bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermodynamics of polymolecular duplexes between phosphate‐methylated DNA and natural DNA
Authors: Moody Maurice R. , van Genderen Marcel H. P. , Buck Henk M. 
Published: December 2004

AbstractPhosphate‐methylated (P.M.) DNA possesses a very high affinity for complementary natural DNA, as a result of the absence of interstrand electrostatic repulsions. In this study, a model system phosphate‐methylated d[Cn] with natural d(Gk) (n < k)is chosen for an investigation of the thermodynamic properties that determine duplex stability. The enthalpy change of a melting transition is shown to be considerably larger than is observed for corresponding natural DNA duplexes. It is found that ΔH of GG/CC nearest neighbor pairwise interaction equals −15.6 kcal/mol, compared to −11.0 kcal/mol for the natural analog. The entropy change is strongly dependent on the length of the natural DNA strand and the number of phosphate‐methylated DNA oligomers hybridized. The results are explained by means of a model in which a cooperative effect for subsequent hybridizations of phosphate‐methylated DNA oligomers is assumed, thus giving additional stability.
Condensation of DNA by trivalent cations. 1. Effects of DNA length and topology on the size and shape of condensed particles
Authors: Arscott Patricia G. , Li An‐Zhi , Bloomfield Victor A. 
Published: December 2004

AbstractIn vitro condensation of DNA by multivalent cations can provide useful insights into the physical factors governing folding and packaging of DNA in vivo. We have made a detailed study of hexammine cobalt (III) induced condensation of 2700 and 1350 base pair (bp) fragments of plasmid pUCl2 DNA by electron microscopy and laser light scattering. The condensed DNA takes the form of toroids and rods. Both are present in all condensates, but the proportion of toroids is higher with the larger fragments. The intact, closed circular plasmid produces smaller particles than the linear fragments. The size of a particle is independent of DNA fragment length. Two hours after adding the condensing agent, a typical toroid is about 800 Å in diameter; the outer radius (R1) is ∼ 400 Å, and the inner radius (R2) is ∼ 140 Å for both sets of fragments. These dimensions are relatively stable, but there is sufficient change in both R1 and R2 to produce approximately 50% increase in volume from 2 to 24 h. A typical rod at 2 h is about 1800 Å long and 300 A wide. The distribution of rod lengths is similar to that of mean toroid circumferences π(R1 + R2), and the distribution of rod widths is similar to that of toroidal widths (R1 − R2). The 2700‐bp fragments show a significantly higher ratio of toroids to rods than the 1350‐bp fragments. Both types of particle are multimolecular. The average number of molecules/particle, calculated from the above dimensions, assuming hexagonally packed B‐form DNA with a center‐to‐center spacing of 27 Å, is 13 ± 4 for condensates of 2700‐bp fragments and 26 ± 11 for those of 1350‐bp fragments. Monomolecular condensates of much larger DNAs have similar dimensions, suggesting that size is governed primarily by the balance of attractive and repulsive intermolecular forces rather than by the entropic factors associated with incorporation of a number of small particles into a larger one. The similar dimensions and volumes of toroids and rods indicate that the free energy cost of continual bending in toroids, minus that gained by extra net attraction in a cyclic particle, is comparable to that of abrupt bending or kinking in rods. Although the condensed particles are multimeric, their distinct toroidal or rodlike shapes distinguish them from the random aggregates that would be generally expected from the multimolecular association of large, flexible polymers.
Dielectric study on hydration of B‐, A‐, and Z‐DNA
Authors: Umehara Toshihiro , Kuwabara Shinichi , Mashimo Satoru , Yagihara Shin 
Published: December 2004

AbstractDielectric relaxation peak due to bound water was found around 100 MHz in poly(dG‐dC) · poly(dG‐dC) and calf thymus DNA in water–ethanol mixtures with NaCl buffer. Relaxation time and strength show a transition for poly(dG‐dC) · poly(dG‐dC) at anethanol composition Cw = 0.45 (w/w) where the structural transition from B‐ to Z‐DNA takes place. It has been suggested that the transition is caused by removal of the bound water molecules preferentially from the phosphate groups. If the bound water molecules are removed equally from the phosphate groups and the grooves, the structural transition from B to A takes place. By analogy with hydration of tropocollagen, it was found that 19 water molecules per one nucleotide are at least necessary to keep B‐DNA. Thirteen molecules are bound to A‐DNA and 9 molecules to Z‐DNA. Stringlike multimers are proposed as available structures of the bound water.
Raman spectroscopic study of the effects of Ca2+, Mg2+, Zn2+, and Cd2+ ions on calf thymus DNA: Binding sites and conformational changes
Authors: Langlais Marc , Tajmir‐Riahi Heidar All , Savoie Rodrigue 
Published: December 2004

AbstractThe interaction of Mg2+, Ca2+, Zn2, and Cd2+ with calf thymus DNA has been investigated by Raman spectroscopy. These spectra reveal that all of these ions, and particularly Zn2+, bind to phosphate groups of DNA, causing a slight structural change in the polynucleotide at very small metal: DNA(P) concentration ratio (ca. 1 : 30). This results in increased base‐stacking interactions, with negligible change of the B conformation of DNA. Contrary to Zn2+ and Cd2+, which interact extensively with the nucleic bases (particularly at the N7 position of guanine), the alkaline‐earth metal ions are bound almost exclusively to the phosphate groups. The affinity of both the Zn2+ and Cd2+ ions for G‐C base pairs is comparable, but the Cd2+ ions interact more extensively with A · T pairs than Zn2+ ions. Interstrand cross‐linking through the N3 atom of cytosine is suggested in the presence of Zn2+, but not Cd2+.
The role of extrahelical peptides in stabilization of collagen fibrils
Authors: Wallace Donald G. 
Published: December 2004

AbstractA quantitative model for fibril assembly of type I collagen was extended to include the explicit effect of extrahelical peptides. The collagen molecule was simulated by rod‐like sequences to which short, rigid tails were connected by “nondimensional” flexible joints. Three collagen structures were studied: (1) intact collagen, simulated by a rod of axial ratio 200 (The axial ratio x was taken as a segment length) with two tails of length x = 1 and x = 2, respectively, appended to each end; (2) pepsin‐digested collagen, simulated by one rigid segment of length 200 and one tail of length 1; and (3) pronase‐digested collagen, by a single rigid segment of length x = 200. Phase equilibria of such structures were calculated, using a lattice theory of Matheson and Flory, and the relation of the polymer–solvent interaction parameter χ to the equilibrium solubility was determined. The χ for each collagen species was then related to temperature (T) and ionic strength (I), based on the approximation that local (per segment) stabilization of collagen fibrils was due to hydrophobic and electrostatic forces only. Solubility vs temperature curves for all three collagen species were computed and compared to published experimental data. From the χ factors for each species, the composite χ was resolved into components representing energetic contributions of the extrahelical peptides relative to the helix, which were interpreted in terms of hydrophobic or electrostatic interactions stabilizing the collagen fibril.
Opioid peptides in micellar systems: Conformational analysis by CD and by one‐dimensional and two‐dimensional 1H‐nmr spectroscopy
Authors: Zetta Lucia , Consonni Roberto , Marco Antonio De , Longhi Renato , Manera Ernesto , Vecchio Giuseppe 
Published: December 2004

Abstractβ‐Endorphin has been studies iin SDS micelles by one‐ and two‐dimensional nmr spectroscopy (1D and 2D nmr), and to explore the influence of peptide length and composition on the polypeptide structure, the investigation was extended to a number of fragments. The nmr results are compared with those obtained from CD experiments and discussed in terms of a secondary structure that involves the central region of β‐endorphin.
Chiroptical labeling of folded polypeptide conformations: The thioamide probe
Authors: Hollósi M. , Kollát E. , Kajtár J. , Kajtár M. , Fasman G. D. 
Published: December 2004

AbstractThis paper reports the chiroptical properties of thionated N‐acyl amino acid and N‐acyl dipeptide N′‐methylamide models. It was found that the optical activity of the thioamide chromophore is dominated by the chiral contribution of perturbants attached to Cα at the N‐H side of the thioamide group. The appearance of a strong negative ππ* band near 270 nm is indicative of the semiextended conformation of this residue. The ϕ ∼ −70°, ψ ⩾ 120° set of torsion angles is compatible with a type II βt‐turn or a γt‐turn conformation with the perturbing N‐H side residue in the i + 1 position of the turn. (The subscript t or tt denotes that one or both of the H‐bonded moieties is thioamide.) Earlier data show that both βt‐ and γt‐turns may be fixed by CS ⃛H‐N(CO) intramolecular H bonds. The appearance of one or two weak nπ* bands and a positive ππ* band at about 270 nm is characteristic of type II βt‐turns containing the H‐bonded thioamide group attached to the glycine residue in position i + 2. The extended conformation (ϕ ∼ −140°, ψ ∼ 140°) of a residue after the thioamide group gives rise to a negative nπ* and a positive ππ* band of comparable magnitude. Peptid1e sequences with alternating thioamide–amide–thioamide backbone tend to adopt 1t ⇆ 4t H‐bonded βtt conformations. CD studies show that type II βtt‐turns have unique chiroptical properties: the ππ* region is dominated by an exceedingly strong negative band near 260 nm (|Δε| = 19–24) accompanied by a weaker band at higher wavelength values.
The secondary structure of turkey gizzard myosin light chain kinase and the nature of its interaction with calmodulin
Authors: Garone Louise , Albaugh Sharon , Steiner Robert F. 
Published: December 2004

AbstractThe enzymatic activities of native myosin light chain kinases are subject to modification by interaction with Ca2+‐calmodulin (CaM). The interaction between myosin light chain kinase isolated from turkey gizzard (tgMLCK) and calmodulin isolated from bovine testes (CaMbt) and wheat germ (CaMwg) has been examined by means of the intrinsic tryptophan fluorescence of tgMLCK and the fluorescence of extrinsic fluorescent labels located at Cys‐27 and Tyr‐139 of CaMwg and Tyr‐99 of CaMbt. Static and dynamic fluorescence measurements provide evidence for the involvement of the former two sites in the zone of contact with lesser involvement of the site marked by the probe at Tyr‐99. Complex formation protected the primary cleavage site in CaMbt (Lys‐77) from proteolysis by trypsin. These results are consistent with involvement of the N‐ and C‐terminal lobes of CaM in stabilization of the complex with tgMLCK, but cannot rule out participation of the connecting strand in the interaction. CD measurements extending to 175 nm, obtained using synchrotron radiation, indicate the following secondary structure content for tgMLCK: 17 ± 2% α‐helix, 22 ± 3% antiparailel β‐sheet, 3 ± 1% parallel β‐sheet, 24 ± 2% β‐turns, and 34 ± 2% random coil. Similar measurements of the CD spectra of CaMbt and of the 1 : 1 :: CaMbt : tgMLCK complex presently indicate that neither protein undergoes major secondary structure rearrangement during their interaction, although subtle changes in the CD spectrum of tgMLCK appear to be correlated with the interaction with CaM.
A numerical counterion condensation analysis of the B‐Z transition of DNA
Authors: Fenley Marcia O. , Manning Gerald S. , Olson Wilma K. 
Published: December 2004

AbstractWe examine the salt dependence of the B‐Z transition in DNA by means of the counterion condensation theory adapted to structurally realistic coordinates of the phosphate groups. The ionic contribution to the free energy difference ΔG is computed for both the ZI and ZII conformations over broad ranges of NaCl and MgCl2 concentrations and polymer lengths. For the solvent we employ both a constant‐dielectric model (dielectric constant set to 78.3) and a dielectric saturation model (distance‐dependent dielectric constant). Where comparison can be made, the results for the constant‐dielectric model are similar to those obtained by other workers for the same model but with different computational methods. The existence of a low‐salt transition, and its location when it does occur, depends strongly on the DNA length and on the dielectric model. The behavior of ZI and ZII are qualitatively similar throughout the entire salt range for the constant‐dielectric model, but qualitatively different if dielectric saturation is simulated, as we think is necessary for a realistic description. The ionic ΔG, in the presence of dielectric saturation, bears comparison with the high‐salt trend of the measured total ΔG if “Z‐DNA” is predominantly ZI, but not if it is predominantly ZII.
The molecular dimensions of G‐actin in solution as studied by dynamic light scattering
Authors: Patkowski A. , Eimer W. , Seils J. , Schneider G. , Jockusch B. M. , Dorfmüller Th. 
Published: December 2004

AbstractThe rotational and the translational diffusion coefficients of G‐actin in solution have been obtained by polarized and depolarized dynamic light scattering, respectively. Modeling the shape of the molecule by a biaxial ellipsoid of revolution, the hydrodynamic dimensions were calculated from the Perrin equations. In completion to previous hydrodynamic measurements, a combination of both light scattering experiments provides direct information about the anisotropic form of G‐actin in solution. The result indicates that the form of G‐actin in solution is not significantly different from the overall structure in the solid state as obtained by x‐ray crystallography.
The divalent cation‐binding sites of gramicidin A transmembrane ion‐channel
Authors: Golovanov A. P. , Barsukov I. L. , Arseniev A. S. , Bystrov V. F. , Sukhanov S. V. , Barsukov L. I. 
Published: December 2004

AbstractThe conductance of the gramicidin A single channels in glycerolmonooleate membranes is strongly reduced in the presence of Mn2+ cations. The nmr experiments were performed for N‐terminal to N‐terminal gramicidin A dimer formed by two right‐handed single‐stranded helixes incorporated into the sodium dodecyl sulfate micelles in the presence of Mn2+ ions. Dependence of the nonselective spin–lattice relaxation rates of the gramicidin A protons on Mn2+ concentration was analyzed to determine coordinates of the divalent cation binding sites. It is inferred that Mn2+ ions are bound at the channel mouths at distances of 6.4, 8.6, and 8.8 Å (±2 Å) from the oxygen atoms of exposed carbonyl groups of D‐Leu 12, 14, and 10, respectively. The bounded Mn2+ retains its hydrate shell, the size of which (≈ 6 Å) exceeds the inner pore diameter (≈ 4 Å). That makes the gramicidin A channel impermeable for divalent cations.
Synthetic immunogens. Part IV: Conformational studies on gastrin conjugates with the human immunoglobulin G1 hinge peptide 225‐232/225′‐232′
Authors: Moroder Luis , Bali Jean‐Pierre , Kobayashi Yuji 
Published: December 2004

AbstractHybrids of the double‐chain bis‐cystinyl fragment 225‐232/225′‐232′ of human immunoglobulin G1 (IgG1) with the human little‐gastrin sequence 2‐17 were found to induce in animals a strong antigastrin humoral immune response with antibody titers comparable to those raised with conventional gastrin/carrier‐protein conjugates. The observed gastrin receptor‐like specificity of the polyclonal antibodies led to the assumption that the gastrin component of the hybrids is still capable of folding into its preferred bioactive structure and thus to express a similar conformational epitope in the dynamic process of recognition by the B‐cell receptors. CD measurements on these hybrid compounds in aqueous and aqueous organic media confirmed the free conformational space for the antigenic gastrin moiety, which is essentially randomly coiled in aqueous solution but retains its ability to fold into the gastrin‐specific ordered structure in aqueous organic media as used to mimic the water‐limited environment of peptides while interacting with target cells at receptor level. The absence of reciprocal conformational restriction in such hybrid molecules suggests that a compact, rigid heterodetic cyclic structure as the hinge peptide is well suited for the multiple attachment of antigenic sequences in view of the preparation of fully synthetic immunogens.
Conformational analysis of bacitracin A, a naturally occurring lariat
Authors: Pons Miquel , Feliz Miguel , Molins M. Antònia , Giralt Ernest 
Published: December 2004

AbstractThe proton nmr spectra of bacitracin A in H2O and DMSO‐d6 have been assigned and the conformational behavior of the peptide in the two solvents has been compared. Although bacitracin A shows a conformational equilibrium between at least two conformations differing in the relative position of the cyclic and linear domains of the molecule, the spectra in water can be interpreted in terms of a preferred conformation in which the linear part is folded over the cyclic moiety and a turn is present around Ile8‐DPhe9.
Fluorescence and CD studies on the conformation of the gastrin releasing peptide in solution and in the presence of model membranes
Authors: Cavatorta P. , Sartor G. , Neyroz P. , Farruggia C. , Franzoni L. , Szabo A. G. , Spisni A. 
Published: December 2004

AbstractThe conformation of the heptacosapeptide hormone, gastrin releasing peptide, has been studied in buffer and in the presence of lipids, using static and dynamic fluorescence and CD. The results obtained show that, in buffer, the hormone exists in a collection of flexible, random coil type conformers, characterized by a β‐turn between residues 14‐19. On the other hand, organic solvents can induce some degree of ordered secondary structure in the peptide chain.The marked changes, observed in CD and fluorescence spectra upon addition of lysolecitin micelles and dimyristoylphosphatidylserine vesicles, clearly show that the peptide interacts with lipids, assuming a lipid specific configuration. Interestingly, no significative spectroscopic changes are produced by exposure to dimyristoylphosphatidylcholine vesicles both in the gel and liquid‐chrystalline phases, suggesting a requirement for negatively charged lipids during the process of hormone–membrane interaction.
Conformational energy minimization by simulated annealing using molecular dynamics: Some improvements to the monitoring procedure
Authors: Lelj F. , Grimaldi P. , Cristinziano P. L. 
Published: December 2004

AbstractThe possibility of using molecular dynamics techniques as a tool for simulated annealing is tested in the case of the molecule of biological interest N‐acetyl, N′‐methyl amides of 3(S)‐hydroxy, 4(S)‐amino 6‐methyl heptanoic acid [(3S, 4S)‐statine] and of its (3R,4S) diastereomer. The approach is able to reach global minimum in the conformational space in the case of the mentioned molecule. A description of the method is given. The use of fractional fluctuations of the internal potential energy as an indicator able to point out transition from a given minimum region to a deeper one is investigated. The results about the lowest energy conformation of (3S,4S) diastereomer are in fairly good accordance with the results obtained in the case of search within the whole Conformational hyperspace.
Conformational and binding studies on peptides related to domains I and III of calmodulin
Authors: Foffani Maria Teresa , Battistutta Roberto , Calderan Andrea , Ruzza Paolo , Borin Gianfranco , Peggion Evaristo 
Published: December 2004

AbstractThe conformational and ion‐binding properties of two peptide fragments of 25 amino acid residues corresponding to the helix‐loop sequences of domains I and III of calmodulin (CaM) were investigated by CD and Tb3+‐mediated fluorescence spectroscopy. Both peptides exhibit very similar ion binding properties either in water or trifluoroethanol (TFE), and do not allow the differentiation of the two domains in the native protein in terms of their binding capacity. An aggregation phenomenon was observed in TFE with increase of the α‐helical content. We suggest that the aggregation involves an interaction between the hydrophilic surfaces of amphiphilic α‐helices in a way similar to inverse micelle formation.
Toward nonpeptidal substance P mimetic analogues: Design, synthesis, and biological activity
Authors: Chorev Michael , Roubini Eli , Gilon Chaim , Selincer Zvi 
Published: December 2004

Abstract1,4‐Piperazine and 4‐hydroxy proline, two small cyclic polyfunctional systems with defined stereochemistry, were introduced as “molecular scaffolds.” We define a “bioactive topology,” which is a derived putative low‐energy conformation obtained through theoretical conformational analysis of substance P. Substitution of these molecular scaffolds by pharmacophors characteristic of the bioactive topology of the C‐terminal hexapeptide of substance P resulted in active, partially nonpeptidal substance P mimetic agonists. The study discusses the concepts arid tools used to achieve this structural transformation, and points out the need to address flexibility–rigidity issues in an attempt to maintain sufficient molecular plasticity.
Pharmacology of neurokinin receptors
Authors: Regoli D. , Nantel F. 
Published: December 2004

AbstractThe neurokinins are a group of naturally occurring peptides with the common C‐terminal sequence Phe‐X‐Gly‐Leu‐Met · NH2. They include substance P (SP), neurokinin A (NKA), and neurokinin B (NKB). SP and NKA are coded on the same gene, the PPT‐A, while NKB is coded on a separate gene, the PPT‐B. Neurokinins are present in the central nervous system and in peripheral organs where they exert various actions. They act on three receptors–NK‐1, NK‐2, and NK‐3–characterized through pharmacological, biochemical, and histochemical studies. Selective agonists for each neurokinin receptor were developed and evaluated on isolated smooth muscle preparations containing only one neurokinin receptor type. All three neurokinin receptors were cloned and expressed in Xenopus oocytes. Relative affinities of those receptors to neurokinins are the same as in their respective smooth muscle preparation. Finally, the mechanism of action of SP on histamine release from rat peritoneal mast cell has been studied and a direct activation of G proteins by peptides with basic amino acids is proposed as a working hypothesis.
Conformational analysis of two cyclic disulfide peptides
Authors: García‐Echeverría C. , Siligardi G. , Mascagni P. , Gibbons W. , Giralt E. , Pons M. 
Published: December 2004

AbstractComplete nmr and CD studies of two cyclic tetrapeptides with disulfide bonds,
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bonds have been carried out in different solvents to investigate the formation and stabilization of β‐turn structures and to determine the stereochemistry of the disulfide linkage. Both peptides have three‐dimensional structures with a type II β‐turn, as derived from quantitative nuclear Overhauser effect data. The combined use of CD and nmr indicates that the dihedral angle of the disulfide bridge is different in the two peptides, although the chirality is maintained.