bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular dynamics simulations of a winter flounder “antifreeze” polypeptide in aqueous solution
Authors: McDonald Shawn M. , Brady John W. , Clancy Paulette 
Published: December 2004

AbstractA winter flounder antifreeze polypeptide (HPLC‐6) has been studied in vacuo and in aqueous solution using molecular dynamics computer simulation techniques. The helical conformation of this polypeptide was found to be stable both in vacuum and in solution. The major stabilizing interactions were found to be the main‐chain hydrogen bonds, a salt‐bridge interaction, and solute–solvent hydrogen bonds. A significant bending in the middle of the polypeptide chain was observed both in vacuo and in solvent at 300 K. Possible causes of the bending are discussed. From simulations of mutant polypeptide molecules in vacuo, it is concluded that the bend in the native polypeptide was caused by side chain to backbone hydrogen bond competition involving the Thr 24 side chain and facilitated by strains on the helix resulting from the Lys 18‐Glu 22 salt bridge. © 1993 John Wiley & Sons, Inc.
Structural versatility of peptides from Cα, α‐disubstituted glycines: Crystal‐state conformational analysis of homopeptides from Cα‐methyl, Cα‐benzylglycine [(αMe)Phe]n
Authors: Valle Giovanni , Pantano Monica , Formaggio Fernando , Crisma Marco , Toniolo Claudio , Précigoux Gilles , Sulzenbacher Gerlind , Boesten Wilhelmus H. J. , Broxterman Quirinus B. , Schoemaker Hans E. , Kamphuis Johan 
Published: December 2004

AbstractThe molecular and crystal structures of one derivative and three homopeptides (from the di‐to the tetrapeptide level) of the chiral, Cα, α‐disubstituted glycine Cα‐methyl, Cα‐benzylglycine [(αMe)Phe], have been determined by x‐ray diffraction. The derivative is mClAc‐D‐(αMe)Phe‐OH, and the peptides are pBrBz‐[D‐(αMe)Phe]2‐NHMe, pBrBz‐[D‐(αMe)Phe]3‐OH hemihydrate, and pBrBz‐[D‐(αMe)Phe]4‐OtBu sesquihydrate. All (αMe)Phe residues prefer ϕ,ψ torsion angles in the helical region of the conformational map. The dipeptide methylamide and the tripeptide carboxylic acid adopt a β‐turn conformation with a 1 ← 4 CO…︁HN intramolecular H bond. The structure of the tripeptide carboxylic acid is further stabilized by a 1 ← 4 CO…︁HO intramolecular H bond, forming an “oxy‐analogue” of a β‐turn. The tetrapeptide ester is folded in a regular (incipient) 310‐helix. In general, the relationship between (αMe)Phe chirality and helix screw sense is opposite to that exhibited by protein amino acids. A comparison is made with the conclusions extracted from published work on homopeptides from other Cα‐methylated α‐amino acids. © 1993 John Wiley & Sons, Inc.
Solid‐Phase synthesis and stability of triple‐helical peptides incorporating native collagen sequences
Authors: Fields Cynthia G. , Lovdahl Christine M. , Miles Andrew J. , Hageini Vickie L. Matthias , Fields Gregg B. 
Published: December 2004

AbstractA generally applicable solid‐phase methodology has been developed for the synthesis of triple‐helical polypeptides incorporating native collagen sequences. Three nascent peptide chains are C‐terminal linked through one Nα‐amino and two Nε‐amino groups of Lys, while repeating Gly‐Pro‐Hyp triplets induce triple helicity. Different protecting group strategies, including several three‐dimensionally orthogonal schemes, have been utilized for the synthesis of four homotrimeric triple‐helical polypeptides (THPs) of 79–124 residues, three of which incorporate native type IV collagen sequences. Highly efficient assemblies were achieved by 9‐fluorenylmethoxycarbonyl (Fmoc) Nα‐amino group protection, in situ 2‐(1H‐benzotriazole‐l‐yl)‐1,1,3,3‐tetramethyluronium hexafluorophosphate mediated couplings, and 1,8‐diazabicyclo [5.4.0] undec‐7‐ene mediated Fmoc group removal. THPs were characterized by Edman degradation sequencing, size‐exclusion chromatography, mass spectrometry, reversed‐phase high performance liquid chromatography, and CD spectroscopy. THP thermal stabilities ranged from 35 to 59°C, with chain length and Hyp content being the influential factors. Melting temperatures and van't Hoff enthalpies for peptide triple‐helical denaturation could be correlated well to Hyp content. The THP synthetic protocol developed here will allow for the study of both structure and biological activity of specific collagen sequences in homotrimeric and heterotrimeric forms. © 1993 John Wiley & Sons, Inc.
127I‐NMR studies of anion binding to κ‐carrageenan
Authors: Zhang Wei , Furó István 
Published: December 2004

AbstractA preliminary 127I‐NMR relaxation study of the binding of the I− ion to κ‐carrageenan is presented. Signal loss caused by motional correlation times out of extreme narrowing makes it difficult to analyze line widths. Longitudinal relaxation times are more suitable for a comprehensive relaxation study. From the observation of nonextreme motional narrowing, the lower limit of the residence time at the binding site is estimated to be on the order of 10 ns. © 1993 John Wiley & Sons, Inc.
The effects of Cu2+ and Pb2+ on the solution structure of calf thymus DNA: DNA condensation and denaturation studied by fourier transform IR difference spectroscopy
Authors: Tajmir‐Riahi Heidar‐Ali , Naoui Mancef , Ahmad Rohana 
Published: December 2004

AbstractThe interaction of calf thymus DNA with Cu2+and Pb2+ was studied in aqueous solution at pH 6.5 with metal/DNA (P) (P = phosphate) molar ratios (r) 1/80, 1/40, 1/20, 1/10, 1/4, 1/2, and 1, using Fourier Transform ir (FTIR) spectroscopy. Correlations between the ir spectral changes, metal ion binding mode, DNA condensation, and denaturation, as well as conformational features, were established.Spectroscopic evidence has shown that at low metal/DNA (P) molar rations 1/80 and 1/40, copper and lead ions bind mainly to the PO of the backbone, resulting in increased base‐stacking interaction and duplex stability. The major copper ion base binding via G‐C base pairs begins at r > 1/40, while the lead ion base binding occurs at r > 1/20 with the A‐T base pairs. The denaturation of DNA begins at r = 1/10 and continues up to r = 1/2 in the presence of copper ions, whereas a partial destabilization of the helical structure was observed for the lead ion at high metal ion concentration (r = 1/2). Metal‐DNA binding also results in DNA condensation. No major departure from the B‐family structure was observed, upon DNA interaction with these metal ions. © 1993 John Wiley & Sons, Inc.
Quantitative two‐dimensional nmr study of dermenkephalin, a highly potent and selective δ‐opioid peptide
Authors: Naim Mohammed , Charpentier Stéphane , Nicolas Pierre , Baron Daniel 
Published: December 2004

AbstractDermenkephalin, H‐Tyr‐(D) Met‐Phe‐His‐Leu‐Met‐Asp‐NH2, a highly potent and selective δ‐opioid peptide isolated from frog skin, was studied in DMSO‐d6 solution by two‐dimensional nmr spectroscopy, including the determination of NH temperature coefficients, the evaluation of 3J coupling constants from phase‐sensitive correlated spectroscopy (COSY) and the volumes of nuclear Overhauser effect (NOE) correlations. The two‐dimensional NOE spectroscopy (NOESY) spectrum of dermenkephalin revealed sequential, medium‐, and long‐range effects. To put this information on a quantitative basis, special attention was devoted to J cross‐peak suppression, quantification of the NOE volumes and analysis of the overlaps, normalization of the NOEs against diagonal peaks and Hββ′ geminal interactions. Although most of the dihedral angles deduced from the 3JNα coupling constants together with several Niαi and αiNi + 1 NOEs pointed to a partially extended peptide backbone, several Ni Ni + 1 NOEs and βi Ni + 1 interactions argued in favor of a folded structure. Moreover, several long‐range correlations of strong intensities were found that supported a close spatial proximity between the side chains of D‐Met2 and Met6, Tyr1 and His4, Tyr1 and Asp7, and His4 and the C‐terminal amide group. In Phe, the g− rotamer in the side chain is deduced from the 3Jαβ coupling constants and αβ and Nβ NOE correlations. Whereas the amide proton dependency was not indicative of stable hydrogen bonds, the nonuniform values of the temperature coefficient may reflect an equilibrium mixture of folded and extended conformers. The overall data should provide realistic starting models for energy minimization and modelization studies. © 1993 John Wiley & Sons, Inc.
Solution conformation study of substance P methyl ester and [Nle10]‐neurokinin A (4–10) by nmr spectroscopy
Authors: Zhang Min , Wong Tuck C. 
Published: December 2004

AbstractHigh‐resolution proton spectra at 500 MHz of two tachykinin peptides, substance P methyl ester (SPOMe) and [Nle10]‐neurokinin A (4–10), have been obtained in dimethylsulfoxide (DMSO), and for SPOMe, also in 2, 2, 2‐trifluoroethanol (TFE)/water mixtures. Complete chemical shift assignments for these peptides were made based on two‐dimensional (2D) nmr techniques, correlated spectroscopy and total COSY. J coupling measurement and nuclear Overhauser effect spectroscopy (NOESY) were then used to determine the conformation of these peptides in the various solvents. Based on the J coupling, NOE correlations, and temperature coefficients of the NH resonances, it is concluded that these two peptides exist in DMSO at room temperature as a mixture of conformers that are primarily extended. For SPOMe in TFE/water with high TFE content, however, helical structures are found to be present, and they become quite clear at temperatures between 270 and 280 K. The variation of the 13C chemical shifts of the Cα (the secondary shift) with TFE contents corroborates this conclusion. The NOE and Cα shifts show that the main helical region for SPOMe lies between 4P and 9G. The C‐terminus segment LMNH2 is found to be quite flexible, which appears to be quite common for neurokinin‐1 selective peptides. © 1993 John Wiley & Sons, Inc.
Synthesis and biological evaluation of novel NK‐1 tachykinin receptor antagonists: The use of cycloalkyl amino acids as a template
Authors: Sisto Alessandro , Bonelli Fabio , Centini Felice , Fincham Christopher I. , Potier Edoardo , Monteagudo Edith , Lombardi Paolo , Arcamone Federico , Goso Cristina , Manzini Stefano , Giolitti Alessandro , Maggi Carlo A. , Venanzi Mariano , Pispisa Basilio 
Published: December 2004

AbstractIn the course of a program aimed at synthesizing novel, potent NK‐1 tachykinin receptor antagonists, we developed upon a bioactive model by comparing the low energy structures of a series of peptide and nonpeptide Substance P antagonists. The comparison was based on the super imposition of the aromatic rings, assuming that the rest of the molecule behaves predominantly as a template to arrange the key aromatic groups in the right spatial position. A series of 2‐aminocyclohexane carboxylic acid analogues were then selected as the best templates for reproducing the postulated bioactive structure, leading to several pseudo‐peptides with interesting biological activity. According to the molecular modeling, these compounds exhibit a neat parallel facing of the indolyl and naphthyl groups at about 3 Å distance. Ultraviolet absorption and steady state fluorescence measurements support this conclusion, showing a linear correlation between the spectral properties and the binding affinity of these analogues. Stacking of the indole ring with naphthalene gives rise to a complex characterized by a well‐defined molar extinction coefficient. Consistently, steady state and lifetime fluorescence measurements suggest that the quenching process is ascribable to ground‐state interactions between the chromophores. Implications of the π stacking propensity of aromatic groups in the biological activity of the compounds examined are briefly discussed. © 1995 John Wiley & Sons, Inc.
Design and operation of a pilot‐plant fermentor for the continuous propagation of filamentous microorganisms
Authors: Means C. W. , Savage G. M. , Reusser F. , Koepsell H. J. 
Published: December 2004

AbstractA multi‐stage pilot fermentor was designed which consists of nine stainless steel cylindrical compartments 2 ft. in length and 8 in. in diameter, joined end to end, giving a tube with a total length of 18 ft. The whole apparatus was mounted with its axis in a horizontal plane. Each compartment was sealed off from its neighboring compartment by a separatory plate having a 1‐in. overflow hole in the upper half. Shafts 9½ feet long extended from each end of the fermentor through the compartments to the center. Agitation was provided by a multitude of stainless steel blades mounted at right angles to the shafts and spaced at regular intervals along the shafts. Stationary, stainless steel comb‐shaped baffle plates were installed vertically at the bottom of each compartment to increase mixing efficiency. Constant leaving and re‐entering of the fermentation liquor by the blades upon rotation imparts a shattering of the liquid surface thus preventing the accumulation of mycelial aggregates on the walls above the fermentation liquor. The mechanical performance of the described fermentor has proved excellent and several trial fermentations (antibiotic formation and steroid bioconversion) are described.
Microbial production of amino acids. I. The synthesis of lysine and threonine by ustilago species
Authors: Ericson L.‐E. , Kurz W. G. 
Published: December 2004

AbstractThe ability of a number of Ustilago species, especiallyUstilago maydis(DC.) Cda., to produce lysine and threonine was investigated. The organisms were grown in shake flasks or in 10‐l. fermentors. Lysine and threonine were found to be excreted into the medium both in the free and bound form. The bound amino acids could be released by acid hydrolysis or by enzymes from autolyzed cells. The optimal conditions for the release by autolysis were, in the case ofUstilago maydis(DC.) Cda., pH 4.3 and 45°C. An enzyme that could liberate lysine from the bound form(s) occurring in the broth was extracted from cells ofUstilago maydis(DC.) Cda. It exhibited an apparent pH optimum near 4.0. The effect of pH and temperature during the growth phase on the yield of lysine and threonine was studied in 10‐l. fermentations.
Antimicrobial agents as liquid chemosterilizers
Authors: Borick P. M. 
Published: December 2004

AbstractMany antimicrobial agents are available for commercial use, but only a few are truly sporicidal and can be used as chemosterilizers. The action of ethylene oxide, propylene oxide, and β‐propiolactone is well documented. Strong acids, e.g., hydrochloric acid, or alkalis may be used as chemosterilizers but their use is extremely limited. The synthetic phenolics accompanied by boiling were recommended, but heat cannot always be employed. Chlorine and iodine have been used in higher concentrations. The use of 8% formaldehyde or 20% formalin was suggested by Spaulding.17 Other aldehydes possess antimicrobial potency. According to work performed in our laboratories, the sporicidal activity of certain alcoholic, saturated dialdehyde solutions equalled or surpassed that of formaldehyde. These included glyoxal, succinaldehyde, and glutaraldehyde. Aqueous alkaline glutaraldehyde solutions killed the most resistant bacterial spores, e.g., B. subtilis and Cl. tetani, within a few hours (Borick1,2). Glutaraldehyde, a 5‐carbon dialdehyde, was shown to be a chemosterilizer when tested by various methods, destroying bacteria, including M. tuberculosis, fungi, and viruses. Acid glutaraldehyde solutions stored at room temperature are highly stable, whereas alkaline solutions show a significant change in pH and a diminution of glutaraldehyde concentration on alkalinization. For this reason, fresh (not over 2 weeks old) alkaline glutaraldehyde solutions can be used as chemosterilizers.
The effect of ethanol on continuous culture stability
Authors: Zines D. O. , Rogers P. L. 
Published: December 2004

AbstractThe stability characteristics of a continuous culture system were studied following the addition of the natural product inhibitor, ethanol. For a steady state culture of Klebsiella (Aerobacter) aerogenes there was a linear dependence of growth rate on ethanol concentration. Following impulse and step addition of the inhibitor, response patterns of the growth rate (μ) and overall metabolism (Qo2, QCo2, QAC) were observed. A mathematical model of the transient behavior of a product‐limited system is proposed, and analog computer solutions fitted to the experimental data. The transient response of the growth rate could best be described by second or higher order equations, e.g.,

with values of the second order time constant (T2) = 5 min, and damping coefficient (ξ) = 0.4.
Kinetic model identification in mixed populations using continuous culture data
Authors: Chiu S. Y. , Erickson L. E. , Fan L. T. , Kao I. C. 
Published: December 2004

AbstractThe kinetic behavior of heterogeneous microbial populations of sewage origin was studied in a single‐stage, isothermal, continuous flow, completely mixed aeration tank. A series of experiments were carried out at various dilutions rates using glucose as the limiting substrate. The cell dry weight and substrate concentration in terms of chemical oxygen demand (COD) were continuously monitored. The results indicate that reproducible steady‐state conditions can generally be obtained; however, multiple steady states were observed at dilution rates near washout. At low dilution rates (below about 0.1 hr−1) the contribution of microorganism decay became appreciable. Using the multiresponse data of cell dry weight and COD, the parameter values in various existing growth models were estimated. The analyses of variance and residuals revealed that models proposed by Moser, Monod, and Contois, each with a decay term added, were significantly better than the other models which were tested.
Emulsification and degradation of “Bunker C” fuel oil by microorganisms
Authors: Zajic J. E. , Supplisson B. 
Published: December 2004

AbstractAn enrichment culture procedure has been used to isolate mixed culture systems which grow upon “Bunker C” fuel oil. When inoculated into a mineral salts aqueous medium containing Bunker C oil, the mixed cultures initiate oil emulsification. Emulsification usually is observed in 24–48 hr. The role of microbes in this emulsification will be discussed. It appears that certain metabolic products produced by the microbe possess properties of surfactants. Bacteria and fungi have been isolated which possess the ability to cause emulsification. Freeze‐dried biomass is also capable of emulsifying oil. Chromatographic analyses of biodegraded Bunker C fuel oil show that microorganisms selectively metabolize the n‐paraffin fraction.
Growth models of cultures with two liquid phases. VI. Parameter estimation and statistical analysis
Authors: Shah P. S. , Erickson L. E. , Fan L. T. , Prokop A. 
Published: December 2004

AbstractParameter estimation studies have been conducted employing mathematical models developed previously by the investigators and experimental data collected by the last author. A batch fermentation process in which Candida lipolytica were cultured on n‐hexadecane dissolved in dewaxed gas oil was employed to obtain the experimental data. The kinetic data from a number of batch experiments conducted at different initial substrate concentrations and different dispersed phase volume fractions were analyzed assuming that, the basic model parameters (maximum specific growth rate, saturation constant, substrate phase equilibrium constant, adsorption constant, desorption constant, etc.) did not change from experiment to experiment. The Gauss‐Newton method with modification by Greenstadt, Eisenpress, Bard, and Carroll was used to minimize the conventional sum of squares criterion on the IBM 300/50 computer. The individual confidence intervals were obtained for each individual parameter. Tin‐ models were compared employing the F‐test for equality of variances and an analysis of residuals. For the two best models, the estimated parameter values were compared with available experimental information. The results showed good agreement between the experimental data and the values predicted by the mathematical models. The results presented in this work did suggest that growth on small segregated drops may be more important than continuous phase growth on dissolved substrate.
Diffusion influences in denaturable insolubilized enzyme catalysis
Authors: Ollis David F. 
Published: December 2004

AbstractThe influence of diffusion on the apparent thermal stability of a reversibly or irreversibly denaturable enzyme is examined theoretically when he enzyme is uniformly distributed in a porous solid. If the overall reaction rate is influenced by diffusion through the catalyst, the insolubilized catalyst is shown to yield an apparently more thermally stable enzyme even though the maximal velocity Vm, and the Michaelis constant, Km, are the same for the free and insolubilized forms of enzyme.Brief consideration is given to the experimental conditions needed to clearly demonstrate whether insolubilization does or does not effect the thermal stability of the enzyme.
Conversion of benzylpenicillin to 6‐aminopenicillanic acid in a batch reactor and continuous feed stirred tank reactor using immobilized penicillin amidase
Authors: Warburton D. , Dunnill P. , Lilly M. D. 
Published: December 2004

AbstractA rate equation has been derived to describe the hydrolysis of benzylpenicillin to 6‐aminopenicillanic acid by penicillin amidase. The integrated from of the rate equation has been shown to predict satisfactorily the progress of the reaction in a batch reactor using either soluble or immobilized penicillin amidase. The rate equation was also used to predict the performance of a continuous feed stirred tank reactor containing immobilized enzyme. There was good agreement with experimental measurements.
Oxygen transfer into mycelial pellets
Authors: Kobayashi Takeshi , Van Dedem G. , Mooyoung M. 
Published: December 2004

AbstractThe oxygen uptake rate in mycelial pellets of Aspergillus niger was studied experimentally and theoretically. The specific rate of respiration of mycelial pellets was found to decrease significantly with increasing pellet size. The distribution of respiratory activity in the mycelial pellets was evaluated and the specific rate of respiration of disrupted mycelia showed adaptation to the concentration of oxygen in the medium. The decrease of the specific rate of respiration of the mycelial pellets could be estimated according to diameter, mycelial density, oxygen diffusivity, and adaptation to the concentration of oxygen. Good agreement was found between the theoretical analysis and the experimental data.
Fed‐batch hydrocarbon fermentation with colloidal emulsion feed
Authors: Yoshida Fumitake , Yamane Tsuneo , Nakamoto Ken‐Ichiro 
Published: December 2004

AbstractCandida tropicalis was cultured with n‐hexadecane, dispersed in water as submicron droplets, as the only carbon substrate; the emulsion being fed continuously into a fermentor containing only an aqueous medium (fed‐batch culture). The results have demonstrated that the organism takes up hydrocarbon accommodated in the aqueous phase as submicron droplets. The cell/substrate yield for the linear growth phase, where growth was limited by the supply of the substrate, was much higher than the yield for the exponential growth phase.
Preparation of immobilized invertase
Authors: Maeda Hidekatsu , Suzuki Hideo , Sakimae Akihiro 
Published: December 2004

AbstractImmobilized invertase was prepared by ionically binding the enzyme to diethylaminoacetyl cellulose (DEAA‐cellulose). DEAA‐cellulose‐invertase complex was quite stable to electrolyte in the range of pH 5–7. Bound invertase was less active than the native enzyme, and approximately 55–70% of the enzyme activity was lost on binding. The complex was stable for 9 days' continuous inversion in a column system at 30°C, but was rather unstable at 40°C. Heat stability and the effect of temperature on the reaction rate of the complex were almost identical with those of the native enzyme.