bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational analysis of endothelin‐1: Effects of solvation free energy
Authors: Hempel J. C. , Fine R. M. , Hassan M. , Ghoul W. , Guaragna A. , Koerber S. C. , Li Z. , Hagler A. T. 
Published: December 2004

AbstractIn order to investigate conformational preferences of the 21‐residue peptide hormone endothelin‐1 (ET‐1), an extensive conformational search was carried out in vacuo using a combination of high temperature molecular dynamics / annealing and a Monte Carlo / minimization search in torsion angle space. Fully minimized conformations from the search were grouped into families using a clustering technique based on rms fitting over the Cartesian coordinates of the atoms of the peptide backbone of the ring region. A wide range of local energy minima were identified even though two disulfide bridges (Cys1‐Cys15 and Cys3‐Cys11) constrain the structure of the peptide. Low energy conformers of ET‐1 as a nonionized species in vacuo arestabilized by intramolecular interaction of the ring region (residues 1‐15) with the tail (residues 16–21). Strained conformations for individual residues are observed. Conformational similarity to protein loops is established by matching to protein crystal structuresIn order to assess the influence of aqueous environment on conformational preference, the electrostatic contribution to the solvation energy was calculated for ET‐1 as a fully ionized species (Asp8, Lys9, Glu10, Asp18, N‐ and C‐terminus) using a continuum electrostatics model (DelPhi) for each of the conformed generated in vacuo, and the total solvation free energy was estimated by adding a hydrophobic contribution proportional to solvent accessible surface area. Solvation dramatically alters the relative energetics of ET‐1 conformers from that calculated in vacuo. Conformers of ET‐1 favored by the electrostatic salvation energy in water include conformers with helical secondary structure in the region of residues 9–15.Perhaps of most importance, it was demonstrated that the contribution tosolvation by an individual charge depends not only on its solvent accessibility but on the proximity of other charges, i.e., it is a cooperative effect. This was shown by the calculation of electrostatic solvation energy as afunction of conformation with individual charges systematically turned “on” and “off”. The cooperative effect of multiple charges on solvation demonstrated in this manner calls into question models that relate solvation energysimply to solvent accessibility by atom or residue alone. © 1995 John Wiley & Sons, Inc.
Comparison of base inclination in ribo‐GC and deoxybribo‐GC polymers, and synthesis of poly(rGrC)‐poly(rGrC)
Authors: Jin Xiaokui , Johnson W. Curtis 
Published: December 2004

AbstractThe inclination angle between the base normal and the helix axis, and the axes around which the bases incline, are measured for ribo‐GC polymers in buffer by using flow linear dichroism (LD), and compared to measurements for deoxyribo‐GC polymers in buffer and under dehydrating conditions. A new method is designed to synthesize poly(rGrC) ‐poly(rGrC), which is not available commercially, in large quantities. The LD of this RNA reveals inclination angles that are similar to the B‐form DNA in buffer, although the axes are different. The CD of poly(dGdC)‐poly(dGdC) under the dehydrating conditions is similar to poly(rGrC)‐poly(rGrC), indicating it is in the A form, and the LD gives larger inclination angles than either the B form or the corresponding RNA. Poly(dG)‐poly(dC) is in the A form in buffer. Comparison among poly(rG)‐poly(rC) in buffer, and poly (dG)‐poly(dC) in buffer and under dehydrating conditions, reveals similar inclination angles and axes, although the LD shows that the DNA has the largest inclination angles. Except for poly(rGrC)‐poly(rGrC), which has a unique reduced dichroism, all the axes for G are similar, as are the axes for C. © 1995 John Wiley & Sons, Inc.
The use of spectral decomposition via the convex constraint algorithm in interpreting the CD‐observed unfolding transitions of C coils
Authors: Holtzer Marilyn Emerson , Holtzer Alfred 
Published: December 2004

AbstractDecomposition of CD spectra for the unfolding of both coiled‐coil and single‐helical molecules is carried out via the convex constraint algorithm (CCA) [A. Perczel, M. Hollósi, G. Tusnády, and G. D. Fasman (1991) Protein Engineering, Vol. 4, pp. 669–679]. Examined are (1) our thermal unfolding data for rabbit αα‐tropomyosin and chicken gizzard γγ‐ tropomyosin coiled coils, and for a35‐residue, tropomyosin‐model peptide that forms single helices, not coiled coils; (2) extent pH‐induced unfolding data for 50‐ and 400‐residue poly‐L‐glutamic acid. Each set of spectra shows a sharp isodichroic point near 203 nm. We find here that the CCA is of sharply limited use for analyzing such data. The component spectra obtained for a given substance not only depend on the particular experimental spectra included and on the chosen number of component spectra, but all pass through the experimental isodichroic point. The latter is physically unlikely for more than three component spectra, and physically impossible for conformers, such as β structures, having known isodichroic points elsewhere. Our conclusions are in contrast to those of an extant decomposition via CCA of thermal spectra for rabbit αα‐tropomyosin [N. J. Greenfield and S. E. Hitchcock‐DeGregori(1993) Protein Science, Vol. 2, pp. 1263‐1273] that postulates the existence of five conformers, including β structures, in the unfolding. Moreover, an extant diagnostic based on the θ222/θ208 ratio and allegedly distinguishing between spectra for coiled coil and for single α‐helix is shown here to be unreliable. © 1995 John Wiley & Sons, Inc.
Hydration of cis and trans N‐methylformamide as revealed by the use of 17O‐NMR, molecular mechanics, and ab initio calculations
Authors: Gerothanassis Ioannis P. , Demetropoulos Ioannis N. , Vakka Constantina 
Published: December 2004

AbstractThe solvation of cis and trans N‐methylformamide (NMF) by water was investigated using a combination of 17O‐nmr spectroscopy, classical molecular mechanics [MM2(77) and MM2(87)] force field, and ab initio 4‐31G* gradient optimization calculations. In dilute aqueous solution, the 17O‐nmr spectra of NMF indicate strong shielding by 66.9 and 66.1 ppm for the cis and trans amide oxygens, respectively, compared to those values obtained in dilute toluene solution. This demonstrates that both isomers are equally solvated by molecules of water, which are further hydrogen bonded to molecules of water of the bulk solvent. Molecular mechanics simulations were carried out for cis and trans NMF in a cluster of water molecules. Radial distribution functions show structural contacts by several water molecules at the amide CO and NH group, which are significantly more pronounced with MM2 (87) calculations. Ab initio 4‐31G* gradient optimization calculations on the supermolecule trans NMF‐(H2O)3 indicates the presence of more than two hydrogen‐bond contacts at the carbonyl oxygen. This is in agreement with MM2 calculations and provides further evidence for multiple acceptor properties of the amide oxygen and an out of the amide plane arrangement of the bound molecules of water. Comparison of the integration data to the first radial distribution function (rdf) minima shows that the local solvation of the CO and NH groups is very similar for both cis and trans isomers. The intermolecular geometric parameters of the supermolecule trans NMA–(H2O)3 and the first rdf maxima resulting from MM2 (87) and MM2 (77) calculations are compared with distribution of water molecules around the CO and NH groups of peptides and proteins resulting from x‐ray and neutron diffraction experiments. The rdfs involving the methyl group of NMF demonstrate the nonrandom distribution of solvent sites with first maxima in reasonable agreement with distribution of water molecules around the apolar side chain of amino acid residues in proteins. © 1995 John Wiley & Sons, Inc.
Influence of proline‐14 substitution on the secondary structure in a synthetic analogue of alamethicin
Authors: Brachais Laurent , Duclohier Hervé , Mayer Catherine , Davoust Daniel , Molle Gérard 
Published: December 2004

AbstractDue to the bend introduced by proline 14 in the conformation of alamethicin (AcUPUAUQUVUGLUPVUUEQFol), the role of this residue was assumed essential in the barrel‐stave model for voltage‐gated ion channels. Taking advantage of a previous synthetic alamethicin analogue (L2) in which all eight α‐aminoisobutyric(U) Were replaced by leucines (AcLPLALAQLVLGLLPVLLEQFol), another analogue (L5) was synthesized in order to test the effects ofproline‐14 substitution by an alanine (AcLPLALAQLVLGLLPVLLEQFol). Previous conductance experiments showed that both high voltage dependence and multistate behavior were conserved. In order to complement these functional results, a conformational study of L5 has been undertaken and compared to L2 using CD. high field nmr, and molecular dynamics. Results show that L5 presents a better ordered structure than L2 particularly in the region of the substitution and in the C‐terminal part. These results are discussed as regards the previous hypothesis of the nonessential character of helix bending for the gating of voltage‐dependent ion channels. © 1995 John Wiley & Sons, Inc.
Properties of auricularia auricula‐judae β‐D‐glucan in dilute solution
Authors: Zhang Lina , Yang Liqun 
Published: December 2004

AbstractA Water‐soluble glucan A was isolated from the fruit body of Auricularia auricula‐judae. It is composed of a backbone chain of β‐(1 → 3)‐linked D‐glucose residues, two out of three glucose residues being substituted at C‐6 positions with a single glucose unit. The weight average molecular weight Mw, number average molecular weight Mn, and intrinsic viscosity [η] of the fractionated samples were studied at 25°C in water and in dimethylsulfoxide (DMSO). The Mark‐Houwink equation was established as [η] = 6. 10 × 10−4 Mw1.14 for the glucan A having Mw ranging from 9 × 105 to 1.6 × 106 in water. The values of [η] in water are far higher than those in DMSO, but the values of Mn measured in water are the same as those in DMSO. Analysis of Mw and [η] in terms of the known theories for rods and wormlike chains yielded 1030 ± 100 nm−1, 90 ± 20 nm, 1.3 ± 0.3 nm, and 0.26 ± 0.03 nm for molar mass per unit contour length ML, persistence length q, diameter d, and contour length h per main‐chain glucose residue, respectively. The present data suggest that glucan A dissolves in water as single‐stranded helical chains and in DMSO as semiflexible chains. © 1995 John Wiley & Sons, Inc.
Anomalous temperature fluorescence quenching of N‐Trp terminal peptides
Authors: Brancaleon L , Crippa P. R. , Diemmi D 
Published: December 2004

AbstractThe photophysics of Trp‐containing peptides is extremely affected by the position of the indole ring with respect to the substituents. In this work an unusual temperature fluorescence quenching behavior is presented. The N‐tryptophan terminal peptides (N‐ Trp) show an increase of the static emission intensity as rising the temperature from 10 to about 40°C. The anomaly is typical of the N‐Trp terminal peptides since neither tryptophan (Trp) nor glycyl‐tryptophan (Gly‐Trp) and alanyl‐tryptophan (Ala‐Trp) show the same trend; a similar behavior is not detected in the C‐tryptophan terminals. The other important features are the wavelength and pH dependence of the effect. The anomaly is in fact detected only at neutral pH and for excitation wavelength near the red edge of the UVB absorption band of indole. An interpretation of the anomaly is suggested, though more sophisticated techniques are needed to better focus the problem; the model proposed involves the superimposition of a ground state effect (the temperature‐induced equilibrium shift from the zwitterionic to the anionic form of the peptides) and an excited state mechanism. At present no unique interpretation can be provided about the excited state mechanism that favors the anomaly and some suggestions are discussed. © 1995 John Wiley & Sons, Inc.
Novel biopolymers for drug discovery
Authors: Moran Edmund J. , Wilson Troy E. , Cho Charles Y. , Cherry Sara R. , Schultz Peter G. 
Published: December 2004

AbstractThe solid phase synthesis and generation of libraries of “unnatural biopolymers” is described. These polymers are characterized by novel backbones and building blocks, the properties of which may modify their pharmacological and folding properties. © 1994 John Wiley & Sons, Inc.
Peptides in membranes: Helicity and hydrophobicity
Authors: Deber Charles M. , Li Shun‐Cheng 
Published: December 2004

AbstractSynthetic model membrane‐interactive peptides—both of natural and designed sequence—have become convenient and systematic tools for determination of how the membrane‐spanning segments within integral membrane proteins confer protein structure and biology. Conformational studies on these peptides demonstrate that the α‐helix is the natural choice of conformation for a peptide segment in a membrane, and that a helical conformation will arise “automatically” in a peptide above a threshold hydrophobicity that allows it to associate stably with the membrane. Environmental and sequential contexts thus impart conformational versatility to many of the amino acids, thereby providing a mechanism for producing the diverse structural and functional properties of proteins. © 1994 John Wiley & Sons, Inc.
The suitability of a monofunctional reagent of an undecagold cluster for phasing data collected from the large ribosomal subunits from Bacillus stearothermophilus
Authors: Bartels Heike , Bennett William S. , Hansen Harly A. S. , Eisenstein Miriam , Weinstein Shulamith , Müssig Jutta , Volkmann Niels , Schlünzen Frank , Agmon Ilana , Franceschi Francois , Yonath Ada 
Published: December 2004

AbstractAn electron density map of the large ribosomal subunit from Bacillus stearothermophilus was obtained at 26 Å resolution by single isomorphous replacement (SIR) from a derivative formed by specific quantitative labeling with a dense undecagold cluster. For derivalization, a mono‐functional reagent of this cluster was bound to a sulfhydryl group of a purified ribosomal protein. which was in turn reconstituted with core particles of a mutant lacking this protein. The native, mutated, and derivatzed 50S ribosomal subunits crystallize under the same conditions in the same space group. Under favorable conditions, crystals of the derivatized subunit proved to be isomorphous with the native ones, whereas the crystals of the mutant may have somewhat different packing.After resolving the SIR phase ambiguity by solvent flattening, the electron density shows a packing that is consistent with the noncrystallographic symmetry found by Patterson searches as well as with the motif observed in electron micrographs of thin sections of the crystals. These studies established that phase information can be obtained from heavy metal clusters, even when the crystals under investigation are unstable and weakly diffracting. These results encouraged further effort at the construction of specifically derivatized crystals from other ribosomal particles that diffract to higher resolution. © 1994 John Wiley & Sons, Inc.
Effect of UV‐irradiated nitrogen gas on biological nitrogen fixation in batch cultures of Azotobacter vinelandii
Authors: Zacharias Bengt 
Published: December 2004

AbstractIn batch cultures of Azotobacter vinelandii exposed to air and ultraviolet‐irradiated nitrogen, an increases in nitrogen fixation, compared to that of cultures exposed to air and non‐irradiated nitrogen, has been noted. This supports the hypothesis that an ionized nitrogen molecule is important for the biological nitrogen fixation.
Production of eburicoic acid by submerged cultures of Polyporus sulfureus
Authors: Pan S. C. , Frazier W. R. 
Published: December 2004

AbstractA process has been developed whereby eburicoic acid, a triterpenoid acid, can be produced by growing Polyporus sulfureus in submerged form in either shake flasks or tank fermentors equipped with aeration and agitation systems.
Volume increase of kernels of corn and sorghum accompanying absorption of liquid water
Authors: Fan Liang‐Tseng , Chu Pu‐Shan , Shellenberger John A. 
Published: December 2004

AbstractThe linearity between weight and volume increases, which takes place when kernels of corn and sorghum are immersed in water, was established experimentally. The rate of volume increase was correlated according to an equation analogous to the diffusion equation. The coefficients of volume increase obeyed the Arrehenius equation. The results would be of practical value in designing steeping vessels, as well as of theoretical interest in elucidating the mechanism of water diffusion in cereal grains.
Experiments with lysis of living cells of Eremothecium ashbyii and of Methanomonas by microbial enzymes
Authors: Carenberg C. O. , Hedén C.‐G. 
Published: December 2004

AbstractThe possibility to use microorganisms as human food is limited by several factors. The intact cell is resistant to digestion, the cell wall is unbalanced in essential amino acids, and the nucleic acids are said to be harmful. For using single cell protein as food it may thus be necessary to disrupt the cell wall and separate the protein from nucleic acid. This paper is concerned with the production and properties of extracellular enzymes able to lyse cell walls of microorganisms. Soil bacteria and actinomycetes have been cultivated and lytic enzymes from these organisms have been used to lyse living cells of the yeast like organism E. ashbyii. Efforts were also made to use these enzymes for lysing cell of a Methanomonas sp.
Respiratory relationships of a symbiotic algal‐bacterial culture for wastewater nutrient removal
Authors: Humenik F. J. , Hanna G. P. 
Published: December 2004

AbstractA continuous symbiotic algal‐bacterial system was developed consisting essentially of a mixed Chlorella‐activated sludge culture which would efficiently remove nutrients from wastewater under aerobic conditions without supplementary aeration. Oxygen decline data were fitted to a mathematical model used to predict respiratory rates, photosynthetic oxygenation, and steady‐state oxygen concentrations. Stable relative biological populations and a dissolved oxygen concentration of about 2 mg/1 were maintained during steady‐state operation with daily harvesting of excess biomass. Respiratory and physiological relationships indicated that the carbon dioxide‐oxygen balance is a primary control that governs the steady‐state operation of a symbiotic algal‐bacterial culture. The close association of the algae and bacteria resulted in an algal‐bacterial floc with settled rapidly yielding a clear supernatant.
Dialysis fermentation. II. Kinetic analysis of salicylic acid production via cell growth and maintenance
Authors: Abbott Bernard J. , Gerhardt Philipp 
Published: December 2004

AbstractA kinetic analysis was made of the relationship between salicylate production from naphthalene and growth of Pseudomonas fluorescens in semicontinuous dialysis culture. The specific rates both of product formation and growth initially were increased by the diffusional withdrawal of salicylate, but subsequently were reduced to low levels despite continued salicylate removal. Productivity and growth were correlated by the Luedeking‐Piret equation in an initial nondialysis period and in the early stages of dialysis fermentation, when specific growth rates exceeded. 005 hr−1. Below this level of growth at later stages of dialysis fermentation, the specific production rate was correlated only with total cell mass by a proportionality constant of .035 hr−1, which was attributed to maintenance metabolism. Maintenance accounted for about 84% of the total salicylate produced, while growth‐associated metabolism accounted for the remainder.
The supply of oxygen to submerged cultures of BHK 21 cells
Authors: Radlett P. J. , Telling R. C. , Whitside J. P. , Maskell M. A. 
Published: December 2004

AbstractOxygen solution rates were measured in 4, 30, and 100 liter culture vessels, and the oxygen demand of growing BHK 21 cells estimated. This data was used to calculate the minimal sparged air rates necessary to satisfy oxygen demand throughout the cell growth cycle, and in this way adequate oxygen was supplied without the damaging effects of excessive sparging. Comparable results were obtained when oxygen was supplied by this method and when pO2 was controlled at 80 mmHg, but both cell growth rate and maximum cell density were reduced when pO2 was controlled at other values.
Growth models of cultures with two liquid phases. VII. Substrate dissolved in dispersed phase; effect of dispersed phase volume and temperature
Authors: Prokop A. , Erickson L. E. 
Published: December 2004

AbstractThe effects of dispersed phase volume and temperature on the batch growth of Candida lipolytica on gas oil are investigated. Growth parameters are presented for two sets of experiments. The shape of growth curves was basically similar to the system composed of n‐hexadecane dissolved in dewaxed gas oil, in spite of the complex nature of the substance. All of the batch growth curves exhibited a linear growth region. The rate of linear growth and its length varied with change in dispersed phase volume. The effect of temperature on growth rate was investigated for temperatures ranging from 23°C to 34°C. The results show a smaller activation energy during linear growth than during the early stages of batch growth. These results are analyzed from the viewpoint of growth models presented previously. The results indicate that growth at drop surfaces is important and that segregation effects may be important.
Microbiological studies on the formation of gramicidin S synthetases
Authors: Matteo C. C. , Glade M. , Tanaka A. , Piret J. , Demain A. L. 
Published: December 2004

AbstractRapid and extensive growth of Bacillus brevis ATCC 9999 was obtained in a complex medium containing yeast extract and peptone. Gramicidin S (GS) production in this medium reached 2.5 g/liter and 0.25 g/g dry cell weight. GS synthetase I production was also high in this complex medium. Chemically defined media were also developed for this strain. In a glycerol‐ammonium sulfate‐Tris‐salts medium, the culture grew about 40% as well (rate and extent) as in complex medium. Although GS production was low (0.23 g GS/liter), peak specific activity of GS synthetase I was as high as on complex medium. Nutritional experiments showed that growth was stimulated by glutamine, methionine, proline, arginine, and histidine. Addition of these amino acids almost doubled the rate and extent of growth and GS production on a volumetric basis. However the increase in GS was due merely to the increased cell density; GS synthetase I specific activity was in fact decreased by the supplement. Complex medium is better than defined medium for GS and GS synthetase production due to increased cell density and a slower rate of synthetase disappearance.
Solution of immobilized enzyme problems by collocation methods
Authors: Ramachandran P. A. 
Published: December 2004

AbstractA method of solution to the problem of enzyme effectiveness factor has been presented. For a rapid estimation of the same, a graphical procedure is discussed which is sufficiently accurate for many practical situations. Applications to systems with rate dependent on position in the pellet and substrate and product inhibition is discussed. The case of concentration dependent diffusivity (facilitated diffusion) can also be solved by a simple transformation.
Microbial growth on hydrocarbons—some experimental results
Authors: Velankar S. K. , Barnett S. M. , Houston C. W. , Thompson A. R. 
Published: December 2004

AbstractA simple mechanism of hydrocarbon uptake by microorganisms is examined. This model considers the presence of micelles of surface active agents as essential for growth of microbial cells on hydrocarbon substrates. Larger hydrocarbon droplets serving as reservoirs may also be present. Experimental results to support the model are presented. The results of others are explained on the basis of this model.