Δε220 of nucleohistone, indicating that polylysine interferes very little with the structure of the less basic halves of bound histones. The implications of these studies with respect to chromatin structure are discussed.
The low‐temperature mechanical relaxation of elastin. I. The dry protein
Authors: Pezzin G. , Scandola M. , Gotte L. 
Published: May 2005

AbstractThe low‐temperature relaxation of native ox Ligamentum nuchae elastin and of two purified elastin samples has been investigated in the dry state by means of the Rheovibron DDV II viscoelastometer, at the fixed frequencies of 3.5, 11, 35, and 110 Hz. Besides the glass transition at about 200°C, a relatively strong secondary loss‐tangent peak, whose activation energy is about 13 kcal/mol, is found for all samples below room temperature. The peak maximum is at −71°C for the 3.5‐Hz frequency. On the basis of its location, intensity, and width, it is attributed to a main‐chain relaxation of the pure protein. When suitable reduced variables are used, the loss‐tangent‐temperature curves obtained at different frequencies can be satisfactorily superimposed to give a master curve. Comparison of the data with the prediction of a semiempirical viscoelastic model can also be considered satisfactory.
Preferential solvent binding and change in conformation of bovine serum albumin in 2‐chloroethanol–water mixed solvents
Authors: Maes Eddie 
Published: May 2005

AbstractSolvent binding to bovine serum albumin in 2‐chloroethanol‐water mixed solvents of different composition, measured previously by Inoue and Timasheff (Biopolymers (1972) 11, 737–43) is applied to a hydrodynamic study of the solvated protein.From sedimentation and diffusion data, the apparent molecular weight of the solvated protein particle can be calculated, provided an average partial specific volume, computed from the composition of the particle, is introduced in Svedberg's equation. The unsolvated molecular weight of the protein can than be calculated by subtraction of the bound solvent. Further data on the hydrodynamic particle (f/fmin and axial ratio of the equivalent ellipsoid) are readily calculated from these experiments, and reinforce the supposition that 2‐chloroethanol is a strong helix‐inducing solvent.
High‐resolution nmr study of yeast tRNA and the native and denatured conformers of yeast tRNA
Authors: Rordorf B. F. , Kearns D. R. , Hawkins Erin , Chang S. H. 
Published: May 2005

AbstractThe high‐resolution nmr spectrum of baker's yeast tRNA, a recently sequenced non‐denaturable tRNA, has been compared with the spectra of the native and denatured conformers of the closely related species tRNA. Because of the presence of many common base pairs in the different tRNA's, it is possible to assign most of the low‐field resonances to specific secondary‐structure base pairs. A comparison of the observed positions of the various resonances with those predicted by a semiempirical ring‐current shift theory shows a root‐mean‐square deviation of 0.14, 0.11, and 0.12 ppm for tRNA (native), and tRNA (denatured), respectively. These results support the ring‐current shift theory currently used to interpret the low‐field nmr spectra of the tRNA molecules. Differences between the predicted and observed positions of some resonances provide new evidence for higher order effects such as shifts from second nearest neighbors, anomalous shifts exerted by G·U base pairs, and tertiary‐structure effects. A model that was previously proposed for the denatured conformer of tRNA is also supported.
Circular dichroism studies of an elastin crosslinked peptide
Authors: Foster J. A. , Bruenger E. , Rubin L. , Imberman M. , Kagan H. , Mecham R. , Franzblau C. 
Published: May 2005

AbstractCircular dichroic studies of a desmosine crosslinked peptide reveal a hitherto undescribed elastin spectrum possessing a weak negative band at 230–235 nm, a weak positive band at 215 nm, and a maximum negative band at 190 nm. The spectrum is sensitive to both pH and temperature displaying increased ellipticity of the 215‐nm band at acidic pH and low temperature. The general shape of the spectrum and its behaviour toward temperature changes suggest the presence of an extended helical conformation. Susceptibility of insoluble elastin to digestion with chymotrypsin is increased tenfold at low temperature (4°C), supporting the contention that the conformational change of the type described above occurs in insoluble elastin. Such changes in conformation would result in increased availability of aromatic amino‐acid resiudues to peptide bond cleavage.
Sedimentation of generalized systems of interacting particles. III. Concentration‐dependent sedimentation and extension to other transport methods
Authors: Claverie Jean‐Michel 
Published: May 2005

AbstractThe simulation method presented in the previous papers is related to the concentration‐dependent sedimentation–diffusion. It can be shown that the efficiency of the program described previously is maintained. A simulation of a system exhibiting the Johnston–Ogston effect is presented.Through the similarity of their continuity equations with the Lamm equation, electrophoresis, molecular sieve, and chromatography are treated. A general simulation of transport for systems of many interacting components is thus presented, which is able to take into account kinetically controlled chemical reactions and nonideal phenomena.
Infinite dilution viscoelastic properties of poly(γ‐benzyl‐L‐glutamate) in m‐cresol
Authors: Ookubo Norio , Komatsubara Michiro , Nakajima Haruhiko , Wada Yasaku 
Published: May 2005

AbstractThe real and imaginary parts of complex viscosity, η′ and η″, are measured for dilute solutions of poly(γ‐benzyl‐L‐glutamate) in m‐cresol, a helicogenic solvent. The frequency range is 2.2–525 kHz; the concentration range 0.2–5 g/dl; the temperature 30°C, and the molecular weights Mr are 6.4 × 104–17 × 104. The dispersion curve of extrapolated intrinsic dynamic viscosity [η′] of samples with Mr > 105 is interpreted in terms of three mechanisms appearing from low to high frequencies: end‐over‐end rotation, flexural deformation, and side‐chain motion. For a sample with Mr < 105, the flexural relaxation disappears and a plateau of [η′] is distinctly observed between rotational and side‐chain relaxations. Rotational relaxation times of all the samples obey the Kirkwood–Auer theory. The strong concentration dependence of rotational relaxation time is explained by collisions of molecules rather than association. Flexural relaxation times calculated from a theory by assuming the persistence length as 1200 Å are consistent with observed dispersion curves of [η′].
Conformational energy calculations for dinucleotide molecules. A systematic study of dinucleotide conformation, with application to diadenosine pyrophosphate
Authors: Thornton Janet M. , Bayley Peter M. 
Published: May 2005

AbstractA systematic study of the conformational states of the dinucleotide diadenosine 5′,5′‐pyrophosphate (AppA), an analog of the coenzyme NAD+, has been made using semi‐empirical energy calculations. Taking low‐energy mononucleotide structures as starting conformations, energy minimizations have been performed. The most stable structures exhibit stacking interactions between the adenine bases; there are many different stacked states of similar energy; their stability is derived from nonbonded interactions primarily between the bases but also from base–sugar interactions. The most common form of stacking in the most stable structures was found to be antiparallel A‐A helix. These findings are consistent with the experimental data, which suggest that AppA adopts predominantly a stacked state in solution, and this state incorporates a variety of stacked conformations.
Contribution of side‐chain chromophores to the optical activity of proteins: Model compound studies. IV. The indole chromophore of yohimbinic acid
Authors: Goux Warren J. , Kadesch Thomas R. , Hooker Thomas M 
Published: May 2005

AbstractThe optical properties of the indole chromophore of the indole alkaloid yohimbinic acid have been investigated as a function of molecular conformation. Theoretical rotatory strengths have been calculated and compared with experimental circular dichroism spectra. Optical data that may be suitable for calculating the chiroptical properties of the near ultraviolet electronic transitions of the indole chromophores, which occur in tryptophan residues of proteins, have been developed. The far ultraviolet transitions of yohimbinic acid have also been investigated.
N‐acetylchitosan gel: A polyhydrate of chitin
Authors: Hirano Shigehiro , Yamaguchi Ryuji 
Published: May 2005

AbstractN‐Acetylchitosan gel, a polyhydrate of chitin, and partially O‐acetylated N‐acetylchitosan gel were produced by a facile acetylation of chitosan with acetic anhydride in 10% acetic acid and in aqueous acetic acid/methanol at room temperature. Under the same conditions, a series of N‐acylchitosan gels was produced in reaction with the other carboxylic anhydrides. The gels thus produced were colorless, transparent and rigid, and stable on heating. The gels were insoluble in cold and boiling water, formic acid, aqueous acids, and the other solvents examined. Significant changes in specific rotation occurred in the acylation of chitosan and its aggregation.
Studies of peptide conformation: Backbone folding of tetrapeptide derivatives in methanol and water
Authors: Kopple Kenneth D. , Go Anita 
Published: May 2005

AbstractDerivatives of tetrapeptide sequences considered likely to form β‐turns were investigated by the study of their proton magnetic resonances in methanol and in water. Differential broadening of N—H resonances by an added nitroxyl was used to indicate the presence of the sequestered N—H proton expected in β‐turn conformations. Transfer of magnetic saturation from solvent water protons to N—H protons was also examined. The evidence is consistent with significant contributions by β‐turn‐like backbones to the conformational averages in methanol of the sequences Gly‐L‐Pro‐D‐Val‐Gly, D(or L)‐Val‐L‐Pro‐Gly‐Gly, and Gly‐L‐Pro‐L‐Asn‐Gly, but not the sequence Gly‐D‐Ala‐L‐Val‐Gly. It is suggested that a Type I turn, Likely in Gly‐L‐Pro‐L‐Asn‐Gly derivatives, is characterized by sequestered N—H protons of both the third and fourth residues. For all of the peptide derivatives, save possibly Ac‐L‐Val‐L‐Pro‐Gly‐Gly‐NHNH2, contributions from folded structures in water are not detectable by line‐broadening experiments. However, the transfer of saturation experiments may be interpreted as indicating some degree of chain folding in water.
Synthesis of a cross‐linked polypentapeptide of tropoelastin
Authors: Okamoto K. , Urry D. W. 
Published: May 2005

AbstractThe synthesis of a cross‐linked polypentapeptide (an insoluble product) by means of a cross‐linking reaction between a lysine‐containing (1%) polypentapeptide and a glutamic acid‐containing (2%) polypentapeptide is described, following description of the synthesis and polymerization of the corresponding pentapeptide p‐nitrophenyl esters. The pentapeptide p‐nitrophenylesters—H‐Val1‐Pro2‐Gly3‐Val4‐Gly5‐ONp, H‐Val1‐Pro2‐Gly3‐Lys4(ε‐Z)‐Gly5‐ONp, and H‐Val1‐Pro2‐Gly3‐Glu4‐Gly5‐ONp—prior to polymerizing and the polypentapeptides prior to cross‐linking were analyzed by proton and carbon‐13 magnetic resonance. The cross‐linking reaction was achieved in the coacervate state by intermolecular primary amide bond formation. The coupling reagent was a water‐soluble carbodiimide (1‐cyclohexyl‐3‐(2‐N‐methylmorpholinoethyl)‐carbodiimide‐p‐toluenesulfonate).
Transition temperature and enthalpy change dependence on stabilizing and destabilizing ions in the helix–coil transition in native tendon collagen
Authors: Lim Jong Jin 
Published: May 2005

AbstractThe transition temperatures tt and enthalpy changes ΔH in the helix–coil transition of solid tendon collagen soaked in a solution containing one of the following stabilizing or destabilizing agents, HCHO, NaF, NaCl, NaI, NaBr, NaOH, NH2CONH2, CaCl2, MgCl2, were measured as a function of molar concentration by a calorimetric method. The temperature and the enthalpy changes accompanying the transition behaved in a similar manner: when the tt was depressed by the presence of ions, similar behaviour was observed in ΔH. Both parameters (tt and ΔH) increased for HCHO, and decreased for NaF and NaCl at concentrations lower than 0.2 M. Above 0.2 M they increased for NaF and NaCl, and decreased in the presence of the other reagents listed above. The average tt and the ΔH observed in collagen soaked in water were 63.5°C and 12.3 cal/g, respectively. In addition to the parameters mentioned above, the molar effectiveness of the various reagents was obtained for the cases where there was a linear relationship between the tt and molar concentration of the reagent in the solution.Since both the tt and the ΔH were observed to vary, the entropy change (ΔS) accompanying the transition was calculated using thermodynamic relations. In order to explain the ΔS observed as a function of ionic concentration, the thermodynamic relationships have been obtained from a partition function under suitable assumptions. Since the partition function is dependent on the number of hydrogen bonds responsible for collagen stability, the result obtained has been compared with the values predicted by the two most quoted models for collagen. The present study is in accordance with the Ramachandran model for collagen structure, which predicts more than one hydrogen bond per three residues.
A configurational interpretation of the axial phosphate spacing in polynucleotide helices and random coils
Authors: Olson Wilma K. , Manning Gerald S. 
Published: May 2005

AbstractThe structural implications arising from the observation (set forth in the preceding paper) that the charge density of a single‐stranded randomly coiling polynucleotide chain is approximately equal to that of one strand of the familiar double helix are here examined. A computational scheme is described to obtain (using bond lengths, valence bond angles, and internal rotation angles) the mean phosphate–phosphate spacing parameter b along the chain axes of any single‐stranded polynucleotide molecule. Attention is then focused upon the computed interphosphate spacing associated with both the theoretical randomly coiling polynucleotide that reproduces the observed experimental unperturbed dimensions and the familiar single‐stranded helix. The calculations clearly demonstrate that the parameter b only weakly reflects the spatial configuration of the chain. The approximate equivalence of the b values associated with the single‐stranded helix and the unperturbed randomly coiling polynucleotide is not indicative of strong configurational similarities between the two forms. The familiar helix is composed of a sequence of identically conformed compact structural residues while the random coil is characterized by a variety of chain‐repeating residues of which a large proportion are extended units.
Study of thermal denaturation of lysozyme and other globular proteins by light‐scattering spectroscopy
Authors: Nicoli D. F. , Benedek G. B. 
Published: May 2005

AbstractThe technique of intensity correlation light‐scattering spectroscopy has been used to accurately determine the extent of physical swelling of lysozyme, ribonuclease, and chymotrypsinogen produced by thermal denaturation. The change in hydrodynamic radius is deduced from direct measurements of the diffusion coefficient, carried out in the temperature range 20° to 70°C at various values of pH in the range 1.0 to 3.0 at ionic strengths of from 0.01 M to 0.2 M. An average radius increase of 18% is observed for lysozyme and ribonuclease, with an estimate of 26% for chymotrypsinogen. Analysis of the pH dependence of the transition temperature leads to the conclusion that the lysozyme charge increases by approximately +2e during unfolding. We have applied this value of the charge increase along with the 18% average radius increase to estimate the electrostatic contribution to the free‐energy change for denaturation of lysozyme. The results are consistent with the experimental observation that the transition temperature is nearly independent of ionic strength.
Vibrational analysis of peptides, polypeptides, and proteins. II. β‐Poly(L‐alanine) and β‐poly(L‐alanylglycine)
Authors: Moore W. H. , Krimm S. 
Published: May 2005

AbstractThe normal vibration frequencies of poly(L‐alanine) and poly(L‐alanylglycine) in the antiparallel chain‐pleated sheet structure have been calculated, using the force field for polyglycine I from the previous paper (Biopolymers 15, 2439–2464) plus additional force constants for the methyl group. The agreement with observed ir and Raman bands is very good. This substantiates the excellent transferability of the force field, since polyglycine I was shown to have a rippled‐sheet structure. The amide I and amide II mode splittings are very well accounted for by transition dipole coupling, showing that subtle structural differences are sensitively manifested through this mechanism.
Conformational energy calculations of enzyme‐substrate complexes of lysozyme. I. Energy minimization of monosaccharide and oligosaccharide inhibitors and substrates of lysozyme
Authors: Pincus Matthew R. , Burgess Antony W. , Scheraga Harold A. 
Published: May 2005

AbstractConformational energy calculations were performed on monosaccharide and oligosaccharide inhibitors and substrates of lysozyme to examine the preferred conformations of these molecules. A grid‐search method was used to locate all of the low‐energy conformational regions for N‐acetyl‐β‐D‐glycosamine (NAG), and energy minimization was then carried out in each of these regions. Three stable positions for the N‐acetyl group have ben located, in two of which the plane of the amide unit is normal to the mean plane of the pyranosyl ring. Nine local energy minima were located for the —CH2OH group. The positions of the two vicinal cis —OH groups are determined predominantly by interactions with either the —CH2OH or the N‐acetyl group. The most stable conformations of β‐N‐acetylmuramic acid (NAM) were determined from the study of the low‐energy conformations of NAG. In the two stable orientations for the D‐lactic acid side chain, the O—C—C′ plane (C′ being the carbon atom of the terminal carboxyl group) was found to be normal to the mean plane of the pyranosyl ring. The low‐energy positions for the COOH group of NAM are determined mainly by interactions with neighboring groups.The conformational preferences of the α‐anomers of NAG and NAM were also explored. The calculated conformation of the N‐acetyl group for α‐NAG was quite close to that determined by X‐ray analysis. Two of the three lowest energy conformations of α‐NAM are similar to the corresponding conformations of the β‐anomer. A third low‐energy structure, which has a hydrogen bond from the NH of the N‐acetyl group to the CO of the lactic acid group, corresponds very closely to the X‐ray structure of this molecule.The preferred conformations of the disaccharides NAG–NAG, NAM–NAG and NAG–NAM were also investigated. Two preferred orientations of the reducing pyranosyl ring relative to the nonreducing ring were found for all of these disaccharides, both of which are close to the extended conformation. In one of these conformations, a hydrogen bond can form between the OH group attached to C3 of the reducing sugar and the ring oxygen of the preceding residue. Each conformation can be stabilized further by a hydrogen bond between the CH2OH (donor) of residue i + 1 and the CO of residue i (acceptor). The interactions that determine conformations for all oligosaccharides containing both NAG and NAM are shown to be exclusively intraresidue and nearest neighbor interactions, so that it is possible to predict all stable conformations of oligosaccharides containing NAG and NAM in any sequence.
The random coil → β transition of copolymers of L‐lysine and L‐isoleucine: Potentiometric titration and circular dichroism studies
Authors: Walter Bert , Fasman Gerald D. 
Published: May 2005

AbstractCopolymers of L‐lysine and L‐isoleucine [poly(L‐Lysf,L‐Val1 − f)] containing 4–15% isoleucine were investigated using potentiometric titration and circular dichroism (CD) spectroscopy. With increasing isoleucine content, β‐sheet formation is favored over α‐helix formation at high pH and room temperature. The fraction of β‐sheet present, as a function of pH, calculated from titrations of poly(L‐Lys85.2,L‐Ile14.8), agreed well with data obtained from CD studies for the same copolymer. Thermodynamic parameters were determined from titrations using the method of Zimm and Rice; the partial free energy (ΔG°C → β) at 25° for the coil‐to‐β‐sheet transition for isoleucine was estimated to be −515 cal/mol; from the temperature dependence of free energy, the partial entropy (ΔS°cβ), and the partial free enthalpy (ΔH°c → β) of the coil → β transition for isoleucine is estimated to be 2.6 e.u. and 260 cal/mol, respectively. The partial thermodynamic parameters obtained for lysine are in good agreement with literature values. It is concluded from these studies that isoleucine has a very high potential for a β‐sheet formation.
Influence of fluctuations in electron density on the excess small‐angle X‐ray scattering from dilute solutions of macromolecules
Authors: Carpenter Dewey K. , Mattice Wayne L. 
Published: May 2005

AbstractThe influence on the excess scattering function P(μ) of flutuations in the electron density ρ within a macromolecule is treated, to the approximation that the solvent is a structureless medium of constant electron density ρ0. The results for P(μ) and the apparent value of the mean square radius Rapp2, can be expressed as functions of the excess electron density Δρ: P(μ) = X(μ) + (Δρ)−1Y(μ) + (Δρ)−2Z(μ) and Rapp2 = Rx2 + (Δρ)−1Ry2 + (Δρ)−2Rz2, where X(μ) and Rx2 depend only on the shape of the macromolecule, while Y(μ) and Ry2 as well as Z(μ) and Rz2 depend on the shape and the fluctuations in ρ. By varying the electron density of the solvent, the contributions of the shape and the internal structure of the macromolecule can be resolved. The quantities Rx2, Ry2, and Rz2 are evaluated for seven models to illustrate the relative importance of these contributions for representative structures.