bluuebunny/crossref_metadata_2025_split huggingface dataset:
A probabilistic model for genetic recombination of nonreplicating λ–phage DNA, stimulated by “mismatch repair” of UV photoproducts
Authors: Hays John B. , Hays Judith G. 
Published: May 2005

AbstractGenetic recombination of nonreplicating phage λ‐DNA, during infection of homoimmune lysogenic bacteria, was previously observed to be dramatically stimulated by prior uv irradiation of the phages, even when the Escherichia coli hosts lacked the major uv‐photo‐product excision‐repair system (UvrABC). UvrABC‐independent recombination of circular phage molecules depends on host MutHLS functions and on undermethylation of adenines at GATC sites in the phage DNA, and thus appears to be the result of “mismatch repair” of uv photoproducts. Recombinant frequencies pass through a relatively sharp maximum at 20 J/m2 and decrease at higher doses, whereas most plausible models for the process predict monotonic increases with dose, or a plateau at high uv doses. A uv‐dose‐dependent loss of biological activity (restriction) of all intracellular phage DNA was also observed previously. In order to provide a framework for testing possible explanations for the unusual recombinant‐frequency vs uv‐dose curve, a statistical model was constructed. This model includes probability terms for all possible one‐exchange and two‐exchange recombination processes, and incorporates the assumption that dimer recombinants are more susceptible to restriction than monomer parents (or recombinants), because of their larger target size. By adjustment of model parameters, particularly ϵ, the efficiency per photoproduct of initiation of a recombinational exchange, a theoretical dose–response curve that agreed well with experiment was obtained. The best fit corresponded to ϵ = 0.035, close to the previously observed restriction efficiency of 0.053. In the calculations, the value for h0, the average length of heteroduplex DNA, was taken to be 0.5 λ units, i.e., about 25 kilobase pairs. This estimate for h0 was obtained here by analysis of the density distributions of the progeny of crosses between nonreplicating density‐labeled λ‐phage chromosomes, published by others [M. S. Fox, C. S. Dudney and E. J. Sodergren (1979) Cold Spring Harbor Symposium on Quantitative Biology, Vol. 43, pp. 999–1007].
Comparison of the conformational dynamics of the (1 → 4)‐ and (1 → 6)‐linked α‐D‐glucans using 13C‐NMR relaxation
Authors: Kadkhodaei Mehran , Wu Helen , Brant David A. 
Published: May 2005

AbstractThe conformational dynamics of α‐ (1 → 4)‐ and α‐ (1 → 6)‐glucan homooligomers in the nanosecond time domain have been compared by measuring the 13C‐nmr longitudinal relaxation times T1 for carbons of the terminal and interior sugar residues. Measurements are reported on monomeric glucose and on oligomers containing up to ten glucose residues at room temperature in aqueous solution at concentrations of 3 and 20 g/dL. The carbons of terminal residues display longer relaxation times than do those of interior residues, presumably as a consequence of a greater degree of conformational mobility of the chain ends. The T1s of the reducing terminal residues of all oligomers are significantly longer than those of the corresponding nonreducing termini, a phenomenon that we associate tentatively with the anomeric equilibrium at the reducing end. Carbons of the reducing terminal residues in the β‐anomeric form relax more slowly than their α‐anomeric counterparts. At 20 g/dL the mean T1s for carbons of the terminal and interior residues attain asymptotic behavior with increasing chain length at a chain length of about six residues, and carbons of the α‐ (1 → 4)‐linked maltooligomers relax significantly more slowly than those of the corresponding α‐(1 → 6)‐linked isomaltooligomers. The T1s of both glucan series increase with decreasing concentration. This concentration dependence disappears below 3 g/dL, where the T1s of the two series of homoligomers are no longer distinguishable. This suggests that in dilute aqueous solution at room temperature viscous damping effects predominate over contributions to the T1‐sensitive conformational dynamics from structural differences in the glycosidic linkage region. At 3 g/dL the approach to long chain‐length asymptotic behavior is more protracted than at 20 g/dL, and the T1s of carbons of interior oligomeric residues appear to match the corresponding high‐polymer behavior at a chain length of eight and greater.
Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: A grand canonical Monte Carlo analysis
Authors: Olmsted Martha C. , Anderson Charles F. , Record M. Thomas 
Published: May 2005

AbstractEffects of salt concentration on the stabilities of oligonucleotide helices are analyzed directly in terms of ΔΓN→yN ≡ Γ − ΓNnat, the difference in the salt–nucleotide phosphate preferential interaction coefficients for the denatured state, having yN phosphate charges, and for the native state, having N phosphate charges (y = 1 for hairpin denaturation and y = 0.5 for dimer denaturation). Previous experimental studies of the denaturation of hairpin oligo‐nucleotides (having 18 < N < 44) indicate significant differences between ΔΓN→N and ΔΓ∞, the value determined for the denaturation of the corresponding polynucleotide. These differences are thermodynamic manifestations of the oligoelectrolyte end effect. In contrast, the available data on the denaturation of oligonucleotide dimer helices (N ⩽ 22) imply that differences between ΔΓ∞ and ΔΓN→0.5N, and hence oligoelectrolyte end effects, are small or negligible. To determine the origin of these apparently conflicting implications concerning the importance of oligoelectrolyte end effects, we have calculated the N dependence of ΓN from grand canonical Monte Carlo simulations for an idealized model of the structure and charge distribution of each oligomer conformation. Our calculations are in quantitative agreement with the experimental finding for d(TA) hairpin oligomers that − ΔΓN→N decreases linearly as N−1 increases, and with the extant experimental determinations of ΔΓN→0.5N. These results provide an illustration of how the large electrostatic end effects exhibited by the hairpin denaturation data are masked when ΔΓ∞ is compared with values of ΔΓN→0.5N for short dimer helices (N ⩽ 22). For 0.5N > 24, − ΔΓN→0.5N is predicted to be a linear function of N−1 whose slope has the opposite sign from, and is more salt‐concentration dependent than, the corresponding slope of − ΔΓN→N as a function of N−1. Our calculations also yield predictions about the N dependences of the individual values of ΓN that can be tested by determining Donnan coefficients from membrane dialysis equilibrium experiments. For long enough hairpin and dimer oligonucleotides (yN ⩾ 24), in either native or denatured forms, we predict that the (positive) difference Γ∞ − ΓN increases linearly with increasing N−1. For smaller values of N the difference Γ∞ − ΓN continues to increase with increasing N−1.
The three states of globular proteins: Acid denaturation
Authors: Alonso Darwin O. V. , Dill Ken A. , Stigter Dirk 
Published: May 2005

AbstractWe describe statistical mechanical theory that aims to predict protein stabilities as a function of temperature, pH, and salt concentration, from the physical properties of the constituent amino acids: (1) the number of nonpolar groups, (2) the chain length, (3) the temperature‐dependent free energy of transfer, (4) the pKa's (including those in the native state) and their temperature dependencies. We calculate here the phase diagrams for apomyoglobin and hypothetical variant proteins. The theory captures essential features of protein stability including myoglobin's Tm vs pH as measured by P. L. Privalov [(1979) Advances in Protein Chemistry, Vol. 33, pp. 167–241] and its ionic strength vs pH phase diagram as measured by Y. Goto and A. L. Fink [(1990) Journal of Molecular Biology, Vol. 214, pp. 803–805].The main predictions here are the following: (1) There are three stable states, corresponding to native (N), compact denatured (C), and highly unfolded (U), with transitions between them. (2) In agreement with experiments, the compact denatured state is predicted to have enthalpy closer to U than N because even though there is considerable hydrophobic “clustering” in C, this nevertheless represents a major loss of hydrophobic contacts relative to configurations (N) that have a hydrophobic “core.” (3) C becomes more prominent in the phase diagram with increasing nonpolar content or decreasing chain length, perhaps thus accounting for (a) why lysozyme and α‐lactalbumin differ in their denatured states, and (b) why shortened Staph nuclease molecules are compact. (4) Of major importance for protein calorimetry is Privalov's observation that the enthalpy of folding, ΔH (T, pH) is independent of pH. The theory accounts for this through the prediction that the main electrostatic contribution to stability is not enthalpic; the main contribution is the entropy, mainly due to the different distributions of protons and small ions in the native and denatured states.
Crystal state conformation of three model monomer units for the β‐bend ribbon structure
Authors: Valle G. , Bardi R. , Piazzesi A. M. , Crisma M. , Toniolo C. , Cavicchioni G. , Uma K. , Balaram P. 
Published: May 2005

AbstractThe molecular and crystal structures of three compounds, representing the repeating units of the β‐bend ribbon (an approximate 310‐helix, with an intramolecular hydrogen‐bonding donor every two residues), have been determined by x‐ray diffraction. They are Boc‐Aib‐Hib‐NHBzl, Z‐Aib‐Hib‐NHBzl, and Z‐L‐Hyp‐Aib‐NHMe (Aib, α‐aminoisobutyric acid; Bzl, benzyl; Boc, t‐butyloxycarbonyl; Hyp, hydroxyproline Hib, α‐hydroxyisobutyric acid; Z, benzyloxycarbonyl). The two former compounds are folded in a β‐bend conformation: type III (III′) for Boc‐Aib‐Hib‐NHBzl, while type II (II′) for the Z analogue. Conversely, the structure of Z‐L‐Hyp‐Aib‐NHMe, although not far from a type II β‐bend, is partially open.
On the flexibility of myosin in solution
Authors: Curry James F. , Krause Sonja 
Published: May 2005

AbstractRabbit skeletal muscle myosin from the same rabbit was prepared by two different methods, and then purified by either Sephadex or hydroxylapatite chromatography. The resulting myosin samples were analyzed in 2–10 mM sodium pyrophosphate solutions at pH 9 using transient electric birefringence. The birefringence decay signals were fitted using a Fortran program called DISCRETE and two relaxation times, 49.7 ± 5.6 and 11.2 ± 2.5 μs, were determined. These relaxation times were independent of the method of myosin preparation, the method of myosin purification, the concentration of sodium pyrophosphate between 2 and 10 mM, the concentration of myosin between 0.08 and 1.59 mg/mL, and the temperature between 4.0 and 20.0°C, after correction to 20.0°C. The longer relaxation time is consistent with a rigid, linear myosin molecule. The shorter relaxation time is consistent with myosin that has a completely flexible hinge region in the myosin tail. Both relaxation times are inconsistent with the previously reported single relaxation time of myosin obtained by fitting the birefringence decay data to only 90% of the decay signal. By forcing some of the birefringence decay data in the present work to fit 90% of the decay signal with a single relaxation time, approximately the same relaxation time as previously reported was obtained.
Heterogeneous molecular aggregation and fractal structure in chitosan/acetic acid systems
Authors: Matsumoto Takayoshi , Kawai Masahiro , Masuda Toshiro 
Published: May 2005

AbstractThe influence of deacetylation degree on heterogeneous molecular aggregation has been investigated for chitosan solution in 2 wt % acetic acid aqueous solution using rheological and small‐angle x‐ray scattering (SAXS) methods. Three samples of chitosan, which were designated CS62, CS79, and CS96, were used, and the deacetylation degrees of these samples were 0.62, 0.79 and 0.96, respectively.Rheological properties show that the systems of CS62 and CS96 are homogeneous, and the system of CS79 has a certain heterogeneous structure with a long‐time relaxation mechanism. According to the SAXS measurement, the heterogeneous system has a fractal structure and the fractal dimension is about 1.3.
Molecular dynamics simulation of Lewis blood groups and related oligosaccharides
Authors: Mukhopadhyay Chaitali , Bush C. Allen 
Published: May 2005

AbstractMolecular dynamics simulations without explicit inclusion of solvent molecules have been performed to study the motions of Lewisa and Lewisb blood group oligosaccharides, and two blood group A tetrasaccharides having type I and type II core chains. The blood group H trisaccharide has also been studied and compared with the blood group A type II core chain. The potential energy surface developed by Rasmussen and co‐workers was used with the molecular mechanics code CHARMM. The lowest energy minima of the component disaccharide fragments were obtained from conformational energy mapping. The lowest energy minima of these disaccharide fragments were used to build the tri‐ and tetrasaccharides that were further minimized before the actual heating/equilibration and dynamics simulations. The trajectories of the disaccharide fragments, e.g., Fuc α‐(1 → 4) GlcNAc, Gal β‐(1 → 4) GlcNAc, etc., show transitions among various minima. However, the oligosaccharides were found to be dynamically stable and no transitions to other minimum energy conformations were observed in the time series of the glycosidic dihedral angles even during trajectories as long as 300 ps. The stable conformations of the glycosidic linkages in the oligosaccharides are not necessarily the same as the minimum energy conformation of the corresponding isolated disaccharides. The average fluctuations of the glycosidic angles in the oligosaccharides were well within the range of ±15°. The results of these trajectory calculations were consistent with the relatively rigid single‐conformation models derived for these oligosaccharides from 1H‐nmr data.
Reassessment of the random coil conformation: Vibrational CD study of proline oligopeptides and related polypeptides
Authors: Dukor Rina K. , Keiderling Timothy A. 
Published: May 2005

AbstractThe “random coil” conformational problem is examined by comparison of vibrational CD (VCD) spectra of various polypeptide model systems with that of proline oligomers [(Pro)n] and poly (L‐proline). VCD, ir and uv CD spectra of blocked L‐proline oligopeptides [(Pro)n, n = 2–12] in different solvents are reported and compared to the spectra of poly (L‐proline) II, poly (L‐glutamic acid), and unblocked proline oligomers. Based on the chain‐length dependence of the VCD and electronic CD (BCD) spectra of proline oligomers, it is established that VCD spectra are dominated by short‐range interactions. The VCD of random coil model polypeptides is shown to be identical in shape but smaller in magnitude than poly (L‐proline) II and of similar magnitude to that of (Pro)n (n = 3, 4). Based on the spectral evidence, it is concluded that the “random coil” conformation has a large fraction of helical regions, conformationally similar to the left‐handed, 31 polyproline II helix, as was previously suggested by Krimm and co‐workers. This conclusion is further supported by studies of effects of salt (CaCl2, LiBr, LiClO4), temperature (5–75°C), and pH on the VCD spectra of L‐proline oligomers, poly (L‐proline) II, and poly (L‐glutamic acid). These show that, after each of these perturbations, a significant local ordering remains in the oligomers and polymers studied, and that charged polypeptides such as poly (L‐glutamic acid) are more flexible than are polyproline or even L‐proline oligomers.
A vibrational spectroscopic study of the self‐association of polyinosinic acid and polyguanylic acid in aqueous solution
Authors: Simard Christine , Savoie Rodrigue 
Published: May 2005

AbstractWe have studied by Raman and ir spectroscopy the structure of self‐associated polyinosinic acid and polyguanylic acid in aqueous solution. The results are consistent with the formation of a four‐stranded complex, which melts cooperatively near 60°C in the case of poly (I) in the presence of K+ ions. The conformation of the ribose in both systems is mixed C2′‐endo/C3′‐endo, giving a structure that is intermediate between the extremes proposed previously from x‐ray diffraction studies. Characteristic Raman bands for the C2′‐endo ribose conformation in polyribonucleotides are identified. The four‐stranded structure of poly (I) appears to be very flexible, with ≈15% of the tetrameric segments being disrupted and ≈30% of the ribose units adopting a disordered conformation prior to melting. This disordering process increases to ≈75% above the melting transition, with the remaining ≈25% of the ribose units keeping an ordered C2′‐endo or C3′‐endo conformation. © 1994 John Wiley & Sons, Inc.
Spatial translational motions of base pairs in DNA molecules: Application of the extended matrix generator method
Authors: Marky Nancy L. , Olson Wilma K. 
Published: May 2005

AbstractWe have used the elementary generator matrices outlined in the preceding paper to examine the conformational plasticity of the nucleic acid double helix. Here we investigate kinked DNA structures made up of alternating B‐ and A‐type helices and intrinsically curved duplexes perturbed by the intercalation of ligands. We model the B‐to‐A transition by the lateral translation of adjacent base pairs, and the intercalation of ligands by the vertical displacement of neighboring residues. We report a complete set of average configuration‐dependent parameters, ranging from scalars (i.e., persistence lengths) to first‐ and second‐order tensor parameters (i.e., average second moments of inertia), as well as approximations of the associated spatial distributions of the DNA and their angular correlations. The average structures of short chains (of lengths less than 100 base pairs) with local kinks or intrinsically curved sequences are essentially rigid rods. At the smallest chain lengths (10 base pairs), the kinked and curved chains exhibit similar average properties, although they are structurally perturbed compared to the standard B‐DNA duplex. In contrast, at lengths of 200 base pairs, the curved and kinked chains are more compact on average and are located in a different space from the standard B‐ or A‐DNA helix. While A‐DNA is shorter and thicker than B‐DNA in x‐ray models, the long flexible A‐DNA helix is thinner and more extended on average than its B‐DNA counterpart because of more limited fluctuations in local structure. Curved polymers of 50 base pairs or longer also show significantly greater asymmetry than other DNAs (in terms of the distribution of base pairs with respect to the center of gravity of the chain). The intercalation of drugs in the curved DNA straightens and extends the smoothly deformed template. The dimensions of the average ellipsoidal boundaries defining the configurations of the intercalated polymers are roughly double those of the intrinsically curved chain. The altered proportions and orientations of these density functions reflect the changing shape and flexibility of the double helix. The calculations shed new light on the possible structural role of short A‐DNA fragments in long B‐type duplexes and also offer a model for understanding how GC‐specific intercalative ligands can straighten naturally curved DNA. The mechanism is not immediately obvious from current models of DNA curvature, which attribute the bending of the chain to a perturbed structure in repeating tracts of A · T base pairs. © 1994 John Wiley & Sons, Inc.
Some effects of microbial growths on surfactant properties of fuels
Authors: Krynitsky John A. , McLaren George W. 
Published: May 2005

AbstractFungi and bacteria taken from fuel systems were allowed to grow in jet fuel (or hydrocarbon)–salt solution mixtures and the layers were analyzed for surfactant properties. The fuels included both JP‐4 and JP‐5 types and an alkylate bottom fraction. Controlled surface activity was imparted to some samples by adding minute quantities of either petroleum sulfonates or petroleum naphthenates. Analyses after growth periods of 2 to 14 weeks failed to show any significant increases in the surface active properties of any fuel or hydrocarbon sample. In all cases, there was either little change or else the surfactant effect was reduced slightly. Opposed to these findings, examination of the aqueous bottoms revealed that microbial growths did effect increases in their surface active properties.
Fractionation of cell constituents of Bacillus megaterium in a polymer two‐phase system
Authors: v. Hofsten Bengt , Baird G. David 
Published: May 2005

AbstractThe distribution of various cell constituents of Bacillus megaterium has been studied in an aqueous two‐phase system containing the two polymers dextran and polythylene glycol. The difference in behaviour between cell walls, lipid granules and soluble cell material are such that a considerable fractionation of a suspension of disrupted cells may be obtained after a few counter‐current distributions. A mixture of whole cells and protoplasts can also be fractionated in this phase system. If sodium chloride is added to the phase system, vegetative cells and spores can be separated from each other.
Determination of oxygen and carbon dioxide using a paramagnetic oxygen analyzer
Authors: Phillips K. L. 
Published: May 2005

AbstractA method by which a paramagnetic oxygen analyzer is used to determine oxygen consumption and carbon dioxide production during aerobic fermentation of Torulopsis utilis is described. The volume of carbon dioxide produced is not necessarily related to the volume of oxygen consumed by the microorganisms. For this reason, all carbon dioxide is removed from the effluent gas before it enters the analyzer when determining oxygen consumption. A method for calibrating the analyzer to correct for this removal is outlined. When determining carbon dioxide, effluent gas bypasses the carbon dioxide absorption tower before entering the analyzer. The carbon dioxide which it contains dilutes the oxygen remaining in the gas. The magnitude of this dilution can be used to calculate the percentage of carbon dioxide produced in terms of the air flow to the fermentor. Equipment required to alternately measure and record oxygen consumption and carbon dioxide production is described.
Polyglutamic acid production by Bacillus subtilis NRRL B‐2612 grown on wheat gluten
Authors: Ward R. M. , Anderson R. F. , Dean F. K. 
Published: May 2005

AbstractBacillus subtilis NRRL B‐2612, isolated at this laboratory, was used to produce polyglutamic acid from devitalized wheat gluten. Conditions for production of the polypeptide were investigated. When NRRL B‐2612 was grown on wheat gluten in shaken flasks with phsophate buffer and salts at pH 6.5, yields of polymer reflected a 25–40% incorporation of glutamic acid into polyglutamic acid. Repeated alcoholic precipitation yielded peptides containing between 45 and 90% D‐glutamic acid. Physical and chemical properties of a typical purified polyglutamic acid indicated that the product was a gamma‐linked polypeptide composed of 75% D‐glutamic acid and 25% L‐glutamic acid with a molecular weight of approximately 200,000.
Stability of product limited continuous culture systems
Authors: Mateles R. I. , Goldthwaite R. W. 
Published: May 2005

AbstractAn investigation was made of the stability of product limited continuous cultures of Saccharomyces carlsbergensis and Pseudomonas ovalis. No oscillations were found in pH or glucose concentration during the steady state, and no overshoot resulted from changing from one steady state to another.