bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA sequencing and helix–coil transition. II. Loop entropy and DNA melting
Authors: Azbel M. Ya. 
Published: December 2004

AbstractAn explicit analytical theory of DNA melting is constructed. It accounts for the loop entropy and the elasticity of DNA strands. Explicit analytical formulas are presented for the melting curves of natural DNA and periodic polymers. The nature of the DNA helix–coil transition is investigated, and it is found to crucially depend on the nucleotide sequence.
Preferred phosphodiester conformations in nucleic acids. A virtual bond torsion potential to estimate lone‐pair interactions in a phosphodiester
Authors: Srinivasan A. R. , Yathindra N. , Rao V. S. R. , Prakash S. 
Published: December 2004

AbstractThe lone‐pair orbital interactions arising in a phosphodiester are incorporated into semiempirical conformational energy calculations using a unifold “torsional potential” around the virtual bond linking the ester oxygen atoms. The results explain the observed experimental data better than other methods.
Contribution of electrodiffusion to the dynamics of electrically stimulated changes in mechanical properties of collagen membranes
Authors: Shoenfeld Norman A. , Grodzinsky Alan J. 
Published: December 2004

AbstractWe have studied the kinetics of oscillatory tensile forces in collagen membranes. These forces were generated by sinusoidal electric fields applied across the membrane. Both the magnitude and phase of the measured force changed with frequency over a three‐decade range. The membrane‐separated electrolyte baths had different ionic strength but identical non‐isoelectric pH. Changes in intramembrane ionic strength due to the electric field were calculated over the same frequency range via an electrodiffusion model that was generalized to include convection and electrokinetic coupling. A comparison of the experimental and theoretical phases and amplitudes versus frequency suggests that electrodiffusion is the dominant rate‐limiting process in this electromechanochemical transduction. These results are relevant to electrostatic interactions in connective tissues and to membrane‐based filtration devices in which membrane permeability may be actively varied and controlled by an applied electric field.
Heat capacity changes and partial molal heat capacities of some di‐ and tripeptides in water
Authors: Prasad K. P. , Ahluwalia J. C. 
Published: December 2004

AbstractIntegral enthalpies of solution of several dipeptides and tripeptides in water at low concentrations have been determined at 25 and 35°C. These data have been used to derive the changes in heat capacity on dissolution at infinite dilution ΔC at 30°C. Limiting partial molal heat capacities ΔC have been determined by combining ΔC with Cp2 (heat capacity of pure solid peptides). Using the data on ω‐amino acids and these peptides, the partial molal heat capacity of a peptide group CONH was semiquantitatively estimated.
Polyelectrolyte theory. I. Counterion accumulation, site‐binding, and their insensitivity to polyelectrolyte shape in solutions containing finite salt concentrations
Authors: Guéron M. , Weisbuch G. 
Published: December 2004

AbstractWe have computed the Poisson‐Boltzmann distribution of counterions around polyelectrolytes in solutions containing finite salt concentrations. The polyelectrolytes considered here are highly charged in the sense that ξ > 1, ξ being the linear charge density parameter for cylinders, which is generalized by us to other shapes.Contrary to the situation at zero salt concentration, the counterion distribution is not strongly shape dependent, being similar for cylinders or spheres which have the same superficial charge density and radius of curvature Rc. The distribution resembles that in the neighborhood of a plane with the same charge density.Three regions are distinguished. (1) In the “inner region” which extends up to a distance Rc/2ξ from the surface, the counterion distribution is essentially salt independent. The counterion concentration in the immediate vicinity of the polyelectrolyte surface (CIV) is quite high, typically 1–10M, and proportional to the square of the surface charge density, which is its main determinant. (2) An intermediate region extends out to a distance where the electrostatic potential is equal to κT/e. This distance is comparable to λ for plane and cylinder, and smaller for the sphere. (3) In the outer region, the distribution is hardly influenced by the details of the inner region, on which it cannot, therefore, give much information. Colligative properties are dependent on the distribution in the outer region and are fairly well predicted even by a rudimentary theory.The large value of the CIV implies that site binding must often be significant. It can be computed by applying the mass‐action law to site‐bound counterions in equilibrium with the counterions in the neighborhood, whose concentration is the CIV, the relevant equilibrium constant being that for the binding of counterions to isolated monomer sites. Because the CIV is insensitive to salt concentration, this will also be the case for site binding. With the graphs provided, one can compute the extent of sitebinding within the Poisson‐Boltzmann framework.The “condensation radius,” i.e., the radius encompassing a counterionic charge 1 − ξ−1 around a cylinder, is found to be large. It varies with salt concentration and tends to infinity as the salt is diluted. Neither this radius nor the charge fraction 1 − ξ−1 of condensation theory plays any special role in the counterion distribution.The “finite‐salt” results apply to salt concentrations, typically as low as 1–10 mM. This encompasses, among others, all experiments on biological polyelectrolytes.
Time‐dependent phosphorescence anisotropy measurements of the slow rotational motions of proteins in viscous solution
Authors: Strambini Giovanni B. , Galley William C. 
Published: December 2004

AbstractA method of monitoring slow rotational motions of proteins from the decay of the intrinsic phosphorescence is described. The phosphorescence is excited with a 10‐μsec pulse of vertically polarized light from an air gap lamp, and the anisotropy was computed as a function of time from the simultaneously detected vertically and horizontally polarized components of the emission. The approach is illustrated with time‐dependent measurements of the anisotropy of the tryptophan phosphorescence of Staphylococcus aureus nuclease, bovine carbonic anhydrase, and liver alcohol dehydrogenase in glycerol‐phosphate buffer between −90 and −70°C. The temperature‐ and molecular‐weight dependence of the exponential decays in the anisotropy indicate that overall rotation of the proteins is at the origin of the depolarization. The potential of the approach as a probe of the slow rotational motions of proteins in membranes and other macromolecular complexes is stressed.
Nearest‐neighbor and next‐nearest‐neighbor effects in the proton NMR spectra of the oligoribonucleotides ApGpX and CpApX
Authors: Everett Jeremy R. , Hughes Donald W. , Bell Russell A. , Alkema Dirk , Neilson Thomas , Romaniuk Paul J. 
Published: December 2004

AbstractThe variable‐temperature proton nmr spectra of the oligoribonucleotides in the series CpApX and the series ApGpX, X = A, G, C, U, together with the parent dimers CpA and ApG have been measured. A complete analysis of all the nonexchangeable base proton resonances and ribose H‐1′ proton resonances was made. The presence of trends in the shielding abilities of the various bases at both the nearest‐neighbor and next‐nearest‐neighbor positions were identified. The observed shieldings could be used to predict the chemical shifts of protons in related systems. Based on the empirical results from ribodinucleoside monophosphates, the temperature‐dependent behavior of the J1′2′ coupling constants of the triribonucleotides suggested that the compounds in the CpApX series stacked from the 5′‐end to the 3′‐end, while those in the ApGpX series stacked from the 3′‐end to the 5′‐end.
On the blue color of triiodide ions in starch and starch fractions. II. Characterization of the changes in absorption and circular dichroism spectra of triiodide ions in amylose with the DP
Authors: Handa Takashi , Yajima Hirofumi 
Published: December 2004

AbstractThree steps appeared in the color change of triiodide ions in amylose with the degree of polymerization (DP), associated with the change in the CD spectra. First, the shoulder around 480 nm developed strikingly from the achromic point of DP 10 to DP 30. Second, the blue color developed critically from DP 30 and deepened on going to DP 100, where the consistent increase in the intensities of the absorption and mutually split CD bands (+,−) was observed. Third, the deep bluing associated with the shallowing of the dual CD band was observed above DP 100. This change depended strongly on the mixing rate of I2 with amylose in the presence of excess KI. In particular, the signs of the dual CD band changed from (+,−) to (+,+) for high‐DP amyloses at high I2 in the rapid‐mixing system. The first and second phenomena are explained in terms of the enhancements in the short‐ and long‐axis transitions dipoles of the ions in the dimeric unit, respectively, being associated with the change in their spatial configuration due to the augmented shear from the stepwise promotion in the types and number of hydrogen bonds in the complex with the DP. The third phenomenon was attributed to the interactions of the skewed ions located in the knot portions and in the associated helices of the aggregate.
Transport properties of particles with segmental flexibility. II. Decay of fluorescence polarization anisotropy from hinged macromolecules
Authors: Harvey Stephen C. , Cheung Herbert C. 
Published: December 2004

AbstractAn algorithm is presented for the Monte Carlo simulation of the decay of fluorescence polarization from segmentally flexible molecules. Based on the random walk model of Brownian motion, the treatment explicitly follows the stochastic changes in the diffusion coefficients as the molecule bends. It includes the effects of a linear restoring force opposing the bending and the effects of hydrodynamic coupling between the translational, rotational, and bending motions. One application is presented: the simulation of anisotropy decay curves for hinged rods. A variety of decay curves are obtained, including single‐ and multiexponential behavior, and the following conclusions are reached: (1) increasing the flexibility is usually, but not always, accompanied by a more rapid rate of depolarization; (2) reducing the size of the fluorescent subunit will usually, but not always, increase the rate of depolarization; and (3) the complex interplay between the effects of molecular shape, relative sizes of the subunits, restoring force, and orientation of the transition dipoles renders it unlikely that any simple method can be used to interpret anisotrophy data without simulation. In particular, it is not possible to determine the extent of bending by fitting the data with the two‐exponential approximation used by some investigators in the past.
13C‐nmr spectroscopy of red algal galactans
Authors: Usov Anatoly I. , Yarotsky Sergey V. , Shashkov Alexandr S. 
Published: December 2004

Abstract13C‐nmr spectra of red seaweed galactans, belonging to the agar and carrageenan groups or having the “intermediate” type of structure, were interpreted on the basis of 13C‐nmr spectra of model compounds. Signal assignments have been made for most of the known extreme structures of such galactans. 13C‐nmr spectroscopy was shown to be a rapid and convenient method of structural analysis, which permits one to determine the type of galactan structure, the absolute configurations of its constituents (galactose and 3,6‐anhydrogalactose), and the positions of the sulfate and O‐methyl groups in a polysaccharide molecule.
Circular dichroism of nucleic acid monomers. I. Calculated adenosine and 2′‐deoxyadenosine CD spectra
Authors: Moore Dexter S. 
Published: December 2004

AbstractA combination of the DeVoe and Kirkwood polarizability concepts is developed to calculate CD spectra of nucleic acid monomers. The method is perfectly general and applies to any system where the constituents have absorption properties which are widely separated in terms of frequency. The theory is applied to calculate the CD spectra of adenosine and 2′‐deoxyadenosine conformers. Bond polarizabilities are evaluated for the ribosyl moiety of adenosine, as a function of glycosidic rotational angles and polarizability anisotropies. It is found that a wide range of C‐C and C‐O bond polarizabilities give similar CD results. Isotropic atom polarizabilities are also evaluated. It is found that the CD results using these polarizabilities do not differ significantly from those obtained with bond polarizabilities. The CD spectra of adenosine and 2′‐deoxyadenosine are calculated for three x‐ray diffraction determined geometries: A‐form RNA, B‐form DNA, and C‐form DNA. The results indicate that the monomer CD spectra are strongly dependent on the precise geometry and appear to be of importance in understanding the spectra of oligomers and polymers. The deoxyadenosine conformers are found to have calculated CD spectra which are less intense than those of the ribosyl conformers. These results indicate that the measured differences between the CD magnitudes of ribo‐ and deoxyriboadenosine are due to the presence or absence of the 2′‐hydroxyl. Weighted averaged adenosine CD spectra are calculated with the aid of probability distributions from conformational energy calculations. The results suggest a new method for obtaining empirical monomer parameters for use in optical calculations. The calculations in this paper indicate for the first time that DeVoe theory, in combination with the Kirkwood theory, provides a useful method for the calculation of the CD spectra of nonpolymeric molecules.
Fluorescence quenching of methyl‐2‐aminobenzoate in the presence of beta‐cyclodextrin: A model for the dynamic quenching of chromophores in hydrophobic regions of biopolymers
Authors: De Korte Aart , Langlois Richard , Cantor Charles R. 
Published: December 2004

AbstractThe binding constant of methyl‐2‐aminobenzoate to beta‐cyclodextrin was determined by fluorescence titration to be 92.1M−1 at 25°C in pH 7 buffer. Beta‐cyclodextrin dramatically protects methyl‐2‐aminobenzoate against quenching by iodate and protects, though much less efficiently, against the smaller quencher, iodide. The observed decrease in fluorescence lifetime of the methyl‐2‐aminobenzoate‐beta‐cyclodextrin complex on addition of quencher indicates that the quenching mechanism is collisional (dynamic). The dependence of quenching rate on solvent viscosity is less than expected from simple theoretical considerations. However, the extent of beta‐cyclodextrin protection is essentially viscosity‐independent. These model studies show the usefulness of iodate as a quencher and encourage further attempts at quantitative interpretation of quenching studies on chromophores attached to biopolymers.
Variation in the degree of branching of the glycogens and an approximate relationship between average exterior chain length and iodine staining
Authors: Fales Frank W. 
Published: December 2004

AbstractPrecise evaluation of the branching characteristics of glycogen complex from a variety of sources was made by replicate determinations of end groups by a reproducible periodate oxidation method and by replicate determinations of the percentage degradation by exhaustive β‐amylase activity. Also, the iodine staining characteristics of these samples were studied. The following observations were made. During the synthesis of glycogen by baker's yeast, there was a significant increase in the average chain length of the glycogen, and the maximal optical absorbance AM of the glycogen–iodine complex doubled. The AM decreased linearly with increasing temperature, and increases in iodine concentration caused increases in both the AM and the wavelength of maximal absorbance. There was a general increase in the AM of the glycogen with increasing exterior chain length, but there were minor deviations due to some dependence on the source of the glycogen. Unlike the linear relationship between the AM per chain and the average chain length of the amyloses, the AM per chain was exponentially related to the average exterior chain length of the glycogens.
Axial ranking of residues in collagen in relation to edge association and fibril formation
Authors: Kumar Narinder G. , Cunningham Leon W. 
Published: December 2004

AbstractIn our earlier analysis of intermolecular interactions between collagen molecules, a major concern with the program employed is that it compared numbers of interactions between residues located on edges of defined, identical width and thus would not necessarily compare the same number of residues in each edge. This would be particularly true of some values of θ where well‐defined vertical ranking of residues occurs. We have examined ranking of residues in relation to intermolecular edge association between bovine skin [α1(I)]3 model collagen molecules by utilizing two different methods of counting intermolecular interactions between residues. The interaction peaks at θ = 27.69° and 36.00° are absent or relatively less intense in the plots obtained by utilizing radial distances between interacting residues instead of vertical bands of defined width. These studies suggest caution in accepting recently reported analyses of superhelix coiling of the collagen molecule which point to values of 27.69° or 36.00° for the twist of the superhelix. Although intramolecular interactions clearly point to interaction of collagen molecules at D intervals, they are insufficiently restricted in distribution to provide a reliable estimate of the superhelix angle by procedures so far employed.
Solid‐state conformation of copolymers of β‐benzyl‐L‐aspartate with L‐alanine, L‐leucine, L‐valine, γ‐benzyl‐L‐glutamate, or ϵ‐carbobenzoxy‐L‐lysine
Authors: Sederel Willem L. , Bantjes Adriaan , Feijen Jan , Anderson James M. 
Published: December 2004

AbstractThe solid‐state conformation of copolymers of β‐benzyl‐L‐aspartate [L‐Asp(OBzl)] with L‐leucine (L‐Leu), L‐alanine (L‐Ala), L‐valine (L‐Val), γ‐benzyl‐L‐glutamate [L‐Glu(OBzl)], or ϵ‐carbobenzoxy‐L‐lysine (Cbz‐L‐Lys) has been studied by ir spectroscopy and circular dichroism (CD). The ir spectra in the region of the amide I and II bands and in the region of 700–250 cm−1 have been determined. The results from the ir studies are in good agreement with data obtained by CD experiments. Incorporation of the amino acid residues mentioned above into poly[L‐Asp(OBzl)] induces a change from the left‐handed into the right‐handed α‐helix. This conformational change for the poly[L‐Asp(OBzl)] copolymers was observed in the following composition ranges: L‐Leu, 0–15 mol %; L‐Ala, 0–32 mol %; L‐Val, 0–8 mol %; L‐Glu(OBzl), 3–10 mol %; and Cbz‐L‐Lys, 0–9 mol %.
Local hydrophobicity stabilizes secondary structures in proteins
Authors: Kanehisa Minoru I. , Tsong Tian Yow 
Published: December 2004

AbstractThe probability of occurrence of helix and β‐sheet residues in 47 globular proteins was determined as a function of local hydrophobicity, which was defined by the sum of the Nozaki‐Tanford transfer free energies at two nearest‐neighbors on both sides of the amino acid sequence. In general, hydrophilic amino acids favor neither helix nor β‐sheet formations when neighbor residues are also hydrophilic but favor helix formation at higher local hydrophobicity. On the other hand, some hydrophobic amino acids such as Met, Leu, and Ile favor helix formation when neighbor residues are hydrophilic. None of the hydrophobic amino acids favor β‐sheet formation with hydrophilic neighbors, but most of them strongly favor β‐sheet formation at high local hydrophobicity. When the average of 20 amino acids is taken, both helix and β‐sheet residue probabilities are higher at higher local hydrophobicity, although the increase is steeper for β‐sheets. Therefore, β‐sheet formation is more influenced by local hydrophobicity than helix formation. Generally, helices are nearer the surface and tend to have hydrophilic and hydrophobic faces at opposite sides. The tendency of alternating regions of hydrophilic and hydrophobic residues in a helical sequence was revealed by calculating the correlation of the Nozaki‐Tanford values. Such amphipathic helices may be important in protein–protein and protein–lipid interactions and in forming hydrophilic channels in the membrane. The choice of 30 nonhomologous proteins as the data set did not alter the above results.
1H‐ and 13C‐nmr studies on caffeine and its interaction with nucleic acids
Authors: Kan Lou‐sing , Borer Philip N. , Cheng Doris M. , Ts'o Paul O. P. 
Published: December 2004

AbstractThe relative orientation of caffeine in stacks formed by self‐association in aqueous solution has been evaluated by both 1H‐ and 13C‐nmr spectroscopy. The data, which were interpreted through the calculation of ring‐current and atomic diamagnetic anisotropic effects of the caffeine molecule, suggest two caffeine bases may stack in a nearly orthogonal manner. The interactions between caffeine and adenylyl‐3′,5′‐adenosine, polyadenylic acid, and ribo‐(A‐A‐G‐C‐U‐U)2 helix were also studied by nmr at different caffeine/base ratios and at varying temperatures. The results show that caffeine tends to stack on the top of the terminal purine bases or to insert (the single‐stranded) or to intercalate (the double‐stranded) between purine bases.
On the blue color of triiodide ions in starch and starch fractions. III. Resonance Raman spectra of bluing species in amylose
Authors: Handa Takashi , Yajima Hirofumi , Kajiura Teruo 
Published: December 2004

AbstractIn order to clarify the characteristics of the basic units responsible for the blue coloring of iodine/iodide in amylose, we made a resonance Raman spectroscopic study at several KI concentrations using excitation by Ar+, He‐Ne, and Kr+ lasers and amyloses with the degrees of polymerization (DP) of 30, 100, 300, and 1000. Similar Raman spectra were observed, regardless of the KI and I2 concentrations, DP, and excitation wavelengths. Four Raman lines appearing at 159, 111, 55, and 27 cm−1 were obviously fundamental tones, with a degree of depolarization ρ of ca. 1/3 for every spectrum. However, the internal ratios of the intensities of the 159, 55, and 27 cm−1 lines to that of the 111‐cm−1 line decreased with increasing KI concentration. Based on the value of ρ, the assignment of the fundamental lines was made by taking a schematic model of the true motions as a projection in separately analyzing the modes of stretching and bending vibrations for a pseudolinear polyiodide chain, which we found to be perturbed by the external forces of the amylose lattice. In accordance with the variation of the force constants from the assignment of the spectra associated with the change in the composition of the bound species, it was concluded that the basic unit changed from I to I through I with decreasing KI concentration.