bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational analysis of acetyl‐L‐phenylalanine p‐acetyl and p‐valeryl anilides
Authors: Petkov D. D. , Ivanov P. M. , Stoineva I. B. 
Published: May 2005

AbstractEmpirical force‐field calculations and ir and 1H‐nmr spectra indicate that five‐membered (C5) and seven‐membered (C) hydrogen‐bonded rings are the preferred conformations of acetyl‐L‐Phe p‐acetyl and p‐valeryl anilides in nonpolar media. The C5/C ratio was found to be dependent on the dryness of the solute and the solvent. This fact and the results from conformational‐energy calculations suggest that a molecule of water participates in the stabilization of the C conformation.
Crystal structure of Boc‐Ala‐Aib‐Ala‐Aib‐Aib‐methyl ester, a pentapeptide fragment of the channel‐forming ionophore suzukacillin
Authors: Francis A. K. , Iqbal M. , Balaram P. , Vijayan M. 
Published: May 2005

Abstractt‐Buthyoxycarbonyl‐L‐alanyl‐α‐aminiosobutyryl‐L‐alanyl‐α‐aminoisobutyryl‐α‐aminoisobutyric acid methyl ester (t‐Boc‐L‐Ala‐Aib‐L‐Ala‐Aib‐Aib‐OMe), C24H43N5O8, an end‐protected pentapeptide with a sequence corresponding to the 6th through the 10th residues in suzukacillin, crystallizes in the orthorhombic space group P212121 with a = 11.671, b = 14.534, c = 17.906 Å and z = 4. The molecule exists as a right‐handed 310‐helix with a pitch of 6.026 Å. The helix is stabilized by three 4 → 1 hydrogen bonds with the NH groups of Ala(3), Aib(4), and Aib(5) hydrogen bonding to the carbonyl oxygens of t‐Boc, Ala(1), and Aib(2), respectively. The helical molecules arrange themselves in a head‐to‐tail fashion along the a direction in such a way that the NH groups of Ala(1) and Aib(2) hydrogen bond to the carbonyl oxygens of Aib(4) and Aib(5), respectively, of a translationally related molecule. The helical columns thus formed close‐pack nearly hexagonally to form the crystal.
X‐Ray conformational study of the DNA duplex in solution
Authors: Grassian V. , Brady G. W. , Benham C. J. 
Published: May 2005

AbstractEarlier x‐ray studies on dissolved linear DNA molecules were interpreted on the assumption that the molecules scattered as rigid rods. Improvement in equipment and advances in theory of the scattering from randomly oriented helices prompted us into a reinvestigation of this problem. Careful measurements were made on the scattering from both linear calf thymus DNA and from circular plasmid C0P608 superhelical DNA. Contrary to the earlier work, we find that the scattering patterns show a helical character, with maxima corresponding to those of a helix with pitch angle of 62°, close to that of the C‐W helix. The patterns for both types of DNA, although similar, show a 5% displacement of the maximum in the superhelical form, just that expected when the C‐W helix is superimposed on a superhelix axis. Introduction of intercalators (PtTS) causes a progressive extension of the helix, as shown by a shift to larger angles and a fading out of the maximum. In the concentration range of 40 mg/mL, interfernce peaks develop, the result of an apparent stacking of the chains, with an interchain distance of ∼35 Å.
Total intensity light scattering from short, optically anisotropic wormlike chains
Authors: Allison Stuart A. 
Published: May 2005

AbstractSimple exact equations are derived for intensity light scattering from optically anisotropic wormlike chains in the absence of excluded volume. The results are valid at low scattering angles (q2 〈R2G〉 ≲ 1) for all sormilke chains from rigid rods to random couils. The present work and an earlier theory [Nagai, K. (1972) Polym. J. 3, 67–83] appear to be equivalent, although they were both derived using different methods. The present work is primarily concerned with short wormlike chains, since intensity light scattering from short fragments may provide valuable information about DNA flexibility. By using the results of this work to reanalyze some older light‐scattering studies [Godfrey, J. E. & Eisenberg, H. (1976) Biophys. Chem. 5, 301–318], it is shown that anisotropy corrections to polarized light‐scattering measurements have been overcorrected in the past. It can be anticipated that future light‐scattering experiments will determine the base‐pair anisotropy.
Monomolecular condensation of λ‐DNA induced by cobalt hexammine
Authors: Widom Jonathan , Baldwin Robert L. 
Published: May 2005

AbstractMeasurements of static and dynamic light scattering have been used to distinguish between monomolecular DNA condensation and aggregation of condensed molecules. In low salt, using Co3+(NH3)6 as the condensing agent, and at λ‐DNA concentrations below 0.2 μg/mL, the transition curves for monomolecular condensation and aggregation are well separated for times of 16 h. In these conditions, the intensity of scattered light (90°) and also the diffusion coefficient of the condensed DNA show reasonable values for monomolecular condensation that are independent of DNA concentration and also of Na+ Co3+(NH3)6 concentrations for which monomolecular condensation is complete. At higher Co3+(NH3)6 concentrations, which produce aggregation (as judged by the intensity of scattered light), the diffusion coefficient decreases sharply.The transition curve for monomolecular condensation is independent of DNA concentration but shows a hysteresis loop. The kinetics of condensation are slow in the forward direction and fast in the reverse direction, indicating that the actual transition curve is measured closely by reversal experiments. Aggregation is blocked kinetically in both the forward and reverse directions when Co3+(NH3)6 is the condensing agent at low Na+ concentrations. When spermine or spermidine is the condensing agent and observations are made at 16 h, it is not possible to separate the transition curves for monomolecular condensation and for aggregation in conditions that are successful with Co3+(NH3)6.Some interesting properties of monomolecular condensation are noted. (1) The transition is not a two‐state reaction, as judged by measurements of the diffusion coefficient through the transition zone. (2) The transition for monomolecular condensation is diffuse. (3) The dimensions of the monomolecular condensates have been calculated from the translational diffusion coefficient for an assumed toroidal shape by the formula derived by Allison and coworkers [(1981) Biopolymers 20, 469–488]. These dimensions are in reasonable agreement with ones deduced from electron microscopy by Chattoraj and coworkers [(1978) J. Mol. Biol. 121, 327–337]. (4) The phase diagram relating the Na+ to the Co3+(NH3)6 concentrations needed for condensation has a slope of 0.6 in a log–log plot. According to numerical solutions of Manning's theory for the atmospheric binding of competing cations to DNA, this means that condensation occurs at a late stage in the replacement of Na+ by Co3+(NH3)6 around the DNA. The fraction of DNA phosphate charge neutralized at condensation is computed to be in the neighborhood of 0.9, as found by Wilson and Bloomfield [(1979) Biochemistry 18, 2192–2196], but to vary with the Na+ concentration.
Inhibition of cation‐induced DNA condensation by intercalating dyes
Authors: Widom Jonathan , Baldwin Robert L. 
Published: May 2005

AbstractSeveral intercalating dyes are shown to inhibit the cation‐induced condensation of λ‐DNA when Co3+(NH3)6 is the condensing agent. The dyes that have been studied are ethidium, propidium, proflavin, quinacrine, and actinomycin D. Earlier work has shown that intercalating dyes inhibit ψ‐DNA condensation. [Lerman, L. S. (1971) Prog. Mol. Subcell. Biol. 2, 382–391; Cheng, S. & Mohr, S. C. (1975) Biopolymers 14, 663–674.] Dye‐induced decondensation of intramolecularly condensed DNA has been studied by making use of conditions in which Co3+(NH3)6 produces intramolecular condensation without significant aggregation. Some aggregation is caused, however, during dye‐induced decondensation. Dye titration curves of DNA decondensation have been measured by excess light scattering to monitor decondensation and by fluorescence to monitor intercalation. All of the dyes studied act as competing cations in displacing the condensing cation Co3+(NH3)6 from the DNA. Competition occurs both in and below the transition zone for condensation. The effectiveness of a dye as a competing cation increases with its net positive charge. Before decondensation begins, no intercalated dye can be detected, suggesting that intercalation might be incompatible with the proper helix packing needed for cation‐induced DNA condensation. To test this last point, methidium–spermine was synthesized: it contains an intercalating methidium head group combined with a polyamine tail. Methidium–spermine is found to cause λ‐DNA condensation, but aggregation accompanies condensation, as has been found earlier for spermine and spermidine. Fluorescence and absorption spectra indicate that the methidium group is intercalated when the DNA is condensed, indicating that intercalation need not be incompatible with DNA condensation. The presence of aggregates among the condensed DNA molecules makes this last conclusion tentative.
Conformational and functional properties of hemoglobin in perturbed solvent: Kinetics of O2 release
Authors: Cordone Lorenzo , Cupane Antonio , Fornili Sandro L. 
Published: May 2005

AbstractWe studied the kinetics of O2 release by oxyhemoglobin caused by sodium dithionite, in the presence and in the absence of organic cosolvents (monohydric alcohols and formamide) at 10°C. This study was performed by using standard stopped‐flow techniques coupled with microprocessor‐based data acquisition. We have fitted the experimental data to a mathematical expression obtained on the basis of a two‐state model that takes into account the kinetic heterogeneity between α‐ and β‐chains and the presence of αβ‐dimers in oxyhemoglobin solutions. Results indicate that the cosolvents mainly affect the allosteric parameter L, i.e., the T ⇄ R conformational equilibrium of hemoglobin, leaving the intrinsic deoxygenation rates of both R and T states almost unaltered. The L values obtained in the present work are in excellent agreement with analogous values previously estimated from oxygen equilibrium measurements.
Flexibility of collagen determined from dilute solution viscoelastic measurements
Authors: Nestler F. Henry M. , Hvidt Søren , Ferry John D. , Veis Arthur 
Published: May 2005

AbstractThe frequency dependences of the storage and loss shear moduli, G′ and G″, of pronase‐treated collagen dissolved in acetate buffer at pH 4.0 were measured at 17.0°C by use of the Birnboim‐Schrag multiple lumped resonator apparatus. Some of the solutions contained 70% glycerol. The infinite‐dilution moduli were determined and compared with theoretical models for a rigid cylinder and a semiflexible rod. Only the latter could fit the data. A rotational time of 144 μs and a slowest flexural relaxation time of 21 μs, both reduced to water at 20°C, were determined from the fit. The intrinsic viscosity and rotational relaxation time correspond to a semiflexible rod with persistence length of about 170 nm and a Young's modulus of 4 × 1010 dyn/cm2.
Modeling biological macromolecules in solution. II. The general tri‐axial ellipsoid
Authors: Harding Stephen E. , Rowe Arthur J. 
Published: May 2005

AbstractThe use of the general (tri‐axial) ellipsoid as a model for the conformation of biological macromolecules in solution is discussed. The recent derivation of an expression for the viscosity increment of dispersions of tri‐axial ellipsoids [S. E. Harding et al. (1979) IRCS Med. Sci. 7, 33; and (1981) J. Colloid Interface Sci. 79, 7–13] makes the fitting of such a model possible by the derivation of appropriate volume‐independent functions. We now derive these volume‐independent functions for tri‐axial ellipsoids and investigate by exhaustive computer simulation the possibility of deriving the two axial ratios (a/b, b/c) from data of various types, in every case containing plausible experimental error. It is shown that transport properties alone cannot be used to yield estimates for the axial ratios, given current experimental precision. However, a combination of transport and rotational diffusion properties is more promising, and an algorithm is developed and tested that will reliably yield estimates from simulated data obtained by the methods of sedimentation, viscosity, and electric birefringence.
Effect of finite ionic size on the solution of the Poisson‐Boltzmann equation: Application to the binding of divalent metal ions to DNA
Authors: Granot Joseph 
Published: May 2005

AbstractThe nonlinear Poisson‐Boltzmann equation is solved for a cylindrical polyelectrolyte solution containing mono‐ and divalent counterions and monovalent coions. The finite size of the ions is taken into account by the introduction of the distances of closest approach between the ionic charges and the surface of the polyelectrolyte. The choice of these distances is based on the physicochemical properties of the polyelectrolyte and ions in solution. The effects of the finite ionic size on the distribution of the counterions around the polyelectrolyte and on the local ion concentration and the integrated charge fraction of the divalent cations in the vicinity of the polyelectrolyte are discussed. Theoretical predictions regarding the overall extent of binding and the extent of inner‐sphere binding of divalent counterions to rodlike polyions are compared with the results of nmr studies of the binding of divalent metal ions to DNA.
Proton NMR studies of partially modified retro–inverso peptides
Authors: Ribeiro Anthony , Chorev Michael , Goodman Murray 
Published: May 2005

AbstractHigh‐resolution 1H‐nmr analyses are presented for partially modified retro‐inverso derivatives of peptides with emphasis on enkephalins. Studies in DMSO‐d6 reveal the unique as well as common characteristics of the non‐amino acid residues incorporated into these modified peptides. The complete assignment of 1,1‐diaminoalkyl and malonyl, as well as of amino acid, residues provides the basis for the exploration of the conformational features induced in peptides by such topochemical modifications.
Reversing‐pulse electric birefringence of poly(γ‐benzyl‐L‐glutamate). I. Transient behavior of fractionated samples in the low electric field region
Authors: Ueda Kazuyoshi , Nomura Minoru , Yamaoka Kiwamu 
Published: May 2005

AbstractReversing‐pulse electric birefringence (RPEB) was measured for the first time for four fractionated poly(γ‐benzyl‐L‐glutamate), [Glu(OBzl)]n, samples in N,N‐dimethylformamide (DMF) at 20°C and at 535 nm. The RPEB signal showed a deep minimum for each sample on reversal of an applied electric field. The profiles of the reverse‐transient signal were analyzed by taking into account the polydispersity for the continuous distribution of molecular lengths. The best set of three quantities (lw, lw/ln, (βw)2/2γw), which determine a signal profile, was evaluated for each sample. By combining the experimental data of intrinsic viscosity and RPEB, the diameter of a cylinder, which is assumed for the [Glu(OBzl)]n helix, was found to be 17 Å. The value (βw)2/2γw, which is related to the ratio of weight‐average permanent dipole moment μw, and electric polarizability anisotropy Δαw, was found to be in the range of 20–45. This indicates that the former contributes predominantly to electric field orientation, but the latter also should not be ignored. With the three parameters from the reverse portion, the rise and decay curves were regenerated theoretically in excellent agreement with experimental signals.
Infrared spectroscopic study of C7 intramolecular hydrogen bonds in peptides
Authors: Rao Ch. Pulla , Balaram P. , Rao C. N. R. 
Published: May 2005

AbstractThe ir‐spectra in the NH stretching region of Piv‐Pro‐NHMe and Boc‐Pro‐NHMe have been studied in carbon tetrachloride and chloroform solutions over a wide range of concentrations. Based on the concentration dependence of the NH stretching bands, it has been shown that the characteristic NH stretching band due to the C7 intramolecular hydrogen bond is around 3335 cm−1. Intermolecular hydrogen bonding also occurs to a small extent in these peptides, giving rise to a slight concentration dependence of the NH stretching bands. The band around 3335 cm−1 need not necessarily be due to C7 hydrogen bonds alone as proposed by Tsuboi et al. or to intermolecular hydrogen bonding alone as proposed by Maxfield et al.; this conclusion is supported by studies on Boc‐Leu‐NHMe, which undergoes only intermolecular hydrogen bonding. We have shown that Z‐Aib‐Aib‐OMe and Z‐Aib‐Ala‐OMe form C7 intramolecular hydrogen bonds in addition to C5 intramolecular hydrogen bonds. The present studies also show that all the peptides studied exist in more than one conformation in solution.
Computer building of β‐helical polypeptide models
Authors: Koeppe Roger E. , Kimura Michio 
Published: May 2005

AbstractA general method is presented for computing the atomic coordinates of helices in which a dipeptide is the repeating unit. The method will generate both single‐ and double‐stranded model helices having idealized bond lengths and angles, and any arbitrary, user‐specified, pitch and number of residues per turn. The variation of inter‐ and intrastrand hydrogen bonds with pitch and number of residues per turn can thus be examined. An application of the method is the construction of a β‐helix having pitch of 6.3 Å per turn and 4.85 residues per turn, a model which can pack nicely into the unit cell of crystals of cation‐bound gramicidin A.
Conformational change in yeast tRNAAsp
Authors: Huong P. V. , Audry E. , Giege R. , Moras D. , Thierry J. C. , Comarmond M. B. 
Published: May 2005

AbstractThe structure of yeast tRNAAsp in aqueous solutions has been analyzed in the light of results obtained from Raman spectra recorded at from 5 to 82°C and compared to those of tRNAPhe. Firm evidence is given of a reversible conformation transition for tRNAAsp at 20°C. This transition is observed for the first time in the tRNA series. The low‐temperature conformation appears to have a more regular ribose–phosphate backbone and a more effective G base‐stacking. This conformational change, which occurs essentially in the D loop, could be connected to the existence of two (A and B) crystal forms obtained depending on crystallization conditions. The melting temperatures, which are different for each base stacking in tRNAAsp, lie in a range of about 70°C, much higher than for tRNAPhe. This fact is interpreted by a higher ratio of G‐C base pairs in tRNAAsp.
Structure of a cellulose I–ethylenediamine complex
Authors: Lee David M. , Burnfield Keith E. , Blackwell John 
Published: May 2005

AbstractThe structure of a crystalline cellulose I–ethylenediamine complex has been determined by x‐ray diffraction methods as part of an investigation of cellulose–solvent interaction. The complex studied is that formed when native ramie fibers are swollen in ethylenediamine and then vacuum‐dried. The unit cell is monoclinic with dimensions a = 12.87 Å, b = 9.52 Å, c = 10.35 Å, and γ = 118.8°, and it contains disaccharide segments of two chains, with one ethylenediamine per glucose residue. The refined model contains parallel cellulose chains that are linked by hydrogen‐bonded ethylenediamine molecules. The chains along the b‐axis are packed in register, leading to stacks of chains analogous to those in chitin. All the hydroxyl groups are satisfactorily hydrogen‐bonded and each ethylenediamine forms four donor and two acceptor hydrogen bonds. From this work it can be seen that the interaction of cellulose I with ethylenediamine involves scission of the intermolecular hydrogen bonds followed by disruption of the stacks of quarter‐staggered chains.
Interactions of molecules with nucleic acids. VII. Intercalation and T·A specificity of daunomycin in DNA
Authors: Newlin Donald D. , Miller Kenneth J. , Pilch Daniel F. 
Published: May 2005

AbstractIntercalation complexes of daunomicin(+1) with tetramer duplexes in DNA are studied with the theoretically determined intercalation sites (I, −0.4), (II, −0.4), and (III, −1.4). These sites occur with base pairs separated by 6.76 Å for helical angles of 26°, 22°, and 8° about the intercalation site. Site I is preferred, and this is in agreement with experimental unwinding angles. Optimum binding positions and conformations are established, and these are in agreement with experimental results from crystal structures. A systematic procedure is devised to study base‐pair and base‐sequence specificity, which results in the demonstration that the most stable sequences are mainly ↑BP1, T·A, DAUN, A·T, BP4↓ and ↑BP1, T·A, DAUN, G·C, BP4↓, i.e., with the TpA and CpG (pyrimidine)p(purine) sequences about the intercalation site. These 32 possible sequences are found among the 40 most stable complexes. These theoretical calculations of intercalation complexes with daunomicin(+1) provide the first example in which a drug specifically selects the base pair T·A and prefers it in a particular sequence about the intercalation site. This specificity is in agreement with some experimental results. Problems associated with the interpretation of specificity are discussed in terms of the base, base‐pair, and base‐sequence resulting from the DNA site and the DNA–drug interactions. T·A specificity is rationalized by noting that the 2′deoxyribo‐5′‐monophosphate backbone attached to A is slightly more negative than that on the other nucleotides. Hence, a preference exists for binding to the protonated daunosamine (+1) groups. Stereographic projections of daunomycinone and daunomycin(+1) in a bond model and in a space‐filling model with steric contours illustrate the results.
Transport properties of rigid and flexible macromolecules by brownian dynamics simulation
Authors: Allison S. A. , McCammon J. A. 
Published: May 2005

AbstractThe method of Ermak and McCammon [Ermak, D. L. & McCammon, J. A. (1978) J. Chem. Phys. 69, 1352–1360] is used to simulate the Brownian dynamics of a system of identical, interacting beads. In the present study, we use the method to obtain transport coefficients for a variety of rigid and flexible structures modeled as arrays of spherical subunits. Constraints are enforced using the SHAKE algorithm or a modification, SHAKE‐HI, that is described for the first time. In SHAKE‐HI, hydrodynamic interactions between subunits are taken into account when the constraints are enforced. Use of SHAKE‐HI yields transport coefficients that are in perfect agreement with those obtained by other methods. The primary advantage of the present method is its generality. We also propose that multistep Brownian dynamics may be important in simulating actual experiments (such as fluorescence depolarization) on well‐defined model systems that possess an arbitrary degree of internal flexibility.