bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermodynamic functions of biopolymer hydration. II. Enthalpy–entropy compensation in hydrophilic hydration processes
Authors: Lüscher‐mattli Madeleine , Rüegg Max 
Published: May 2005

AbstractThe thermodynamic functions of biopolymer hydration were investigated by multitemperature vapor pressure studies. Desorption measurements were performed that allowed determination of reversible isotherms in the hydration range of 0.1 to 0.3–0.5 g H2O/g dry polymer. These isotherms are accessible to thermodynamic interpretation and are relevant to the interaction of water with biopolymers in their solution conformation. The results obtained on a series of different biopolymers (lysozyme, α‐chymotrypsin, apo‐lactoferrin, and desoxyribonucleic acid), show the following common features of interest: (1) The differential excess enthalpies (ΔHe) and entropies (ΔSe) are negative, and exhibit pronounced anomalies in a well‐defined low‐humidity range (approx. 0.1 g H2O/g dry polymer). These initial extrema are interpretable by structural changes, induced in the native biopolymer structures by water removal below a critical degree of hydration. (2) The ΔHe and ΔSe terms exhibit statistically significant linear enthalpy–entropy compensation effects in all biopolymer–water systems investigated. The compensation temperatures \documentclass{article}\pagestyle{empty}\begin{document}$ \hat \beta = \overline {\Delta H} ^e /\overline {\Delta S} ^e $\end{document} are approximately identical for all biopolymers, ranging from 360 to 500 K. The compensation effects are attributable to phase transitions of water molecules between the bulk liquid and the inner‐sphere hydration shell of native biopolymers. (3) The negative excess free energies (ΔGe) decrease monotonically with increasing water content and are close to zero at 0.3 to 0.5 g H2O/g polymer. This result indicates that only transitions between the bulk liquid and the inner‐sphere hydration shell are associated with significant net free energy effects. The outer‐sphere hydration water is thermodynamically comparable to bulk water. The importance of the proportionality factor \documentclass{article}\pagestyle{empty}\begin{document}$ \hat \beta $\end{document} in the control of the free energy term is discussed.
Physicochemical properties of pectic acid. I. Thermodynamic evidence of a pH‐induced conformational transition in aqueous solution
Authors: Cesàro A. , Ciana A. , Delben F. , Manzini G. , Paoletti S. 
Published: May 2005

AbstractOn the basis of measurements of enthalpy of dissociation and of dilution, an interamolecular conformational transition induced by pH change is shown for pectic acid in aqueous solution. Additional evidence is given by potentiometic, viscometric, and chiroptical results. The transition from a more rigid, probably H‐bonded, structure prevailing at low pH to a more extended one at around neutrality is accompanied by a ΔH value of about 500 cal/equiv and a ΔS value of 1.6 cal/equiv K in water at 25°C. The addition of salts increases the stability of the rigid conformation without changing the general features of the phenomenon. Dilatometric measurements suggest that the transition is accompanied by practically no change in the overall solvation of the polymer chain.
Borate complexes of amphotericin B: Polymeric species and aggregates in aqueous solutions
Authors: Strauss George , Kral Frank 
Published: May 2005

AbstractAmphotericin B, a polyene macrolide antibiotic, exists in aqueous solution as a poorly soluble, high‐molecular‐weight aggregate. A borate complex of this polyene was prepared that has greater solubility and is less aggregated. In aqueous solution this borate complex exists as a mixture of several molecular species differing in borate content, molecular weight, and molecular conformation. The solubility varied with pH and was minimal at neutrality. Throughout the pH range it was one to two orders of magnitude higher than that of the parent compound. The molecular size distribution, as determined by differential ultrafiltration, showed a progressive increase in the weight fraction of aggregates going from acid to alkaline solutions. The sizes of aggregates ranged from under 25 to over 100 molecules. The borate content of the complexes increased with increasing pH. No borate was complexed in acid solutions. This indicated that amphotericin B and borate ions can complex to form copolymer chains of varying length in which these species alternate, since both are bifunctional. The complexation equilibrium is favored by high pH. Absorption and CD spectra indicated that the polyene molecules can stack reversibly to form dimers. Dimerization constants calculated from the spectra were highest in neutral solution and declined with increasing acidity or alkalinity. In alkaline solutions the polymer chains are long and extended, with minimal stacking. In neutral solution the chains are shorter and extensively stacked. In acid solutions no borate complexes are formed, and the polyenes are stacked to an intermediate degree. The very different effects of pH and concentration on the degree of complexation with borate and on the degree of dimerization of the polyenes shows that these equilibria are independent of each other.
Semiflexibility of collagens in solution
Authors: Saito Takahide , Iso Naomichi , Mizuno Haruo , Onda Nobuhiko , Yamato Hideyuki , Odashima Hiroshi 
Published: May 2005

AbstractThe persistence length of lugworm cuticle collagen in 0.1M acetic acid was evaluated as 1600 ∼ 1800 Å by Yamakawa‐Fujii's model for a wormlike chain from the sedimentation constant and the intrinsic viscosity. The persistence length was further examined for a series of sample “collagen sonicates” produced by varying the duration of sonic irradiation. To estimate the salt effect on the persistence length, measurements were made over a range of NaCl concentrations from 0 to 0.1M. The results showed that the cuticle collagen and collagen sonicates had identical values of persistence length and that the neutral salt effect for the cuticle collagen was far smaller than that for DNA.
Simulations of the solvent structure for macromolecules. III. Determination of the Na+ counter ion structure
Authors: Clementi Enrico , Corongiu Giorgina 
Published: May 2005

AbstractWe report on a computer experiment in which, using Monte Carlo techniques, we considered a three‐turn (30‐base‐pairs) B‐DNA fragment as a solute and a set of 1200 water molecules and 60 sodium counterions (at a temperature of 300 K) as a solvent. From a statistical analysis of the Monte Carlo simulation (applied to the water molecules and counterions in the B‐DNA field), we determined that the counterions themselves conform to two helical structures intertwined with the two strands. The strutures of the water molecules solvating both counterion helices and the two B‐DNA strands are fully analyzed and described in detail. A model for base‐pair recognition based on the above findings is proposed. Aspects of the unwinding mechanism are discussed.
Interactions of DNA with divalent metal ions. IV. Competitive studies of Mn2+ binding to AT‐ and GC‐rich DNAs
Authors: Granot Joseph , Assa‐Munt Nuria , Kearns David R. 
Published: May 2005

AbstractIt has been inferred from previous studies that Mn2+ ions bind preferentially to G·C base pairs in DNA, and it has even been suggested that this preference for G·C pairs might be responsible for some of the Mn2+ specific effects observed in various biochemical reactions. In this paper we investigate the AT/GC preference of Mn2+ by direct competition studies in which AT‐rich DNA was dialyzed against GC‐rich DNA in the presence of varying amounts of Mn2+. Analysis of these results demonstrates that over a wide range of Mn2+/DNA(P) molar ratios, Mn2+ binds to A·T and to G·C base pairs with virtually identical affinity, although in a somewhat different mode. Both the present and previous nmr, uv, CD, and melting studies are discussed in terms of the different modes of binding of Mn2+ to single‐ and double‐stranded DNA.
Influence of surfactants on the conformation of β‐lactoglobulin B using circular dichroism
Authors: Damon Amy Jo Hillquist , Kresheck Gordon C. 
Published: May 2005

AbstractThe effect of several surfactants on the secondary structure of bovine β‐lactoglobulin B was determined from the circular dichroism spectra. The spectra were measured at several concentrations of surfactant ranging from 1 mg/mL to the critical micelle concentration. The surfactants studied were sodium dodecyl, decyl, and octyl sulfate, sodium dodecyl sarcosinate, dodecyltrimethylammonium bromide. The data were analyzed using the method of Chen et al. [Biochemistry (1974) 13, 3350–3359] to determine the percentage of α‐helix, β‐sheet, and unordered form at each surfactant concentration. In every case, an increase in structured form and a 20–25% decrease in the amount of unordered form was noted when the surfactant concentration reached the critical micelle concentration. However, the relative amounts of the two structured forms present depend on the surfactant used. The profile of the secondary structure of the protein also varied from surfactant to surfactant as the protein was titrated, probably reflecting the delicate balance between ionic and nonionic forces that governs the secondary structure of β‐lactoglobulin and most other globular proteins in aqueous solution.
Flow birefringence of T7 phage DNA: Dependence on salt concentration
Authors: Cairney Kim L. , Harrington Rodney E. 
Published: May 2005

AbstractWe have determined extinction angles and flow birefringence of T7 bacteriophage DNA over a wide range of shear, polymer concentration, and solvent ionic strength. From these data, information on the simple salt dependence of coil permeability to solvent and on short‐range intrachain interactions (persistence length) was obtained. At all ionic strengths, our results are consistent with a partially draining coil in the Gaussian subchain dynamical theory of Rouse‐Zimm‐Tschoegl‐Bloomfield. Salt dependence of persistence length is comparable to, although somewhat less than, that obtained previously using similar methods with a fivefold higher‐molecular‐weight DNA (T2 bacteriophage DNA). Possible reasons for observed discrepancies are analyzed, and the results of this work are compared in detail to other current studies of solvent ionic strength dependence in persistence length and hydrodynamic properties of DNA.
Conformational dependence of the vicinal proton coupling constant for the CαCβ bond in peptides
Authors: Cung M. T. , Marraud M. 
Published: May 2005

AbstractWe use the nmr data concerning the CαHCβH fragment in eight peptides with rigid side chains to parametrize a Karplus correlation between the vicinal proton Jαβ coupling constant and the dihedral angle θ. When considering molecules containing the fragment CαHαCβHβHβ′, the three‐dimensional structure of the model peptides does not need to be known with accurate precision, since each set of Jαβ and Jαβ′ coupling constants is then related to the coefficients of the Karplus equation. A good correlation is observed with the Karplus equation,

which is in substantial agreement with the Jαβ coupling constants reported for rigid as well as rotating CαCβ bonds in peptides.
Interaction of poly C with cis‐ and trans‐diamminedichloroplatinum (II): Secondary structure effects
Authors: Strommen Dennis P. , Peticolas Warner L. 
Published: May 2005

AbstractThe interactions of the ribonucleotide poly C with cis‐ and trans‐diamminedichloroplatinum (II) were probed with Raman spectroscopy. Both platinum compounds attack the N‐1 position of the cytosine residue, while the trans form appears to attack the PO2− as well. Raman difference spectra obtained from samples of poly C containing similar amounts of the respective Pt compounds indicate that the trans form is able to disrupt the secondary structure of poly C to a greater degree than the cis form. This latter observation may be a contributing factor in the low therapeutic index exhibited by the trans form.
Polynucleotide folding in yeast tRNAPhe: Elucidation of short‐, medium‐, and long‐range interactions of sugar–phosphate–sugar backbone and base using a “blocked” nucleotide probe
Authors: Malathi R. , Yathindra N. 
Published: May 2005

AbstractIt has recently been proposed that the repeating backbone nucleotide may be regarded as consisting of two blocks of equal magnitude representable by two virtual bonds. Implicit consideration of the nucleotide (ψ,ψ) and internucleotide (ω′,ω) geometry that generate variety in polynucleotide conformations, and of the constancy of the repeating structural moieties (P‐C4′ and C4′‐P) independent of the above rotations, has enabled us to utilize this scheme in the study of ordered structures such as di‐, oligonucleotides and, most significantly, tRNA. The polynucleotide folding dictated by short‐, intermediate‐, and long‐range interactions in the monoclinic and orthorhombic forms is described and compared through circular plots depicting the virtual bond torsions and distance plots constructed independently for backbone as well as bases. The torsions and the bond angles associated with the virtual bonds afford a clear distinction between ordered helical segments from loops and bends of tRNA. Lower virtual bond torsions (−60° to 60°) concomitant with higher values of virtual bond angles characterize various bend regions, while torsions around 160°–210° typify ordered helical strands. The distance plot elucidates the type of interaction associated with various sub‐structures (helix–helix, helix–loop, and loop–loop) that form the constituents of different structural domains. Several other features such as the manifestation of the P10 loop and the approximate twofold symmetry in the tRNA molecule are conspicuous on the distance plot.
Theory of DNA condensation: Collapse versus aggregation
Authors: Post Carol Beth , Zimm Bruno H. 
Published: May 2005

AbstractIn an unfavorable solvent environment, DNA (and other polymers) undergo a conformational transition to a collapsed form, accompanied by a dramatic reduction in the effective volume of the molecule. Solvent conditions leading to the collapse are the same as those that cause aggregation. We give here a thermodynamic description of the collapse and its relations to aggregation (or precipitation). This is formulated in terms of the Flory‐Huggins theory of the thermodynamics of polymer solutions. The results show that it is possible for three different states of DNA to be stable under different conditions: (1) the extended random coil, (2) the collapsed coil, and (3) a concentrated phase of aggregated random coils. The collapsed coil is predicted to be stable against aggregation only at high dilutions, of the order of parts per million. For DNA the transition between the extended coil and the collapsed coil is predicted to be discontinuous, in the sense that intermediate states are not present, because of the relatively high stiffness of the chain. The transition should appear diffuse because of the small size of the single molecule in comparison to macroscopic systems.
A fully nonequilibrium concerted model for enzymes
Authors: Shiner J. S. 
Published: May 2005

AbstractThe concerted model of Monod, Wyman, and Changeux is generalized so that all effects of interactions for an enzyme operating at a nonequilibrium stationary state are considered. In contrast to the original model, which is based on an analogy to equilibrium ligand binding, the generalization may show both “positive” and “negative cooperativity” in both catalytic binding and conformational processes. Furthermore, in contrast to any equilibrium binding model, the Hill coefficients may be greater than the number of sites n. For catalysis, the maximum value is 2n, and for conformational changes, n + 1. These points are illustrated by two cases that yield simpler analytic expressions. The first obtains when catalysis occurs on a much faster time scale than the conformational changes, and the second, when this situation is reversed.
Conformational studies of diastereoisomeric cyclo(alanyl‐phenylalanyl) with the coupling constants 1H–1H, 15N–1H, 13C–1H, and 13C–15N
Authors: Vicar Jaroslav , Blaha Karel , Piriou François , Juy Michel , Lam‐thanh Hung , Fermandjian Serge 
Published: May 2005

AbstractThe cyclodipeptides cyclo(L‐alanyl‐L‐phenylalanyl) and cyclo(D‐alanyl‐L‐phenylalanyl) were synthesized with various atoms substituted by the isotopes 15N and 13C. Thus, the coupling constants 15N–1H, 13C–1H, and 13C–15N could be obtained, in addition to the commonly used 1H–1H constants. The applicability of these coupling constants for obtaining conformational information on side chains and substituted 2,5‐piperazinedione rings is discussed.
Linear dichroism studies of nucleic acids. II. Calculation of reduced dichroism curves of A‐and B‐form DNA
Authors: Matsuoka Yukio , Nordén Bengt 
Published: May 2005

AbstractWe have calculated the uv linear dichroism for the A‐ and B‐forms of DNA using π‐π* transition moments and band components determined from the free DNA bases. The reduced dichroism (LDR) as a function of wavelength is estimated is in the 220–300‐nm region, for both the oriented‐gas model and a simple exciton model. For B‐form DNA, LDR is obtained to −1.48S (S being the orientation factor) over the whole wavelenth region by both models. For A‐form DNA, LDR is not constant, but changes monotonically from about −1.15S at 220 nm to about −1.35S to −1.45S at 300 nm, depending on base combination and degree of interaction (−1.35S for the oriented gas). It is emphasized that a common assumption of a single “effective” transition moment of the principal band at 260 nm may not generally be made because of the extensive overlap of differently polarized bands. The possibility of using the reduced dichroism curve for characterizing the secondary structure of DNA is discussed.
Molecular structure of t‐butyloxycarbonyl‐Leu‐Aib‐Pro‐Val‐Aib‐methyl ester, a fragment of alamethicin and suzukacillin: A 310‐helical pentapeptide
Authors: Rao Ch. Pulla , Balaram P. 
Published: May 2005

AbstractThe pentapeptide Boc‐Leu‐Aib‐Pro‐Val‐Aib‐OMe, a fragment of alamethicin and suzukacillin, crystallizes in the space group P21, with a = 11.034 (2), b = 10.894 (2), c = 15.483 (2) Å, β = 104.80 (2)° and Z = 2. The crystal structure has been solved by direct methods and refined to an R value of 0.069. The peptide backbone folds into a right‐handed 310‐helical conformation, stabilized by two intramolecular 4 → 1 hydrogen bonds between the Leu(1) CO and Val(4) NH and Aib(2) CO and Aib(5) NH groups. The solid‐state conformation is consistent with results of spectroscopic analysis in solution.
Structure of a cellulose II‐hydrazine complex
Authors: Lee David M. , Blackwell John , Litt M. H. 
Published: May 2005

AbstractThe structure of a crystalline cellulose II‐hydrazine complex has been determined by x‐ray diffraction methods as part of an investigation of cellulose‐solvent interaction. The complex studied was that formed when Fortisan fibers were swollen in hydrazine and then vacuumdried. The unit cell is monoclinic with dimensions a = 9.37 Å, b = 19.88 Å, c = 10.39 Å, and γ = 120.0° and contains disaccharide segments of four chains, with one hydrazine per glucose residue. In view of the limited x‐ray intensity data, the structure has been determined based on an approximate unit cell containing two chain segments, with a = 4.69 Å, using the linked‐atom least‐squares refinement procedures. The refined model contains antiparallel cellulose chains that are linked by both intermolecular hydrogen bonds and hydrogen‐bonded hydrazine molecules. The parallel chains in the 020 planes are packed in register, leading to stacks of chains analogous to those in chitin. All the hydroxyl groups are satisfactorily hydrogen‐bonded, and each hydrazine forms four donor and two acceptor hydrogen bonds, including an NH…N bond between hydrazines. From this work it can be seen that the interaction of cellulose II with hydrazine involves scission of the intermolecular hydrogen bonds followed by disruption of the stacks of quarter‐staggered chains. The latter effect is probably necessary for hydrazine to act as a cellulose solvent.
Multinuclear magnetic resonance studies of monomers and diemrs containing 2′‐fluoro‐2′‐deoxyadenosine
Authors: Cheng Doris M. , Kan Lou‐Sing , Ts'o Paul O. P. , Uesugi Seiichi , Takatsuka Yoko , Ikehara Morio 
Published: May 2005

AbstractA series of 2′‐fluorinated adenosine compounds, dAfl, dAflp, pdAfl, dAfl‐A, A‐dAfl, and dAfl‐dAfl, have been investigated by nmr spectroscopies. The 1H‐, 19F‐, and 31P‐nmr data provide structural information from different parts of these moleucles. The pKa of the phosphate group of these two 2′‐fluoro‐2′‐deoxyadenosine monophosphates was found to be the same as that of hte parent adenosine monophosphate. As for the pentose conformation, the 3E population is greatly increased as a result of the fluorine substitution at the C2′ position. However, the populations of conformers of gg (C4′‐C5′) and g′g′ (C5′‐O5′) and the average angle ϕ′(C3′‐O3′) of the 2′‐fluoro compounds remain unchanged as compared to the natural riboadenosine monomer and dimer (A‐A). Thefefore, the backbone conformation of the 2′‐fluoro‐2′‐deoxy‐adenosine, its monophosphates and dimers, resembles that of RNA. The extent of base‐base overlapping in these 2′‐fluoro‐2′‐deoxy‐adenosine‐containing dimers is also found to be similar to or even greater than A‐A. Thus, the conformations of these compounds can be considered as those in the RNA family.These fluorocompounds also serve as models for a careful study on the 19F‐nmr in nucleic acid. The 19F chemical‐shift values are sensitive to the environment of the fluorine atom such as ionic structure of the neighboring group(s) (phosphate of base), solvation, and ring‐ruccent anisotropic effect from the base(s). Qualitatively, the change of the 19F chemical‐shift values (up to 2 ppm) is much larger than that of 1H‐nmr (up to 0.5 ppm) in the dimers. Using dAfl·poly(U), poly(dAfl)·poly(dAfl), and poly(dAfl)·poly(U) helix–coil transition as model systems, the linewidth of 19F in dAfl‐ residues reflects effectively the mobility of the unit in the nucleic acid complex as calibrated by uv data and by 1H‐nmr. Therefore, application of 19F‐nmr spectroscopy on fluorine‐substituted nucleic acid can also be used to detect nucleic acid‐nucleic acid interaction in complicated systems.
Laser light scattering of PBLG in DMF
Authors: Kubota K. , Chu B. 
Published: May 2005

AbstractWe report measurements of static and dynamic properties of poly(γ‐benzyl‐L‐glutamate) (PBLG) in dimethyl formamide at 25 °C using laser light scattering. Correlation‐function profile analyses were performed using the histogram method. The resultant average linewidth and dispersion were reconfirmed using the cumulants method. We were able to determine the molecular‐weight distribution of PBLG using the histogram method and to confirm the polydispersity for rod polymers in solution to be roughly Mw/Mn ∼ 1 + μ2/Γ2. In our analysis of the Rayleigh linewidth, we used both the rigid‐rod model and the Fujime approach involving rod flexibility. We obtained very reasonable agreement between the Fujime theory and our experiments and concluded that for most stiff polymers of interest, it would be more appropriate to use the Fujime approach, which could also yield a rod‐flexibility parameter. In semidilute solutions, we observed two effects, namely, a maximum in the diffusion coefficient and a broadening of the linewidth distribution function at both low and high frequencies, which were not predicted by the Doi‐Edwards theory.