bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformation of LiDNA in solutions of LiCl
Authors: Borochov Nina , Eisenberg Henryk 
Published: May 2005

AbstractWe have derived radii of gyratin, Rg, from the absolute intensity of the scattered light of mondisperse linear Col E1 LiDNA in solution at various LiCl concentrations up to 5M. The second virial coefficients, A2, decrease strongly with increasing LiCl concentration, and vanish between 3 and 5M LiCl. It was thus possible to calculate a limiting value at a high salt concentration of 28.5 nm for the persistence length, a0, of LiDNA, without the necessity of applying excluded‐volume corrections. The value obtained is in good agreement with the value previously obtained for NaDNA at high NaCl concentrations, and can be identified with the high salt limit of DNA flexibility, with long‐range electrostatic interactions effectively screened. Sedimentation coefficients in the ultracentrifuge and apparent and translational diffusion coefficients (at finite and vanishing scattering vectors, respectively) from dynamic laser‐light scattering have also been obtained up to 5M LiCl. From the sedimentation and apparent diffusion, D(90), (at 90° scattering angle only) above 5M, and up to 9M LiCl, it could be shown that the solutions are stable for reasonable periods of time, and the molecular parameters vary smoothly and moderately at high salt. Conformational transitions were not observed and precipitation occurs between 9 and 10M LiCl.
Theoretical π‐π* absorption, circular dichroic, and linear dichroic spectra of collagen triple helices
Authors: Caldwell James W. , Applequist Jon 
Published: May 2005

AbstractAbsorption, CD, and LD spectra of the π‐π* transition near 200 nm are calculated for poly(Gly‐X‐Y) (X,Y = Gly, Ala, Pro) in four conformations proposed for collagen like triple helices in the recent literature. A dipole interaction model is used with the same optical paramenters as in previous studies of polypeptide spectra. The CD spectra are sensitive to backbone structure and amino acid composition, although the experimentally observed negative peak near 200 nm is a general feature of most the calculated spectra. Interchain interactions significantly affect the CD spectra in most cases. Calculations for (Gly‐Pro‐Ala)3 and (Gly‐Ala‐Pro)3 in the triple helical structure of Fraser, MacRae, and Suzuki [(1979) J. Mol. Biol. 129, 463–481] show absorption, CD, and LD spectra in fairly good agreement with experiment. The characteristics of the π‐π* normal modes responsible for the calculated spectra are compared with those of the component bands resolved from the experimental spectra of collagen by Mandel and Holzwarth [(1973) Biopolymers 12, 655–674].
Kinetic studies of the complex formation in the ternary system of amylose, SDS, and iodine
Authors: Yamamoto Masako , Harada Shoji , Sano Takayuki , Yasunaga Tatsuya , Tatsumoto Nobuhide 
Published: May 2005

AbstractComplex formation in the ternary system of amylose (degree of polymerization,DP, 1100), SDS, and iodine was studied statically by spectrophotometry and amperometric titration and kinetically by the pressure‐jump method. It was clarified that (1) iodine (I3−) to some extent binds to amylose saturated with SDS to form an inclusion complex (ASI system); (2) the binding of SDS apparently transforms amylose ofDP1100 to that of much lowerDP(less than 60) from the viewpoint of iodine binding; and (3) iodine binds to sites unoccupied by SDS in the center of the helical segment of amylose. Pressure‐jump relaxation phenomenon was not observed in solutions in which iodine was dissolved prior to SDS (AIS system), but it was observed in the ASI system; it is ascribed to the association and dissociation of three molecules of iodine in the center of the amylose helix. Comparison of the rate constants in the ASI system with those in the amylose (DP32) and iodine system indicates that iodine runs to and from the helical segment of amylose perpendicularly to the axial plane in the former, while it runs horizontally in the latter. We discuss the order of ligand mixing on the resulting structure of the ternary complexes of amylose, SDS, and iodine.
Molecular model for the complex between Concanavalin A and a biantennary‐complex class glycopeptide
Authors: Carver J. P. , MacKenzie A. E. , Hardman K. D. 
Published: May 2005

AbstractA molecular model for the complex formed between the jack bean lectin concanavalin A (Con A) and glycopeptides of the complex biantennary class is described. The model was derived using coordinates for Con A determined by x‐ray crystalographic refinement techniques, with 1.75‐Å resolution data, and coordinates for the glycopeptides obtained from 1H‐nmr measurements, using the nuclear Overhauser effect. Previous solution and crystallographic studies provided several constraints on the possible mode of interaction of the lectin and the glycopeptide. Examination of the model suggests that the glycopeptide binding site is defined by four loops on the protein surface made up by amino acid residues: 12–18, 98–102, 205–208, and 226–229. Within these loops, it favorable interactions with high‐affinity ligands and tose responsible for the unfavourable interactions with poor ligands.
Membrane proteins as light‐energy transducers
Authors: Ovchinnikov Yu. A. 
Published: May 2005

AbstractMonoclonal antibodies to different parts of bacteriorhodopsin were raised to define its topography in the membrane. It is shown that the amino acid residue Glu 194 is a part of an antigenic determinant and should be located on the membrane surface. We found that the removal of the C‐terminal 17 amino acid sequence does not affect the efficiency of the proton transport in bacteriorhodopsin. From a combination of proteolysis and secondary structure prediction methods an experimentally testable structural model for bovine rhodopsin is presented. The complete amino acid sequence of the transducin γ‐subunit consisting of 69 residues was determined.
Studies on proline‐containing tetrapeptide models of β‐turns
Authors: Hollośi M. , Kawai M. , Fasman G. D. 
Published: May 2005

AbstractThe synthesis of a series of protected tetrapeptides of the general formula Cbz‐Gly‐X2‐Y3‐Gly‐OR (R = stearyl or methyl, X and/or Y = proline) is described. Detailed CD studies have been performed to evaluate the contribution of proline‐containing β‐turns to the CD spectra of proteins. The CD spectra of all the models are dominated by the chiral contribution of the proline residue. In polar, proton‐donating solvents, a poly‐proline II‐like spectrum was observed in almost all cases. The tetrapeptide model Cbz‐Gly‐Gly‐Pro‐Gly‐OStearyl, in acetonitrile shows a type C spectrum that has not been previously reported for linear peptides. The ir and nmr data on this model support the assumption of that of a type III β‐turn, exhibiting a type C spectrum, participate in the conformational equilibrium. The most interesting finding of the CD studies is the observation of a type D spectrum (according to the classification of Woody [Woody, R. W. (1974) in Peptides, Polypeptides and Proteins, Blout, E. R. Bovey, F. A. Lotan, N. & Goodman, M. (Eds.), Wiley, New York]) for models Cbz‐Gly‐Pro‐Asp(OBut)‐Gly‐OStearyl and Cbz‐Gly‐Pro‐Ser(OBut)‐Gly‐OStearyl in cyclohexane. The results of the CD measurements ae discussed in correlation with ir and nmr data and with recent literature.
The octamers d(CGCGCGCG) and d(CGCATGCG) both crystallize as Z‐DNA in the same hexagonal lattice
Authors: Fujii Satoshi , Wang Andrew H.‐J. , Quigley Gary J. , Westerink Henk , Van Der Marel Gijs , Van Boom Jacques H. , Rich Alexander 
Published: May 2005

AbstractBoth (dC‐dG)4 and d(CGCATGCG) crystallize in hexagonal lattices and their three‐dimensional structure has been solved by x‐ray diffraction analysis. Both molecules are found to form Z‐DNA, although the fine details of the structure cannot be visualized due to the statistical disordering of the molecules along the c‐axis, which is brought about by the symmetry constraints of the space group. This represents the first time in which the unmodified dinucleotide sequences CpAp and TpGp have been found to form Z‐DNA in a crystalline lattice.
Determinations of atomic partial charges for nucleic acid constituents from x‐ray diffraction data. I. 2′‐Deoxycytidine‐5′‐monophosphate
Authors: Pearlman David A. , Kim Sung‐Hou 
Published: May 2005

AbstractThe first experimentally derived set of partial charges for a nucleotide has been determined. A high‐resolution x‐ray data set (5122 independent observed reflections to sin(θ)/λ = 0.995 Å−1) has been collected at T = −150°C for 2′‐deoxycytidine‐5′‐monophosphate monohydrate in the zwitterionic form. Radial refinement was carried out on the data, a refinement method that allows variation of atomic valence sphere radii and populations and hence directly yields the partial charges of atoms in a structure [Coppens, P., Guru Row, T. N., Leung, P., Stevens, E. D., Becker, P. J. & Yang, Y. W. (1979) Acta Crystallogr., Sect. A 35, 63–72]. The atomic partial charges thus determined are in general qualitative agreement with theoretical values, but significant differences exist, indicating a reassessment of the applicability of the theoretical sets currently in use is necessary. The ab initio charges determined by Nuss and Kollman [(1979) J. Med. Chem. 22, 1517–1524] are closest to experiment in the sugar and base regions, while the Del Re charges of Renugopalakrishnan et al. [(1971) Biopolymers 10, 1159–1167] match best in the phosphate region. The presence of an additional hydrogen on N3 appears to have a small effect on the charge densities of all base atoms, rather than a large localized effect on adjacent atoms. Inspection of deformation density maps for the hydrogen bonds in this crystal suggests possible differences between those bonds that include a nitrogen atom as part of the bond and those that do not.
Thermodynamics of the daunomycin–DNA interaction: Ionic strength dependence of the enthalpy and entropy
Authors: Chaires Jonathan B. 
Published: May 2005

AbstractFluorescence and absorbance methods were used to study the interaction of daunomycin with calf‐thymus DNA over a wide range of temperatures and NaCl concentrations. van't Hoff analysis provided estimates for the enthalpy of the binding reaction over the NaCl range of 0.05–1.0 M. Daunomycin binding is exothermic over this entire range, and the favorable binding free energy arises primarily from the large, negative enthalpy. Both the enthalpy change and entropy change are strong functions of ionic strength. Possible molecular contributions to the enthalpy and entropy are discussed, leading to the tentative conclusion that hydrogen‐bonding interactions at the interacalation site are the primary contributors to the observed thermodynamic parameters. The dependence of the enthalpy on the ionic strength is well beyond the predictions of current polyelectrolyte theory and cannot be fully accounted for. The enthalpy and entropy changes observed compensate one another to produce relatively small free‐energy changes over the range of solution conditions studied.
Dielectric effects in biopolymers: The theory of ionic saturation revisited
Authors: Hingerty B. E. , Ritchie R. H. , Ferrell T. L. , Turner J. E. 
Published: May 2005

AbstractElectrostatic effects are believed to determine the molecular structure and function of macromolecules in many ways. In metallo‐based enzymes and in metal–macromolecule interactions in solution, these effects may predominate. In order to tackle metal ion–nucleic acid interactions theoretically, we propose a modification of Debye's distance‐dependent dielectric function first proposed more than 50 years ago. This function more closely approximates physical reality at small interatomic separations. Our theory yields a dielectric function that gives reasonable agreement with experimental data in preliminary calculations.
Conformation of double‐stranded polydeoxynucleotides in solution by proton two‐dimensional nuclear overhauser enhancement spectroscopy
Authors: Borah Babul , Cohen Jack S. , Bax Ad 
Published: May 2005

AbstractProton 2D‐NOE spectroscopy has been used to investigate the three‐dimensional conformations of several sonicated polydeoxynucleotides in solution. The observed pattern of cross peaks indicate that poly(dA‐dT) · poly(dA‐dT) in all salt concentrations studied (up to 6.6M CsF), and poly(dG‐m5dC) · poly(dG‐m5dC) in low salt (0.1M NaCl) are righthanded B‐structures. Poly(dG‐m5dC) · poly(dG‐m5dC) in Mg2+ (3 mM) solution exhibits a pattern characteristic of the left‐handed Z‐form. These results for poly(dA‐dT) · poly(dA‐dT) are in contrast to suggestions that this copolymer exists as a left‐handed form, either in low or high salt. We present pure absorption‐mode 2D‐NOE spectra that enable us to compare several distances and define the conformations of these polydeoxynucleotides in solution.
The physical origin of the low solubility of nonpolar solutes in water
Authors: Lee B. 
Published: May 2005

AbstractElementary but general statistical‐mechanical relations are derived that relate the thermodynamic properties of the dissolution process to those of the pure solvent. A number of conclusions are drawn from qualitative arguments that these relations suggest. These include the following: (1) The low solubility of nonpolar solutes in water arises not from the fact that water molecules can form hydrogen bonds, but rather from the fact that they are small in size. (2) The large entropy decrease attending the transfer of an inert solute from a nonaqueous solvent to water is largely due to the decrease in entropy of the nonaqueous solvent as the solvent–solvent interaction is restored on removal of the solute from it. (3) It is improper to use values of thermodynamic quantities obtained from small‐molecule transfer studies for those that involve macromolecular folding and interaction.
Base tilt of poly[d(A)]–poly[d(T)] and poly[d(AT)]–poly[d(AT)] in solution determined by linear dichroism
Authors: Edmondson Stephen P. , Johnson W. Curtis 
Published: May 2005

AbstractWe have measured the CD, isotropic absorption, and LD of poly[d(A)]–poly[d(T)] and poly[d(AT)]–poly[d(AT)] in the vacuum‐uv spectral region. The reduced dichroism (LD divided by isotropic absorption) varied as a function of wavelength and was independent of shear gradient. Thus, the bases are not perpendicular to the helix axis in solution. Since the directions of the transition dipoles are known, the orientations of the bases in the polymers can be calculated from the reduced dichroism spectra. The results show that the base normals are tilted at angles greater than 25°, with respect to the helix axis, and thymine is tilted more than adenine for both polymers. The tilt axes of adenine and thymine are not parallel, indicating a large propeller twist. Space‐filling models of poly[d(A)]–poly[d(T)] and poly[(AT)]–poly[d(AT)] are built based on our results, and the conformations of the two (A + T) polymers in solution are discussed.
Conformation of cyclic analogs of enkephalin. III. Effect of varying ring size
Authors: Hall David , Pavitt Nicola 
Published: May 2005

AbstractA comparative study has been made using molecular mechanics of the ring entity of the active enkephalin analogs, Tyr‐cyclo(‐Nω‐D‐XXX‐Gly‐Phe‐Leu‐), where XXX is variously A2pr, A2bu, and Orn. Several conformations are favored for all three, and the lower‐energy models are compatible with a Gly3‐Phe4 bend in the active form of enkephalin. Some difficulties in assuming standard geometries in conformational surveys are illustrated.
Crystal structure of the α‐helical undecapeptide Boc‐L‐Ala‐Aib‐Ala‐Aib‐Ala‐Glu(OBzl)‐Ala‐Aib‐Ala‐Aib‐Ala‐OMe
Authors: Bosch R. , Jung G. , Schmitt H. , Winter W. 
Published: May 2005

AbstractThe x‐ray structure of Boc‐L‐Ala‐Aib‐Ala‐Aib‐Ala‐Glu(OBzl)‐Ala‐Aib‐Ala‐Aib‐Ala‐OMe(I) represents the first α‐helix determined by direct methods. This undecapeptide is a model of the N‐terminus of alamethicin, and it exhibits voltage‐dependent pores in bilayer membranes at a higher voltage and concentration than alamethicin. The molecule crystallizes in the monoclinic space group P21 with a = 10.602(1), b = 23.884(3), c = 13.622(1) Å, β = 95.61(6)°, and Z = 2. It adopts a right‐handed α‐helical conformation in the solid state with intramolecular 5 → 1 hydrogen bonds. An additional intramolecular hydrogen bond is bifurcated, forming a stronger 4 → 1 interaction (i.e., a β‐turn III) and a weaker 5 → 1 interaction, thus prolonging the α‐helical part up to 9 residues. The α‐helix radius of 2.1 Å, the height per residue (distance Ni … Ni + 4) of 1.53 Å, the resulting length of the α‐helical part of 13.8 Å (9 residues) resp. 15.3 Å (10 residues), the van der Waals radius (4.7 Å), and the minimal diameter of pores formed by aggregation of 3–10 α‐helices were calculated omitting the Glu(OBzl) side chain. In the crystal, the α‐helices are linked head to tail via two hydrogen bridges forming continuous chains. Adjacent helices are oriented in antiparallel with their helix axes and have only van der Waals contacts.
Crystal structure of Boc‐Leu‐Aib‐Pro‐Val‐Aib‐Aib‐Glu(OBzl)‐Gln‐Phl × H2O, the C‐terminal nonapeptide of the voltage‐dependent ionophore alamethicin
Authors: Bosch R. , Jung G. , Schmitt H. , Winter W. 
Published: May 2005

AbstractBoc‐L‐Leu‐Aib‐Pro‐Val‐Aib‐Aib‐Glu(OBzl)‐Gln‐Phl (Boc = t‐butyloxycarbonyl, Aib = α‐aminoisobutyric acid, Bzl = benzyl, Phl = phenylalaninol), C59H90N10O14, the protected C‐terminal nonapeptide with the sequence 12–20 of alamethicin, crystallizes in the orthorhombic space group P212121 with a = 15.666, b = 16.192, c = 26.876 Å, and Z = 4. The molecular conformation is right‐handed helical with three α‐(5 → 1 hydrogen bonds) and three β‐turns (4 → 1 hydrogen bonds). All but two of the hydrogen bonds are significantly longer than the usual value and show bifurcation to some extent. The α/3‐helical nonapeptide molecules are arranged head‐to‐tail along the a direction. The resulting linear antiparallel chains are linked by a weak intermolecular hydrogen bridge, thus forming a two‐dimensional layer structure in the ab plane. The conformation of this nonapeptide is almost identical with that of the corresponding C‐terminal part found by x‐ray crystallography of the eicosapeptide alamethicin.
Influence of supercoiling on DNA structure: Laser Raman spectroscopy of the plasmid pBR322
Authors: Vasmel Henk 
Published: May 2005

AbstractWe report high‐resolution Raman spectra obtained from the circularly closed double stranded DNA (Form I) of the plasmid pBR322 and from its corresponding linear form (Form III). Comparison of the Raman spectra of the two forms demonstrates that, at a superhelical density (σ) of −0.069, which is of the same order as those found for most naturally occurring circularly closed DNAs, no major structural transitions occur under the influence of supercoiling. It is shown that at least 98% of all bases are fully basepaired, and that the conformation of the sugar–phosphate backbone is essentially identical to that of linear DNA. Thus, the structural influence of supercoiling, under these conditions, is confined to minor stretches of the plasmid DNA.
Torsional dynamics and rigidity of fractionated poly(dGdC)
Authors: Fujimoto Bryant S. , Shibata John H. , Schurr Rebecca L. , Schurr J. Michael 
Published: May 2005

AbstractTime‐resolved fluorescence polarization anisotropy measurements were performed on two fractionated samples of duplex poly(dGdC) containing 230 (+40, −30) base pairs (bp) and 590 ± 40 bp. Deconvolution using the intermediate zone formula for the twisting correlation functions (which is not valid for such short DNAs) yields apparent torsion constants for these two samples that are disparate and, in any case, too low. By similarly deconvoluting simulated data constructed from the correct twisting correlation functions, it can be inferred that these two samples actually exhibit the same torsion constant, α = (4.0 ± 0.4) × 10−12 dyn cm. Within the experimental uncertainties, this value is the same as that reported previously from this laboratory for linear ϕ29 and linearized M13mp7 DNAs. The 590‐bp sample exhibited a peculiar evolution of its apparent torsional rigidity from a very high initial value, \documentclass{article}\pagestyle{empty}\begin{document}$ \hat \alpha $\end{document} = (11 ± 1) × 10−12 dyn cm, to a normal value over a period of several months, during which time many very small fragments appeared to be dissociated from, or annealed out, of the predominant high‐molecular‐weight species. Possible interpretations of these observations are discussed.
Guanine residue: A normal‐coordinate analysis of the vibrational spectra
Authors: Majoube Michel 
Published: May 2005

AbstractThe force field established for guanine is applied here to guanine‐containing biopolymers by considering the model compound 9‐methylguanine, in which the methyl group is taken as a dynamic unit whose mass is concentrated on the carbon. In‐plane normal‐mode frequencies for this model compound and its N‐deuterated analog are calculated. Band frequencies observed for guanine residue in Raman biopolymer spectra, such as those for DNA, RNA, or poly(G), are associated with calculated modes having similar wavelengths. They are discussed by taking into account observed and calculated D, 15N, and 18O isotopic shifts. The atomic displacements for the normal modes corresponding to the principal bands are illustrated and a number of assignments proposed.
Raman spectroscopic elucidation of DNA backbone conformations for poly(dG‐dT) · poly(dA‐dC) and poly(dA‐dT) · poly(dA‐dT) in CsF solution
Authors: Fodor Stephen P. A. , Starr Philip A. , Spiro Thomas G. 
Published: May 2005

AbstractRaman spectra have been recorded for poly(dG‐dT) · poly(dA‐dC) and poly(dA‐dT) · poly(dA‐dT) in low salt and at high concentrations of CsF. Poly(dG‐dT) · poly(dA‐dC) shows no change in the 682‐cm−1 guanine mode, demonstrating the absence of the Z‐structure at high salt. The 790‐cm−1 phosphodiester symmetric stretch, however, shifts up 5 cm−1 in 4.3M CsF, suggesting a slight conformational change, associated with ion binding or hydration changes. Poly(dA‐dT) · poly(dA‐dT) shows an additional broad band at 816 cm−1, attributed to the phosphodiester modes associated with the C3′‐endo deoxyribose units in the alternating B‐structure. In this case, both the 841‐ and the 816‐cm−1 asymmetric phosphodiester stretches, associated with the C2′‐ and C3′‐endo units, shift down on addition of CsF in a sequential manner. Correlation of this sequence with that previously observed for the two 31P‐nmr resonances, establishes that the phosphodiester stretching frequencies depend on the conformation of the 5′‐sugar, and not on the 3′‐sugar.
Theory of gel electrophoresis of DNA
Authors: Lumpkin Oscar J. , Déjardin Philippe , Zimm Bruno H. 
Published: May 2005

AbstractA theory of the electrophoresis of DNA through gels with large interfiber spacing, such as dilute agarose, is presented. We assume that the DNA molecule moves along its axis through a “tube” in a neutral gel under the influence of the electric field. The tube is random except for possible bias due to the effects of the field. When the field is small, we easily recover the inverse‐length dependence of the mobility found previously by de Gennes and by Doi and Edwards. At higher fields, a new effect appears; the tube becomes oriented because the field biases the direction of the leading end of the chain as it moves to form an extension of the tube. This leads to an increase of the mobility with increasing field by adding a field‐dependent but length‐independent term to the mobility expression. In agreement with experiment, we find that the field effect can be important at fields as low as 1 V/cm and that the effect can seriously decrease the sensitivity of the mobility to chain length. We also examine the fluctuation of the migration distance, the degree of orientation induced by the field, and the transient effects occurring when the feld direction is rotated by a right angle.