bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the interaction of daunomycin with synthetic alternating DNAs: Sequence specificity and polyelectrolyte effects on the intercalation equilibrium
Authors: Xodo Luigi Emilio , Manzini Giorgio , Ruggiero João , Quadrifoglio Franco 
Published: December 2004

AbstractThe interaction of daunomycin with ctDNA and six purine–pyrimidine alternating poly‐deoxynucleotides has been studied using fluorometric and uv‐visible absorption methods. In the explored binding range of r > 0.05, the intercalation of the drug into the DNAs proved to be anticooperative, as indicated by the pronounced upward curvature of all the Scatchard plots obtained. The experimental data have been analyzed according to the recent theory of Friedman and Manning, which describes the polyelectrolyte effects on the site binding equilibria, drug intercalation included. We found that, accounting for the polyelectrolyte effects in the neighbor site exclusion model, the experimental data were nearly equally well described, in a wide range of binding ratios, by assuming the presence of sequence specificity effects (site size = 2 base pairs, exclusion parameter n = 1) or its absence (site size = 1 base pair, n = 1.7). The relevant results are as follows: (a) Daunomycin binds to all the DNAs considered with a stoichiometry of approximately 1 drug for every two base pairs. (b) The anticooperative nature of the interaction is essentially polyelectrolytic in origin. (c) The binding affinity shown by the drug for the different sites considered decreases in the order of Gm5C > AT > AC‐GT > IC > GC > AU, indicating a stabilizing effect of the —CH3 group in position 5 of the pyrimidines. (d) The extent of quenching of the intrinsic fluorescence of daunomycin in the presence of DNA is bound to the presence, at the intercalation site, of a guanine residue, since GC, Gm5C, and AC‐GT sites induce a nearly total quenching, whereas AT, AU, and IC sites act only partially in this respect. The structural results obtained from the daunomycin‐d[(CGTACG)]2 crystal suggest that the 2‐NH2 group of guanine might be responsible for such a phenomenon. The influence of both the temperature and the ionic strength on the free energy of drug intercalation into ctDNA, poly[d(G‐C)] : poly[d(G‐C)], and poly[d(A‐C)] : poly[d(G‐T)] is examined and discussed.
CD studies of double‐stranded polydeoxynucleotides composed of repeating units of contiguous homopurine residues
Authors: Gudibande Satyanarayana R. , Jayasena Sumedha D. , Behe Michael J. 
Published: December 2004

AbstractDouble‐stranded synthetic polydeoxynucleotides of the general form poly[d(GnCn)] · poly[d(GnCn)], poly[d(GnC)] · poly[d(GCn)], and poly[d(AnTn)] · poly[d(AnTn)] have been synthesized. When n = 4 or larger, the CD spectra of polymers of the form poly[d(GnCn)] · poly[d(GnCn)] or poly[d(GnC)] · poly[d(GCn)] closely resemble the spectrum of poly[dG] · poly[dC], suggesting that a string of four continguous guanosine residues is sufficient to induce a conformation resembling that of the polypurine · polypyrimidine. With polymers of the form poly[d(AnTn)] · poly[d(AnTn)], however, the CD spectrum only gradually approaches that of poly[dA] · poly[dT].
DNA gel electrophoresis: Effect of field intensity and agarose concentration on band inversion
Authors: Slater Gary W. , Turmel Chantal , Lalande Marc , Noolandi Jaan 
Published: December 2004

AbstractWe study the effect of electric field intensity and agarose gel concentration on the anomalous electrophoretic mobility recently predicted by the biased reptation model and experimentally observed for linear DNA fragments electrophoresed in continuous electric fields. We show that high fields and low agarose concentrations eliminate the physical mechanism responsible for anomalous DNA mobility and band inversion, in good agreement with theory, thus restoring the monotonic mobility–size relationship necessary for unambiguous interpretation of the results of DNA gel electrophoresis.
Modeling cation‐driven (proto)fibrin coagulation
Authors: Marx Gerard 
Published: December 2004

AbstractThe coagulation mechanism of thrombin‐ and reptilase‐activated fibrinogen is the focus of this report. Three types of gels were evaluated for their sensitivity to physiologic levels of Ca(II) and Zn(II): Fibrin gel formed directly by adding thrombin or reptilase to fibrinogen, protofibrin gel generated by adding Ca(II) and Zn(II) to soluble fibrin oligomers (protofibrills), and gels induced by sudden pH increase of fibrin monomer (pH 4.9–7.4). The turbidity and viscoelasticity of reptilase‐ and thrombin‐activated fibrin are similarly sensitive to Ca(II) and Zn(II) scanning electron micrographs (SEM) of fibrin gels from pH jump experiments show that their constituent fibers are relatively homogeneous and only mildly affected by divalent cations. This contrasts with the cation sensitivity of normally formed fibrin and protofibrin gels. Based on these and previously published experiments, a graphic shorthand is developed to describe the directionality of linear and lateral polymerization modes that result in cation‐driven (proto)fibrin gelation.
Analysis of dihedral angles distribution: The doublets distribution determines polypeptides conformations
Authors: Unger Ron , Harel David , Wherland Scot , Sussman Joel L. 
Published: December 2004

AbstractIt is possible to construct fragments of protein structures by using the known values for the fixed bond lengths, bond angles, and torsion angles, and “dialing” in the dihedral angles ϕ and ψ. By choosing these angles in different ways, it is possible to create different populations of fragments and to investigate their properties. We analyzed the following populations: Real fragments taken randomly from known structures. Reconstructed fragments, which are constructed, using the “fixed geometry” assumption, from a set of consecutive pairs of dihedral angles drawn from known structures. Random fragments that are constructed from a random set of dihedral angles from known structures, and doublet‐preserving fragments, which are constructed from a set of dihedral angles drawn at random from known structures in a way such that the distribution of two consecutive pairs of dihedral angles in this population is similar to that distribution in the known structures. We examine the fixed geometry assumption and demonstrate that even reconstructed fragments contain many atomic collisions. We show that random fragments have only slightly more interatomic collisions than the reconstructed fragments. Nevertheless, the population of random fragments is structurally different from the population of reconstructed fragments. On the other hand, we show that the doublet‐preserving fragments exhibit properties that are similar to the real population. Thus the doublet preserving random population can be used to simulate the structure of short polypeptides.
Solution structure of human growth hormone‐releasing factor fragment (1–29) by CD: Characteristic conformational change on phospholipid membrane
Authors: Honda Shinya , Ohashi Shinichi , Morii Hisayuki , Uedaira Hatsuho 
Published: December 2004

AbstractThe conformations of synthetic human growth hormone‐releasing factor fragment (1‐29) in the presence and the absence of l, 2‐dimyristoyl‐sn‐glycero‐3‐phosphorylglycerol liposome as well as in aqueous 2, 2, 2‐trifluoroethanol solution were investigated by CD spectroscopy. The secondary structure of the peptide in each solution was analyzed by two methods. Both results show that the peptide has an unordered structure in the aqueous solution. whereas it folds into helical structure in the aqueous alcohol and in the phospholipid solution. In addition, although the peptide exists as almost complete helix in the 50 vol % aqueous alcohol (80–90% helicity), it does not reach full helicity even in the solution containing excess amount of phospholipid liposome (maximum 65–70% helicity). The conformational difference is explained by the characteristic amphipathy of the peptide, i.e., the necessity to twist the separated amphipathic helical parts in the interaction with the phospholipid membrane probably makes the helicity of the peptide decrease.
Vibrational studies of the disulfide group in proteins. Part V. Correlation of SS stretch frequencies with the CCSS dihedral angle in known protein disulfide bridges
Authors: Qian Weili , Krimm Samuel 
Published: December 2004

AbstractNormal mode calculations have been done on 92 disulfide bridges in 25 known protein structures in order to correlate the SS stretch frequency with the CCSS dihedral angle. It is possible to classify the frequencies into four major categories, which provide a more detailed classification scheme than previously proposed from dialkyl disulfide correlations.
Computer modeling of polysaccharide–polysaccharide interactions: An approach to the κ‐carrageenan–mannan case
Authors: Tvaroska Igor , Rochas Cyrille , Taravel François‐R. , Turquois Tristan 
Published: December 2004

AbstractA computer program SAINT has been developed for the investigation of the structure and for the prediction of minimum‐energy structure of polysaccharide–polysaccharide complexes. The energy minimization is carried out on internal geometrical parameters—namely bond angles, torsional angles, and five parameters describing the mutual orientations of polysaccharide chains. For this purpose, the nonderivative method of conjugated directions is used. This procedure was applied to computer modeling of an idealized model of the binary gelling κ‐carrageenan and galactomannan system. It is shown that the interaction between two chains influences the structure of the individual polysaccharide molecule and that in the minimum‐energy structures of the complex, the conformation of the chains does not correspond to the lowest energy.
Molecular dynamics simulation of poly(spiropyran‐L‐glutamate): Influence of chromophore isomerization
Authors: Pachter Ruth , Cooper Thomas M. , Natarajan L. V. , Obermeier Keith A. , Crane Robert L. , Adams W. Wade 
Published: December 2004

AbstractA study of the influence of the spiropyran to merocyanine ring opening on a model of poly(spiropyran‐L‐glutamate) as implied by the experimental data (T. M. Cooper, K. A. Obermeier, L. V. Natarajan, and R. L. Crane (1992) Photochemistry and Photobiology, 55, 1–7) is presented. The individual chromophore is studied by the AM1 semiempirical approach, while molecular mechanics and dynamics calculations are employed in the analysis of the poly(spiropyran‐L‐glutamate) model. It is shown that the α‐helical secondary structure is less conserved in the polypeptide substituted with the merocyanine form of the chromophore. In particular, larger side‐chain flexibility, increased backbone hydrogen‐bond lengths, as well as a larger helix bending are calculated. Furthermore, a random conformational minimization calculation finds the intrinsic behavior of the spiropyran molecular system as being more of a helix “maker” than its merocyanine analogue. The interactions of the chromophore substituent with other side chains prove, in part, that an early event in the decay of the α‐helical structure is the formation of hydrogen bonds between the carboxylic acid groups and the merocyanine oxygens. The results lend support to the experimental observation that the merocyanine group destabilizes the α‐helical framework of the polypeptide, thus possibly allowing the entry of solvent molecules into the α‐helical core, while spiropyran in its closed form shields it from the solvent. © 1992 John Wiley & Sons, Inc.
Solution conformation of maltose from optical rotation: A procedure for evaluating carbohydrate force fields
Authors: Stevens Eugene S. 
Published: December 2004

AbstractAs one means of evaluating the various force fields that are being developed for the molecular modeling of carbohydrate structures, the statistically averaged optical rotation of β‐maltose can be calculated using the energy surface to be tested in combination with the detailed conformation dependence of β‐maltose optical rotation presented here. Comparison with the observed rotation will indicate the quality of the force field, especially with respect to the parameterization of solvent effects. © 1992 John Wiley & Sons, Inc.
Hydrodynamic modes of arbitrarily shaped flexible macromolecules: Influence on dynamic light scattering
Authors: Goldstein Robert F. 
Published: December 2004

AbstractThe diffusional motions of flexible macromolecules are analyzed with an increasingly realistic Rouse–Zimm model, i.e., by modeling the molecule as an arbitrary set of spheres connected by nearly harmonic springs. New features include (1) nearly arbitrary arrangements of spheres, (2) arbitrary arrangements of translational and torsional springs, (3) significant anharmonic corrections to the elastic potential surface, and (4) inclusion of torsional damping and various hydrodynamic cross‐coupling effects (including two types of translational‐rotational coupling) with no additional fitted parameters.The hydrodynamic interactions [R. F. Goldstein (1985) Journal of Chemical Physics, Vol. 83, pp. 2390–2397] contain no adjustable parameters other than temperature, viscosity, and the radii and positions of the spheres. These hydrodynamic interactions allow accurate calculations of rigid body diffusion as well as flexible motions.Given the positions, radii, and spring constant matrix, one can calculate a full set of three‐dimensional diffusional modes. Because one uses an off‐diagonal hydrodynamic resistance matrix instead of a diagonal mass matrix, the diffusional modes are different in structure from vacuum normal modes, and give rise to different rms motions in the laboratory frame. These hydrodynamic modes include the effects of vibrational‐translational cross‐coupling (i.e., motion along a vibrational coordinate may give rise to a translational force, and vice versa).The diffusional modes are used to simulate dynamic light scattering (DLS). I examine various molecules with different shapes, flexibilities, and with different scattering vectors. Radial and angular motions influence DLS decays differently. These effects are dependent upon the molecular shape (straight, bent, or curved) and type of flexibility (stretching or bending). Furthermore, small cubic corrections to the potential surface can be significant for DLS of certain geometries such as straight rods and semicircles. © 1993 John Wiley & Sons, Inc.
Rayleigh scattering of Mössbauer radiation in hydrated oriented DNA fibers
Authors: Albanese G. , Deriu A. , Cavatorta F. , Rupprecht A. 
Published: December 2004

AbstractThe Rayleigh scattering of Mössbauer radiation has been measured on oriented hydrated fibres of A‐NaDNA. The elastic and inelastic scattering intensities have been determined at different temperatures from 275 to 310 K in the Q range 0.7–3.3 Å−1. The elastic intensity has a main maximum at Q = 1.92 Å−1 due to an ordered structure of water along the DNA double helices. From the temperature dependence of the elastic intensity under the water peak maximum, the mean square displacement of water oxygens in the direction parallel to the DNA axis has been deduced. It varies from 0.110 Å2 at 275 K up to 0.345 Å2 at 310 K. The thermal diffuse scattering intensity is also peaked at the same Q value of the elastic intensity, indicating the presence of coherent vibrational excitations propagating along the ordered water filaments. © 1993 John Wiley & Sons, Inc.
Characterization of the bioactive form and molecular determinants of recognition of cyclic enkephalin peptides at the δ‐opioid receptor
Authors: Chew Clifford , Villar Hugo O. , Loew Gilda H. 
Published: December 2004

AbstractAn extensive and systematic search strategy to determine the conformational profile of 12 cyclic disulfide‐bridged opioid peptides with varying affinities at the δ receptor has been carried out to identify the structure that is recognized by the δ receptor for each analogue. The methods and procedures used here for the conformational search have already been validated for [D‐Pen2, D‐Pen5] enkephalin (DPDPE), one member of this family. Use of these methods led to a low‐energy solution conformation of DPDPE in excellent agreement with all the geometric properties deduced from its solution nmr spectra. Each of the analogue was subjected to the same procedure, involving a combination of molecular dynamics simulations at high and low temperature. The study was repeated in two environmental conditions, an apolar environment, simulated by using a distance‐dependent dielectric constant, and a polar environment by embedding the peptides in a high constant dielectric ( ε = 80). An automated comparison of the different conformers based on their backbone rms and average distance between the key aromatic moieties was followed by graphic analysis using maximum structural overlap. The cross‐comparison of the conformations for each analogue revealed a unique conformer that may be recognized by the δ receptor for each high‐affinity analogue that permitted maintaining the critical elements required for recognition in a simple spatial orientation, while maximizing similarity in other regions. © 1993 John Wiley & Sons, Inc.
Substituent effects on the puckering mode of the cyclobutane ring and the glycosyl bond of cis–syn photodimers
Authors: Kim Jong‐Ki , Wallace John C. , Alderfer James L. 
Published: December 2004

AbstractThe cyclobutane ring (CB) puckering of a cis–syn DNA photodimer (cis–syn d‐T[p]T) differs from that of a cis–syn RNA photodimer (cis–syn r‐U [p] U) [J.‐K. Kim and J. L. Alderfer (1992) Journal of Biomolecular Structure and Dynamics, Vol. 9, p. 1705]. In cis–syn d‐T [p] T, interconversion of the CB ring between CB+ and CB− is observed, while in cis–syn r‐U [p] U only CB− is observed. In the CB+ conformation, the two thymine rings of the dimer are twisted in a right‐handed fashion, as are the bases in B‐form DNA. In case of CB− they are twisted in a left‐handed fashion. The C5 (base) and/or C2′ (sugar) substituents apparently affect the CB ring flexibility in cis–syn d‐T [p] T and cis–syn r‐U [p] U. To study the effects of the C5 substituent on CB ring flexibility, two‐dimensional nuclear Overhauser effect (NOE) and 31P‐nmr experiments were performed on cis–syn d‐T [p] U, cis–syn d‐U [p] T, and cis–syn d‐U [p] U photodimers to investigate the CB puckering mode and overall molecular conformation and dynamics. The NOE results indicate the 5‐methyl group in the photodimer induces conformational flexibility of the CB ring. In cis–syn d‐T [p] U and cis–syn d‐U [p] T, both CB+ and CB− puckering modes are observed. This indicates interconversion between two modes takes place as observed in cis–syn d‐T [p] T. In the case of cis–syn d‐U [p] U, only the puckering CB− mode is observed. All three DNA‐type dimers—cis–syn d‐T [p] U, cis–syn d‐U [p] T, cis–syn d‐U [p] U—show a characteristic flexibility of glycosidic bonds at the 5′ residue; cis–syn d‐T [p] T demonstrates syn–anti interconversion for both the 3′ and 5′ sides, while the others are exclusively anti on the 3′ side. In contrast, the ribophotodimer, cis–syn r‐U [p] U, lacking the C5 methyls and having a C2′‐OH, demonstrates no conformational flexibility in the CB ring or in either of the glycosidic bonds. Differential flexibility of the three DNA‐type dimers (cis–syn d‐T [p] U, cis–syn d‐U [p] T, cis–syn d‐U [p] U) and the RNA dimer (cis–syn r‐U [p] U) in the sugar‐phosphate backbone region is also apparent from the temperature dependence of the 31P chemical shifts of these photodimers compared to their normal dimer analogues. Over the temperature range 18‐63°C, the chemical shift change is reduced 22–42% in three DNA‐type dimers, while it is reduced 71% in cis–syn r‐U [p] U, suggesting the RNA‐type dimer is more rigid. © 1993 John Wiley & Sons, Inc.
Molecular dynamics simulations of poly(dA)·poly(dT): Comparisons between implicit and explicit solvent representations
Authors: Fritsch V. , Ravishanker G. , Beveridge D. L , Westhof E. 
Published: December 2004

AbstractThe program AMBER 3.0 has been used to generate molecular dynamics trajectories of a poly (dA)·poly (dT) decamer. The simulations were performed using different methods to treat solvent effects. Results of a simulation including 18 counterions NH and 4109 water molecules under (N, P, T) conditions were compared to simulation runs with implicit solvent representation in which solvent screening effects were represented by the use of a sigmoidal distance‐dependent dielectric function. In the latter case, the system was simulated under microcanonical (N, V, E) and canonical (N, V, T) conditions. For the fully hydrated system simulation, a preequilibration protocol was developed since it was observed that long and progressive periods of heating and equilibration on the overall system were necessary in order to avoid energetic collisions between the solute and the solvent molecules, leading to severe irreversible deformation of the solute. A detailed analysis of DNA conformations, sugar puckers, and stability of the hydrogen bonds, Watson–Crick and three‐center H bonds, is reported. The results show that DNA remains essentially in the B conformer with a tendency in the hydrated model to adopt a slightly distorted, unwound, and stretched conformation in comparison to standard B‐DNA. Concerning sugar puckers, the mean pseudorotation phases of the adenine residues are systematically higher than those of the thymine residues, except in the case of the hydrated model for which a particular behavior is observed for the adenine strand. In this case, the terminal bases oscillate between C2′,‐endo and O4′,‐endo and the central ones stay in the C3′,‐endo domain. The mean lifetimes of the internal Watson–Crick H‐bond (A)HN6O4(T) are also dependent on the base pairs included in the calculation, excepted for the implicit solvent simulation at constant temperature. The three‐center H bonds have very small mean lifetimes in all three cases of MD simulation. In the minor groove of the hydrated model, a spine of hydration is found as observed by x‐ray crystallography and other theoretical simulations. On the basis of the rms deviations, it appears that the fully hydrated simulation has not reached a plateau at the end of the run, while the implicit simulation at constant energy seems to have converged. At constant temperature, very large oscillations in rms deviations are observed. © 1993 John Wiley & Sons, Inc.
Structural changes in 16S RNA from Escherichia coli upon unfolding by urea
Authors: Timchenko A. A. , Langowski J. , Serdyuk I. N. 
Published: December 2004

AbstractThe urea‐induced unfolding of 16S RNA at low ionic strength has been studied by dynamic light scattering, uv spectroscopy, and some hydrodynamic methods. Three components could be resolved in the photon correlation spectra of scattered light, using the inverse Laplace transform SIPP program [G. R. Danovich and I. N. Serdyuk (1983) in Photon Correlation Techniques in Fluid Mechanics, vol. B38, E. O. Schulz‐Dubois, Ed., Springer, Berlin/Heidelberg, New York, p. 315]. One component is assigned to the center‐of‐mass translation of the RNA, another one to a combination of translational and internal motion, and the last to diffusion of urea clusters. The hydrodynamic dimensions of RNA increase strongly upon transition from 4 to 6M urea. We conclude that up to 2M urea, 16S RNA is highly elongated, and coiled above 4M urea, with a great increase of the hydrodynamic dimensions of RNA being observed upon transition from 4 to 6M urea. A scheme for RNA unfolding is proposed. © 1993 John Wiley & Sons, Inc.