bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic light scattering studies of porcine submaxillary mucin fractions in dilute solution at intermediate scattering vectors
Authors: Varma B. K. , Demers A. , Jamieson A. M. , Blackwell J. , Jentoft Neil 
Published: December 2004

AbstractWe report dynamic light scattering measurements over a wide range of scattering vectors for fractionated samples of porcine submaxillary mucin (PSM) glycoproteins in two different solvents: 0.1M NaCl, and 6M GdnHCl. The relaxation spectrum has been successfully resolved into a slow mode corresponding to pure translational diffusion and a fast mode containing information on the relaxation times for intramolecular motion. Analysis of the slow mode permits a light scattering evaluation of the polydispersity of these high molecular weight mucin glycoprotein fractions. Determination of the longest intramolecular relaxation times τ1 shows that these are much longer for the PSM fractions in 0.1M NaCl compared to 6M GdnHCl. These data are consistent with earlier studies showing that the chain conformation is the same in both solvents, but that in 0.1M NaCl, the PSM glycoprotein undergoes a self‐association process that is end‐to‐end in nature. Since the τ1 value is intimately related to the viscoelastic behavior of PSM solutions and gels, it is interesting to speculate that the end‐to‐end association process may be physiologically important.
Modeling DNA supercoils and knots with B‐spline functions
Authors: Hao Ming‐Hong , Olson Wilma K. 
Published: December 2004

AbstractA method is offered to model the complex trajectories of closed circular DNA supercoils and knots. The trajectories are approximated by polygons and analytical expressions of the curves are generated from the polygons with B‐spline functions. The resulting curves are used to evaluate the writhe and elastic energy of a series of interrelated supercoils, and to generate detailed atomic models of the deformed double helix.
The 9‐fluorenylmethyloxycarbonyl group as a 5′‐OH protection in oligonucleotide synthesis
Authors: Ma Yunxi , Sonveaux Etienne 
Published: December 2004

AbstractOligo‐DNAs are synthesized on a solid support using the 9‐fluorenylmethyloxycarbonyl group as a 5′‐OH base labile protection. The synthesis of the pure protected nucleotides, a relevant phosphoramidite‐type strategy of coupling, and the optimization of the deprotection steps are described. This new synthetic method is an alternative to the standard protocol that avoids acidic conditions.
Structure of DNA hydration shells studied by Raman spectroscopy
Authors: Tao N. J. , Lindsay S. M. , Rupprecht A. 
Published: December 2004

AbstractWe have used Raman scattering to study the water O‐H stretching modes at ∼ 3450 and ∼ 3220 cm−1 in DNA films as a function of relative humidity (r.h.). The intensity of the 3220‐cm−1 band vanishes as the r.h. is decreased from 98% to around 80%, which indicates that the hydrogen‐bond network of water is disrupted in the primary hydration shell (which therefore cannot have an “ice‐like” structure). The number of water molecules in the primary hydration shell was determined from the intensity of the ∼ 3200‐cm−1 band as about 30 water molecules per nucleotide pair. The ∼ 3400‐cm−1 O‐H stretch band was used for determining the total water content, and this band persists at 0% r.h., implying that 5–6 tightly bound water molecules per nucleotide pair remain. The frequency of the ∼ 3400‐cm−1 O‐H stretch mode is lower by 30 to 45 cm−1 in the primary hydration shell compared to free water. The water content as a function of r.h. obtained from these experiments agrees with gravimetric measurements. The disappearance of the ∼ 3200‐cm−1 band and the shift of the ∼ 3400‐cm−1 O‐H stretch band provide a reliable way of measuring the hydration number of DNA.
Conformation of a bulge‐containing oligomer from a hot‐spot sequence by NMR and energy minimization
Authors: Woodson Sarah A. , Crothers Donald M. 
Published: December 2004

AbstractTwo‐dimensional nmr data on a bulge‐containing oligodeoxyribonucleotide, 5′dGATGGGCAG · dCTGACCCATC, and a regular oligomer of similar sequence, 5′dGATGGCAG · dCTGCCATC, are presented. The nonexchangeable protons are assigned from sequential nuclear Overhauser effect spectroscopy (NOESY) connectivities. The two‐dimensional NOE (NOESY) and correlated (COSY) spectra of the bulge‐containing oligomer are compared to those of the perfect 8‐mer. Experimental proton‐proton distances are determined from NOESY spectra acquired with mixing times of 100, 150, and 200 ms, using comparable distances in the B‐DNA region of the molecule as a calibration. With this approach, measured distances do not depend systematically on mixing time. Energy minimization techniques are used to calculate a three‐dimensional structure for the bulge‐containing oligomer in agreement with the nmr data. The helix is of the B family, with the extra adenine stacked into the helix, and the helix axis is bent by 20°.
Counterion diffusion in heparin solutions
Authors: Tivant P. , Perera A. , Turq P. , Belloni L. 
Published: December 2004

AbstractThe physiological importance of heparin is due to its strong interaction with bivalent counterions, especially Ca2+. A diffusional approach of this property is presented in this article: the observable is the self‐diffusion coefficient of the counterions, as a function of the ratio of the polyelectrolyte over the added salt concentrations. All the results are in agreement with a simple “quasi‐chemical model” in which two different states are assumed for the counterions: “free” or “bound.” The proportions of these two types of ions are calculated according to the distribution function of the counterions around the polyion. We assume that those of counterions located at a distance closer than a, the characteristic distance, are bound; the others are free. The ionic distribution function is evaluated by a numerical integration of a cell model Poisson–Boltzmann equation. Finally, this model leads to a very good agreement with the experimental results, if the radius of heparin polyion is assumed to be 6 and 10 Å.
Sequence dependence of the B‐A conformational transition of DNA
Authors: Mazur J. , Sarai A. , Jernigan R. L. 
Published: December 2004

AbstractWe have studied, by conformational analysis, the sequence dependence of DNA conformational transition between B‐ and A‐forms. We have considered intramolecular interactions between base pairs, without backbone, to examine their role in the conformational transition between B‐ and A‐forms, and found that base pairs themselves usually have intrinsic conformational preferences for the B‐ or A‐form. Calculation of all ten possible base steps shows that the base combinations, CC (or GG), GC, AT, and TA, have tendencies to assume the A‐conformation. Results show that it is particularly easy to slide along the long axis of the base pair for these steps, with AT and CC showing especially flat energies. These calculations show that a preference for the B‐ or A‐conformation depends on the electrostatic energy parameters, in particular, on dielectric and shielding constants; the A‐conformations are mainly stabilized by electrostatic interactions between favorably juxtaposed atomic charges on base pairs; however, the B‐conformation generally has more favorable van der Waals interactions than the A‐form. These sequence‐dependent conformational preference and environmental effects agree roughly with experimental observations, suggesting that the origin of the conformational polymorphism is attributable to the intrinsic conformational preference of base pairs.
Ca2+ binding cyclic octapeptides having an alternating sar and a hydrophobic amino acid in the sequence
Authors: Kimura Shunsaku , Ozeki Eiichi , Imanishi Yukio 
Published: December 2004

AbstractCyclic octapeptides having alternating Sar and hydrophobic amino acid sequences, such as cyclo[Lys(Z)‐Sar‐Leu‐Sar‐Leu‐Sar‐Leu‐Sar] (C8KL), cyclo[Glu(OMe)‐Sar‐Lys(Z)‐Sar‐Leu‐Sar‐Leu‐Sar] (C8KE), and cyclo[Lys(Suc)‐Sar‐Leu‐Sar‐Leu‐Sar‐Leu‐Sar][C8K(Suc)L, Suc represents succinic acid], were synthesized. These cyclic octapeptides formed a complex selectively with Ca2+. Upon complexation, trans peptide bonds of Sar residues were isomerized to cis peptide bonds. C8KL and C8KE showed very similar characteristics of Ca2+ binding, extraction of Ca2‐ from an aqueous solution to a chloroform solution, and Ca2+ transport through a liquid chloroform membrane. C8KL transported Ca2+ across the lipid bilayer membrane above the phase‐transition temperature, while C8KE and C8K(Suc)L did not. Therefore, the transport of Ca2+ through the lipid bilayer membrane is very sensitive to the hydrophobicity of the carrier molecule.
Ca2+ transport through lipid membrane by diastereomer cyclic octapeptides
Authors: Kimura Shunsaku , Ozeki Eiichi , Imanishi Yukio 
Published: December 2004

AbstractEffects of the nature and orientation of a side chain in cyclic octapeptides on Ca2+ transport were examined by using cyclo[L‐Lys(Z)‐Sar‐LLeu‐Sar]2 (C8‐L), cyclo[L‐Lys(Z)‐Sar]4 (C8KS), and their diastereomer cyclic octapeptides, cyclo[L‐Lys(Z)‐Sar‐D‐Leu‐Sar]2 (C8‐D) and cyclo[L‐Lys(Z)‐Sar‐D‐Lys(Z)‐Sar]2 (C8Kk). All these cyclic octapeptides were found to take a single conformation in CDCl3, and the conformation was C2‐symmetric for C8‐L and C8‐D, and C4‐symmetric for C8KS and C8Kk. They formed a complex with Ca2+. Upon complexation, C8KS accompanied isomerization of peptide bonds, but C8‐D retained the arrangement of peptide bonds. The amount of Ca2+ extracted from an aqueous solution to a chloroform solution by all L cyclic octapeptide C8‐L or C8KS was about twice that of Na+, but 6 ∼ 8‐fold smaller than that by C8‐D or C8Kk including D units. These cyclic octapeptides were capable of transporting Ca2+ through a lipid membrane above the phase transition temperature, and the transport rate decreased in the order of C8Kk ∼ C8KS > C8‐D > C8‐L.
Two γ‐bends in the backbone conformation of [D‐ala2]‐leucine enkephalin in solution
Authors: Dhingra M. M. , Saran Anil 
Published: December 2004

AbstractThe solution conformation of [D‐Ala2]‐leucine enkephalin in its zwitterionic form in DMSO‐d6 has been monitored by one‐ and two‐dimensional proton magnetic resonance spectroscopy at 500 MHz. The resonances from the labile amide protons and the nonlabile protons have been assigned from the shift correlated spectroscopy. The chemical shift of the amide and C‐α protons are found to vary with temperature but in opposite directions, except the C‐α proton of the terminal tyrosine residue. This behaviour has been explained by the shifting of equilibrium between the zwitterionic and neutral forms of the [D‐Ala2]‐leucine enkephalin and probably conformational changes accompanying temperature variation. The low values of the temperature coefficients of leucine and glycine amide protons indicate that these protons are either intramolecularly hydrogen bonded or solvent shielded. The observation of sequential cross peaks in the nuclear Overhauser effect spectra obtained at various mixing times, τm (200–900 ms), indicate an extended backbone, which does not corroborate with the presence of a folded structure, i.e., β‐bend type structure. The estimate of interproton distances in conjunction with the low values of temperature coefficients of the leucine and glycine amide protons and vicinal coupling constants 3J have been rationalized by the predominance of two γ‐bends in the backbone conformation of [D‐Ala2]‐leucine enkephalin. The γ‐bend around the D‐Ala residue has Φ = 80° and ψ = 270°, while the one around Phe it has Φ = 285° and ψ = 90°.
A calorimetric approach to the study of the interactions of cytidine‐3′‐phosphate with bovine seminal ribonuclease
Authors: Ambrosino Rita , Barone Guido , Castronuovo Giuseppina , Cultrera Orazio , Di Donato Alberto , Elia Vittorio 
Published: December 2004

AbstractA calorimetric study at 25°C is reported on the interaction between allosteric bovine seminal ribonuclease and cytidine‐3′‐phosphate. The results are compared with those obtained under identical experimental conditions for the interaction of pancreatic ribonuclease A and the same nucleotide. The analysis of the data provides evidence that the binding sites of seminal ribonuclease for cytidine‐3′‐phosphate are not equivalent, in agreement with previous equilibrium dialysis studies. A model with two sites with different affinities toward the nucleotide, the site with higher affinity resembling the binding site of pancreatic ribonuclease, is proposed. The values calculated for the thermodynamic parameters provide an insight of the forces involved in the interaction of the two enzymes with the nucleotide.
Long‐range structural effects in supercolied DNA: Statistical thermodynamics reveals a correlation between calculated cooperative melting and contextual influence on cruciform extrusion
Authors: Schaeffer Francis , Yeramian Edouard , Lilley David M. J. 
Published: December 2004

AbstractWe have previously described [K. M. Sullivan and D. M. J. Lilley (1986) Cell 47, 817–827] a set of sequences, called C‐type inducing sequences, which cause cruciform extrusion by adjacent inverted repeats to occur by an abnormal kinetic pathway involving a large denatured region of DNA. In this paper we apply statistical thermodynamic DNA helix melting theory to these sequences. We find a marked correlation between the ability of sequences to confer C‐type cruciform character experimentally and their calculated propensity to undergo cooperative melting, and no exceptions have been found. The correlations are both qualitative and quantitative. Thus the ColE1 flanking sequences behave as single melting units, while the DNA of the S‐type plasmid pIRbke8 exhibits no propensity to melt in the region of the bke cruciform. The results of the calculations are also fully consistent with the following experimental observations:

the ability of the isolated colL and colR fragments of the ColE1 flanking sequences, as well as the short sequence col30, to confer C‐type character;
C‐type induction by an A + T rich Drosophila sequence;
low‐temperature cruciform extrusion by an (AT)34 sequence;
the effect of changing sequences at a site 90 base pairs (bp) removed from the inverted repeat;
the effects of systematic deletion of the colL sequence; and
the effects of insertion of various sequences in between the colL sequence and the xke inverted repeat.
These studies show that telestability effects on thermal denaturation as predicted from equilibrium helix melting theory of linear DNA molecules may explain all the features that are revealed by studying the extrusion of cruciforms in circular DNA molecules subjected to superhelical stress.
The sieving of spheres during agarose gel electrophoresis: Quantitation and modeling
Authors: Griess Gary A. , Moreno Elena T. , Easom Richard A. , Serwer Philip 
Published: December 2004

AbstractBy use of agarose gel electrophoresis, the sieving of spherical particles in agarose gels has been quantitated and modeled for spheres with a radius (R) between 13.3 and 149 mm. For quantitation, the electrophoretic mobility has been determined as a function of agarose percentage (A). Because a previously used model of sieving [D. Rodbard and A. Chrambach (1970) Proc. Natl. Acad. Sci. USA 65, 970–977] was found incompatible with some of these data, alternative models have been tested. By use of an underivatized agarose, two models, both based on the assumption of a single effective pore radius (PE) for each A, were found to yield PE values that were independent of R and that were in agreement with values of PE obtained independently (PE = 118 nm × A−0.74): sieving by altered hydrodynamics in a cylindrical tube of radius, PE, and sieving by steric exclusion from a circular hole of radius, PE. The same analysis applied to a 6.5% hydroxyethylated commercial agarose yileded a steeper PE vs A plot and also agreement of the above tow models with the data. The PE vs A plot was significantly altered by both further hydroxyethylation and factors that cause variation in the electro‐osmosis found in commercial agarose.
Orientational and rotational velocity correlation functions for water‐hydrating B‐ and Z‐DNA double helices
Authors: Swamy Kandadai N. , Clementi Enrico 
Published: December 2004

AbstractThe molecular dynamics simulations reported earlier for the structure and dynamics of water molecules hydrating B‐ and Z‐DNA double helices are analyzed for the orientational correlation functions and the proton rotational velocity autocorrelation functions. The spectra of the rotational velocity autocorrelation functions obtained from the simulation results are compared with the neutron inelastic scattering experiments on hydrated Na‐DNA samples. The results predict a small frequency component associated with water molecules bound to the double helices that disappears for waters away from the double helix.
Aggregation of amphotericin B in the presence of γ‐cyclodextin
Authors: Kajtár M. , Vikmon M. , Morlin E. , Szejtli J. 
Published: December 2004

AbstractThe macrolide antibiotic amphotericin B (AmB) forms an inclusion complex with γ‐cyclodextrin (γ‐CDx), resulting in a molecularly dispersed state of the drug. The state of aggregation of AmB in different solvents has been studied by absorption (uv‐vis) and CD spectroscopy. While in aqueous solutions AmB forms colloid‐like multimolecular aggregates, in the presence of γ‐CDx true solutions can be prepared, which show similar spectral properties as AmB dissolved in organic solvents. The AmB–γ‐CDx complex can be isolated as an amorphous, stable, water‐soluble powder, indicatin that γ‐CDx is a good carrier for the solubilization of this antibiotic. Using γ‐CDx as a carrier, the danger of precipitation of the drug during parenteral or intravenous administration can be largely reduced.
The CD of two‐chain coiled coils: Experiments on tropomyosin and tropomyosin segments in the tyrosin/disulfide spectral region
Authors: Holtzer Marilyn Emerson , Kumar Swatantar , Holtzer Alfred , Crimmins Dan L. 
Published: December 2004

AbstractCD experiments are reported for several coiled‐coil species in the tyrosine/disulfide ( ∼ 250–350‐nm) region. Intact noncross‐linked tropomyosin ( ∼ 3°C) shows a negative nonsymmetric band maximal at 280 nm. This spectrum is the sum over six tyrosines/chain, and has conformational significance, since it disappears on denaturation. Experiments on an excised coiled‐coil segment, each of whose chains comprise residues 11–127 of the tropomyosin sequence and only one tyrosine (Y60), reveal that not all tyrosines are alike. The spectrum at 3°C shows a small negative maximum at ∼ 285 nm and a substantial, hitherto unknown, positive band at ∼ 270 nm, the latter masked in the parent protein by the negative contribution from the other tyrosines. A noncross‐linked coiled‐coil segment comprising residues 142–281, in which Y60 is absent, shows no such positive band. This peculiarity of Y60 is confirmed by absorbance spectra, with the extinction coefficient of Y60 larger in benign media than the average of the other tyrosines. Intact (3°C) C190 cross‐linked tropomyosin is known to yield, besides tyrosine contributions, a positive maximum at ∼ 300 nm. Subtracting the corresponding data for noncross‐linked tropomyosin shows that the disulfide spectrum itself actually has two equal, partly resolved bands at, respectively, 250 and 280 nm. The existence of a chiral disulfide argues for a relatively rigid, perhaps strained, local coiled coil. A C190 cross‐linked segment, comprising residues 142–281 shows a chiral disulfide spectrum like tropomyosin's, but another segment, comprising residues 168–284, shows none; thus removal of residues 142–167 causes loss of chirality at C190, over 20 residues away. These spectra thus contain important information on the subtle local differences in coiled‐coil structures.
A temperature‐dependent Z to B to single‐strand transition in d(CGCG)
Authors: Thomas Gerald A. , Peticolas Warner L. 
Published: December 2004

AbstractA thermally induced left‐ to right‐handed helical interconversion for the self‐complementary tetradeoxynucleotide d(CGCG) has been observed in the presence of NaCl at concentrations from 1.5 to 2.25M. Analysis of the Raman spectrum of d(CGCG) in aqueous solution as a function of temperature indicates that at low temperature a left‐handed Z‐helical form is the predominant species. An increase in temperature results in a decrease in the population of the left‐handed form and an increase in the population of the right‐handed form. Further elevation in temperature results in extensive disruption of base stacking and a loss of secondary structure. This unstacking presumably represents dissociation to a single‐stranded structure. The data suggest that a temperature‐dependent Z to B to single‐strand transition occurs under the conditions employed. A direct Z to single‐strand conversion was not identified. In contrast to previous examples, the thermally induced left‐ to right‐handed helical conversion for d(CGCG) can occur in the absence of chemically modified nucleic acid bases, alcohol solutions, or divalent ions.
Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first‐order phase transition
Authors: Shakhnovich Evgeny I. , Finkelstein Alexey V. 
Published: December 2004

AbstractA theory of equilibrium denaturation of proteins is suggested. According to this theory, a cornerstone of protein denaturation is disruption of tight packing of side chains in protein core. Investigation of this disruption is the object of this paper. It is shown that this disruption is an “all‐or‐none” transition (independent of how compact is the denatured state of a protein and independent of the protein–solvent interactions) because expansion of a globule must exceed some threshold to release rotational isomerization of side chains. Smaller expansion cannot produce entropy compensation of nonbonded energy loss; this is the origin of a free‐energy barrier (transition state) between the native and denatured states. The density of the transition state is so high that the solvent cannot penetrate into protein in this state. The results obtained in this paper make it possible to present in the following paper a general phase diagram of protein molecule in solution.
A CD determination of the α‐helix contents of the coat proteins of four filamentous bacteriophages: fd, IKe, Pf1, and Pf3
Authors: Clack Beatrice A. , Gray Donald M. 
Published: December 2004

AbstractThe CD spectra of four filamentous bacteriophages—fd, IKe, Pf1, and Pf3— were analyzed to determine the α‐helix contents of their major coat proteins. Measured spectra included the 192‐nm band so that analyses could be carried out over the full wavelength range of the reference spectra for protein secondary structures available (a) from globular proteins [J. T. Yang, C.‐S. C. Wu, and H. M. Martinez (1986) Methods in Enzymology 130, 208–269] and (b) from poly(L‐lysine) [N. Greenfield and G. D. Fasman (1960) Biochemistry 8, 4108–4116]. Extended analyses were also performed with the addition of the spectrum of a model β‐turn to the Greenfield and Fasman reference set, with the spectrum of a short α‐helix in the Yang et al. reference set, and with an estimate of the spectrum of Trp added to both reference sets. The reference set based on the simple poly(L‐lysine) polypetide, plus a spectrum of a model β‐turn or of Trp, gave reasonably good fits to the measured spectra for all four phages and yielded the largest percentages of α‐helix. The class I phages—fd and IKe—had large percentages of α‐helix of 98 ± 2 and 97 ± 5%, respectively, while the two class II phages—Pf1 and Pf3— had similar but smaller α‐helix contents of 83 ± 6 and 84 ± 2, respectively. While these α‐helix contents were within the ranges previously reported from CD spectra of these phages in solution, they were more precise, and they indicated that the coat proteins of the intact phages have CD spectra that are probably modeled better by the reference spectra of polypeptides than by those of globular proteins.