bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incorporation of diacids into the polyglycine II structure: Model studies
Authors: Navarro Eloísa , Tereshko Valya , Subirana Juan A , Puiggalí Jordi 
Published: December 2004

AbstractAliphatic diacids Eare often incorporated into polypeptide structures in order to obtain model compounds for hormones, protein turns, etc. They are also fundamental components of many commercial polyamides. On the other hand glycine, the simplest amino acid, shows unique conformational features. In order to better understand the structure of such compounds, we have synthetized and determined the molecular structure of three models represented by the general formula CH3‐CH2CH2‐NH‐CO‐CH2NH‐CO‐(CH2)n‐2‐CO‐NH‐CH2CO‐NH‐CH2CH2CH3, with n = 3, 4, or 6. Conformational differences have been found in the dicarboxylic moiety, whereas glycine always has the polyglycine II conformation. The ‐CO‐(CH2)n‐2‐CO‐ segment adopts a folded conjformation: SS, TGT, and SḠTGS̄ for n = 3, 4, and 6, respectively. Molecular packing is always pseiidohexagonal and a network of hydrogen bonds oriented in three directions at 120° is formed. The results are of interest in order to provide information about polyamides in which gljrine residues are incorporated. Our results confirm the tendency of glycine residues to adopt the polyglycine II conformation in its copolymers with aliphatic compounds. © 1995 John Wiley & Sons, Inc.
Influence of sample pH on the conformational backbone dynamics of a pseudotripeptide (H‐Tyr‐TicΨ[CH2‐NH] Phe‐OH) incorporating a reduced peptide bond: An NMR investigation
Authors: Carpenter K. A. , Wilkes B. C. , Schiller P. W. 
Published: December 2004

AbstractIn the present paper we investigate the influence of sample pH on the conformational and dynamical properties of the pseudotripeptide H‐Tyr‐TicΨ[CH2NH]Phe‐OH(TIP[Ψ]:Tic: l, 2, 3, 4,‐tetrahydroisoquinoline‐3‐carboxylic acid) using various one‐ and two‐dimensional nmt techniques in conjunction with molecular modeling. Studies were conducted at three different pH levels‐corresponding to the zwitterionic peptide containing a formal positive charge(pH 3. 1).the deprotonated molecule(pH 9. 1), and a situation at neutral pH(pH 7. 2) involving both protonated and deprotonated states of the reduced peptide bond. Analysis of the one‐dimensional1H‐nmr spectra reveals that in solution TIP[Ψ]is in slow dynamic exchange between conformations containing cis and trans configurations of the Tyr‐Tic bond. An nmr pH dependence study of the cis:trans ratio indicated that the exchange process was governed by the protonation state of the reduced bond amine. From the nmr data, reduced peptide bond pKavalues of 6. 5 and 7. 5 were determined for the cis and trans conformers, respectively. It was concluded that conformations containing a trans Tyr‐Tic bond are stabilized at law pH by an intramolecular hydrogen bond between the Tyr carbonyl and the reduced peptide bond protonated amine. This observation was corroborated by molecular mechanics investigations that revealed low energy trans structures compatible with nmr structural data, and furthermore, were consistently characterized by the existence of a strong N+ HO C interaction closing a seven‐membered cycle. The dynamics of cis‐trans isomerization about the Tyr‐Tic peptide bond were probed by nmr exchange experiments. The selective presaturation of exchanging resonances carried out at several temperatures between 50 and 70°C allowed the determination of isomerization rate constants as well as thermodynamic activation parameters. ΔG≠ values were in close agreement with the cis → trans energy barrier found in X‐Pro peptide fragments (∼83 kJ/mol).A large entropic barrier determined for the trans → cis conversion of TIP[Ψ](5. 7 JK−1 mol−1 at pH 3. 1; 6. 5 JK−1 mol−1 at pH 9. 1) is discussed in terms of decreased solvent molecular ordering around the conformers possessing a trans Tyr‐Tic bond. Evidence that the neutral form of the reduced peptide bond gains rigidity upon protonation was obtained from relaxation measurements in the rotating frame. TJp measurements of several protons in the vicinity of the reduced peptide bond were made as a function of spin‐lock field. Quantitative analysis of the relaxation data indicated that chemical shift fluctuations in the 10−4‐10−5s range were more pronounced in the case of deprotonated TIP[Ψ]. Results of molecular dynamics simulations in addition to 3Jαβ coupling constant measurements support the experimentally observed greater flexibility in the C‐terminal region of TIP[Ψ]. © 1995 John Wiley & Sons, Inc.
The conformation of an alamethicin in methanol by multinuclear NMR spetroscopy and distance geometry/simulated annealing
Authors: Yee Adelinda A , Babiuk Randal , O'Neil Joe D. J 
Published: December 2004

AbstractThe solution conformation of the antibiotic peptide alamethicin was investigated using multi‐nuclear spectroscopy and the distance geometry/simulated annealing algorithms from the program DSPACE. 1H‐, 13C‐, and 15N‐nmr chemical shifts and homonuclear 1H coupling constants suggest that the molecule is flexible in the vicinity of Gly‐11 and Leu‐12. The temperature dependence of the amide proton chemical shifts indicates that there is flexibility in the middle of the 20 residue peptide and provides evidence that, at the very N‐terminus, the molecule adopts a 310‐helical conformation. The large differences in the 13C chemical shifts of the pro‐R and pro‐S methyls of the α‐aminoisobutyric acid residues were used to constrain those residues to the right‐handed helical conformation in the distance geometry/simulated annealing algorithms. A family of 24 structures was generated but did not converge to a common conformation when superimposed over the entire polypeptide sequence. The molecules did converge to a helical conformation over residues 1–10 and residues 13–18. The lack of convergence when the entire lengths of the molecules are superimposed is explained by the flexibility of the peptide near Gly‐11/Leu‐12. The results suggest that the protein consists of two helices connected by a flexible “hinge.” The flexibility of the molecule is discussed with respect to the macrodipole model of voltage gating. © 1995 John Wiley & Sons, Inc.
The use of light‐directed combinatorial peptide synthesis in epitope mapping
Authors: Holmes Christopher P. , Adams Cynthia L. , Kochersperger Lynn M. , Mortensen Richard B. , Aldwin Lois A. 
Published: December 2004

AbstractThe application of light‐directed combinatorial peptide synthesis to epitope mapping is described. Photolithography and solid phase peptide synthesis were combined in an automated fashion to assemble arrays containing 1024 peptide sequences on a glass support in ten steps with the precise location of each peptide known. The simultaneous synthesis of two slides containing three arrays of peptidtes each allowed for the independent screening of both a monoclonal antibody (mAb) and its Fab fragment at two different concentrations. A binary synthesis strategy was used to assemble the arrays, resulting in all deletions and truncations possible within the FLRRQFKVVT sequence being present and available for screening. The relative binding interactions of each peptide was determined by incubating the arrays with either mAb D32.39 and goat antimouse immunoglobulin G–FITC or mAb D32.39 Fab‐FITC conjugate, followed by scanning the surface for fluorescence with an epifluorescence microscope. The fragment RQFKVVT was found to bind lightly to both the mAb and Fab fragment while tethered to the surface, and was measured to have 0.49 n M affinity in solution. The frame‐shifted RRQFKVV sequence was found to have lower affinity both in solution (1.3 m M) and on the surface. The fragment RQFKVV was determined to be responsible for antibody recognition and was found to bind tightly when tethered to the surface, yet exhibited no binding in solution as the free acid, suggesting the requirement of an amidated C‐terminus or an additional flunking residue. A deletion analysis revealed that the novel RQFKVT sequence exhibited higher affinity than the RQFKVV sequence while tethered to the surface. © 1994 John Wiley & Sons, Inc.
Exploring the peptide 310‐helix ⇆ α–helix equilibrium with double label electron spin resonance
Authors: Fiori Wayne R. , Millhauser Glenn L. 
Published: December 2004

AbstractOver the last several years we have used spin labeling as a means for exploring the structure of helical peptides. Two nitroxide labels are engineered into a peptide sequence and distances are ranked with electron spin resonance (ESR). We have found that there is a significant amount of 310–helix in 16–residue model peptides containing only L–amino acids. This review covers several facets of the methodology including spin labeling strategy, interpretation of ESR spectra and the influence of molecular dynamics on the spectral line shapes. Also covered are recent findings of a length–dependent 3l0‐helix → α‐helix transition and the role of Arg+ in the stabilization of specific helix structures. © 1994 John Wiley & Sons, Inc.
The conformational analysis of peptides using fourier transform IR spectroscopy
Authors: Haris Parvez I. , Chapman Dennis 
Published: December 2004

AbstractFourier transform infrared spectroscopy (FTIR) can be used for conformational analysis of peptides in a wide range of environments. Measurements can be performed in aqueous solution, organic solvents, detergent micelles as well as in phospholipid membranes. Information on the secondary structure of peptides can be derived from the analysis of the strong amide I band. Orientation of secondary structural elements within a lipid bilayer matrix can be determined by means of polarized attenuated total reflectance–FTIR spectroscopy. Hydrogen–deuterium exchange can be monitored by the analysis of the, amide II band. This review gives some example of peptide systems studied by FTIR spectroscopy. Studies on alamethicin and α‐aminoisobutyric acid containing peptides have shown that FTIR spectroscopy is a sensitive tool for identifying 310‐helical structures. Changes in the structure of the magainins upon interaction with charged lipids were detected using FTIR spectroscopy. Tachyplesin is an example of a β‐sheet containing membrane active peptide. Polarized ir spectroscopy reveals that the antiparallel β‐sheet structures of tachyplesin are oriented parallel to the membrane surface. Synthesis of peptides corresponding to functionally/structurally important regions of large proteins is becoming increasingly popular. FTIR spectroscopy has been used to analyze the structure of synthetic peptides corresponding to the ion‐selective pore of the voltage‐gated potassium channel. In biomembrane systems these peptides adopt a highly helical structure. Under conditions, where these peptides are aggregated the presence of some intermolecular β‐sheet structure can also be detected. © 1994 John Wiley & Sons, Inc.
A model for enzymatic isomerization of D‐glucose to D‐fructose in a batch reactor
Authors: Sproull Robert D. , Lim Henry C. , Schneider Daniel R. 
Published: December 2004

AbstractUsing whole cells containing glucose isomerase, mathematical models for the enzymatic conversion of D‐glucose to D‐fructose and for the inactivation of the enzyme catalyst have been postulated and verified experimentally. The heat of reaction, the equilibrium constant, and the individual rate constants and their activation energies have been estimated. The model can be used to predict the time course for the enzymatic production of fructose in a batch reactor within the tested experimental range of 40–80°C.
The production of foot‐and‐mouth disease virus from BHK 21 C 13 cells grown on the surface of glass spheres
Authors: Spier R. E. , Whiteside J. P. 
Published: December 2004

AbstractIn view of the advantages which are associated with the use of the BHK monolayer cell for the production of foot‐and‐mouth disease (FMD) virus, a unit system using glass spheres was developed to grow BHK monolayer cells and to test the susceptibility of such cells to FMD virus. The yield of cells and their susceptibility compares favorably with BHK monolayer cells which have been grown in Roux bottles.
The production of foot‐and‐mouth disease virus from BHK 21 C 13 cells grown on the surface of DEAE sephadex A50 beads
Authors: Spier R. E. , Whiteside J. P. 
Published: December 2004

AbstractMethods are described which make possible the production of foot‐and‐mouth disease (FMD) virus from BHK 21 C13 monolayer cells which have been grown on the surface of serum coated DEAE Sephadex A50 beads. The yield of cells and their susceptibility to infection by FMD virus are equivalent to conventional Roux monolayer systems. The potential for the commercial application of the DEAE Sephadex A50 system is discussed in relation to other unit process monolayer systems and in particular to the system in which cells are cultured in a deep bed of small glass spheres.
Effects of immobilization on the kinetics of enzyme‐catalyzed reactions. I. Glucose oxidase in a recirculation reactor system
Authors: Ramachandran K. B. , Perlmutter D. D. 
Published: December 2004

AbstractGlucose oxidase from Aspergillus niger was immobilized on nonporous glass beads by covalent bonding and its kinetics were studied in a packed‐column recycle reactor. The optimum pH of the immobilized enzyme was the same as that of soluble enzyme; however, immobilized glucose oxidase showed a sharper pH‐activity profile than that of the soluble enzyme. The kinetic behavior of immobilized glucose oxidase at optimum pH and 25°C was similar to that of the soluble enzyme, but the immobilized material showed increased temperature sensitivity. Immobilized glucose oxidase showed no loss in activity on storage at 4°C for nearly ten weeks. On continuous use for 60 hr, the immobilized enzyme showed about a 40% loss in activity but no change in the kinetic constant.
Time delay in simple chemostat models
Authors: Macdonald N. 
Published: December 2004

AbstractThe models of Monod and Williams, for the growth of unicellular organisms in chemostats, give strongly damped transients in the biomass and cell number when the flow rate of the chemostat is changed. A simple trick is used to incorporate time delay in these models while still allowing a conventional stability analysis. For long enough time delays the equilibrium point is unstable and limit cycles can be computed. Results obtained using Williams' model, with weakly damped transients as a result of using moderately long time delay, are compared with his data in which cell numbers show weak damping but biomass shows strong damping.
Pilot scale exponential growth of Escherichia coli W to high cell concentration with temperature variation
Authors: Bauer S. , White M. D. 
Published: December 2004

AbstractAn efficient method to grow Escherichia coli W to high cell concentrations on the pilot scale is described and discussed. The method involves growth linked introduction of glucose; and ammonia to the culture, sparing with oxygen, and maintenance of aerobic conditions by gradually decreasing the temperature in the culture in order to keep the oxygen demand within the limits of the capacity of supply. Under these conditions the linear rate of cell mass production is actually the result of exponential growth with a gradually decreasing growth‐rate constant.About 10 kg packed cells were produced in a 50 liter working‐volume fermentor in one run of 13 hr. The concentration of the cells at the end of the growth was about 47 g dry cells/liter. The expenditure for nutrients was minimal and the controls were of simple automatic nature. From the determined yield constants for glucose, nitrogen, phosphorus, and oxygen it may be inferred that the cells grown by this method are similar to those grown exponentially at constant temperature.
Optimal control of a semibatch fermentation
Authors: Ohno Hiromu , Nakanishi Eiji , Takamatsu Takeichiro 
Published: December 2004

AbstractThis work is concerned with the optimization study of the semibatch fermentation by which an amino acid is produced. The particular fermentation studied is the synthesis of lysine by the auxotrophic mutant. Applying Green's theorem to the maximization problem was proposed, and it succeeded in determining the feed rate of the substrate that maximized the production rate of the desired product.
Biosynthesis of flavors by Penicillium roqueforti
Authors: Kinsella John E. , Hwang Dan 
Published: December 2004

AbstractThe development of the unique flavor of blue type cheese depends on the concerted action of numerous enzymes of Penicillium roqueforti involved in protein and lipid metabolism. Protease(s) by degrading casein modify the texture and background flavor of the ripening cheese. Lipase by hydrolyzing milk triglycerides provides flavorful fatty acids and precursors of methyl ketones. The enzyme complex involved in the partial oxidation of free fatty acids and the properties of β‐ketoacyl decarboxylase which generates the major flavor components of blue cheese are discussed. Fermentation of P. roqueforti for the rapid production of methyl ketones is briefly reviewed.
The chemistry of some microbially induced flavor defects in milk and dairy foods
Authors: Morgan M. E. 
Published: December 2004

AbstractThe “malty” flavor defect that commonly develops in raw milk produced in certain areas of North America and Europe has long been known to be due to the metabolic activity of Streptococcus lactis var. maltigenes. The identification of the aldehydes and alcohols responsible for this flavor defect and the mechanisms involved in their formation from amino acids are discussed.Pseudomonas fragi, a common psychrophilic recontaminant, is responsible for development of “fruity” flavors in processed dairy products by virtue of the organisms ability to hydrolyze milk fat and esterify certain of the lower fatty acids with ethanol. A similar esterase is present in certain lactic cultures used in the manufacture of cheddar cheese.The “musty potato” aroma first described in eggs and milk and other dairy products due to the growth of Pseudomonas graveolens (Pseudomonas taetrolens) continues to be reported as a defect in eggs and carcass meats. Pseudomonas perolens has been found to produce a similar aroma in spoiling fish. Vapors entrained from milk and fish tissue cultures of these organisms, collected on porous polymer traps and analyzed by GLC‐alkali flame and GLC‐MS systems, revealed both organisms produce 2‐methoxy‐3‐alkylpyrazines. 2‐Methyoxy‐3‐isopropylpyrazine was found to be responsible for the musty potato aroma. A possible mechanism for the formation of pyrazines is discussed.
Aerobic microbial growth in semisolid matrices: Heat and mass transfer limitation
Authors: Finger S. M. , Hatch R. T. , Regan T. M. 
Published: December 2004

AbstractA conceptual model of aerobic microbial growth in semisolid matrices was developed as a first step in the prediction of the rate of breakdown of semisolid cellulosic material. The conceptual model was described by a series of equations simplified by the assumption of steady‐state microbial activity, and heat and mass transfer limitation. Temperature and oxygen distribution in compost piles were measured experimentally at the Butler County Mushroom Farm, Butler County, Pennsylvania, to test the validity of these assumptions. The compost piles consisted of ground corn husks, straw, and race horse manure. The data fit with the model was excellent with deviations between model predictions (as solved by an analog computer) and actual temperature measurements never exceeding 3°C. The effects of compost pile geometry, external temperature, compost density, external oxygen concentration, and insulation at the bottom of the pile were then predicted using a digital computer to solve the model. The predictions show that the maximum breakdown rate occurs for an optimum height (which depends upon the system), insulating the base increases the breakdown rate, increasing the external temperature increases the initial breakdown rate but decreases the pseudo‐steady‐state breakdown rate and the uniformity, and any increase in the external oxygen concentration increases the breakdown rate but decreases the uniformity.
Utilization of cellulosic materials through enzymatic hydrolysis. II. Preliminary assessment of an integrated processing scheme
Authors: Wilke Charles R. , Cysewski Gerald R. , Der Yang Ren , Von Stockar Urs 
Published: December 2004

AbstractAn integrated processing scheme is described for the conversion of a cellulosic waste (newsprint) to sugars by enzymatic hydrolysis and then to ethanol and yeast by fermentation. The unconverted solids are burned to produce process energy requirements and surplus electrical power. Preliminary designs and cost studies are developed to provide a rough perspective on the potential economic feasibility of this method of cellulose utilization.
Computer‐aided baker's yeast fermentations
Authors: Wang Henry Y. , Cooney Charles L. , Wang Daniel I. C. 
Published: December 2004

AbstractThe economics of yeast production depend heavily upon the cellular yield coefficient on the carbon source and the volumetric productivity of the process. The application of an on‐line computer to maximize these two terms during the fermentation requires a continuous method of measuring cell density and growth rate. U fortunately, a direct sensor for biomass concentration suitable for use in industrial fermentations is not available. Material balancing, with the aid of on‐line computer monitoring, offers an indirect method of measurement. Laboratory results from baker's yeast production in a 14‐liter fermentor (with a PDP‐11/10 computer for on‐line analyses) show this indirect measurement technique to be a viable alternative. From the oxygen uptake and carbon dioxide production data, gas flow rate, and ammonia addition rate, the cell density during the fermentation has been estimated and found to compare well with actual fermentation data.
Production of schardinger β‐dextrin by soluble and immobilized cyclodextrin glycosyltransferase of an alkalophilic Bacillus sp.
Authors: Nakamura N. , Horikoshi K. 
Published: December 2004

AbstractSucciylated cyclodextrin glycosyltransferase (EC.3.2.1.19) of an alkalophilic Bacillus sp. was adsorbed on a vinylpyridine copolymer. The enzyme had about 25% of the activity of soluble enzyme added. No increase of pH or thermal stability of the enzyme was observed by the adsorption, whereas optimum temperature for the enzyme action was shifted from 50 to 55°C. The enzyme converted starch to cyclodextrins without significant loss of activity under the conditions of 4 times reusing of 6 hr conversion by the batch system or 2 weeks continuous reaction by the column system at 55°C and pH 8.0. About 46% of the potato starch solution [15% (w/v)] was converted to cyclodextrins by the enzyme, and 52% was converted by the simultaneous action of the enzyme and alkaline pullulanase of alkalophilic Bacullus sp.(No.202‐1). These values were almost the same as those obtained by the soluble enzyme or enzyme system.
A method using solubility to predict dry matter digestibility of cellulosic materials
Authors: Chiang Lin Chang , Dunlap Charles E. 
Published: December 2004

AbstractA rapid chemical procedure based on the solubility of a holocellulose sample in a system of dimethyl sulfoxide with paraformaldehyde has been developed to provide a laboratory method for predicting dry matter digestibility of cellulose containing samples. The amount of dry matter solubilized by the chemical procedure was closely correlated with anaerobic, in vitro, rumen fluid digestion and with digestibility as measured by aerobic Cellulomonas, sp. bacteria. The quantity of solvent and dissolving time had little effect on solubility over a wide range. The method is rapid, well suited for various cellulosic materials, and may be carried out with simple equipment and facilities.