bluuebunny/crossref_metadata_2025_split huggingface dataset:
The origin of the A to B transition in DNA fibers and films
Authors: Lindsay S. M. , Lee S. A. , Powell J. W. , Weidlich T. , Demarco C. , Lewen G. D. , Tao N. J. , Rupprecht A. 
Published: December 2004

AbstractWe have studied the hydration of Na‐DNA and Li‐DNA fibers and films, measuring water contents, x‐ray fiber diffraction patterns, low‐frequency Raman spectra (below 100 cm−1), high‐frequency Raman spectra (600–1000 cm−1), and swelling, as a function of relative humidity. Most samples gain weight equilibrium (though not conformational equilibrium) in one day. The volume occupied by a base pair as the DNA is hydrated (obtained from the x‐ray and swelling data) shows anomalies for the case of Na‐DNA in the region where the A‐form occurs. Our Raman and x‐ray data reproduce the well‐known features of the established conformational transitions, but we find evidence in the Raman spectra and optical properties of a transition to what may be a disordered B‐like conformation in Na‐DNA below 40% relative humidity. We have studied the effects of crystallinity on the A to B transition. We find that the transition to the B‐form is impeded in highly crystalline samples. In most samples, the transition occurs in three days (after putting the sample at 92% relative humidity) but in highly crystalline samples, the transition may take months. By comparing the high‐frequency Raman spectra of highly ordered and disordered films, we show that the extent of crystallinity controls the amount of A‐DNA formed when ethanol is used to dehydrate the films. We show that rapid dehydration (by laser heating) does not result in a B to A transition. A fiber that gives A‐type x‐ray reflections probably contains B‐like material in noncrystalline regions. The low‐frequency Raman spectrum is dominated by a band at about 25 cm−1 in both Na‐ and Li‐DNA. Another band is seen near 35 cm−1 in Na‐DNA at humidities where the sample is in the A‐form. In contrast to earlier reports, we find that the Raman intensity does not depend on fiber orientation relative to the scattering vector. The “35‐cm−1” band is largely depolarized (i.e. vertical polarization incident and horizontal polarization scattered, VH, or vice versa, HV) while the “25‐cm−1” band appears in both VV, VH and HV polarizations. These bands are all weaker in HH polarization. The “25‐cm−1” band may be due to a shearing motion of the phosphates and their associated counterions, while the “35‐cm−1” band may be characteristic of A‐DNA crystallites. We consider mass‐loading, relaxational coupling to the hydration shell, and softening of interatomic potentials as possible explanations of the observed softening of the low‐frequency Raman bands on hydration. Relaxation data suggest that the added water binds tightly (on these time scales) and a mass‐loading model accounts for the observed softening rather well.We conclude that the A to B transition is not driven by softening of the “25‐cm−1” band. Rather, it is most probably a consequence of crystal‐packing forces, with the more regular A‐form favored in crystals when these forces are strong.
CD of ethidium bromide complexes with normal and electrophoretically anomalous DNA restriction fragments
Authors: Slobodyansky Elizabeth , Stellwagen John , Stellwagen Nancy C. 
Published: December 2004

AbstractThe equilibrium binding of ethidium bromide (EB) to two small 147 base‐pair (bp) DNA restriction fragments, which exhibit different mobilities in polyacrylamide gels, was investigated by CD. Two larger DNA restriction fragments and calf thymus DNA were also studied for comparison. Difference spectra were calculated by subtracting the spectrum of the pure DNA from the spectra of its DNA–EB complexes. The D/P ratios ranged from 0.03 to 1.0. The difference CD spectra of all fragments are characterized by bands with maxima near 310, 275, and 207 nm, and minima near 290, 253, 225, and 190 nm. The band near 310 nm, which has a shoulder at about 335 nm, has zero intensity at D/P ≤ 0.05, and rises to a plateau value, different for each fragment, at D/P ≃ 0.3 for large fragments (≥ 1400 bp), and D/P ∼ 0.7 for the two small 147 bp fragments. The minimum near 290 nm is markedly blue shifted with increasing D/P, the wavelength of the extremum corresponding approximately to the wavelength of the uv absorption maximum of the DNA–EB complex. The negative amplitude of this band at D/P = 1.0 depends on the molecular weight of the DNA. The difference CD maximum near 275 nm is positive at low D/P ratios, increases and goes through a maximum at D/P = 0.06–0.1, and then becomes increasingly negative with increasing D/P. The amplitude of the negative ellipticity per added dye is constant at high D/P ratios, suggesting that the transition can be attributed to outside‐bound EB molecules. The ellipticities at 310, 290, and 253 nm increase in absolute magnitude with increasing D/P at approximately the same rate, suggesting that all three bands are associated with the same optical and/or conformational transition. For the two small 147 bp fragments the fractional increases in amplitude of these bands parallel the fractional increase in length of the DNA upon binding EB, determined by electric birefringence measurements. The titration of the restriction fragments with EB was also followed by optical absorption. Two end points are observed, the first at a D/P ratio of ∼ 0.1, reflecting the transition between intercalated and outside‐bound dye molecules, and the second at D/P ≃ 1.0, the equivalence point of the titration.
A revisit to the three‐dimensional structure of B‐type starch
Authors: Imberty Anne , Perez Serge 
Published: December 2004

AbstractA new three‐dimensional structure of B‐starch is proposed in which the unit cell contains 12 glucose residues located in two left‐handed, parallel‐stranded double helices packed in a parallel register; 36 water molecules are located between these helices. Chains are crystallized in the hexagonal space group P61, with lattice parameters a = b = 1.85 nm, c = 1.04 nm. The space group symmetry was derived from an exhaustive analysis of the large body of structural studies published so far. Diffraction data used in this work were taken from the previously reported x‐ray fiber diffractogram [H.C. Wu and A. Sarko (1978), Carbohydrate Research, 61, 7–25] after adequate reindexing. The final R factor is 0.145 for the three‐dimensional data. The repeating unit consists of a maltose molecule where the glucose residues have the 4C1 pyranose conformation and are α(1 → 4) linked. The conformation of the glycosidic linkage is characterized by torsion angles (Φ, Ψ) that take the values (83.8°, −144.6°) and (84.3°, −144.1°), whereas the valence angles at the glycosidic bridge have a magnitude of 115.8° and 116.5°, respectively. The primary hydroxyl groups exist in a gauche–gauche conformation. There is no intramolecular hydrogen bond. Within the double helix, interstrand stabilization is achieved without any steric conflict and through the occurrence of O(2)…O(6) type of hydrogen bonds. The model presented here, with an hydration around 27% w/w, corresponds to a well‐ordered crystalline sample, since all the water molecules could be located with no apparent sign of a disorder. Half of the water molecules are tightly bound to the double helices; the remainder forms a complex network centered around the sixfold screw axis of the unit cell. The consistency of the present structural model, with both physicochemical and biochemical aspects of the crystalline component of tuber starch granules, is analyzed.
On the multiple‐minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method—tests on poly(L‐alanine)
Authors: Ripoll Daniel R. , Scheraga Harold A. 
Published: December 2004

AbstractA new approach to the multiple‐minima problem in protein folding is presented. It is assumed that the molecule is driven toward the native structure by three types of mechanism. The first one involves an optimization of the electrostatic interactions, whereby the molecule evolves toward conformations in which the charge distribution becomes energetically more favorable. The second mechanism involves a Monte Carlo–energy minimization approach, and the third one is a backtrack mechanism that acts in the opposite direction, increasing the energy—the third type of movement provides a means to perturb the molecule when it is trapped in a stable but energetically unfavorable local energy minimum. This paper describes the implementation of a model based on these mechanisms, and illustrates its effectiveness by computations on different arbitrary starting conformations of a terminally blocked 19‐residue chain of poly(L‐alanine) for which the global minimum apparently corresponds to the right‐handed α‐helix. In all cases, the global minimum was attained, even when the starting conformation was a left‐handed α‐helix. In the latter case, the trajectory of conformations passed through partially melted forms of the left‐handed α‐helix (because of electrostatic defects at the ends), and then through the formation of structures leading to the more stable right‐handed α‐helix.
Direct product‐matrix method treatment of macromolecular binding
Authors: Woodbury Charles P. 
Published: December 2004

AbstractA major limitation of the well‐known matrix method treatment of linear polymer systems is the large size of the transfer matrix required to account simultaneously for such factors as polymer conformation, polymer sequence, ligand binding, etc. This paper shows how to combine such factors by using a direct product of small matrices, one for each factor, to generate the large transfer matrix. The properties of the direct product operation can be used to simplify considerably the calculation of eigenvalues and eigenvectors of the transfer matrix. This permits one to develop fairly simply the statistical thermodynamics of relatively complicated macromolecular binding systems involving a large number of states for the individual polymer sites. Applications include treatments of sequence‐specific binding of ligands, sequence‐specific conformational changes, and the combination of the two processes.
Micellization and interactions with phospholipid vesicles of the lipopeptide iturin a, as monitored by time‐resolved fluorescence of a D‐tyrosyl residue
Authors: Harnois I. , Genest D. , Brochon J. C. , Ptak M. 
Published: December 2004

AbstractThe micellization and the interactions with lipid vesicles of the antifungal cyclic lipopeptide iturin A have been investigated by nanosecond pulse fluorometry of a D‐tyrosyl residue. We show that this lipopeptide has three conformers in solution whose proportions are modified during the micellization process. Below the critical micellar concentration (CMC) iturin A does not self‐associate inside the bilayer. Above the CMC all the molecules of iturin A interact with the vesicles and self‐associate inside the membrane.
Order–Disorder conformation change of xanthan in 0.01M aqueous sodium chloride: Dimensional behavior
Authors: Liu Wei , Norisuye Takashi 
Published: December 2004

AbstractWeight‐average molecular weights Mw, second virial coefficients, and z‐average radii of gyration 〈S2〉 were determined by light scattering as a function of temperature T for four sodium salt samples of xanthan in 0.01M aqueous NaCl, in which the polysaccharide undergoes an order–disorder conformation change with increasing T. The data for 〈S2〉 and Mw at 25 and 80°C, the lowest and highest temperatures studied, confirmed the previous conclusion that the predominant conformation at the former T, i.e., in the ordered state, is a double helix, while that at the latter T, i.e., in the disordered state, is a dimerized coil expanded by electrostatic repulsions between charged groups of the polymer. As T was increased from 25 to 80°C, 〈S2〉 sigmoidally decreased or increased depending on the dimer's molecular weight. This temperature dependence of 〈S2〉 and that determined elsewhere for a high molecular weight sample were found to be described almost quantitatively by a simple dimer model in which the double helix melts from both ends, when the double‐helical fraction in the dimer at a given T estimated previously from optical rotation data was used.
Chromatography and electron microscopy of cross‐linked fibrin polymers—a new model describing the cross‐linking at the DD‐trans contact of the fibrin molecules
Authors: Selmayr E. , Deffner M. , Bachmann L. , Müller‐Berghaus G. 
Published: December 2004

AbstractPolymerization of fibrin molecules results in the formation of a double‐stranded protofibril. Although convincing data have not been presented, it is classically believed that γ‐chain cross‐linking of fibrin molecules occurs between the longitudinal end‐to‐end contacts (DD‐long contacts) of the molecules within each of the two strands of a protofibril (intrastrand cross‐linking). In this investigation the question addressed was whether γ‐chain cross‐linking takes place across the two strands (interstrand cross‐linking) between the transversal half‐staggered contacts of the molecules. Demonstration of double‐stranded protofibrils in the presence of urea would indicate an interstrand cross‐linking, whereas in the case of intrastrand cross‐linking, the chaotropic agent urea would dissociate the double‐stranded structure to form single‐stranded fibrils. Protofibrils were obtained by generating soluble cross‐linked fibrin polymers (sXLFbP): After incubation of souble fibrin polymers with Factor XIIIa at 37°C, the polymerization and cross‐linking reaction was stopped by the addition of 6M urea and EDTA. Gel filtration of the reaction mixture in the presence of 3M urea was effect in separating sXLFbP from monomeric molecules. The sXLFbP‐containing fractions were adsorbed onto mica in the presence of different concentrations of urea and investigated by electron microscopy after rotary shadowing. In the presence of 3M urea the sXLFbP appeared as double‐stranded protofibrils. In the presence of 4M urea some parts of the double‐stranded structure were found to be unfolded whereas in the presence of 6M urea multiple‐bended single‐stranded fibrils were observed. SDS‐polyacrylamide gel electrophoresis of the sXLFbP demonstrated no γ‐chain cross‐linking within the protofibrils. Ultracentrifugation of the sXLFbP showed that in the presence of 3M urea noncross‐linked fibrin polymers dissociated to monomeric molecules. When sXLFbP was centrifuged into 6M urea on sucrose density gradients, no reduction of the polymer size could be observed. The data indicate that γ‐chain cross‐linking occurs between the transversal contacts of the fibrin molecules within a protofibril, thus generating interstrand cross‐linking. A model of the cross‐linking of polymerized fibrin molecules is developed and the term DD‐trans contact is proposed for this specific alignment of the D‐domains.
Helix–Coil transition of plasmid dna by adiabatic differential scanning microcalorimetry
Authors: Maeda Y. , Takahashi K. , Yamaki H. , Ohtsubo E. 
Published: December 2004

AbstractAdiabatic differential scanning microcalorimetry, which provides curves of the heat capacity vs temperature, was carried out for the DNA of plasmid pJL3‐TB5 (5277 base pairs in length). The calorimetry curve shows nine peaks ranging from 81 to 96°C in 1 × SSC buffer at a heating rate of 0.25°C, due to the stepwise helix–coil transition of the DNA along the molecular chain. The theoretical melting curve, which can be constructed by calculation from the entire nucleotide sequence of the plasmid DNA by the helix–coil transition theory, is then compared with the calorimetry curve. The two curves resemble each other remarkably well, particularly when a parameter for the methylated adenine residues at GATC sites by Dam methylase is used appropriately. This allows us to assign each peak in the calorimetry curve to the melting of the respective regions of the plasmid DNA sequence. The local stability of the helix–coil transition along the DNA chain is closely related to the functional regions coded by pJL3‐TB5, such as genes, transcriptional promoters, and particular sites generated by recombination of two different sequences in vivo and in vitro.
Spectrophotometric and nmr analysis of the interaction of fluorinated mono‐ and bifunctional interacalators with DNA, poly(dA‐dT), and poly(dG‐dC)
Authors: Delbarre A. , Brown S. C. , James T. L. , Shafer R. H. 
Published: December 2004

AbstractWe have synthesized and investigated the DNA binding properties of three fluorinated acridine derivatives—a monomer (I), a short dimer (II) and a long dimer (III). Only III has a sufficiently long chain bridging the two acridine nuclei to permit binding by bisintercalation. Analysis of the equilibrium and kinetic binding properties of these compounds to poly(dA‐dT) demonstrates that they behave very similarly to their unfluorinated parent compounds. Helix extension, as determined by viscosity measurements, shows that both compounds I and II bind by monointercalation while III binds by bisintercalation. These results are confirmed by 19F‐nmr analysis, which indicates, in particular, that the two chromophores of III share the same molecular environment as that of I in the presence of either calf thymus DNA or poly(dA‐dT). Negative nuclear Overhauser effects in the presence of DNA indicate tight binding such that the motion of the ligands is governed by the polynucleotide dynamics. Optical titrations establish that in 4M NaCl, both I and III bind to calf thymus DNA, but no binding was observed with poly(dG‐dC). This result is in contrast to those for dimers of ethidium, which show substantial binding to polynucleotides under high salt conditions. Nuclear magnetic resonance experiments, however, carried out at considerably higher concentrations, show that compound I does indeed bind to poly(dG‐dC) under these high salt conditions, albeit weakly, and leads to a conversion of the polynucleotide from a left‐handed to a right‐handed conformation.
A lipid vesicle system for probing voltage‐dependent peptide–lipid interactions: Application to alamethicin channel formation
Authors: Woolley G. Andrew , Deber Charles M. 
Published: December 2004

AbstractA membrance potential is shown to be established in phosphatidylcholine/cholesterol unilamellar vesicles using valinomycin in conjunction with a potassium ion gradient; this potential is monitored using the externally added fluorescent dye Safranine O. In the same system, transmembrance calcium fluxes are then detected using the (internally trapped) fluorescent dye Quin‐2. The calcium‐transport behavior of the channel‐forming peptide alamethicin is shown to be potential dependent in this system, in contrast to calcium transport by the ionophore Br‐A23187, which is unaffected by the potential. The observation of this potential‐dependent behavior for alamethicin suggests that this vesicle system may be suitable for direct spectroscopic observation of the voitage‐gating process.
Bicyclic peptides: Solution conformation and Ca2+ binding of the heterodetic bicyclic decapeptide cyclo(Glu1‐Leu2‐Pro3‐Gly4‐Ser5‐Ile6‐Pro7‐Ala8)‐cyclo(1γ → 5β) Phe9‐Gly10
Authors: Zanotti Giancarlo , Pinnen Francesco , Lucente Gino , Paolillo Livio , D'Auria Gabriella , Trivellone Enrico , D'Alagni Maria 
Published: December 2004

AbstractThe conformational behavior of a heterodetic bicyclic decapeptide (BCPLT) in the absence and in the presence of calcium ions has been studied by means of mono and two‐dimensional nmr techniques. Free BCPLT possesses a quite compact structure stabilized by intramolecular bonds and turns. In the structure a cluster of carbonyls is located in a cavity that is supposed to be the cation binding site.
Biologically significant conformation of the Saccharomyces cerevisiae α‐factor
Authors: Naider Fred , Jelicks Linda A. , Becker Jeffrey M. , Broido Michelle S. 
Published: December 2004

AbstractThe conformation of the tridecapeptide α‐factor of the yeast Saccharomyces cerevisiae was examined in both solution and in the presence of lipid vesicles. CD, differential scanning calorimetry, and phosphorus nmr all indicate that this mating pheromone interacts with lipid vesicles. In both aqueous and organic solution of the α‐factor is a flexible molecule that exhibits features of a type II β‐turn spanning the center of the peptide. Two‐dimensional Nuclear Overhauser enhancement spectroscopy gives evidence that the β‐turn is stabilized on interaction of the peptide with lipid vesicles. Our current belief is that the β‐turn may play an important role in the biologically active conformation of the α‐factor.
Conformational analysis of cyclolinopeptide A, a cyclic nonapeptide: Nuclear overhauser effect and energy minimization studies
Authors: Raghothama S. , Ramakrishnan C. , Balasubramanian D. , Balaram P. 
Published: December 2004

AbstractThe conformation of cyclolinopeptide A [cyclo(Pro–Pro–Phe–Phe–Leu–Ile–Ile–Leu–Val)], a naturally occurring cyclic nonapeptide has been investigated in dimethylsulfoxide solution by 270 MHz 1H‐nmr. A complete assignment of all CαH and NH resonances has been accomplished using two‐dimensional correlated spectroscopy and nuclear Overhauser effects (NOEs). Analysis of interresidue NOEs and J values permit construction of a molecular model for the cyclic peptide backbone. The crude model derived from nmr has been used as a starting point for energy minimization, which yields a refined structure largely compatible with nmr observations. The major features of the conformation of cyclolinopeptide A are a Type VI β‐turn centered at Pro(1)‐Pro(2), with a cis peptide bond between these residues and a γ‐turn (C7) structure centered at Ile(6). Two intramolecular hydrogen bonds Val(9) CO—Phe(3)NH (4 → 1) and Leu(5) CO—Ile(7)NH (3 → 1) are observed in the low‐energy conformation. The limited solvent accessibility observed for the Val(9) and Leu(5) NH groups in the nmr studies are rationalized in terms of steric shielding.
Low‐frequency dynamics and Raman scattering of crystals, of B‐, A‐, and Z‐DNA, and fibers of C‐DNA
Authors: Lamba Om. P. , Wang A. H.‐J. , Thomas George J. 
Published: December 2004

AbstractNormal modes of vibration of DNA in the low‐frequency region (10–300 cm−1 interval) have been identified from Raman spectra of crystals of B‐DNA [d(CGCAAATTTGCG)], A‐DNA [r(GCG)d(CGC) and d(CCCCGGGG)], and Z‐DNA [d(CGCGCG) and d(CGCGTG)]. The lowest vibrational frequencies detected in the canonical DNA structures—at 18 ± 2 cm−1 in the B‐DNA crystal, near 24 ± 2 cm−1 in A‐DNA crystals, and near 30 ± 2 cm−1 in Z‐DNA crystals—are shown to correlate well with the degree of DNA hydration in the crystals structures, as well as with the level of hydration in calf thymus DNA fibers. These findings support the assignment [H. Urabe et al. (1985) J. Chem. Phys. 82, 531–535; C. Demarco et al. (1985) Biopolymers 24, 2035–2040] of the lowest frequency Raman band of each DNA to a helix mode, which is dependent primarily upon the degree of helix hydration, rather than upon the intrahelical conformation. The present results show also that B‐, A‐, C‐, and Z‐DNA structures can be distinguished from one another on the basis of their characteristics Raman intensity profiles in the region of 40–140 cm−1, even through all structures display two rather similar and complex bands centered within the intervals of 66–72 and 90–120 cm−1. The similarity of Raman frequencies for B‐, A‐, C‐, and Z‐DNA suggests that these modes originate from concerted motions of the bases (librations), which are not strongly dependent upon helix backbone geometry or handedness. Correlation of the Raman frequencies and intensities with the DNA base compositions suggests that the complex band near 90–120 cm−1 in all double‐helix structures is due to in‐plane librational motions of the bases, which involve stretching of the purine‐pyrimidine hydrogen bonds. This would explain the centering of the band at higher frequencies in structures containing G ⃛ C pairs (> 100 cm−1) than in structures containing A ⃛ T pairs (< 100 cm−1), consistent with the strengths of G ⃛ C and A ⃛ T hydrogen bonding.