bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthesis and spectroscopic characterization of insulin derivatives containing one or two poly(ethylene oxide) chains at specific positions
Authors: Ehrat M. , Luisi P. L. 
Published: December 2004

AbstractWe describe a synthetic method aimed at specifically coupling poly(ethylene oxide) (PEO) to proteins without altering their spectroscopic properties. To do so, we have first modified the alcohol end group of PEO to an acid end group (PEO‐COOH). Coupling of PEO‐COOH to Gly A1 methylsulfonylethyloxycarbonyl (Msc) protected insulin yielded NαB1,NϵB29‐(PEO)2‐insulin. Conversely, coupling of PEO‐COOH to insulin whose Gly A1 and Lys B29 amino groups were protected with Msc yielded NαB1‐PEO‐insulin. The products were obtained in a spectroscopically pure form and characterized by uv and CD spectroscopy. Conformational and biological studies are in progress.
Methods for the analysis of the kinetics of cooperative binding of ligands to a two‐site lattice
Authors: Edgerton Mary E. , Handler Frank A. , Wu Cheng‐Wen 
Published: December 2004

AbstractSolutions are obtained that describe the time dependence of the reversible binding of a ligand to a two‐site lattice. The binding may be cooperative. Three methods are used to obtain these solutions: the separation of on/off processes with a variable transformation, the asymptotic series analysis, and the singular perturbation procedure. Applications to parameter calculation from experimental data are presented. This kinetic system is such that it is difficult to extract all kinetic parameters from data analysis, and the implications for each method are also discussed.
Effects of composition and polymerization conditions on crosslinked polymer supports based on N‐acrylyl pyrrolidine and N,N‐dimethyl acrylamide for peptide synthesis
Authors: Varadarajan K. , Fiat D. 
Published: December 2004

AbstractPoly(N‐acrylyl pyrrolidine‐co‐N,N′‐bis(acrylyl) 1,2‐diaminoethane‐co‐N‐Acrylyl 1,6‐diamino hexane HCl) with 2,5,8,11,12,15, and 20% degrees of crosslinking (DC) and poly‐(N,N′‐dimethylacrylaminde‐co‐N,N′‐bis(acrylyl) 1,2‐diaminoethane‐co‐N‐acrylyl 1,6‐diamino hexane HCl) with 2,5,10, and 15% DC have been synthesized in an entirely beaded form by reverse‐phase suspension polymerization. The monomer‐to‐water ratio was kept constant for all these polymers. With the exception of 2% crosslinked resins in the PAP and PDMA groups, all the resins exhibited favorable swelling properties in solvents normally used for peptide synthesis and the percent incorporation of the first amino acid residue was close to 100 for DC of up to 20%. This is explained as due to the flexible and polar characteristics of the crosslinking agent, N,N′‐bis(acrylyl) 1,2‐diaminoethane. Between 5 and 20% DC the degree of swelling of the resins changes only slightly with increasing DC. This effect of DC on the swelling and percent incorporation of the first amino acid residue is more favorable for peptide synthesis than in the case of divinyl benzene crosslinked poly(styrene).
Differences in structure and stability between normal and deuterated proteins (phycocyanin)
Authors: Chen Chang‐Hwei , Liu I‐Wen , MacColl Robert , Berns Donald S. 
Published: December 2004

AbstractDifferential scanning microcalorimetry was used to investigate the enthalpy (ΔHd) and the temperature (td) of thermal denaturation of normal and deuterated phycocyanins isolated from two blue‐green algae, Plectonema calothricoides and Phormidium luridum. Values of td in deuterated proteins are about 5°C lower than those in normal proteins. The magnitudes of ΔHd in deuterated proteins are 18–36% lower than in normal proteins. The heatcapacity change (ΔCp) in protein unfolding is essentially the same (2 kcal/mol/K) for deuterated and normal proteins within the experimental error. At close to physiological temperature (27°C), the differences in thermodynamic functions in the native and denatured states are much higher in normal proteins than in deuterated proteins. CD was employed to evaluate both the secondary structures and urea denaturation of these two types of proteins. In P. luridum, deuterated protein is about 8% higher in α‐helix content; in P. calothricoides it is not significantly higher. Deuterated proteins are less resistant to the denaturant urea than are normal proteins: the denaturant concentration at the midpoint of the denaturation curve is 0.6–1.2 mol/L lower in the deuterated proteins. The apparent free energies of unfolding of deuterated proteins at zero denaturant concentration are 1.1–1.5 kcal/mol less than for normal proteins.
Salt‐dependent conformational transitions in the self‐complementary deoxydodecanucleotide d(CGCAATTCGCG): Evidence for hairpin formation
Authors: Marky Luis A. , Blumenfeld Kenneth S. , Kozlowski Sharon , Breslauer Kenneth J. 
Published: December 2004

AbstractDifferential scanning calorimetry (DSC), temperature‐dependent uv‐absorption spectroscopy, and temperature‐dependent CD were used to monitor and characterize the salt‐dependent, thermally induced structural transitions in the deoxydodecanucleotide d(CGCGAATTCGCG). At the high oligomer concentrations required for DSC, the calorimetric scans revealed a single, monophasic transition curve at all salt concentrations. Based on previous nmr melting studies under similar conditions, we conclude that these monophasic transitions correspond to the cooperative duplex‐to‐single‐strand conversion of the dodecamer. By contrast, at the lower oligomer concentrations used for the spectroscopic studies, the shapes of the uv and CD melting curves were found to depend on the concentration of the added salt. At high salt (≥0.1M Na+), a single, monophasic transition curve was observed. At lower salt (⩽0.01M Na+), the CD and uv melting curves exhibit biphasic behavior. Based on the concentration dependence, the enthalpy, and the cooperativity of each transition in the biphasic curve, we conclude that at low salt and low oligomer concentrations, the dodecamer melts in a sequential manner involving initial disruption of a duplex structure and subsequent disruption of a hairpin structure.
Geometry and mechanics of DNA superhelicity
Authors: Benham Craig J. 
Published: December 2004

AbstractThis paper analyzes the elastic equilibrium conformations of duplex DNA constrained by the constancy of its molecular linking number, Lk. The DNA is regarded as having the mechanical properties of a homogeneous, linearly elastic substance with symmetric cross section. Integral representations of the writhing number Wr and of Lk are developed, in terms of which the equilibria are given as solutions to an isoperimetric problem. It is shown that the Euler angles defining equilibrium conformations must obey equations identical to those governing unconstrained equilibria. A scaling law is developed stating that molecules supercoiled the same amount ΔLk will have geometrically similar elastic equilibria regardless of their length. Thus, comparisons among molecules of properties related to their large‐scale tertiary structure should be referred to differences in ΔLk rather than to their superhelix densities. Specific conditions on the elastic equilibrium conformations are developed that are necessary for ring closure. The equilibrium superhelical conformations accessible to closed‐ring molecules are shown to approximate toroidal helices. Questions relating to the stability and nonuniqueness of equilibria are treated briefly. A comparison is made between these toroidal conformations and interwound configurations, which are shown to be stable, although they are not equilibria in the present sense. It is suggested that entropic factors are responsible for favouring the toroidal conformation in solution.
X‐Ray diffraction studies on the structure of hydrated collagen
Authors: Sasaki Naoki , Shiwa Shinichi , Yagihara Shin , Hikichi Kunio 
Published: December 2004

AbstractThe temperature dependence of the humidity‐sensitive spacing, d, related to the lateral packing of collagen molecules was measured for fully hydrated collagen. In the vicinity of 0°C, a sudden change in d was observed, which was reversible with temperature. In the diffraction profile, below 0°C, a set of diffraction peaks identified with the hexagonal crystalline form of ice was observed. With the reduction in water content, the intensity of the set of diffraction peaks decreased and was found to be zero at a water content of 0.38 g/g collagen. These results were considered to be caused by the frozen water in collagen fibril below 0°C. According to the water content dependence of d, it was considered that up to a certain water content water absorbed would be stowed in the intermolecular space of collagen and above that water content water molecules would aggregate to make pools, i. e., extrafibrillar spaces. The unfreezable bound water was considered to be located in the intermolecular space of collagen. Size of the extrafibrillar space, determined from the intensity analysis of a smallangle x‐ray scattering pattern, corroborates the speculation that the water showed in the extrafibrillar space is freezable and free. The formation of the hexagonal crystalline form of ice in the extrafibrillar space was considered to cause the sudden change in d at 0°C.
Multistep brownian dynamics: Application to short wormlike chains
Authors: Allison S. A. , McCammon J. A. 
Published: December 2004

AbstractBrownian dynamics simulations of short wormlike chains are carried out using the method of Ermak and McCammon [(1978) J. Chem. Phys. 69, 1352–1360]. Following Hagerman and Zimm [(1981) Biopolymers 20, 1481–1502], the wormlike chain is modeled as a string of beads. In each simulation, the dynamic evolution of an ensemble of 100 randomly generated chains is calculated for a period of from 3 to 200 ns. Two different “experiments,” fluorescence depolarization and dynamic light scattering, were performed in these simulations. Since we are primarily interested in the bending motions and not the torsional motions in this work, we have placed the transition moments along the local symmetry axis of the wormlike chain in the fluorescence depolarization “experiment.” As predicted by the Barkley and Zimm theory [(1979) J. Chem. Phys. 70, 2991–3008], a considerable amount of rapid bending motion was detected by fluorescence depolarization, though not as much as predicted by theory. We conclude that these differences are primarily due to differences between the model used in the theory and the simulations. The light‐scattering experiment was found to be insensitive to internal motion in the low scattering angle limit.
Intercalation of cationic dyes in the DNA double helix: Introductory theory
Authors: Bustamante Carlos , Stigter Dirk 
Published: December 2004

AbstractThe effect of salt on the intercalation of acridine dyes and DNA is rather well explained by the Gouy‐Chapman double‐layer theory as applied to a cylinder model of the DNA–dye complex. The free energy of transfer of a dye ion from the bulk solution to the complex is divided into several parts, one of which, ΔF0, accounts for the short‐range, nonelectrostatic interactions. The assumption that ΔF0 should not depend on the amount of dye in the complex leads to an internal dielectric constant of the cylinder of about Di = 7. The scatter in ΔF0 values, as calculated from individual experimental points, is of order 0.5 kT per dye ion. This scatter is large enough to mask possible effects of heterogeneity in DNA sequences. The calculations are made for a long cylinder with radius 10 Å, with the DNA phosphate charges smeared uniformly at the surface, a uniform spacing of dye charges at the cylinder axis, and a length of b = 3.37 Å per base pair. Each intercalated dye ion also adds a length b to the total length of the cylinder. The salt‐dependent part of the electric free energy of intercalation, ΔF1, is tabulated for complexes with r = 0–0.24 dye ions per DNA phosphate in 0.002–0.2M monovalent salt and dye solutions.
Most‐probable distribution at enzyme depolymerization of polysaccharides
Authors: Mazur A. K. 
Published: December 2004

AbstractSeveral research groups have studied depolymerizing processes by enzyme cleavage using product distribution. Although only the shortest chain products can be measured experimentally, interpretation of much evidence requires an assumption of the nature of high polymer distribution. The present work analyzes the high polymer distribution of products on the basis of mathematical models suggested for the two most widespread α‐amylase action‐mechanisms. The most‐probable distribution was found to be distorted by hydrolysis only for the shortest chain products. The size of the distorted region is directly dependent on the characteristics of a specific enzyme. We studied the distribution of products for substrates of varying composition to show that it approaches the most‐probable distribution at depolymerization.
Molecular conformations and 8‐CH exchange rates of purine ribo‐ and deoxyribonucleotides: Investigation by Raman spectroscopy
Authors: Benevides James M. , Lemeur Danielle , Thomas George J. 
Published: December 2004

AbstractThe rate of deuterium exchange of the 8‐CH group in a purine deoxyribonucleotide, is the same as the 8‐CH exchange rate in the corresponding purine ribonucleotide, with the exception of 5′‐nucleotides of guanine. The observed 20% slower rate of 8‐CH exchange in 5′‐dGMP versus 5′‐rGMP, over the temperature range 50–80°C, are attributable to differences in molecular conformation, including differences in ring puckering of the furanose substituents. Minor differences in 8‐CH exhange rates are observed between 5′‐and cyclic (3′:5′)‐deoxyribonucleotides of a given purine, which are similar to those observed previously between corresponding 5′‐ and cyclic ribonucleotides that have been attributed to the charge difference of their respective phosphate groups [Ferreira, S. A. & Thomas, G. J., Jr. (1981) J. Raman Spectrosc. 11, 508–514]. The coupling of guanine and furanose ring structures in the 5′‐nucleotides is also evident from the vibrational frequencies of the guanine ring, which are strongly dependent on the pucker of the attached furanose moiety. Raman difference spectroscopy clearly reveals the dependence of purine nucleotide spectra on sugar‐ring pucker. In the case of GMP, the guanine characteristic ring breathing mode near 600–700 cm−1 depends for its exact position and intensity on the proportion of C3′‐endo (668 cm−1) and C2′‐endo (682 cm−1) conformers in equilibrium with one another. The Raman intensity ratio I(668)/I(682) is proposed as a measure of the conformer ratio C3′‐endo/C2′‐endo in 5′‐dGMP with possible application also to nucleic acids. Among cyclic nucleotides, differences in spectra of deoxyribo‐ and ribo‐ forms also appear to be related to differences of molecular conformation.
Study of polysaccharides by the fluorescence method. III. Chain length dependence of the micro‐Brownian motion of amylose in an aqueous solution
Authors: Kitamura Sinichi , Tanahashi Hiroshi , Kuge Takashi 
Published: December 2004

AbstractThe fluorescence polarization method was applied to the investigation of the micro‐Brownian motion of amylose chains having a wide range of degree of polymerization (DP). We prepared two types of fluorescent conjugates of amylose: amylose conjugated with fluorescein randomly throughout the chain (F‐amylose) and amylose conjugated locally on a terminal segment (t‐F‐amylose). The degree of fluorescence polarization of these conjugates was measured by changing the solvent viscosity at a constant temperature (25°C). The data obtained were analyzed by a Perrin‐type equation to calculate the mean rotational relaxation time, 〈ρ〉. By examination of the plots of 〈ρ〉 vs DP, and by comparison of 〈ρ〉 with the theoretical rotational relaxation time of the whole molecule at a given DP, it was found that 〈ρ〉 mainly reflects the segmental motion of the amylose chain in the high‐DP range. Thus, the fact that 〈ρ〉 for t‐F‐amylose is much smaller than that for F‐amylose at a sufficiently high DP shows that a terminal segment undergoes a more rapid micro‐Brownian motion than interior segments. In the low‐DP range, we felt that the rotational diffusion of the whole molecule contributes significantly to the relaxation process. We also examined, for comparison, the segmental motion of dextran and pullulan in a similar manner and found that these segmental motions are more rapid than those of amylose. Based on the results obtained, the segmental mobility and conformation of the amylose molecule are discussed in relation to its chain length.
Quasi‐harmonic method for studying very low frequency modes in proteins
Authors: Levy R. M. , Srinivasan A. R. , Olson W. K. , McCammon J. A. 
Published: December 2004

AbstractA quasi‐harmonic approximation is described for studying very low frequency vibrations and flexible paths in proteins. The force constants of the empirical potential function are quadratic approximations to the potentials of mean force; they are evaluated from a molecular dynamics simulation of a protein based on a detailed anharmonic potential. The method is used to identify very low frequency (∼1 cm−1) normal modes for the protein pancreatic trypsin inhibitor. A simplified model for the protein is used, for which each residue is represented by a single interaction center. The quasi‐harmonic force constants of the virtual internal coordinates are evaluated and the normal‐mode frequencies and eigenvectors are obtained. Conformations corresponding to distortions along selected low‐frequency modes are analyzed.
Dynamic light scattering as a probe of superhelical DNA–intercalating agent interaction
Authors: Newman Jay 
Published: December 2004

AbstractPolarized dynamic light‐scattering measurements on superhelical pBR322‐plasmid DNA solutions in 0.2M NaCl, 2 mM NaPi, pH 7.0, 2 mM EDTA result in a translational diffusion coefficient D = (3.77 ± 0.10) × 10−8 cm2/s for the native molecule. Modeling the DNA, in the simplest approximation, as a 10 × 440‐nm effective hydrodynamic rigid rod yields a good fit to the apparent diffusion coefficient angular‐dependence data up to 70°; the model fails at higher angles, probably due to the effects of flexibility or branching of the rod. Diffusion coefficient titration experiments with a platinum complex intercalating agent (PtTS) result in a titratable superhelix density of σ = −0.079 ± 0.008 under our experimental conditions, corresponding to about 34 superhelical turns in the native DNA. The DNA contour length predicted by our two independent results, the rod dimensions and the number of superhelical turns, is in excellent agreement with the contour length calculated from the number of base pairs, supporting the hydrodynamic approximation of an effective rodlike structure for this small DNA molecule in solution.
Analysis of the high‐ and low‐spin soret bands of horse‐heart metmyoglobin complexes
Authors: Anusiem A. C. I. , Kelleher M. 
Published: December 2004

AbstractInterest in the thermodynamics of the iron‐binding site in hemoproteins has increased in recent years due to refinements in x‐ray crystallographic studies of hemoproteins [see Deathage, J. F., Lee, R. S., Anderson, C. M. & Moffat, K. (1976) J. Mol. Biol. 104, 687–706; Heidner, E. J., Ladner, R. C. & Perutz, M. F. (1976) J. Mol. Biol. 104, 707–722; Deathage, J. F., Lee, R. S. & Moffat, K. (1976) J. Mol. Biol. 104, 723–728; Ladner, R. C., Heidner, E. J. & Perutz, M. F. (1976) J. Mol. Biol. 114, 385–414; Fermi, G. & Perutz, M. F. (1977) J. Mol. Biol. 114, 421–431; Takano, T. (1977) J. Mol. Biol. 110, 537–568 and 569–589], the synthesis and x‐ray analysis of model heme compounds [see Scheidt, W. R. (1977) Acc. Chem. Res. 10, 339–345; Kastner, M. E., Scheidt, W. R., Mashino, T. & Reed, C. A. (1978) J. Am. Chem. Soc. 100, 666–667; Mashiko, T., Kastner, M. E., Spartalian, K., Scheidt, W. R. & Reed, C. A. (1978) J. Am. Chem. Soc. 100, 6354–6362; Hill, H. A. O., Skite, P. P., Buchler, J. W., Luchr, H., Tonn, M., Gregson, A. K. & Pellizer, G. (1979) Chem. Commun. 4, 151–152; and Scheidt, W. R., Cohen, I. A. & Kastner, M. E. (1979) Biochemistry 18, 3546–3556], and the numerous data on heme–protein interactions that account for the differences observed in ligand binding between the various species of animals. Numerous probes have been used and provide information about the structure and thermodynamics of the binding site, but no single probe can provide the complete picture [see Iizuka, T. & Yonetani, T. (1970) Adv. Biophys. 1, 157–182; Smith, D. W. & Williams, R. J. P. (1970) Struct. Bond. 7, 1–45; and Spiro, T. G. (1975) Biochim. Biophys. Acta 416, 169–189].
The speed of sound in DNA
Authors: Hakim M. B. , Lindsay S. M. , Powell J. 
Published: December 2004

AbstractWe have used Brillouin scattering to determine the speed of sound in (and hence longitudinal modulus of) A‐ and B‐DNA fibers. The speed of sound is very sensitive to the degree of hydration of the fibers, and measurements have to be made at laser powers below 5 mW to avoid local heating and dehydration. Under those conditions, we obtain sound speed perpendicular to the fiber axis of about 2.2 and 1.9 km/s in A‐ and B‐DNA fibers, respectively. A‐DNA fibers show a small anisotropy with sound speeds along the fiber axis higher by up to 10% B‐DNA fibers appear to be isotropic.
Conformation of P‐form DNA
Authors: Zehfus Micheal H. , Johnson W. Curtis 
Published: December 2004

AbstractThe P‐Form of DNA has been studied by use of ir spectroscopy and electron microscopy (EM). The ir data show that the P‐form has little or no hydrogen bonding, while the data from EM show that the P‐form has a condensed tertiary structure. In earlier work, we demonstrated that the P‐form is devoid of base stacking. When that information is combined with the new ir data, we conclude that the P‐Form is denatured because it lacks any of the interactions associated with a normal secondary structure. This is in apparent contradiction to earlier work that showed that the P‐form may be easily transformed back to a native state by adding water. However, the lack of secondary structure can be overcome by the presence of a collapsed tertiary state that does not allow non‐hydrogen‐bonded strands to separate. Thus, the complementary strands can renature quickly on addition of water. The collapse to a condensed tertiary structure occurs when roughly 90% of the charge on the DNA molecule is neutralized by counterion condensation, as calculated by the Manning polyelectrolyte theory, and is consistent with other collapsed DNA states in this respect. This structure explains all physical properties of the P‐form that have been observed.