bluuebunny/crossref_metadata_2025_split huggingface dataset:
The contribution of proximity and orientation to catalytic reaction rates
Authors: Delisi Charles , Crothers Donald M. 
Published: December 2004

AbstractWe present calculations of the possible magnitude of propinquity which has been proposed to play an important role in enzymic catalysis. The effect has been evaluated as in the past by calculating the ratio of bimolecular to intramolecular reaction rates. The ratio is estimated for intramolecular catalysis in rigid systems as well as for systems with five and six rotatable bonds. Our method differs from others mainly in the way cyclization has been treated.The reaction rate (in all cases) is proportional to the probability that the reactive units have the appropriate spatial and orientational positioning for reaction. This probability is obtained by evaluating a distance distribution function within the spatial and angular intervals to which the units are constrained after reaction. For the bimolecular case we have made the usual assumption that the distribution function is uniform. For the intramolecular reaction, neither the spatial nor the angular part of the distribution function is uniform. The pertinent parameters in this case are the bond lengths and angles, and the statistical weight matrices describing torsional rotation. The difficulty in obtaining analytical expressions for the distribution function is circumvented by using Monte Carlo methods.It is argued that the spatial contribution to rate accelerations in rigid systems can be as high as 107 M, depending upon the size of the volume to which the reactive units are constrained after reaction. The limitation on the smallest physically reasonable volume is estimated from considerations of energy requirements and vibrational amplitudes. Accelerations by five‐ and six‐membered ring cyclizations were estimated at 103 M, the six‐membered ring exhibiting the smaller rate enhancement.
Conformational changes in transfer RNA. I. Equilibrium theory
Authors: De Lisi Charles 
Published: December 2004

AbstractWe report the results of semi‐empirical calculations describing thermodynamic properties of transfer RNA conformations. The most important new features of the procedure are: (1) the use of parameters obtained from model oligoribonucleotides to evaluate the free energy of helical regions and small hairpin loops, and (2) the use of a model which is somewhat more realistic than the freely jointed chain for evaluating internal loops and intermediate size hairpin loops. The new parameters lead to important quantitative and qualitative differences from predictions which would have been made in the past and lead to a priori predictions of tRNA melting temperatures which are within about 6°C of the experimental values. The results suggest the following conclusions: (1) The early melting transition observed in several tRNA's is partly the result of tertiary unfolding, and partly the result of the loss of some secondary structure. (2) The part of the secondary structure which melts during the early transition is different for different tRNA's. For fMet and Tyr from E. coli, the calculations predict that the dihydrouradiene arm melts out early. For yeast Phe the acceptor stem and anticodon helix melt first. (3) The results also suggest the possibility that tertiary unfolding and early secondary structural melting do not occur independently but are coupled, so that the two types of structure are probably mutually stabilizing.
Structural components of alginic acid. I. The crystalline structure of poly‐β‐D‐mannuronic acid. Results of X‐ray diffraction and polarized infrared studies
Authors: Atkins E. D. T. , Nieduszynski I. A. , Mackie W. , Parker K. D. , Smolko E. E. 
Published: December 2004

AbstractA Structure determination of the naturally occuring marine algal polysaccharide poly‐β‐D‐mannuronic acid is described. The structure consists of 1e → 4e linked D‐mannuronic acid chains with the monosaccharide units in the C1 chair conformation. The X‐ray fiber diffraction photograph obtained from bundles of fibers prepared from Fucus vesiculosus has been indexed to an orthorhombic unit cell in which a =7.6 Å, b (fiber axis) = 10.4 Å, c = 8.6 Å, the unit cell containing two disaccharide chain segments with space group P212121.A sheet‐like structure involving one intra‐chain, one intra‐sheet, and one inter‐sheet hydrogen bond per monosaccharide is proposed. Features of the chain‐packing arrangement are compared with mannan.
The conformational stability of ribosomal proteins L7 and L12 from E. coli. I. Circular dichroism study of the changes induced by ionic strength and solvents
Authors: Boublik Miloslav , Brot Nathan , Weissbach Herbert 
Published: December 2004

AbstractRibosomal proteins L7 and L12 are the only acidic proteins found on the 50S ribosomal subunit of Escherichia coli. The effect of ionic strength, helix‐promoting solvents and denaturating agents on the conformation of these proteins has been studied. It has been established that the helicity of L7 and L12 proteins (approx. 45–50% α helix) can be increased to 60–70% when they are exposed to helix‐promoting solvents such as methanol or ethanol in the presence of 0.1M salt. High ionic strength by itself was without any effect on the conformation of the proteins. However, the solvent, 2,2,2‐trifluoroethanol increased the content of α helices up to 80% even in the absence of salt. Denaturating agents like urea (6M) or guanidine HCl (6M), decreased the content of the ordered structure below 20%. All conformational changes induced by salt or solvents were completely reversible and characterized by a broad transition showing a low degree of cooperativity. This might indicate the presence of discrete segments with variations in amino acid sequences and ordered structures with different stabilities.
Dielectric relaxation and orientation of DNA molecules
Authors: Hanss M. , Bernengo J. C. 
Published: December 2004

AbstractA conductivity dispersion has been measured at very low frequencies (VLF) on several concentrated DNA solutions. By measuring simultaneously their electric birefringence decay, it is shown that the dielectric relaxation (which is related to the conductivity dispersion) is due to the molecular orientation. Different polarization mechanisms are discussed. It is concluded that the DNA polarizability measured in the VLF range can only be explained by the orientation of a permanent ionic dipole. It is suggested that such permanent dipoles could be caused by small differences in the ionic composition between the two molecular “ends;” the difference could either be stable (asymmetrical localization of protein impurities for instance) or transient (fluctuating dipoles explained by the Kirkwood‐Schumaker theory).
Conformational studies on alamethicin
Authors: Burgess A. W. , Leach S. J. 
Published: December 2004

AbstractA conformational analysis has been carried out for the cyclic peptide antibiotic alamethicin. Unlikely structures were first eliminated by constructing van der Waals' energy maps for near‐neighbor contacts and using these maps to generate forty complete alamethicin structures free of steric overlaps. The energies of the forty conformations were minimized; optimizing all dihedral angles first in sets and then simultaneously, to give a family of five low‐energy structures. In the conformation of lowest energy three of the seven α‐amino isobutyric acid residues occur in a six‐residue α‐helix and three at the two chain reversals. Judged by the change in conformational energy as a function of the change in dihedral angle, the flexibility of the chain is determined by both the type of peptide unit and its position in the molecule.The model has features consistent with reported circular dichorism and surface balance measurements and has two polar centers separated by a lipophilic region. It does not contain the large central pore required by some theories for the action of alamethicin on cell membrances. It therefore probably acts by altering membrance structres rather than by shuttling ions through a pore in the membrance.
Molecular mobility of polypeptides containing proline as determined by 13C magnetic resonance
Authors: Torchia D. A. , Lyerla J. R. 
Published: December 2004

AbstractThe molecular conformations and dynamics of poly(L‐prolyl), poly(hydroxyl‐L‐prolyl), poly(L‐prolyl‐glycyl), poly(hydroxyl‐L‐prolyl), and poly(glycyl‐glycyl‐L‐prolyl‐glycyl), in aqueous solution, have been studied using 13C pulse Fourier transform nmr spectroscopy. From a measurement of the intensities of major and minor resonances in the spectra of the copolypeptides, it was determined that 15–20% of the glycyl‐prolyl and glycyl‐hydroxyprolyl peptide bonds are cis. Effective rotational correlation times (τeff), obtained from measurements of spin‐lattice relaxation times (T1) of individual backbone and side‐chain carbons, demonstrated that backbone reorientation is approximately isotropic for the five polypeptides and is characterized by correlation times of ca. 0.3–0.6 nanoseconds as a result of rapid segmental motion. In a given polypeptide glycyl and pyrrolidine residues were found to have the same backbone correlation times, but backbone carbon τeff values did decrease as the glycyl content of the peptides increased. A semi‐quantitative analysis of Cβ, Cγ, and Cδ correlation times suggests that rapid ring motion in both prolyl and hydroxyprolyl involves primarily Cγ and Cβ, with the prolyl ring being more mobile than the hydroxyprolyl ring.
Flexibility of DNA
Authors: Schellman John A. 
Published: December 2004

AbstractA model for the flexibility of DNA is proposed that is based on discrete variations in the direction of propagation in going from one subunit to the next. Expansion of the local free energy in terms of the local bending gives a Gaussian distribution function. The assumption of the independence of local bends on neighbors lead to very simple formulae for the persistence length and the characteristic ratio. Emphasis, however, is placed on the application of the formulae for molecules of finite size where the persistence length and C∞ are not defined. The formulae are worked out for two models, which should serve as limits for the real physical situation.
Kinetics of protein subunit interactions: Simulation of a polymerization overshoot
Authors: Scheele Robert B. , Schuster Todd M. 
Published: December 2004

AbstractTheoretical calculations of the kinetics of a polymerization reaction have been carried out for a scheme in which there is a nucleation step that is slow relative to subsequent propagation steps.A transient maximum (overshoot) in molecular weight can be expected in such reversibly self‐associating systems when polymerization is initiated suddenly. The extent of overshoot decreases with increasing initial concentration of true equilibrium is strongly dependent on the rate of nucleus formation and the rate of depolymerization when the absolute values of both are small relative to the rate of propagation.
Conformational analysis of DNA–basic polypeptide complexes: Possible models of nucleoprotamines and nucleohistones
Authors: De Santis P. , Forni E. , Rizzo R. 
Published: December 2004

AbstractConformational analysis of DNA–basic polypeptide complexes, based on stereo‐chemical criteria and energy calculations and experimental results, is reported. Three types of polypeptide conformations were selected: the distorted β conformation similar to that proposed by Feughelmann et al.; a structure characterized by a repetition of a right‐handed and left‐handed α helix‐type conformation; and an intermediate structure. A model of the complex between DNA and basic polypeptides was proposed, where the polypeptide chain fits the narrow groove of the B form of DNA. Van der Waals, hydrogen bond, electrostatic, and hydrophobic forces cooperate to stabilize the association complex. This structure also seems to be suitable to represent the molecular model of nucleoprotamines. In the case of nucleohistones, both grooves of DNA are involved in the interaction with the proteins. These have the nonbasic‐rich portion in the α‐helical conformation, whereas the part where a greater proportion of basic amino acids occurs presents a structure similar to nucleoprotamines and complexes between DNA and basic homopolypeptides. The distribution of basic residues of the F2A1(IV) histone on DNA is markedly disproportionate for the two opposite cylindrical sectors of the double helix. This suggests a new mechanism of supercoiling in nucleo‐histones.
Investigation of the base‐pairing structure of the anticodon hairpin from E. coli initiator tRNA by high‐resolution nmr
Authors: Wong K. Lim , Kearns David R. 
Published: December 2004

AbstractThe high‐resolution nmr spectrum of the anticodon hairpin from E. coli tRNAfMet has been obtained at a number of different temperatures. The positions of the resonances from interior Watson‐Crick base pairs are well accounted for (within 0.1 ppm) by a semi‐empirical ring current shift theory, but the terminal base pairs are susceptible to the exact orientation of adjacent bases in single‐stranded regions. From a careful examination of the exact way in which resonances disappear at elevated temperatures, we conclude that melting in the nmr experiments occurs when the lifetime of a base pair is reduced to several milliseconds. On the basis of these experiments we are able to assign an nmr Tm to each individual base pair and these should be useful in interpreting the melting behavior of the intact molecule. An “extra” resonance is observed at ∼11.3 ppm and, on the basis of its position and temperature sensitivity, it is tentatively assigned to the ring nitrogen proton of a “protected” U residue in the anticodon loop. A strong preference for stacking of a nonbase‐paired A residue on an adjacent GC base pair is observed even at temperatures in excess of 52°C.
Electrical birefringence study of monodisperse collagen solutions
Authors: Bernengo J. C. , Roux B. , Herbage D. 
Published: December 2004

AbstractAcid‐soluble collagen solution in 0.1 M acetic acid are studied by electrical birefringence. Specific birefringence is independant of concentration (for c < 100 mg/l.) and follows Kerr's law at low fields. Birefringence decays present a single relaxation time, and reversing pulse experiments show a very low contribution of induced moment compared to permanent dipole orientation. This result is also confirmed by birefringence rise measurements.
Helix–coil transition in nucleoprotein: Renaturation of polylysine–DNA and polylysine–nucleohistone complexes
Authors: Li Hsueh Jei , Chang Catherine , Weiskopf Manuel , Brand Benjamin , Rotter Arnold 
Published: December 2004

AbstractThermal denaturation and renaturation of directly mixed and reconstituted polylysine–DNA, directly mixed polylysine–nucleohistone complexes, and NaCl‐treated nucleohistones in 2.5 × 10−4 M EDTA, pH 8.0 have been studied. At the same input ratio of polylysine to DNA, the percent of renaturation of free base pairs in a directly mixed polylysine–DNA complex is higher than that in a reconstituted complex. For a directly mixed complex, the renaturation of free base pairs is proportional to the fraction of DNA bound by polylysine or inversely proportional to the sizes of free DNA loops. A of large amount of renaturation of free base pairs has also been observed for 0.6 M and 1.6 M NaCl‐treated nucleohistones. The binding of polylysine to nucleohistone enhances the renaturation of histone‐bound base pairs. The percent of renaturation of polylysine–bound base pairs is high and is approximately independent of the extent of binding on DNA by polylysine. This is true in polylysine–DNA complexes prepared either by reconstitution or by directly mixing. It also applies for polylysine–nucleohistone complexes.The model where polylysine‐bound base pairs collapse at Tm′ with two complementary strands still bound by polylysine is favored over the model where polylysine is dissociated from DNA during melting. The low renaturation of histone‐bound base pairs in nucleo‐histone indicates that either histones do not hold two complementary strands of DNA tightly or that histones are fully or partially dissociated from DNA when the nucleo‐histone is fully denatured.
Effects of water on the mechanical properties of gelatin films
Authors: Tanioka Akihiko , Tazawa Takashi , Miyasaka Keizo , Ishikawa Kinzo 
Published: December 2004

AbstractThe mechanical properties of gelatin films were studied in relation to the effect of water, and compared with those of collagen films. The S‐shaped sorption isotherm was separated into an adsorption curve C1 and dissolution curve C2. From the C2 curve, the interaction parameter χ1 of Flory–Huggins' equation was calculated. The χ1 of gelatin were larger than those of collagen at low relative humidities (RH), while they coincided with each other at high RH. It was found that a composite curve was made by shifting stress relaxation curves obtained at different humidities along the log time axis. The shift factor for the formation of the composite curve was analyzed by Fujita–Kishimoto's equation, which was based on the free volume theory. The parameter β, which expressed the extent of the contribution of sorbed water to the increase in the free volume of the system, was 0.05 in the range of C2 from 0 to 0.08 (0–65% RH). This value was much smaller than 0.16 for collagen. The value was 0.16 in the range of C2 higher than 0.08, which was equal to that of the collagen. Dynamic shear modulus G′, loss modulus G″, and tan δ were determined as functions of RH. The gelatin film extended more than 100% at 73% RH under the very small stress of about 107 dyn/cm2. This corresponds to the region where β changes from 0.05 to 0.16, although such a phenomenon was not observed in the collagen film. The wide‐angle X‐ray pattern of extended gelatin was similar to that of renatured collagen fiber.
High‐resolution analysis of the modified quarter‐stagger model of the collagen fibril
Authors: Bruns Romaine R. , Gross Jerome 
Published: December 2004

AbstractThe location of transverse bands within the major repeating period of positively stained collagen fibrils was determined from electron micrographs by an optical averaging procedure. From these data and the published location of bands in SLS crystallites, we have prepared a two‐dimensional representation, accurate to about 25 Å, of the modified quarter‐stagger arrangement of molecules in the collagen fibril. With this information it is possible to demonstrate the relationship of loci on individual collagen molecules within the fibril. For example, the site where the collagen molecule is cleaved by tadpole collagenase, the site where a disaccharide unit is covalently bound to the α1‐CB5 peptide, and the site of carboxyl‐terminal intermolecular cross‐linking all occur in the fibril near the amino‐terminal edge of the “hole zone;” and the site of amino‐terminal cross‐linking occurs near the carboxyl‐terminal edge of the “hole zone.”
Sequential oligopeptides. Conformational studies of the oligopeptides and a polypeptide with the repeating sequence L‐norvalyl‐glycyl‐L‐proline
Authors: Bonora Gian Maria , Toniolo Claudio 
Published: December 2004

AbstractConformational studies of a series of oligopeptides (from the tripeptide to the octadecapeptide) with the repeating sequence L‐norvalyl‐glycyl‐L‐proline and a polytripeptide with this sequence are reported. By means of chiroptical techniques, unordered conformations are found for all oligopeptides in water, trifluoroethanol, and ethylene glycol and for the water‐insoluble polymer in trifluoroethanol. In ethylene glycol the polymer assumes a collagen‐like structure. Infrared studies indicate that all the oligomers, in contrast to the polymer, are unordered in the solid state.
Spin‐labeled polyuridylic acid. Formation of an intermediate structure
Authors: Pan Yu‐Ching E. , Bobst Albert M. 
Published: December 2004

AbstractTemperature‐dependent conformational transitions of spin‐labeled poly(U) at low temperature in spermidine and cesium chloride buffer have been measured by electron spin resonance spectroscopy. The Arrhenius plot shows the existence of the order‐disorder transition at a temperature close to that obtained from absorbance temperature profiles. However, in addition the formation of an intermediate state is observed during the melting of the ordered poly(U) to its random coil.
Conformation and packing analysis of polysaccharides and derivatives. I: Mannan
Authors: Zugenmaier P. 
Published: December 2004

AbstractA previously described procedure for simultaneous optimization of bond lengths and angles was used to test different models for mannan I. Potential hydrogen bonds and the glycosidic angle were included in the optimization. A conformational model with bifurcated intramolecular hydrogen bonds of the type observed in the methyl cellobioside methanol complex showed the best agreement with available exprerimental data. The coordinates of this model were provided by computer calculations. The available X‐ray data, however, were not sufficient for selecting this model; rather, ir data were necessary to furnish the needed information. The different conformational models tested all showed an almost constant virtual bond length O(1)–O(4) of the β‐pyranose residue. This was in contrast to the previously obtained results for the α‐pyranose residues.
Interaction of ethidium bromide with DNA. Optical and electrooptical study
Authors: Houssier Claude , Hardy Bernadette , Fredericq Eugene 
Published: December 2004

AbstractThe binding of ethidium bromide to DNA has been studied by various optical methods. From fluorescence polarization studies, and film, electric linear dichroism, and circular dichroism spectra, we propose assignments of the absorption bands of the dye, which are discussed in connection with wave‐mechanical calculations recently reported.The optical activity induced in the dye absorption bands upon binding to DNA was attributed to various origins depending on the electronic transition considered. The visible absorption band displayed a circular dichroism due to the asymmetry of the binding site and independent of the amount of binding. The transition identified at 378 nm from the circular dichroism and electric dichroism observations was thought to be due to a magnetic‐dipole transition. It remained constant with increasing amounts of dye bound. The main ultraviolet band showed circular dichroism characteristics corresponding to exciton interactions between dye molecules bound to neighboring sites.The electric dichroism observed for the strongly bound dye molecules indicated that the phenanthridinium ring of ethidium bromide was probably not perfectly parallel to the DNA base planes. When the amount of dye bound to DNA exceeded the maximum amount compatible with the exclusion of adjacent binding sites, the electric dichroism decreased owing to the appearance of externally bound dye molecules with no contribution to the dichroism.Sonicated DNA was used to study the lengthening of the DNA molecule upon complexation. Although the viscosity of the complexes increased with the amount of binding, the rotational diffusion coefficient measured by the electric birefringence relaxation was not detectably affected. The absence of variation in the electric birefringence with the binding indicated that the DNA base stacking remained unaltered.