bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acetylcholinesterase in motion: Visualizing conformational changes in crystal structures by a morphing procedure
Authors: Zeev‐Ben‐Mordehai T. , Silman I. , Sussman J. L. 
Published: February 2003

AbstractIn order to visualize and appreciate conformational changes between homologous three‐dimensional (3D) protein structures or protein/inhibitor complexes, we have developed a user‐friendly morphing procedure. It enabled us to detect coordinated conformational changes not easily discernible by analytic methods or by comparison of static images. This procedure was applied to comparison of native Torpedo californica acetylcholinesterase and of complexes with reversible inhibitors and conjugates with covalent inhibitors. It was likewise shown to be valuable for the visualization of conformational differences between acetylcholinesterases from different species. The procedure involves generation, in Cartesian space, of 25 interpolated intermediate structures between the initial and final 3D structures, which then serve as the individual frames in a QuickTime movie. © 2003 Wiley Periodicals, Inc. Biopolymers: 395–406, 2003
Application of the empirical force field to macrocyclic ion carriers, siderophores, and biomimetic analogs
Authors: Felder Clifford E. , Shanzer Abraham 
Published: February 2003

AbstractThe empirical force field (EFF), developed by Prof. Lifson, was applied to the study of macrocyclic alkali ion carriers and to di‐ and tripodal and open chain siderophores and synthetic biomimetic molecules binding transition metals. The highly symmetric nature of these structures facilitated a favorable coordination geometry of the ligating groups about the metal, which helped organize the entire molecule into a fairly rigid structure. In our combined experimental‐theoretical approach, EFF calculations were used to help predict likely candidates to synthesize, and provided a wealth of structural data to complement what we learned from the spectroscopic measurements, while feedback from these measurements allowed us to continue improving the EFF itself. The simple, highly modular design of the biomimetic analogs allowed rapid synthesis and systematic examination of a large number of related structures, as well as facilitating an efficient, piecewise conformational scanning for the theoretical calculations. In the early years, we focused on macrocyclic polylactones and lactams binding monovalent alkali ions, particularly the natural products enniatin and valinomycin, including inside a crystal lattice. Later we switched to bi‐ and tridentate siderophores, natural microbial iron carriers, and synthetic biomimetic analogs—in particular, of enterobactin, ferrichrome, and ferrioxamine B. Over the years a large number of biomimetic siderophores have been prepared, some active in a broad range of microorganisms while others are highly species specific. The results of this work have broad applications in many areas, including the design of novel drugs and antimicrobial agents, helical polymeric structures, and polynuclear metal complexes. © 2003 Wiley Periodicals, Inc. Biopolymers: 407–421, 2003
The dominant interaction between peptide and urea is electrostatic in nature: A molecular dynamics simulation study
Authors: Tobi Dror , Elber Ron , Thirumalai Devarajan 
Published: February 2003

AbstractThe conformational equilibrium of a blocked valine peptide in water and aqueous urea solution is studied using molecular dynamics simulations. Pair correlation functions indicate enhanced concentration of urea near the peptide. Stronger hydrogen bonding of urea–peptide compared to water–peptide is observed with preference for helical conformation. The potential of mean force, computed using umbrella sampling, shows only small differences between urea and water solvation that are difficult to quantify. The changes in solvent structure around the peptide are explained by favorable electrostatic interactions (hydrogen bonds) of urea with the peptide backbone. There is no evidence for significant changes in hydrophobic interactions in the two conformations of the peptide in urea solution. Our simulations suggest that urea denatures proteins by preferentially forming hydrogen bonds to the peptide backbone, reducing the barrier for exposing protein residues to the solvent, and reaching the unfolded state. © 2003 Wiley Periodicals, Inc. Biopolymers: 359–369, 2003
Vibrational spectroscopy and the development of new force fields for biological molecules
Authors: Gerber R. B. , Chaban G. M. , Gregurick S. K. , Brauer B. 
Published: February 2003

AbstractThe role of vibrational spectroscopy in the testing of force fields of biological molecules and in the determination of improved force fields is discussed. Analysis shows that quantitative testing of potential energy surfaces by comparison with spectroscopic data generally requires calculations that include anharmonic couplings between different vibrational modes. Applications of the vibrational self‐consistent field (VSCF) method to calculations of spectroscopy of biological molecules are presented, and comparison with experiment is used to determine the merits and flaws of various types of force fields. The main conclusions include the following: (1) Potential surfaces from ab initio methods at the level of MP2 yield very satisfactory agreement with spectroscopic experimental data. (2) By the test of spectroscopy, ab initio force fields are considerably superior to the standard versions of force fields such as AMBER or OPLS. (3) Much of the spectroscopic weakness of AMBER and OPLS is due to incorrect description of anharmonic coupling between different vibrational modes. (4) Potential surfaces of the QM/MM (Quantum Mechanics/Molecular Mechanics) type, and potentials based on improved versions of semi‐empirical electronic structure theory, which are feasible for large biological molecules, yield encouraging results by the test of vibrational spectroscopy. © 2003 Wiley Periodicals, Inc. Biopolymers: 370–382, 2003
Structure–function relationship studies of bovine parathyroid hormone [bPTH(1–34)] analogues containing α‐amino‐iso‐butyric acid (Aib) residues
Authors: Peggion E. , Mammi S. , Schievano E. , Schiebler L. , Corich M. , Rosenblatt M. , Chorev M. 
Published: February 2003

AbstractThe N‐terminal 1–34 fragments of the parathyroid hormone (PTH) and parathyroid hormone‐related protein (PTHrP) elicit the full spectrum of bone‐related biological activities of the intact native sequences. It has been suggested that the structural elements essential for bioactivity are two helical segments located at the N‐terminal and C‐terminal sequences, connected by hinges or flexible points around positions 12 and 19. In order to assess the relevance of the local conformation around Gly12 upon biological function, we synthesized and characterized the following PTH(1–34) analogues containing Aib residues: (I) A‐V‐S‐E‐I‐Q‐F‐nL‐H‐N‐Aib‐G‐K‐H‐L‐S‐S‐nL‐E‐R‐V‐E‐Nal‐L‐R‐K‐K‐L‐Q‐D‐V‐H‐N‐Y‐NH2 {[Nle8,18, Aib11, Nal23,Tyr34]bPTH(1–34)–NH2}; (II) A‐V‐S‐E‐I‐Q‐F‐nL‐H‐N‐L‐Aib‐K‐H‐L‐S‐S‐nL‐E‐R‐V‐E‐Nal‐L‐R‐K‐K‐L‐Q‐D‐V‐H‐N‐Y‐NH2 {[Nle8,18, Aib12,Nal23,Tyr34]bPTH(1–34)–NH2}; (III) A‐V‐S‐E‐I‐Q‐F‐nL‐H‐N‐L‐G‐Aib‐H‐L‐S‐S‐nL‐E‐R‐V‐E‐Nal‐L‐R‐K‐K‐L‐Q‐D‐V‐H‐N‐Y‐NH2 {[Nle8,18, Aib13, Nal23,Tyr34]bPTH(1–34)–NH2}; (IV) A‐V‐S‐E‐I‐Q‐F‐nL‐H‐N‐Aib‐Aib‐K‐H‐L‐S‐S‐nL‐E‐R‐V‐E‐Nal‐L‐R‐K‐K‐L‐Q‐D‐V‐H‐N‐YNH2 {[Nle8,18, Aib11,12, Nal23,Tyr34]bPTH(1–34)–NH2}; (V) A‐V‐S‐E‐I‐Q‐F‐nL‐H‐N‐L‐Aib‐Aib‐H‐L‐S‐S‐nL‐E‐R‐V‐E‐Nal‐L‐R‐K‐K‐L‐Q‐D‐V‐H‐N‐Y‐NH2 {[Nle8,18, Aib12,13,Nal23,Tyr34]bPTH(1–34)–NH2}. (nL= Nle; Nal= L‐(2‐naphthyl)‐alanine; Aib= α‐amino‐isobutyric acid.) The introduction of Aib residues at position 11 in analogue I or at positions 11 and 12 in analogue IV resulted in a 5–20‐fold lower efficacy and a substantial loss of binding affinity compared to the parent compound [Nle8,18, Nal23,Tyr34]bPTH(1–34)–NH2. Both binding affinity and adenylyl cyclase stimulation activity are largely restored when the Aib residues are introduced at position 12 in analogue II, 13 in analogue III, and 12–13 in analogue V. The conformational properties of the analogues in aqueous solution containing dodecylphosphocholine micelles were studied by CD, two‐dimensional (2D) NMR and computer simulations. The results indicated the presence of two helical segments in all analogues, located at the N‐terminal and C‐terminal sequences. Insertion of Aib residues at positions 12 and 13, or of Aib dyads at positions 11–12 and 12–13, enhances the stability of the N‐terminal helix of all analogues. In all analogues the Aib residues are included in the helical segments. These results confirmed the importance of the helical structure in the N‐terminal activation domain, as well as of the presence of the Leu11 hydrophobic side chain in the native sequence, for PTH‐like bioactivity. © 2003 Wiley Periodicals, Inc. Biopolymers: 437–457, 2003
Effect of low culture temperature on specific productivity, transcription level, and heterogeneity of erythropoietin in Chinese hamster ovary cells
Authors: Yoon Sung Kwan , Song Ji Yong , Lee Gyun Min 
Published: February 2003

AbstractTo determine the effect of low culture temperature on erythropoietin (EPO) production in recombinant Chinese hamster ovary (rCHO) cells, rCHO cells producing EPO (LGE10‐9‐27) were cultivated at 30, 33, and 37°C. At a culture temperature lower than 37°C cell growth was suppressed, but cell viability remained high for a longer culture period. When the culture temperature was lowered from 37°C to 33°C, more than a 2.5‐fold increase in the maximum EPO concentration was achieved. This enhanced EPO production at 33°C was not just because of the extended culture longevity with the decreased release of proteolytic enzymes from dead cells, but mainly because of enhanced qEPO. The qEPO at 33°C was 0.35 ± 0.08 μg/106 cells/h, which was approximately 4‐fold higher than that at 37°C. Although the highest qEPO of 0.49 ± 0.14 μg/106 cells/h was obtained at 30°C, the maximum EPO concentration was lowest because the detrimental effect of lowering culture temperature on cell growth outweighed its beneficial effect on qEPO. Like qEPO, the relative EPO mRNA content increased by lowering culture temperature, indicating that the increased transcription level of EPO was responsible in part for the enhanced qEPO at low culture temperature. The quality of EPO produced at 33°C in regard to isoform pattern, sialic acid content, and in vivo biological activity was comparable to or even better than that produced at 37°C. Taken together, the results obtained demonstrate the potential of the application of low culture temperature to the commercial EPO production in rCHO cells. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 82: 289–298, 2003.
Characterization of an oxygen‐dependent inducible promoter, the Escherichia coli nar promoter, in gram‐negative host strains
Authors: Lee Kil Ho , Cho Moo Hwan , Chung Taeowan , Chang Ho Nam , Lim Sun Ha , Lee Jongwon 
Published: February 2003

AbstractThe Escherichia coli nar promoter is maximally induced under anaerobic conditions in the presence of nitrate ion or under anaerobic only conditions, depending on the genotype of the E. coli nar promoter. Previously, we found that the E. coli nar promoter has some desirable characteristics as an inducible promoter in the E. coli host strains. In this study, the E. coli nar promoter with lacZ gene at the downstream was cloned onto a broad‐host‐range Gram‐negative vector, pBBR122. It was then induced in some other Gram‐negative host strains, such as Agrobacterium, Pseudomonas, and Rhizobium, to determine whether the E. coli nar promoter could be used as an inducible promoter in these strains. From shake‐flask experiments it was found that the wild‐type E. coli nar promoter cloned onto pBBR122, pNW61, was suppressed under aerobic conditions in an Agrobacterium host strain, was partially induced under microaerobic only conditions, and was maximally induced under microaerobic conditions in the presence of nitrate ion. Whereas the mutant‐type E. coli nar promoter cloned onto pBBR122, pNW618, was suppressed under aerobic conditions and was maximally induced under microaerobic conditions, regardless of the presence of nitrate ion. This kind of induction pattern observed for the E. coli nar promoters in the Agrobacterium host strain was similar to that observed for the E. coli nar promoters in the E. coli host strain. On the other hand, it was found that both of the E. coli nar promoters, pNW61 and pNW618, in a Pseudomonas host strain were partially induced under aerobic conditions and were maximally induced under microaerobic conditions, regardless of the presence of nitrate. Finally, it was found that both of the E. coli nar promoters in a Rhizobium host strain were minimally induced, regardless of the presence of oxygen or nitrate ion. Similar induction patterns for the three strains were also observed from fermentor experiments in which the dissolved oxygen (DO) level was tightly controlled. From an evolutionary point of view, the results from the three Gram‐negative host strains indicate that the E. coli nar promoter system, including the promoter and regulatory proteins, was best conserved in the Agrobacterium host strain and the least conserved in the Rhizobium host strain. From an industrial point of view, the results indicate that the E. coli nar promoter system can be used as an oxygen‐dependent inducible promoter in both Agrobacterium and Pseudomonas host strains. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 82: 271–277, 2003.
Rheology, oxygen transfer, and molecular weight characteristics of poly(glutamic acid) fermentation by Bacillus subtilis
Authors: Richard Andrew , Margaritis Argyrios 
Published: February 2003

AbstractPoly(glutamic acid) (PGA) is a water‐soluble, biodegradable biopolymer that is produced by microbial fermentation. Recent research has shown that PGA can be used in drug delivery applications for the controlled release of paclitaxel (Taxol) in cancer treatment. A fundamental understanding of the key fermentation parameters is necessary to optimize the production and molecular weight characteristics of poly(glutamic acid) by Bacillus subtilis for paclitaxel and other applications of pharmaceuticals for controlled release. Because of its high molecular weight, PGA fermentation broths exhibit non‐Newtonian rheology. In this article we present experimental results on the batch fermentation kinetics of PGA production, mass transfer of oxygen, specific oxygen uptake rate, broth rheology, and molecular weight characterization of the PGA biopolymer.© 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 82: 299–305, 2003.
Formation of steady‐state oxygen gradients in vitro: Application to liver zonation
Authors: Allen Jared W. , Bhatia Sangeeta N. 
Published: February 2003

AbstractWe have developed a perfusion bioreactor system that allows the formation of steady state oxygen gradients in cell culture. In this study, gradients were formed in cultures of rat hepatocytes to study the role of oxygen in modulating cellular functions. A model of oxygen transport in our flat‐plate reactor was developed to estimate oxygen distribution at the cell surface. Experimental measurements of outlet oxygen concentration from various flow conditions were used to validate model predictions. We showed that cell viability was maintained over a 24‐h period when operating with a physiologic oxygen gradient at the cell surface from 76 to 5 mmHg O2 at the outlet. Oxygen gradients have been implicated in the maintenance of regional compartmentalized metabolic and detoxification functions in the liver, termed zonation. In this system, physiologic oxygen gradients in reactor cultures contributed to a heterogeneous distribution of phosphoenolpyruvate carboxykinase (predominantly localized upstream) and cytochrome P450 2B (predominantly localized downstream) that correlates with the distribution of these enzymes in vivo. The oxygen gradient chamber provides a means of probing the oxygen effects in vitro over a continuous range of O2 tensions. In addition, this system serves as an in vitro model of zonation that could be further extended to study the role of gradients in ischemia–reperfusion injury, toxicity, and bioartificial liver design. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 82: 253–262, 2003.
Effect of specific oxygen uptake rate on Enterobacter aerogenes energetics: Carbon and reduction degree balances in batch cultivations
Authors: Converti Attilio , Perego Patrizia , Del Borghi Marco 
Published: February 2003

AbstractThe effect of oxygen availability on the metabolism of Enterobacter aerogenes NCIMB 10102 was studied through batch fermentations of glucose performed increasing the specific oxygen uptake rate up to 72.7 mmolO2 C‐molDW−1 h−1. The final concentrations of fermentation products of this biosystem (2,3‐butanediol, hydrogen, acetoin, formate, acetate, carbon dioxide, ethanol, lactate, succinate, and biomass) were utilized to check the use of simple carbon mass and reduction degree balances for the study of microbial energetics even in batch cultivations. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 82: 370–377, 2003.
Computer simulation of the delivery of etanidazole to brain tumor from PLGA wafers: Comparison between linear and double burst release systems
Authors: Tan Wilson Hor Keong , Wang Fangjing , Lee Timothy , Wang Chi‐Hwa 
Published: February 2003

AbstractThis paper presents the computer simulation results on the delivery of Etanidazole (radiosensitizer) to the brain tumor and examines several factors affecting the delivery. The simulation consists of a 3D model of tumor with poly(lactide‐co‐glycolide) (PLGA) wafers with 1% Etanidazole loading implanted in the resected cavity. A zero‐order release device will produce a concentration profile in the tumor which increases with time until the drug in the carrier is depleted. This causes toxicity complications during the later stages of drug treatment. However, for wafers of similar loading, such release results in a higher drug penetration depth and therapeutic index as compared to the double drug burst profile. The numerical accuracy of the model was verified by the similar results obtained in the two‐dimensional and three‐dimensional models. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 82: 278–288, 2003.
Aerobic biological treatment of synthetic municipal wastewater in membrane‐coupled bioreactors
Authors: Klatt Christian G. , LaPara Timothy M. 
Published: February 2003

AbstractMembrane‐coupled bioreactors (MBRs) offer many benefits compared to conventional biological wastewater treatment systems; however, their performance characteristics are poorly understood. Laboratory‐scale MBRs were used to study bacterial adaptations in physiology and community structure. MBRs were fed a mixture of starch, gelatin, and polyoxyethylene‐sorbitan monooleate to simulate the polysaccharide, protein, and lipid components of municipal wastewater. Physiological adaptations were detected by measuring ectoenzyme activity while structural dynamics were studied by denaturing gradient gel electrophoresis of PCR‐amplified 16S rRNA gene fragments. As cell biomass accumulated in the MBRs, pollutant removal efficiency initially improved and then stabilized with respect to effluent concentrations of chemical oxygen demand, protein, and carbohydrate. Comparison of the MBR effluent to filtered reactor fluid indicated that a portion of the observed pollutant removal was due to filtration by the membrane rather than microbial activity. The rates of ectoenzyme‐mediated polysaccharide (α‐glucosidase) and protein (leucine aminopeptidase) hydrolysis became relatively constant once pollutant removal efficiency stabilized. However, the maximum rate of lipid hydrolysis (heptanoate esterase) concomitantly increased more than 10‐fold. Similarly, α‐glucosidase and leucine aminopeptidase ectoenzyme affinities were relatively constant, while the heptanoate esterase affinity increased more than 30‐fold. Community analysis revealed that a substantial community shift occurred within the first 7 days of operation. A Flavobacterium‐like bacterial population dominated the community (>50% of total band intensity) and continued to do so for the remainder of the experiment. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 82: 313–320, 2003.
Effects of intermittent addition of cellulase for production of L‐lactic acid from wastewater sludge by simultaneous saccharification and fermentation
Authors: Nakasaki Kiyohiko , Adachi Tomohiko 
Published: February 2003

AbstractAn attempt was made to create L‐lactic acid, a precursor of poly‐lactic acid, which is a biodegradable plastic, from wastewater sludge from the paper‐manufacturing industry. The sludge contained a high percentage of cellulose and needed to be hydrolyzed to glucose by the action of the cellulase before being treating with lactic acid bacteria. Therefore, a method involving simultaneous saccharification and fermentation (SSF) was carried out. The optimum pH of the SSF for production of the lactic acid by the newly isolated lactic acid bacterium with a high selectively of L‐lactic acid was found out to be around pH = 5.0, and the optimum temperature to be approximately 40°C. On the basis of the measurement of the cell density changes in the lactic acid bacteria, it was ascertained that the bacterial activity could continue at a high level for a relatively long period of time, and that the L‐lactic acid productivity was diminished by the rapid deactivation of the cellulase. With the intermittent addition of cellulase once daily for the sake of compensating for the cellulase deactivation, the L‐lactic acid attained a maximum concentration of 16.9 g/L, i.e., a 72.2% yield based on the potential glucose contained in the sludge under optimum pH and temperature conditions.© 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 82: 263–270, 2003.
Bracketed generic inactivation of rodent retroviruses by low pH treatment for monoclonal antibodies and recombinant proteins
Authors: Brorson Kurt , Krejci Sherrie , Lee Kitty , Hamilton Elizabeth , Stein Kathryn , Xu Yuan 
Published: February 2003

AbstractViral safety is a predominant concern for monoclonal antibodies (mAbs) and other recombinant proteins (RPs) with pharmaceutical applications. Certain commercial purification modules, such as nanofiltration and low‐pH inactivation, have been observed to reliably clear greater than 4 log10 of large enveloped viruses, including endogenous retrovirus. The concept of “bracketed generic clearance” has been proposed for these steps if it could be prospectively demonstrated that viral log10 reduction value (LRV) is not impacted by operating parameters that can vary, within a reasonable range, between commercial processes. In the case of low‐pH inactivation, a common step in mAb purification processes employed after protein A affinity chromatography, these parameters would include pH, time and temperature of incubation, the content of salts, protein concentration, aggregates, impurities, model protein pI, and buffer composition. In this report, we define bracketed generic clearance conditions, using a prospectively defined bracket/matrix approach, where low‐pH inactivation consistently achieves ≥4.6 log10 clearance of xenotropic murine leukemia virus (X‐MLV), a model for rodent endogenous retrovirus. The mechanism of retrovirus inactivation by low‐pH treatment was also investigated. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 82: 321–329, 2003.