bluuebunny/crossref_metadata_2025_split huggingface dataset:
Excluded volume of an intermediate‐molecular‐weight DNA. A Monte Carlo analysis
Authors: Post Carol Beth 
Published: December 2004

AbstractA Monte Carlo procedure wasused to determine the effect of excluded volume on the dimensions of an intermediate‐molecular‐weight DNA for different Na+ concentrations. The calculation of α, the parameter for the linear expansion due to excluded volume, was accomplished by generating sets of chains and, for each set, comparing the average radius of gyration for the set of chains that do not overlap to that averaged over the entire set of chains. Each chain was defined by cylinders linked with free rotation and with bend angles generated according to a weighted Gaussian distribution. The chain parameters—contour lenght, cylinder lenght and diameter—were fixed in order to resemble published light‐scattering experiments on Col E1 DNA. Values for α were less than 1.08. for Na+ concentrations between 0.007 and 1.0M. A previously reported analytical calculation of the excluded‐volume correction of intermediate‐sized DNA gave results that are closely similar to those from the Monte Carlo analysis.
Orientational interactions in low‐concentration DNA solutions
Authors: Marion Christian , Roux Bernard , Hanss Maxime 
Published: December 2004

AbstractThe rotational relaxation tiem τ3 of DNA molecules (Mw ≃ 5 × 106) in solution has been determined by the transient electric birefringence method. The analysis of the birefringence decay makes it possible to study only the higher‐molecular‐weight fraction, the molecules being considered as rigid elongated particles in a short time scale. A marked concentration dependence of the relaxation time has been observed for DNA in low ionic strengths. Above a critical concentration c*, τ3 increases with the DNA concentration, c. The value of c* increases with the ionic strength. For 10−3 ionic strength (with NaCl), c* is about 10 μg/mL; then we observe the same strong concentration dependence of rotational relaxation times as recently reported for rodlike M‐13 viruses [Maguire, J. F., McTague, J. P. & Rondelez, F. (1980) Phys. Rev. Lett. 45, 1891–1894]. These results may be discussed in terms of the Doi‐Edwards theory for rotational relaxation time of rigid macromolecules [Doi, M. (1975) J. Phys. 36, 607–611; Doi, M. & Edwards, S. F. (1978) J. Chem. Soc. Faraday Trans. 74, 918–932] and the critical concentration above which the interactions between the molecules begin to appear allows determining the corresponding molecular length. We observe a very good agreement between the DNA lengths obtained from the c* values and by using the infinite dilution value of τ3 and Broersma's equation. Therefore, only highly diluted solutions can be used if intrinsic molecular properties based on the rotational diffusion of high‐molecular‐weight elongated molecules are studied.
Conformation of 2‐aminofluorene‐modified DNA
Authors: Broyde S. , Hingerty B. 
Published: December 2004

AbstractMinimized potential‐energy calculations were performed to determine the conformation of the 2‐aminofluorene (AF) adduct to dCpdG at guanine C‐8. The AF adduct has many low‐energy conformers in both the anti and the syn domains of the guanine. This is in contrast with the acetylated adduct, (AAF), which greatly prefers the syn domain. Two types of low‐energy guanine anti‐conformations were obtained: (1) conformers that preserve guanine–cytidine stacking and (2) conformers with fluorene–cytidine stacking. Of special importance are conformers with ω′,ω,ψ = g−, g−, g+, characteristic of normal A‐ or B‐helices, which are found in both groups. No conformers of this type were obtained for the acetylated AAF adduct. The guanine–cytidine stacked from with this conformation can be incorporated in the B‐helix without any distortion, with the carcinogen situated at the helix exterior. The fluorene in this model can slide into the helix to yield a fluorene–cytidine stacked minimum‐energy conformation. This requires no denaturation, although one base pair is unstacked and the helix axis is bent. Low‐energy syn‐conformations, similar to those obtained for the AAF adduct, were also computed. These were either guanine‐cytidine stacked or fluorene–cytidine stacked. The syn froms are less likely to be observed in larger DNA polymers of the adduct, since they cause more distortion than the anti‐conformations. However, they might well be observed in crystals of small subunits, and they should contribute significantly to the population in solution.
1H‐Nuclear magnetic resonance study on imidazole–imidazole interaction in L‐histidyl‐L‐histidine and D‐histidyl‐L‐histidine: Analysis including microscopic dissociation series
Authors: Tanokura Masaru 
Published: December 2004

AbstractThe 1H‐nmr titration curves of chemical shifts versus pH were observed for the protons of D,L‐histidyl‐D,L‐histidine as representative of cases with two or more ionizable groups with similar pKa values. The titration curves of L‐histidyl‐L‐histidine and D‐histidyl‐L‐histidine were individually analyzed according to two mathematical models: one of a macroscopic dissociation series and one of a microscopic dissociation series. Most‐probable values and standard deviations were obtained for pKa values and intrinsic chemical shifts. An analysis including the microscopic dissociation series yielded an electrostatic interaction between twoimidazole rings of about 0.3 pH units for L‐histidyl‐L‐histidine and about 0.7 pH units for D‐histidyl‐L‐histidine. The difference of the magnitude of imidazole‐imidazole interactions between L‐histidyl‐L‐histidyne and D‐histidyl‐L‐histidine was interpreted in terms of the spatial arrangement of two imidazole rings in each molecule based on the solution conformation estimated from Gd(III)‐induced relaxation enhancements.
Unwinding kinetics of cooperatively melting regions in DNA
Authors: Suyama Akira , Wada Akiyoshi 
Published: December 2004

AbstractUnwinding of a single cooperatively melting region of ColE1 DNA is investigated by a slow temperature jump in formamide–neutral buffer mixed solvent. The semilogarithmic plots of unwinding relaxation curves show a marked terminal linear region following the fast decay, which occurred within the temperature rise time (1 ∼ 2 s). This longest relaxation is ascribed to the total unwinding of a single cooperatively melting region. The longest relaxation time, τ1, is uniquely determined by the final equilibrium state and becomes shorter as the final temperature increases. Decrease in ionic strength makes τ1 and its fractional amplitude increase, and the relaxation almost approaches single‐exponential decay. The facts that (1) τ1 of a single cooperatively melting region whose unwinding suffers larger frictional resistance does not always unwind more slowly, as was shown by the observations of τ1's of almost the same cooperatively melting region located at different positions on two linearized ColEl DNAs and of τ1's of two cooperatively melting regions on the same linearized ColEl DNA; (2) τ1 has strong dependence on the equilibrium state after a temperature jump; and (3) the observed τ1 is much longer than the expected time of the frictional barrier all demonstrate that the τ1 is limited by chemical but not hydrodynamic processes. The detailed unwinding process of a single cooperatively melting region, elucidated by evidence of a negative apparent activation energy of the rewinding process and by extensive computer simulation of the equilibrium melting process, suggests that the local heterogeneity of G+C content in a cooperatively melting region, as well as its averaged G+C content, strongly affects its unwinding rate. The present study of a single cooperatively melting region is found to be useful to improve our understanding of the detailed mechanism of complex unwinding of large natural DNAs, in which many cooperatively melting regions unwind.
Mechanism of gel formation in κ‐carrageenan
Authors: Rochas C. , Rinaudo M. 
Published: December 2004

AbstractWe present a general view of κ‐carrageenan gelation and some new experimental results concerning their behavior in the presence of Na+, K+, or Rb+ counterions in semidilute concentration. The gelation mechanism is based on the aggregation of helical dimers.
Circular dichroism studies of α‐aminoisobutyric acid‐containing peptides: Chain length and solvent effects in alternating Aib‐L‐Ala and Aib‐L‐Val sequences
Authors: Vijayakumar E. K. S. , Sudha T. S. , Balaram P. 
Published: December 2004

AbstractThe CD spectra of the peptides Boc‐X‐(Aib‐X)n‐OMe (n = 1, 2, 3) and Boc‐(Aib‐X)5‐OMe, where X = L‐Ala or L‐Val have been examined in several solvents. The X = Ala and Val peptides behave similarly in all solvents, suggesting that the Aib residues dominate the folding preferences of these peptides. The decapeptides adopt helical conformations in methanol and trifluoroethanol, with characteristic negative CD bands at 222 and 205 nm. In the heptapeptides, similar spectra with reduced intensities are observed. Comparison with nmr studies suggest that estimates of helical content in oligopeptides by CD methods may lead to erroneous conclusions. The pentapeptides yield solvent‐dependent spectra indicative of conformational perturbations. Peptide association in dioxane results in an unusual spectrum with a single negative band at 210 nm for the decapeptides. Disaggregation is induced by the addition of methanol or water to dioxane solutions. Aggregation of the heptapeptides is less pronounced in dioxane, suggesting that a critical helix length may be necessary to promote association stabilized by helix dipole–dipole interactions.
Vibrational analysis of peptides, polypeptides, and proteins. XVIII. Conformational sensitivity of the α‐helix spectrum: αI‐ and αII‐Poly(L‐alanine)
Authors: Dwivedi Anil M. , Krimm S. 
Published: December 2004

AbstractThe αII‐helix (ϕ = −70.47°, ψ = −35.75°) is a structure having the same n and h as the (standard) αI‐helix (ϕ = −57.37°, ψ = −47.49°). Its conformational angles are commonly found in proteins. Using an improved α‐helix force field, we have compared the vibrational frequencies of these two structures. Despite the small conformational differences, there are significant predicted differences in frequencies, particularly in the amide A, amide I, and amide II bands, and in the conformation‐sensitive region below 900 cm−1. This analysis indicates that αII‐helices are likely to be present in bacteriorhodopsin [Krimm, S. & Dwivedi, A. M. (1982) Science 216, 407–408].
Locally oscillatory motion of RNA helix derived from linear relationships of backbone torsion angles
Authors: Kitamura Kunihiro , Mizuno Hiroshi , Amisaki Takashi , Tomita Ken‐Ichi , Baba Yasumasa 
Published: December 2004

AbstractA linear relationship in each of the torsion angle pairs, α‐β, β‐ϵ, ϵ‐ζ, and α‐γ, has been found by applying a statistical method based on the concept of circular variates to backbone torsion angle data of helical in yeast tTNAPhe. A series of helical dimer models generated with these relationships have been found to be stereochemically acceptable, and the models also indicate that the backbone unit in the RNA helix is geometrically capable of an oscillatory motion with the distance of about 3.4 Å between adjacent bases. The motion of the backbone unit is analogous to that of a helical spring. The adjacent bases, because of being attached to the backbone, oscillate in a manner similar to the oscillatory dimer model proposed by Davis and Tinoco [Davis, R. C. & Tinoco, I., Jr. (1968) Biopolymers 6, 223–242]. Here, the oscillation of the backbone unit in the RNA helix is discussed in terms of two geometrical quantities: the torsion (τ) and curvature (κ) of the helix. On these lines, a stereochemical model of RNA strand separation is proposed.
Interaction of metal ions with gastrointestinal hormones: Binding studies of Mg++ to biologically active analogs of little gastrin and minigastrin
Authors: Peggion E. , Mammi S. , Palumbo M. , Moroder L. , Wünsch E. 
Published: December 2004

AbstractThe interaction of magnesium ions with Des‐Trp1‐Nle12‐minigastrin I (Nle11‐HG‐13) and Nle115‐little gastrin I (Nle15‐HG‐17) has been studied by CD and spectrophotometric techniques in trifluoroethanol. Spectrophotometric titrations using murexide as a metallochromic indicator showed that there are three binding sites for magnesium ions in Nle11‐HG‐13, with binding constants of the order of (6 ± 2) × 106, (1.7 ± 0.5) × 106, and (5.0 ± 0.5) × 105M−1. These figures have been independently confirmed by CD measurements in the far‐uv in the presence of increasing amounts of magnesium ions. Elongation of the peptide chain from Nle11‐HG‐13 to Nle15‐HG‐17 does not provide any additional binding site for the metal ions. In both hormones, we have observed different responses in the near‐ and fur‐uv CD properties with regard to added magnesium. The intensity of the CD bands in the aromatic region changes cooperatively with the ion/hormone molar ratio. These findings lead us to conclude that at the C‐terminal, the biologically important sequence, ‐Trp‐Nle‐Asp‐Phe‐Nh2, is directly involved in the interaction with magnesium.
Circular dichroic studies on Cu(II) interactions with a protamine, scylliorhinine Z3
Authors: Kozlowski H. , Aubert J. P. , Gusse M. , Chevaillier P. , Loucheux‐Lefebvre M. H. 
Published: December 2004

AbstractThe interaction of Cu(II) with the protamine scylliorhinine Z3 was studied by means of CD measurements. At a 1:1 molar ratio, three complexes are formed. (1) In the pH range 5–6.5, the results suggest the formation of a five‐membered chelate ring through the coordination of two nitrogen atoms, the N‐terminal and the contiguous peptide nitrogen. (2) At pH ≥ 6.4, there is involvement of the lateral NH2 group of Arg; at pH 6.5–8, the formation of a 3N cupric complex is strongly suggested. (3) At pH ≥ 8, results indicate the formation of a 4N complex as a major species in Cu(II)‐Z3 solution. The transformation from a 2N to a 3N complex, and from a 3N to a 4N complex was followed with the help of the σ(αNH2) → Cu(II) charge‐transfer dichroic band transitions. At Cu(II):Z3 molar ratios ≥ 2 and at pH > 8, a new dichroic band appears, indicating the involvement of the tyrosine residue side chain in metal‐ion complexation.
Induced optical activity in the complex of poly(L‐arginine) with azo dyes
Authors: Yamamoto Hiroyuki , Nakazawa Ayako 
Published: December 2004

AbstractThe absorption and CD spectra of the complexes of poly(L‐arginine) (PLA) and azo dyes have been measured in aqueous solution. On complexation, Blue‐shifted additional absorption bands were observed. In the wide pH 4–11 range, induced CD was observed at the visible wavelengths corresponding to the blue‐shifted absorption bands. The induced CD arose from the dimeric dye molecules bound to PLA in the α‐helical structure. When a modified analysis of induced CE is made by the excition chirality method, the origin of the induced CD can be assigned to the dipole coupling. The PLA–dye complexes showed the counterlockwise (negative, S) chirality of the transition dipole moments of dyes.
Conformation of a cyclic tetrapeptide related to an analog of enkephalin
Authors: Hall David , Pavitt Nicola 
Published: December 2004

AbstractA systematic survey has been made, using molecular mechanics, of the conformation of cyclo(‐Nγ‐Mabu‐Gly‐Ala‐Ala‐), where Mabu is (R)‐α‐methyl‐γ‐aminobutyric acid. This molecule corresponds to the 14‐membered ring of the conformationally restricted, biologically active, Leu‐enkephalin analog, Tyr‐cyclo(N γ‐D‐A2bu‐Gly‐Phe‐Leu‐), reported by DiMaio and Schiller [(1980) Proc. Natl. Acad. Sci. USA 77, 7162–7166]. There is one extensive low‐energy conformational region, in which the two lowest energy minima are separated by a low barrier; other low‐energy conformations exist but are closely restricted. Assuming that enkephalin in its active form shares conformation features with the cyclic molecule, it is deduced that enkephalin contains a Gly3‐Phe4 type II′ bend and that it could be similar to the model proposed by Clarke et al. [(1978) J. Med. Chem. 21, 600–606].
Characterization of intermediate conformational states in the B↔Z transitions of poly(dGdC) · poly(dGdC)
Authors: Goto Sachio 
Published: December 2004

AbstractTime‐dependent uv absorption and CD spectrum changes in salt‐induced conformational B → Z and Z → B transitions of poly(dGdC) · poly(dGdC) were measured. This polynucleotide does not convert directly from a right‐handed double‐helical B form to a left‐handed double‐helical Z form, but goes through an intermediate, B* form, with the B → B* transition proceeding nearly instantaneously, and then transforms gradually to the Z form. Uv absorption spectra of these B and B* forms are nearly identical, but their CD spectra are quite different. The CD spectrum of the B* form is identical with that obtained for DNA in high salt solutions and is similar to a spectrum which for some time was thought to be a C form. These B and B* forms have the same number of base pairs per turn [Sprecher, C.A., Baase, W.A. & Johnson, Jr., W.C. (1979) Biopolymers 18, 1009–1019]. Kinetic measurements showed that uv absorption and CD intensities at fixed wavelengths do not change in a simple exponential curve. However, both the uv absorption spectrum change in the B → Z transition and the CD spectrum change in the B* → Z transition, respectively, have isosbestic points. In the B → Z transition, no hyperchromicity can be observed. These results suggest that this B* form unfolding or premelting process is a rate‐determining step in the B* → Z transition and makes it easy for the unfolded or premelted polynucleotide to almost immediately fold into the Z form. The double helix does not dissociate into single strands and transforms from the B* form to the Z form point‐by‐point along the chain in a soliton‐like manner of with a small amount of open states in which the bases are unpaired. Also, in the Z → B transition, the polynucleotide does not convert directly from the Z to the B form, but goes through a B*‐like form. In this transition, the uv‐absorption spectra also have an isosbestic point. The reaction velocity in the Z → B transition is much faster than that in the B → Z transition. Possibly, the positive CD band between 265 and 310 nm in the B form comes from a n‐π* transition due to an interaction of the bases with sugarphosphate groups.
Viscoelasticity of rigid macromolecules with irregular shapes in the limit of overwhelming Brownian motion
Authors: Wegener William A. 
Published: December 2004

AbstractWe consider viscoelastic properties of complex rigid macromolecules in fluids undergoing steady or sinusoidal linear shearing. An arbitrary body is hydrodynamically described by six tensors to allow for irregular shapes that couple rotational and translational motions to each other and to the shear field. The viscosity increment ν is obtained for infinitely dilute suspensions in the limit of overwhelming Brownian motion by balancing drag forces and torques with entropic forces and torques. For sinusoidal shearing, ν is a complex number that exhibits five resonances at frequencies matching the j = 2 eigenvalues of the rotational diffusion equation for a stationary fluid. The resonance amplitudes are conveniently expressed in terms of a second‐rank body‐fixed tensor χ that characterizes alignment by the shear field, and special cases of symmetry are considered which reduce the number of contributing terms. Steadyshear methods, which assume a body matches the translational and rotational motions of the fluid element it replaces, are shown to slightly overestimate ν when complex shapes are involved. An algebraic criterion is found to locate the center of viscosity needed in these other methods although our treatment is independent of the choice of position in the body used for calculations. Bead‐model expressions are derived in order to provide numerical treatments of complicated structures. As an example, we examine a long bent rod.
Suppression of the statistical coil state during the α ↔ β transition in homopolypeptides
Authors: Mattice Wayne L. , Scheraga Harold A. 
Published: December 2004

AbstractA matrix formulation of the conformational partition function has been used to examine helix ↔ sheet transitions in homopolyamino acids. α‐Helices are weighted by Zimm‐Bragg parameters σ and s. Antiparallel β‐sheets with tight bends are weighted by the parameters t, δ, and τ, where t is the propagation parameter. In addition, each bend contributes a factor δ, and each residue in the sheet that does not have a partner in the preceding strand contributes a factor τ. The helix can be the dominant conformation in a long chain only if two conditions are satisfied simultaneously: (i) s > 1, and (ii) either s > t, or σ, δ, and τ are assigned values that inflict a greater penalty on antiparallel sheets than on helices. The maximum amount of coil developed during the helix ↔ sheet transition is strongly influenced by the size of τ, but it is only weakly dependent on the size of δ. Previously reported optical rotatory dispersion, CD, laser Raman, and nmr studies of thermally induced α ↔ β transitions in homopolyamino acids, notably poly(L‐lysine), demonstrate that little random coil is present. If the random coil content is to remain small during the helix ↔ sheet transition, τ must be significantly less than unity. A small value for τ means that there is a significant penalty assessed to lysyl residues in an antiparallel sheet that do not have a partner in a preceding strand.
Molecular‐dynamics simulation of phenylalanine transfer RNA. II. Amplitudes, anisotropies, and anharmonicities of atomic motions
Authors: Prabhakaran M. , Harvey Stephen C. , McCammon J. Andrew 
Published: December 2004

AbstractThe atomic motions from a molecular‐dynamics simulation of yeast tRNAPhe are analyzed and compared with those observed in protein simulations. In general, the tRNA motions are of larger amplitude, they are more anisotropic, and they arise from potentials of mean force that are more anharmonic than in the protein case. In both cases, the amplitudes are largest for atoms on the surface of the molecules. On the other hand, the most anisotropic and anharmonic atomic motions are generally found in the interior of the tRNA, while they are found on the surface of the protein. These differences are discussed in terms of the differences in structure between nucleic acids and proteins.
Effect of anisotropic bending rigidity and finite twisting rigidity on statistical properties of DNA model filaments
Authors: Schurr J. Michael 
Published: December 2004

AbstractThe persistence length and effective long‐range bending rigidity are derived for a discrete model of an anisotropically bending filament and shown to be independent of the torsional rigidity. The twisting persistence length is found to be independent of the anisotropic bending rigidity. Other statistical properties are briefly discussed, including the dependence of tangent vector projections on contour length. The dependence of a tensor contraction on contour length is derived for an isotropically bending filament with no equilibrium twist.
Vibrational circular dichroism of polypeptides. IV. Film studies of L‐alanine homo‐oligopeptides
Authors: Narayanan Usha , Keiderling T. A. , Bonora G. M. , Toniolo C. 
Published: December 2004

AbstractVibrational CD (VCD) and ir absorption data are reported for a series of films of Boc‐(L‐Ala)n‐OMe homo‐oligopeptides (n = 3–7) in the amide I and A regions. The data evidenced a sharp change between n = 3 and n = 4, which parallels the onset of β‐structure formation, and another between n = 5 and n = 6, which parallels the full development of β‐structure. This represents the first report of the application of VCD to oligopeptide conformation. The data resembled earlier reported film VCD studies of higher‐molecular‐weight polypeptides of known β‐structure.