bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conformational analysis of CCK‐B agonists using 1H‐nmr and restrained molecular dynamics: Comparison of biologically active Boc‐Trp‐(N‐Me)Nle‐Asp‐Phe‐NH2 and inactive Boc‐Trp‐(N‐Me)Phe‐Asp‐Phe‐NH2
Authors: Goudreau N. , Weng J. H. , Roques B. P. 
Published: December 2004

AbstractThe tetrapeptide Boc‐Trp‐(N‐Me)Nle‐Asp‐Phe‐NH2 is a potent CCK‐B agonist. Replacement in this analogue of the norleucine residue by a phenylalanine, to yield Boc‐Trp‐(N‐Me)Phe‐Asp‐Phe‐NH2, led to a 740‐fold decrease in affinity whereas the same decrease in affinity was not observed in their nonmethylated counterparts. In order to ascertain the conformational preferences of these two N‐methylated tetrapeptides, a study by two‐dimensional (2D) nmr spectroscopy and molecular modeling was undertaken. The solution conformation of the two peptides was examined by 1H‐nmr in a d6‐DMSO/H2O (80 : 20) mixture. A cis‐trans equilibrium, induced by N‐methylation, was observed for both analogues, and the proton spectra of the two retamers were fully characterized in each case. 1H‐1H distance constraints, derived from 2D nuclear Overhauser effect spectroscopy and rotating frame nuclear Overhauser effect spectroscopy experiments, were used as inputs for subsequent restrained molecular dynamics simulations. Comparisons of the nmr and molecular modeling data point toward distinct conformational preferences for these two peptides with an opposite spatial orientation of the Trp residue, and could explain the large difference in their biological activities. Furthermore, the tridimensional structure of Boc‐Trp‐(N‐Me)Nle‐Asp‐Phe‐NH2 could serve as a model for the design of nonpeptide CCK‐B agonists. © 1994 John Wiley & Sons, Inc.
Rheological properties and conformational states of β‐conglycinin gels at acidic pH
Authors: Nagano Takao , Mori Hiroyuki , Nishinari Katsuyoshi 
Published: December 2004

AbstractThe heat‐induced gelation of β‐conglycinin was investigated by dynamic viscoelastic measurements as a function of pH. At pH values below 5.5–6.0, the storage modulus G′ rapidly increased with decreasing pH. The conformational states of both sols and gels of β‐conglycinin were investigated by Fourier transform ir (FTIR) and by differential scanning calorimetry (DSC). The degree of protonation of the carboxyl groups of β‐conglycinin, when examined by FTIR indicated that, as would be expected, the degree of protonation increased with decreasing pH below pH 6.0. DSC measurements suggest that β‐conglycinin tends toward thermal denaturation with decreasing pH (below pH 6.0). Second‐derivative FTIR spectra for β‐conglycinin gels show that a band at 1620 cm−1 (associated with exposed β‐strands) develops with decreasing pH. The results suggest that β‐conglycinin undergoes denaturation with increasing protonation of its carboxyl groups, resulting in an increase in the amount of exposed β‐strands. The exposed β‐strands then intermolecularly bond to form gel networks. This process is promoted with decreasing pH, and as a result, rigid gels form at acidic pH values. © 1994 John Wiley & Sons, Inc.
Solution structure and dynamics of DNA topoisomers: Dynamic light scattering studies and Monte Carlo simulations
Authors: Langowski Jörg , Kapp Ulrike , Klenin Konstantin , Vologodskii Alexander 
Published: December 2004

AbstractUsing dynamic light scattering (DLS), we have measured the diffusion coefficient and internal motions of narrow topoisomer distributions of pUCl8 DNA (2687 base pairs) as a function of linking number. The topoisomer distributions were prepared by C‐18 reversed phase high performance liquid chromatography separation of topoisomerase I/ethidium‐generated topoisomer families. The measured diffusion coefficients agree well with those predicted by a Monte Carlo model for the generation of equilibrium ensembles of DNA topoisomers of defined linking number. The only parameters used in the model were the bending persistence length, torsional rigidity, and hydrodynamic radius of DNA known independently from other techniques. Two different values for the torsional rigidity, α = 4 · 10−12 and 8.8 · 10−12 dyn cm, were used. Intrachain interactions in the DNA were taken into account by using an “effective DNA radius,” which was varied between rDNA = 1–8 nm. The best agreement between the measured and calculated values was obtained for α = 4 · 10−12 dyn cm, rDNA = 4 nm. The internal motions of the DNA topoisomers were characterized by the amplitude of the fast relaxation of the DLS autocorrelation function. Our earlier result that supercoiling leads to a decrease in the amplitude of internal motion was confirmed. In addition, we see a characteristic maximum of the internal motion amplitude at a superhelix density of σ = −0.03. The maximum occurs in the same range as a structural transition in pUC8 dimers previously described by L. Song et al. (1990 J. Mol. Biol. 214, 307–326). © 1994 John Wiley & Sons, Inc.
β‐Alanine containing cyclic peptides with turned structure: The “pseudo type II β‐turn.” VI
Authors: Pavone Vincenzo , Lombardi Angelina , Saviano Michele , Nastri Flavia , Fattorusso Roberto , Maglio Ornella , Isernia Carla , Paolillo Livio , Pedone Carlo 
Published: December 2004

AbstractIn the present paper we describe the synthesis, purification, single crystal x‐ray analysis, and nmr solution characterization, combined with restrained molecular dynamic simulations, of the cyclic hexapeptide cyclo‐(L‐Pro‐L‐Phe‐β‐Ala)2. The peptide was synthesized by classical solution methods and the cyclization of the free hexapeptide was accomplished in good yields in diluted methylene chloride solution using N,N‐dicyclohexyl‐carbodiimide. The compound crystallizes in the monoclinic space group P21 from methanol‐dichloro‐methane solution. The two identical halves of the molecule adopt in the solid state two different conformations. One β‐Ala‐L‐Pro peptide bond is trans, while the second is cis. The molecule is present in dimethylsulfoxide d6 solutions as a mixture of conformational families. One of these corresponds to a C2 symmetrical molecule with both β‐Ala‐Pro cis peptide bonds, while the second major conformation is very similar to that observed in the solid state. All Pro‐Phe segments, both in the solid state and the symmetrical and unsym‐metrical solution conformations, display ϕ,ψ angles close to that of position i + 1 and i + 2 of type II β‐turns. In addition, the segments preceeded by a trans β‐Ala‐Pro peptide bond are characterized by a typical i ← i + 3 hydrogen bond, which is absent in the conformer containing a cis β‐Ala‐Pro peptide bond. The latter conformation corresponds to a new structural domain we define as the “pseudo type II β‐turn.” © 1994 John Wiley & Sons, Inc.
New characteristic signatures from time‐dependent static light scattering during polymer depolymerization, with application to proteoglycan subunit degradation
Authors: Ghosh Snehasish , Reed Wayne F. 
Published: December 2004

AbstractModels were developed for the time‐dependent light scattering intensity for simply branched (“comb”) polymers undergoing one or more of three distinguishable degradation mechanisms: (a) stripping off the side chains, (b) randomly degrading off the side chains, and (c) randomly degrading the backbone. The model equations were applied to the analysis of different types of degradation of simply branched biopolymers—bovine nasal cartilage proteoglycan subunits (or “monomers”); NaOH stripped off the glycosaminoglycan (GAG) chains from the protein backbone [mechanism (a)], whereas hyaluronidase seemed to randomly cleave the GAG side chains [mechanism (b)], and HCl both stripped the GAG side chains and randomly cleaved the protein backbone [combined mechanisms (a) and (c)]. The reactions were followed with time‐dependent multiangle, static light scattering. The time‐resolved total scattering technique allowed degradation rate constants and percentage of material in the branched polymer backbone and side chains to be determined, in addition to the mechanisms involved. These new time‐dependent light scattering profiles are added to the growing library of functions from which deductions can be made concerning polymer structure and associated degradation mechanisms and kinetics. These conclusions, drawn from time‐dependent “batch” light scattering, are substantiated by preliminary size exclusion chromatography results and chemical binding assays for sulfated GAGs. © 1995 John Wiley & Sons, Inc.
Duplex to quadruplex equilibrium of the self‐complementary oligonucleotide d(GGGGCCCC)
Authors: Deng Hong , Braunlin William H. 
Published: December 2004

AbstractThe structure of the deoxyaligonucleotide d(GGGGCCCC) has been monitored by 1H and 31 P NMR, and by gel electrophoresis. In low‐salt solution, this oligonucleotide forms a stable duplex structure. Upon titration with KCl, an equilibrium is established between duplex and quadruplex forms. The quadruplex form is the dominant one at physiological KCl concentrations, despite the fact that fewer hydrogen bonds are formed per strand in the quadruplex than in the duplex. © 1995 John Wiley & Sons, Inc.
Density distribution of calcium‐induced alginate gels. A numerical study
Authors: Mikkelsen Arne , Elgsaeter Arnljot 
Published: December 2004

AbstractCharged polysaccharides often form hydrogels in the presence of cations. In many applications the polymer network density distribution and associated physical properties are of major practical importance. Depending on the detailed conditions, the resulting gel density may vary from fully homogeneous to strongly inhomogeneous.We have established a simple set of coupled chemical reaction–diffusion equations to model the gelling process of calcium‐induced alginate gels. The necessary algorithms for numerical solution of the resulting simultaneous parabolic differential equations have been developed both for one‐dimensional models and three‐ldimensional models with cylindrical or spherical symmetry. The algorithms make use of the Crank–Nicolson implicit finite difference method. The results of the numerical analyses of the gel formation can be divided into several different regimes depending on the physical and chemical parameters of the alginates and the cations. The numerical results are in good agreements with reported experimental results. © 1995 John Wiley & Sons, Inc.
Kinetics of protein folding: Nucleation mechanism, time scales, and pathways
Authors: Guo Zhuyan , Thirumalai D. 
Published: December 2004

AbstractThe kinetics and thermodynamics of protein folding is investigated using low friction Langevin simulation of minimal continuum mode of proteins. We show that the model protein has two characteristic temperatures: (a) Tθ, at which the chain undergoes a collapse transition from an extended conformation; (b) Tf(< Tθ), at which a finite size first‐order transition to the folded state takes place. The kinetics of approach to the native state from initially denatured conformations is probed by several novel correlation functions. We find that the overall kinetics of approach to the native conformation occurs via a three‐stage multiple pathway mechanism. The initial stage, characterized by a series of local dihedral angle transitions, eventually results in the compaction of the protein. Subsequently, the molecule acquires native‐like structures during the second stage of folding. The final stage of folding involves activated transitions from one of the native‐like structures to the native conformation. The first two stages are characterized by a multiplicity of pathways while relatively few paths are involved in the final stage. A detailed analysis of the dynamics of individual trajectories reveals a novel picture of protein folding. We find that afraction of the initial population reaches the native conformation without the formation of any detectable intermediates. This pathway is associated with a nucleation mechanism, i.e., once a critical number of tertiary contacts are established then the native state is reached rapidly. The remaining fraction of molecules become trapped in misfolded structures (stabilized by incorrect tertiary contacts). The slow folding involves transitions over barriers from these structures to the native conformation. The theoretical predictions are compared with recent experiments that probe protein folding kinetics by hydrogen exchange labeling technique. © 1995 John Wiley & Sons, Inc.
The development of potent peptide agonists and antagonists for the endothelin receptors
Authors: Cody Wayne L. , Doherty Annette M. 
Published: December 2004

AbstractThe endothelins (ETs), sarafotoxins (SRTXs), vasoactive intestinal contractor (VIC), and bibrotoxin are a family of potent vasoconstrictor peptides. All peptides in this family possess 21 amino acids arranged in a unique bicyclic motif formed between cystine bridges in the 1–15 and 3–11 positions. Since the discovery of endothelin‐1 (ET‐1) in 1988, significant effort has been focused on the understanding of its structure–activity relationships. The identification of endothelin receptor subtypes has led to the discovery/design of potent peptide agonists and antagonists, along with nonpeptide antagonists of endothelin with varying levels of potency and receptor subtype selectivity. In keeping with the theme of this journal, this review will focus only on the development of peptidic‐based agonists and antagonists of endothelin in addition to their applications in understanding the physiological and/or pathophysiological role of endothelin and its isopeptides. © 1994 John Wiley & Sons, Inc.
Structure–activity relationships of neuropeptide Y analogues with respect to Y1 and Y2 receptors
Authors: Beck‐Sickinger Annette G. , Jung Günther 
Published: December 2004

AbstractSecondary structure investigations, affinities, and activities of neuropeptide Y analogues with respect to the Y1 and the Y2 receptor are reviewed. The results are discussed with respect to the different prerequisites for affinities to both receptor subtypes. The results from a systematic scanning of the hormone using L‐alanine and from a large variety of discontinuous and cyclic analogs suggest that two different conformations of neuropeptide Y are adopted at the Y1 and Y2 receptors. Whereas a C‐terminal turn structure is suggested for Y1 receptor affinity, an α‐helical conformation of the C‐terminus is afforded for good binding to the Y2 receptor. © 1994 John Wiley & Sons, Inc.
Enhancement of cheese flavors with microbial esterases
Authors: Huang H. T. , Dooley J. G. 
Published: December 2004

AbstractThe characteristic flavor of hard Italian cheeses is associated with the presence of fatty acids, particularly butyric acid, liberated from milk fat during the ripening process. To ensure proper development and control of flavor, animal pregastric esterases or lipases are routinely added to the milk before coagulation of the curd. Such esterases are also used to generate flavor in enzyme modified cheese and other dairy products.Esterases from microbial sources have been investigated as agents to enhance flavor in cheese. We have found that an esterase from Mucor miehei exhibits the type of lipolytic activity needed for this application. Romano and fontina cheeses of excellent quality have been prepared by the use of this esterase. It has also been used successfully in the preparation of enzyme modified cheese, and, in turn, processed American cheese.
SCP production by Chaetomium cellulolyticum, a new thermotolerant cellulolytic fungus
Authors: Moo‐Young M. , Chahal D. S. , Swan J. E. , Robinson C. W. 
Published: December 2004

AbstractChaetomium cellulolyticum, a newly isolated cellulolytic fungus, showed 50–100% faster growth rates and over 80% more final biomass‐protein formation than Trichoderma viride, a well‐known high cellulase‐producing cellulolytic organism, when cultivated on Solka‐floc (a purified, predominantly amorphorous form of cellulose) or partially delignified sawdust (consisting of a mixture of hardwoods) as the sole‐carbon source in the fermentation media. However, in both cases, T. viride produced much higher quantities of free cellulases at faster rates and also degraded more substrate than C. cellulolyticum. It is concluded that the synthesis mechanisms and/or the nature of the cellulase complexes of the two types of organisms are quite different such that C. cellulolyticum is more optimal for single‐cell protein (SCP) production, while T. viride is more optimal for the production of extracellular cellulases.It was also found that the amino acid composition of C. cellulolyticum is generally better than that of T. viride and compares favorably with those of the FAO reference protein, alfalfa, and soya meal. In addition, preliminary feeding trials on rats have shown no adverse effects of the SCP produced by C. cellulolyticum fermentations.
Effect of drop interactions on the performance of hydrocarbon fermentors
Authors: Bajpai R. K. , Ramkrishna D. , Prokop A. 
Published: December 2004

AbstractA drop‐interaction model devised by the authors, which successfully predicts experimentally observed drop‐size distributions in stirred batch vessels, has been used to assess the importance of droplet coalescence and redispersion in hydrocarbon fermentation yields. Calculations, which have been made with both n‐alkane and gas–oil fermentations, have been compared with previous calculations based on simpler and, hence, less realistic droplet interaction mechanisms. The comparison shows that the differences in yield are not spectacularly different.
Pore dimensions for accumulating biomass. II. Microbes that form spores and exhibit mycelial growth
Authors: Messing R. A. , Oppermann R. A. , Kolot F. B. 
Published: December 2004

AbstractThe relationship between the dimensions of a spore and the accumulation of that microbe in a porous, inorganic structure has been determined. In order to achieve high accumulation of mycelial growth, at least 70% of the pores of an inorganic carrier should have pore diameters in the range of one times the smallest dimension of the fungal spore but less than about 16 times the largest dimension of that spore. This relationship was established by varying the physical parameters of the carriers as well as their chemical composition.
Studies on the mechanism of enzymatic hydrolysis of cellulosic substances
Authors: Ghose T. K. , Bisaria V. S. 
Published: December 2004

AbstractMost cellulosic substances contain appreciable amounts of cellulose and hemicellulose, which on enzymatic hydrolysis mainly yield a mixture of glucose, cellobiose, and xylose. In this paper, studies on the mechanisms of hydrolysis of bagasse (a complex native cellulosic waste left after extraction of juice from can sugar) by the cellulase enzyme components are described in light of their adsorption characteristics. Simultaneous adsorption of exo‐ and endoglucanases on hydrolyzable cellulosics is the causative factor of the hydrolysis that follows immediately after. It supports the postulate of synergistic enzyme action proposed by Eriksson. Xylanase Pretreatment enhanced the hydrolysis of bagasse owing to the creation of more accessible cellulosic regions that are readily acted upon by exo‐ and endoglucanases. The synergistic action of the purified exoglucanase, endoglucanase, and xylanase has been found to be most effective for hydrolysis of bagasse but not for pure cellulose. Significant quantities of glucose are produced in β‐glucosidase‐free cellulase action on bagasse. Individual and combined action of the purified cellulase components on hydrolysis of native and delignified bagasse are discussed in respect to the release of sugars in the hydrolysate.
Production of microbial lipid: Effects of growth rate and oxygen on lipid synthesis and fatty acid composition of Rhodotorula gracilis
Authors: Choi S. Y. , Ryu Dewey D. Y. , Rhee J. S. 
Published: December 2004

AbstractMicrobial lipids produced by Rhodotorula gracilis NRRL Y‐1091 grown in continuous culture under nitrogen‐limiting condition were evaluated and the effects of growth rate and oxygen concentration on the degree of unsaturatoin of fatty acids studied. As the growth rate increased the protein content of the biomass increased but cell biomass, lipid content, and lipid productivity decreased; the specific lipid production rate remained constant at about 0.012 g lipid/g dry biomass/h. The maximum lipid content recorded was 49.8% (w/w) of the cell mass at a growth rate of 0.02 h−1. The growth rate also affected fatty acid composition; polyunsaturated fatty acids (C18:2 and C18:3) increaded with growth rate while other fatty acids (C16:0, C18:0, C18:1) decreased. Increase in oxygen concentration between 5 and 234μM increased the lipid content without significantly affecting its degree of unsaturation. On the other hand, the degree of unsaturation was significantly affected by specific oxygen uptake rate for this obligate aerobe, Rh. gracilis.
Continuous ethanol production from Jerusalem artichoke tubers. I. Use of free cells of Kluyveromyces marxianus
Authors: Margaritis Argyrios , Bajpai Pratima 
Published: December 2004

AbstractThe Continuous fermentation of Jerusalem artichoke juice to ethanol by free cells of Kluyveromyces marxianus UCD (FST) 55–82 has been studied in a continuous‐stirred‐tank bioreactor at 35°C and pH 4.6. A maximum yield of 90% of the theoretical was obtained at a dilution rate of 0.05 h−1. About 95% of the sugars were utilized at dilution rates lower than 0.15 h−1. Volumetric ethanol productivity and volumetric biomass productivity reached maximum values of 7 g ETOH/L/h and 0.6 g dry wt/L/h, respectively, at a dilution rate of 0.2 h−1. The maintenance energy coefficient for K. marxianus culture was found to be 0.46 g sugar/g biomass/h/ Oscillatory behavior was following a change in dilution rate from a previous steady state and from batch to continuous culture. Values of specific ethanol production rate and specific sugar uptake were found to increase almost linearly with the increase of the dilution rate. The maximum specific ethanol production rate and maximum specific sugar uptake rate were found to be 2.6 g ethanol/g/ cell/h and 7.9 sugars/g cell/h, respectively. Washout occurred at a dilution rate of 0.41 h−1.
Conversion of cheese whey to single‐cell protein
Authors: Sandhu D. K. , Waraich M. K. 
Published: December 2004

AbstractThirteen yeast species belonging to nine genera were screened for the production of single‐cell protein (SCP) using cheese whey as the substrate. Cheese whey supplemented with minerals and yeast extract proved to the best medium for yield, lactose utilization, biomass production, and conversion efficiency. Production of β‐galactosidase was studied in Brettanomyces anomalus, Kluyveromyces fragilis, Trichosporon cutaneum, and Wingea robertsii; the last proved to be the best strain combining high yield with shorter incubation period.
Calorimetric analysis of Escherichia coli in continuous culture
Authors: Ishikawa Yasufumi , Shoda Makoto 
Published: December 2004

AbstractThe heat evolution rate was measured in continuous culture of Escherichia coli k‐12 on glucose‐limiting medium. The specific heat production rate based on the dry cell mass increased in proportion to increase of dilution rate. The specific heat production rate based on a viable cell increased nonlinearly because the cell size varied in each dilution rate. Several thermochemical data were calculated for each dilution rate from the stoichiometric equation which was derived from elementary analysis of the cells. Growth yields based on energy measured directly was found to be less influenced by dilution rate than the growth yield based on consumed glucose. This suggested that the energy efficiency of utilization of catabolic energy for anabolism was almost constant.