bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study of large DNA fragments in agarose gels by transient electric birefringence
Authors: Chu Benjamin , Wang Zhulun , Xu Renliang , Lalande Marc 
Published: December 2004

AbstractThe pulsed‐field gel electrophoresis (PFG) is a newly developing technique used in the fractionation of large DNA fragments. Advances in PFG demand a better understanding in the corresponding mechanisms of DNA dynamics in the gel network. Detailed experiments are needed to verify and to extend existing theoretical predictions as well as to find optimum conditions for effecient separation of large DNA fragments. In the present study, deformation of large DNA fragments (40 ∼ 70 kilobase pairs) imbedded in agarose gels were investigated by using the transient electric birefringence (TEB) technique under both singular polarity and bipolarity electric pulses at low applied electric field strengths (E ≤ 5 V/cm). The steady‐state optical retardation (δs) of DNA molecules is linearly proportional to E2. At a given E, the amplitude of optical retardation [δ(t)] increases monotonically with the pulse width (PW) and then reaches a plateau value [δ(t = 0) = δs] where t = 0 denotes the time when the applied field is turned off or reversed. The field‐free decay time (τ ∼ a few minutes) is several orders of magnitudes slower than that from previous TEB observations using high electric field strengths (E ∼ kV/cm) and short pulse widths (PW ∼ ms). The degree of deformation (stretching and orientation) and the time of restoration to the equilibrium conformation of overall DNA chains have been related to δ and τ. In field inversion measurements, exponentially rising and linearly falling of birefringence signals in the presence of forward/inverse applied fields were observed. The rising and falling of birefringence signals were reproducible under a sequence of alternating pulses. Comparison of our results with literature findings and discussions with theories are presented.
Induction of CD in some anionic dyes by cationic chitosan
Authors: Pal Medini Kanta , Pal Prasun Kumar 
Published: December 2004

AbstractChitosan can be converted into a polycation by dissolving it in an acid, and this polycation (I) induces blue‐shifted metachromasia in suitable anionic dyes, C.I. acid red 88 and C.I. acid orange 7, after reacting with the dyes with 1 : 1 stoichiometry (P/D). Both these dye–polymer systems exhibit strong biphasic CD in the visible range. Biphasic CD, as well as blue‐shifted metachromasia, indicates strong dye–dye interactions in these systems. Monophasic CD are observed only in conditions where metachromasia is partially disrupted due to poor dye–dye interactions.The 21‐helical conformation, as confirmed for the present polymer chitin as well as for neutral chitosan, seems to be inadequate in explaining the observed results with (I).
Molecular dynamics simulations and the conformational mobility of blood group oligosaccharides
Authors: Yan Zhen‐Yi , Bush C. Allen 
Published: December 2004

AbstractMolecular dynamics simulations were carried out without explicit consideration of solvent to explore the conformational mobility of blood group A and H oligosaccharides. The potential energy force field of Rasmussen and co‐workers was used with the CHARMM program on a number of disaccharide and trisaccharide models composed of fucose, galactose, glucose, N‐acetyl glucosamine, and N‐acetyl galactosamine chosen to represent various fragments of blood group oligosaccharides. In agreement with results of earlier studies, stable chair conformations were found for each pyranoside from which no transitions were detected in simulations as long as 800 ps. Exocyclic dihedral angles, including that of C5—C6, generally show numerous transitions on a time scale of approximately 5–30 ps. The dihedral angles of some but not all glycosidic linkages of blood group oligosaccharides show transitions on the time scale of 30–50 ps, implying that the extent of internal motion in blood group oligosaccharides depends strongly on linkage stereochemistry. For certain blood group A and H oligosaccharides that show limited internal motion in these simulations, we argue that the calculations are consistent with our previous analysis of 1H nuclear Overhauser enhancement (NOE) data that imply single conformations over a wide range of temperature and solvent conditions. While the trajectories are consistent with 13C T1 values that have been interpreted as indicating rigid conformations, measurements of 13C‐NOE and T1 as a function of magnetic field strength are proposed as an improved method for experimental detection of the internal motion that is suggested for certain oligosaccharides in these simulations. The results of these simulations differ substantially from those of peptides of a similar molecular weight in that the oligosaccharides show much less internal motion.
Reversibility of acid denaturation of recombinant interferon‐γ
Authors: Arakawa Tsutomu , Hsu Yeuh‐Rong , Narachi Michael A. , Herrera Charles , Rohde Michael F. , Hennigan Paul 
Published: December 2004

AbstractIt has been shown that interferon‐γ (IFN‐γ) loses activity after acid treatment and this property can be used to distinguish it from other types of interferons. Therefore, reversibility of acid denaturation of IFN‐γ was examined using the reconbinant human protein. The fluorescence spectra showed that conformation of the protein is similar before and after acid treatment, suggesting reversibility of the acid denaturation. The antiviral activity of the protein was also identical in the same treatment. However, the antiviral activity was significantly reduced when it was determined by directly diluting the acidic samples into the assay medium containing high salts and serum proteins. Similar results were obtained with the recombinant murine IFN‐γ. This observation demonstrates that acid denaturation of the IFN‐γ is dependent on the way the protein is renatured, and hence that the difference in response to acid treatment between IFN‐γ and other interferons is quantitative rather than qualitative.
ΔV̄0 of the Na+‐induced B‐Z transition of poly[d(G‐C)] is positive
Authors: Macgregor Robert B. , Chen Marilyn Y. 
Published: December 2004

AbstractThe equilibrium between the right‐ and left‐handed conformations of poly[d(G‐C)] in aqueous NaCl shifts towards the right‐handed (B) form with increasing pressure. The optical density at 290 and 260 nm was determined at 50 and 180 MPa for solutions in which approximately equal amounts of the two conformations were present at 0.1 MPa (atmospheric pressure). Interpretation of the observed changes in terms of a two‐state unimolecular reaction mechanism results in an average molar reaction volume (ΔV̄0) equal to 26 cm3 mol−1 at 22°C; that is, the partial molar volume of B form poly [d(G‐C)] is smaller than that of the left‐handed (Z) form. Based upon the thermodynamics of ion‐pair formation in polar solvents, it is proposed that the positive ΔV̄0 reflects a favorable entropy change for the reaction toward the Z conformation. The larger entropy change of the Z form may derive from the release of water molecules from the hydration spheres of the cation and the poly[d(G‐C)] due to the formation of ionic interactions with the Z conformer. The ΔV̄0 of the transition is similar in sign and and magnitude to the calculated molar volume change of the interaction of Na+ with H2PO in water.
Inclusion of ionic interactions in force field calculations of charged biomolecules – DNA structural transitions
Authors: Klement Reinhard , Soumpasis Dikeos M. , Kitzing Eberhard V. , Jovin Thomas M. 
Published: December 2004

AbstractThe potential of mean force (PMF) approach for treating polyion–diffuse ionic cloud interactions [D. M. Soumpasis (1984) Proceedings of the National Academy of Sciences USA 81, 5116–5120] has been combined with the AMBER force field describing intramolecular interactions. The resultant generalized AMBER‐PMF force field enables one to treat the conformational stabilities and structural transitions of charged biomolecules in aqueous electrolytes more realistically. For example, we have used it to calculate the relative stabilities of the B and Z conformations of d(C‐G)6, and the B and heteronomous (H) conformations of dA12 · dT12, as a function of salt concentration. In the case of d(C‐G)6, the predicted B–ZI transition occurs at 2.4M and is essentially driven by the phosphate‐diffuse ionic cloud interactions alone as suggested by the results of earlier PMF calculations. The ZII conformer is less stable than the B form under all conditions. It is found that the helical parameters of the refined B and Z structures change with salt concentration. For example, the helical rise of B‐DNA increases about 10% and the twist angle decreases by the same amount above 1M NaCl.In the range of 0.01–0.3M NaCl, the H form of dA12 · dT12 is found to be more stable than the B form and its stability increases with increasing salt concentration. The computed greater relative stability of the H conformation is likely due to noninclusion of the free energy contribution from the spine of hydration, a feature presumed to stabilize the B form of this sequence.
Electrophoretic charge density and persistence length of DNA as measured by fluorescence microscopy
Authors: Smith Steven B. , Bendich Arnold J. 
Published: December 2004

AbstractIndividual ethidium‐stained DNA molecules, embedded in an agarose gel made with electrophoresis buffer (0.05 molar salt), are observed using a fluorescence microscope. In the first experiment, open circular 66 kilobase pair (kbp) plasmids, immobilized by agarose fibers threaded through their centers, display entropic “rubber” elasticity. The charged molecules extend in an electric field of several volts per centimeter and contract to a compact random coil when the field is removed. The extension of the plasmids as a function of field strength is consistent with the freely jointed chain model when the effective electrophoretic charge density is set at 15 e− per persistence length. In a second experiment, stained linear 48.5 kbp DNA molecules are observed as random coils immobilized in agarose. A measure of their size, here named the “maximal‐X‐extent,” is taken for 100 molecules and found to average 1.47 μ. A Monte Carlo computer simulation of random coils (freely jointed chain model) gives the same maximal‐X‐extent value when the persistence length is set at 0.08 μ.
Microwave dielectric study on hydration of moist collagen
Authors: Shinyashiki Naoki , Asaka Nobuyuki , Mashimo Satoru , Yagihara Shin , Sasaki Naoki 
Published: December 2004

AbstractTwo dielectric relaxation peaks were found in moist collagen by the time domain reflectometry. The low‐frequency peak around 100 MHz moves little as the water content is varied. Its relaxation strength depends on the content and vanishes for completely dried collagen. This process is concluded to be due to water molecules strongly bound to the tropocollagen. Amount of the bound water is estimated as 0.12 g water/g collagen. Twenty‐one water molecules are bound to one repeat of the triple helix. The existence of stringlike water chains is suggested. If the water content is less than 0.5 g water/g collagen, the high frequency peak locates between those of bound and bulk water. Water among the tropocollagen is weakly bound to the collagen. In the higher region it does not change much with the content, being close to that of bulk water. The bulk water appears in this region.
Intramolecular interference effects in dynamic light scattering: Rigid double spirals and superhelical DNAs
Authors: Wu Pengguang , Song Lu , Schurr J. Michael 
Published: December 2004

AbstractA theory is developed for dynamic light scattering (DLS) from rigid double spirals by treating an invisible rigid cylinder with two helical scattering stripes on opposite sides of its cylindrical surface. The exact initial, or first cumulant, diffusion coefficient Dapp(K) is obtained in terms of the translational diffusion coefficients (D∥ and D⟂) parallel and perpendicular to the symmetry axis, the rotational diffusion coefficients (D and D) around the symmetry and transverse axes, the length (L) and radius (b) of the cylindrical surface bearing the stripes, and the pitch (p). Interference effects, namely geometrical antiresonances, between strands, produce deep minima in the static structure factor S(K) and corresponding prominent peaks in Dapp(K). These peaks in Dapp(K) depend sensitively on the rotational dynamics around the symmetry axis, and nearly vanish when D = 0. Some results for single spirals are also presented. A simpler model in which scattering points are attached at opposite ends of an otherwise invisible thin rigid rod is also treated, and shown to exhibit modest minima in S(K) and corresponding maxima in Dapp(K). Confining this rod to a plane containing K enhances the amplitudes of the oscillations in S(K) and Dapp(K), as expected.Rigid double spirals are employed as crude models for interwound supercoiled DNAs in order to assess the possible occurrence of interference effects. Although native supercoiled DNAs exhibit a cylinder diameter that is much too small to exhibit geometrical antiresonances in the presently accessible range of K2, nearly relaxed supercoiled DNAs are predicted to exhibit their first maximum in Dapp(K) just inside this range. Previously reported data for the effect of Escherichia coli single‐strand binding (ssb) protein on the DLS of supercoiled pBR322 DNA cannot be mimicked by a gradual homogeneous reduction of superhelix density with increasing ssb, but instead can be mimicked by inhomogeneous all‐or‐none binding in which uncomplexed native DNAs and nearly relaxed saturated ssb/DNA complexes coexist in varying proportions. Experimental Dapp(K) and S(K) data for a sample of relaxed pUC8 dimers display, respectively, a broad maximum and a corresponding minimum, in qualitative agreement with rough theoretical predictions.
The sieving of rod‐shaped viruses during agarose gel electrophoresis. I. Comparison with the sieving of spheres
Authors: Griess Gary A. , Moreno Elena T. , Herrmann Richard , Serwer Philip 
Published: December 2004

AbstractThe sieving of rod‐shaped viruses during agarose gel electrophoresis is quantitatively analyzed here with a previously proposed model [G. A. Griess et al. (1989) Biopolymers, 28, 1475–1484] that has one radius (PE) of the effective pore at each concentration of gel. By use of this model and an internal spherical size standard, a plot of electrophoretic mobility vs agarose percentage is converted to a plot of the radius of the effective sphere (effective radius) vs PE. Experimentally, when the concentration of the rod‐shaped bacteriophage, fd, is progressively increased, eventually the electrophoretic mobility of fd becomes dependent on its concentration. The concentration of fd at which this occurs decreases as the agarose concentration decreases. After avoiding this dependence on the concentration of sample, the effective radius of rod‐shaped particles, including bacteriophage fd, length variants of fd, and length variants of tobacco mosaic virus, is found to increase as PE increases until a plateau of approximately constant maximum effective radius is reached at P. In the region of this plateau, the effective sphere's measure that best approximates that of the rod is surface area. However, significant disagreement with the data exists for surface area; the maximum effective radius for fd varies as (length)0.69. For fd and its length variants, the value of 2·P/length increases from 0.21 to 0.86 as the length decreases from 2808 to 367 nm. The dependence of effective radius on PE and the proximity of 2·P to the length of the rod are explained by (a) random orientation of rods at PE values in the region of the plateau, and (b) increasingly preferential end‐first orientation (reptation) of the rod as PE decreases below P. This hypothesis of reptation is supported by a significant dependence of electrophoretic mobility on electrical potential gradient for a PE below, but not above, P. The dependence of 2·P/length on length is not rigorously understood, but is qualitatively explained by flexibility of the rods. This apparent flexibility has thus far prevented determination of a rod's axial ratio from quantitation of sieving during agarose gel electrophoresis. The electrical potential dependence of electrophoretic mobility is determined here by a procedure of two‐dimensional agarose gel electrophoresis. This procedure is also useful for detecting rod‐shaped particles in heterogeneous mixtures of predominantly spherical particles.
Stabilization of helical structure in two 17‐residue amphipathic analogues of the C‐terminal peptide of cytochrome c
Authors: Collawn James F. , Paterson Yvonne 
Published: December 2004

AbstractThe conformations of two 17‐residue peptide analogues derived from the C‐terminal sequence of pigeon cytochrome c (native sequence = KAERADLIAYLKQATAK) were examined in aqueous and lipid environments by CD spectroscopy. The two analogues, KKLLKKLIAYLKQATAK (K peptide), and EELLEELIAYLKQATAK (E peptide), were made amphipathic with respect to helical segregation by substituting a 6‐residue sequence at the N‐terminus of the native peptide. Their structures were compared to the native peptide under aqueous conditions of varying pH and temperature, and in the presence of liposomes composed of phosphatidylcholine and phosphatidylserine in the ratio of 9:1. The results indicated that the native peptide remains unstructured under all the conditions examined even though this region of the native molecule is surface exposed and helical. The E peptide, however, was helical under aqueous conditions at 25°C from pH 2–10 with a maximum helicity at pH 4 (54% helix from analysis of CD data). The ellipticity of the E peptide at pH 4 and 8 was concentration dependent, indicating an aggregation phenomenon. In studies in which the CD spectrum was measured at different temperatures, the E peptide became more helical at lower temperatures at pH 4 but not at pH 8. Upon interaction with a lipid membrane in the form of liposomes, there appeared to be a slight destabilization in the structure of the E peptide. The K peptide in an aqueous environment behaved like the native peptide in that it was structureless at all pHs and temperatures examined. In the presence of liposomes, however, this peptide had a high helical content (75% helix from analysis of CD data). These findings suggest that while stabilization of the helix dipole with negative charges at the N‐terminus are important in inducing helical conformation in the E peptide, hydrophobic interactions created during aggregation appear to provide the principal stabilizing force. The results with the K peptide demonstrate that the positive N‐terminal sequence of this peptide is able to interact with the negatively charged head groups in the phospholipid membrane in such a fashion as to stabilize a helical structure that is not apparent in an aqueous environment alone.
Viscoelastic properties of solutions of ovine submaxillary mucin
Authors: Soby Lynn M. , Jamieson Alexander M. , Blackwell John , Jentoft Neil 
Published: December 2004

AbstractThe linear viscoelastic and rheological properties of high molecular weight ovine submaxillary mucin (OSM) solution have been investigated in terms of the Newtonian steadyflow viscosity \documentclass{article}\pagestyle{empty}\begin{document}$ [\eta (\dot{\gamma})] $\end{document}, the complex oscillatory viscosity [η*(ω)], and the storage and loss shear moduli [G′(ω) and G″(ω)]. It was observed that \documentclass{article}\pagestyle{empty}\begin{document}$ \eta (\dot{\gamma}) $\end{document}, η*(ω), and G′(ω) are always higher when OSM is dissolved in 0.1M NaCl than when at the same concentration in 6M GdnHCl. This is consistent with previous observations that submaxillary mucins self‐associate in 0.1M NaCl to form large aggregates, which are disrupted in 6M GdnHCl. As the OSM concentration increases, the appearance of a plateau shear modulus indicates the formation of a gel network in both solvents. The results suggest gelation involves specific intermolecular interactions, perhaps due to hydrophobic forces between interdigitated oligosaccharide side chains. The viscoelastic behavior of OSM solution at high concentration is thus similar to that reported in the literature for porcine gastric mucin (PGM). However, the OSM gels are mechanically weaker, having moduli that are an order of magnitude lower thatn those for PGM gels of comparable concentration. The oligosaccharide side chains of OSM consist of only 1–2 sugar units compared to 10–15 for PGM, but it appears that this is sufficient to allow for intermolecular interaction and the formation of weak gels.
Alanyl dipeptide potential‐derived net atomic charges and bond dipoles, and their variation with molecular conformation
Authors: Williams Donald E. 
Published: December 2004

AbstractThe elctric potential around the alanyl dipeptide in various conformations was calculated from ab initio 6–31G wave functions. Seven conformations were selected to correspond to calculated local energy minima of the isolated molecule. Five additional conformations were selected corresponding to the alanylalanine crystal structure and the polypeptide conformations in a right‐handed α‐helix, left‐handed α‐helix, parallel β‐sheet, and anti‐parallel β‐sheet. The electric potential surrounding each conformer was fitted with either net charges at atomic sites or dipolles at bond sites by least squares. Either choice reproduced the electric potential with relative rms deviations of 1.9–4.8%. Values for net atomic charges or bond dipoles were usually in line with expectations based on electronegativity. The imino and carbonyl groups showed their expected polarities, although there were considerable deviations from zero group charge. Net atomic charges on and near the α‐carbon changed substantially with the conformation angles; bond dipoles around the α‐carbon showed analogous behavior.
Conformational studies of cyclic peptide structures in solution from 1H‐Nmr data by distance geometry calculation and restrained energy minimization
Authors: Senn Hans , Loosli Hans‐Rudolf , Sanner Michel , Braun Werner 
Published: December 2004

AbstractThe three‐dimensional structure of a cyclic bouvardin analogue, cyclo (‐Pro‐MeTyr‐Ala‐MeTyr‐MeTyr‐D‐Ala‐) has been determined by distance geomtry calculation and restrained energy minimization from nmr data. The preparation of the input for the distance geometry calculations, the modification of the amino acid library, and the analysis of the structures were done with the aid of a recently developed software package, GEOM. A great variety of different initial structures were explored to check the uniqueness of the determined solution structure. Calculations with 500 different initial structures and two different strategies led to a uniquely determined backbone conformation with a root mean square deviations value of 0.4 Å. The backbone structure consists of two β‐turns, a β‐II turn at Pro1‐MeTyr2, and a β‐VI turn at MeTyr4‐MeTyr5. The efficiency of the two calculation strategies were compared in order to propose an optimal means for performing distance geometry calculations with cyclic structures.