bluuebunny/crossref_metadata_2025_split huggingface dataset:
Second virial coefficients as a measure of protein–osmolyte interactions
Authors: Weatherly Gresham T. , Pielak Gary J. 
Published: July 2002

AbstractThe cytoplasm contains high concentrations of cosolutes. These cosolutes include macromolecules and small organic molecules called osmolytes. However, most biophysical studies of proteins are conducted in dilute solutions. Two broad classes of models have been used to describe the interaction between osmolytes and proteins. One class focuses on excluded volume effects, while the other focuses on binding between the protein and the osmolyte. To better understand protein–smolyte interactions, we have conducted sedimentation equilibrium analytical ultracentrifugation experiments using ferricytochrome c as a model protein. From these experiments, we determined the second virial coefficients for a series of osmolytes. We have interpreted the second virial coefficient as a measure of both excluded volume and protein–osmolyte binding. We conclude that simple models are not sufficient to understand the interactions between osmolytes and proteins.
The energetic cost of induced fit catalysis: Crystal structures of trypsinogen mutants with enhanced activity and inhibitor affinity
Authors: Pasternak Annette , White Andre , Jeffery Constance J. , Medina Nivia , Cahoon Marguerite , Ringe Dagmar , Hedstrom Lizbeth 
Published: July 2002

AbstractThe contribution of induced fit to enzyme specificity has been much debated, although with little experimental data. Here we probe the effect of induced fit on enzyme specificity using the trypsin(ogen) system. BPTI is known to induce trypsinogen to assume a trypsinlike conformation. Correlations are observed between BPTI affinity and the values of kcat/Km for the hydrolysis of two substrates by eight trypsin(ogen) variants. The slope of both correlations is −1.8. The crystal structures of the BPTI complexes of four variant trypsinogens were also solved. Three of these enzymes, K15A, ΔI16V17/D194N, and ΔI16V17/Q156K trypsinogen, are 10‐ to 100‐fold more active than trypsinogen. The fourth variant, ΔI16V17 trypsinogen, is the lone outlier in the correlations; its activity is lower than expected based on its affinity for BPTI. The S1 site and oxyanion hole, formed by segments 184A–194 and 216–223, are trypsinlike in all of the enzymes. These structural and kinetic data confirm that BPTI induces an active conformation in the trypsin(ogen) variants. Thus, changes in BPTI affinity monitor changes in the energetic cost of inducing a trypsinlike conformation. Although the S1 site and oxyanion hole are similar in all four variants, the N‐terminal and autolysis loop (residues 142–152) segments have different interactions for each variant. These results indicate that zymogen activity is controled by a simple conformational equilibrium between active and inactive conformations, and that the autolysis loop and N‐terminal segments control this equilibrium. Together, these data illustrate that induced fit does not generally contribute to enzyme specificity.
Dopa decarboxylase exhibits low pH half‐transaminase and high pH oxidative deaminase activities toward serotonin (5‐hydroxytryptamine)
Authors: Bertoldi Mariarita , Voltattorni Carla Borri 
Published: July 2002

AbstractDopa decarboxylase (DDC) catalyzes not only the decarboxylation of l‐aromatic amino acids but also side reactions including half‐transamination of d‐aromatic amino acids and oxidative deamination of aromatic amines. The latter reaction produces, in equivalent amounts, an aromatic aldehyde or ketone (depending on the nature of the substrate), and ammonia, accompanied by O2 consumption in a 1 : 2 molar ratio with respect to the products. The kinetic mechanism and the pH dependence of the kinetic parameters have been determined in order to obtain information on the chemical mechanism for this reaction toward 5‐hydroxytryptamine (5‐HT). The initial velocity studies indicate that 5‐HT and O2 bind to the enzyme sequentially, and that d‐Dopa is a competitive inhibitor versus 5‐HT and a noncompetitive inhibitor versus O2. The results are consistent with a mechanism in which 5‐HT binds to DDC before O2. The pH dependency of log V for the oxidative deaminase reaction shows that the enzyme possesses a single ionizing group with a pK value of ∼7.8 that must be unprotonated for catalysis. In addition to an ionizing residue with a pK value of 7.9 similar to that found in the V profile, the (V/K)5‐HT profile exhibits a pK value of 9.8, identical to that of free substrate. This pK was therefore tentatively assigned to the α‐amino group of 5‐HT. No titrable ionizing residue was detected in the (V/K)O2 profile, in the pH range examined. Surprisingly, at pH values lower than 7, where oxidative deamination does not occur to a significant extent, a half‐transamination of 5‐HT takes place. The rate constant of pyridoxamine 5′‐phosphate formation increases below a single pK of ∼6.7. This value mirrors the spectrophotometric pKspec of the shift 420–384 nm of the external aldimine between DDC and 5‐HT. Nevertheless, the analysis of the reaction of DDC with 5‐HT under anaerobic conditions indicates that only half‐transamination occurs with a pH‐independent rate constant over the pH range 6–8.5. A model accounting for these data is proposed that provides alternative pathways leading to oxidative deamination or half‐transamination.
Biochemical and X‐ray crystallographic studies on shikimate kinase: The important structural role of the P‐loop lysine
Authors: Krell Tino , Maclean John , Boam Deborah J. , Cooper Alan , Resmini Marina , Brocklehurst Keith , Kelly Sharon M. , Price Nicholas C. , Lapthorn Adrian J. , Coggins John R. 
Published: July 2002

AbstractShikimate kinase, despite low sequence identity, has been shown to be structurally a member of the nucleoside monophosphate (NMP) kinase family, which includes adenylate kinase. In this paper we have explored the roles of residues in the P‐loop of shikimate kinase, which forms the binding site for nucleotides and is one of the most conserved structural features in proteins. In common with many members of the P‐loop family, shikimate kinase contains a cysteine residue 2 amino acids upstream of the essential lysine residue; the side chains of these residues are shown to form an ion pair. The C13S mutant of shikimate kinase was found to be enzymatically active, whereas the K15M mutant was inactive. However, the latter mutant had both increased thermostability and affinity for ATP when compared to the wild‐type enzyme. The structure of the K15M mutant protein has been determined at 1.8 Å, and shows that the organization of the P‐loop and flanking regions is heavily disturbed. This indicates that, besides its role in catalysis, the P‐loop lysine also has an important structural role. The structure of the K15M mutant also reveals that the formation of an additional arginine/aspartate ion pair is the most likely reason for its increased thermostability. From studies of ligand binding it appears that, like adenylate kinase, shikimate kinase binds substrates randomly and in a synergistic fashion, indicating that the two enzymes have similar catalytic mechanisms.
A Numerical Scheme for Dynamic Systems Containing Fractional
Derivatives
Authors: Yuan Lixia , Agrawal Om P. 
Published: July 2002

Abstract
This paper presents a numerical scheme for dynamic analysis of mechanical systems subjected to damping forces that are proportional to fractional derivatives of displacements. These equations appear in the modeling of frequency dependent viscoelastic damping of materials. In the scheme presented, the fractional differential equation governing the dynamics of a system is transformed into a set of differential equations with no fractional derivative terms. Using Laguerre integral formula, this set is converted to a set of first order ordinary differential equations, which are integrated using a numerical scheme to obtain the response of the system. In contrast to other numerical techniques, this method does not require one to store the past history of the response. Numerical studies show that the solution converges as the number of Laguerre node points increase. Further, results obtained using this scheme agree well with those obtained using analytical techniques.
Modeling of Conjugate Two-Phase Heat Transfer During Depressurization of Pipelines
Authors: Fairuzov Y. V. 
Published: July 2002

AbstractTransient conjugate two-phase heat transfer during depressurization of pipelines containing flashing liquids is examined in this paper. A numerical model for transient flashing liquid flow in a pipe is formulated. The model takes into account the transient radial heat conduction and the forced convection effects. Numerical simulation of flashing two-component (propane and butane) flow is performed in order to investigate the effect of wall friction on the heat transfer conditions in the pipe. The simulation results are compared with predictions of the model that are based on a new formulation of energy equation proposed by the author in an early study. A comparison of the results obtained allows one to determine the range of applicability of the new energy equation formulation. A procedure is proposed for choosing an appropriate model for predicting transient conjugate two-phase heat transfer during releases of flashing liquids from pipes. A criterion of thermodynamic similarity for flashing liquids flows in pipes or channels is formulated. The proposed criterion provides the basis for selecting model fluids and for constructing experimental models of systems containing flashing (volatile) liquids with scaled thermodynamic conditions. An example of its use is given. [S0022-1481(00)02001-6]
On the Enhancement of the Thermal Contact Conductance: Effect of
Loading History
Authors: Li Y. Z. , Madhusudana C. V. , Leonardi E. 
Published: July 2002

Abstract
A resistance to heat flow exists at the junction of two surfaces. It has long been recognized that there exists a hysteresis effect, that is, the value of thermal contact resistance in the unloading process is less than that in the loading process at the same load. However, little work has been done in utilizing this phenomenon to enhance the thermal contact conductance. The present experimental work investigated the effect of loading history; in particular the number of load cycles and overloading pressure, on the thermal contact conductance. It was found that the value of the thermal contact conductance might be enhanced by up to 51 percent. A cost-effective way of enhancing the contact conductance is suggested. [S0022-1481(00)01601-7]
Friction and energy dissipation at the atomic scale: A review
Authors: Singer I. L. 
Published: July 2002

Discussions of energy dissipation during friction processes have captured the attention of engineers and scientists for over 300 years. Why then do we know so little about either dissipation or friction processes? A simple answer is that we cannot see what is taking place at the interface during sliding. Recently, however, devices such as the atomic force microscope have been used to perform friction measurements, characterize contact conditions, and even describe the ‘‘worn surface.’’ Following these and other experimental developments, friction modeling at the atomic level—particularly molecular dynamics (MD) simulations—has brought scientists a step closer to ‘‘seeing’’ what takes place during sliding contact. With these investigations have come some answers and new questions about the modes and mechanisms of energy dissipation at the sliding interface. This article will review recent theoretical and experimental studies of friction processes at the atomic scale. Theoretical treatments range from simple, analytical models of two-dimensional, coupled ball-spring systems at 0 K, to more complex MD simulations of three-dimensional arrays of hydrogen- and hydrocarbon-terminated surfaces at finite temperatures.
Results are presented for the simplest yet most practical cases of sliding contact: sliding without wear. Sliding without friction is seen in weakly interacting systems. Simple models can easily explain the energetics of such friction processes, but MD studies are needed to explore the dynamics (excitation modes, energy pathways,...) of thermally excited atoms interacting in three-dimensional fields. These studies provide the first atomic-scale models for anisotropic friction and boundary lubrication. Friction forces at atomic interfaces must ultimately be measured at the macroscopic level; these measurements, which depend on the mechanical properties of the measuring system, are discussed. Two rather unique experimental studies of friction are also reviewed. The first employs a ‘‘surface force apparatus’’ to measure adhesion and friction between surfactant monolayers. The correlation of adhesion hysteresis and friction provides a new mechanism of friction; moreover, the interpretation for the effect—hysteresis from entanglement of the molecular chains during a phase transformation—implies that the dynamics are taking place at an accessible time scale (seconds to minutes). The second study extends the time domain at which friction can be measured to the nanosecond scale. A quartz-crystal oscillator is used to monitor the viscosity of monolayer liquids and solids against solid surfaces. Interfaces slip angstroms in nanoseconds. Modelers have suggested a variety of mechanisms for this atomic-scale friction process, from defect-mediated sliding to electron drag effects. The article ends by identifying the vast, barely charted time-space domain (micro-to-pico time and length scales) in which experiments are needed to further understand the dynamic aspects of friction processes.
Gold/carbon superfine particles produced in pulsed CO2 laser stimulated plasmas
Authors: Colgate S. O. , Simon C. G. , Boggess S. J. , Moini M. , D’Agostino A. T. , Ammons J. M. 
Published: July 2002

A new technique for the production of composite nano materials was used to produce carbon coated gold superfine particles in the 100 nm size range. Particles were produced in pulsed CO2 laser (2 J/pulse at 3×109 W/cm2 ) stimulated plasmas using solid Au targets and 1:3 mixtures of CH4, CO, or CO2 with He or H2 gases at 1.3 kPa pressure. The particle production rate was dependent on the presence and type of carbonaceous gas species, and the partial and total gas pressures. Thin films of the black superfine particles were deposited on glass, ceramic and metal substrates. X-ray photoelectron spectroscopic analyses showed that Au was in the metallic state in the particles, both before and after thermal annealing, at an average concentration of 95% by mass. Fourier transform ion cyclotron resonance mass spectrometry of gaseous products emitted during thermal and laser anneals identified the major constituents as carbon dioxide and hydrocarbons. Scanning electron microscopy images of thermally annealed films showed that the particles retained their relatively uniform 100 nm diam size, despite significant changes in optical and electrical properties.
This is attributed to loss of the carbon coating on the exterior of the Au particles. While some of the carbon is catalytically oxidized during thermal annealing, the majority remains in the bulk of the film, presumably concentrated at subsurface grain boundaries. Annealing the films in air produced sharp, permanent color changes to purple at 470 K and red/yellow at 493 K due to the loss of the carbon coating from the basic Au particle. Films deposited at 373 K on glass substrates were ∼5× more reflective in the 450–750 nm portion of the spectrum than films deposited at 300 K due to increased particle packing density. Particle films were also annealed using an unfocused CO2 laser beam and a radio-frequency field. A focused argon ion laser beam was used to anneal lines as narrow as 0.5 μm in particle films on glass substrates. The lowest sheet resistance value measured for an unannealed particle film deposited on glass at 298 K was 5600 Ω/square. Resistance versus temperature (in air) measurements across a 2 mm wide gap of a coated ceramic feedthrough exhibited minima of 9 mΩ at 450 K and 4.47 MΩ at 655 K, and a maximum of &gt;20 MΩ from 493–600 K. The temperature dependent electrical and optical properties of the Au/C particle films, especially their high temperature stability relative to traditional gold blacks, make them potential candidates for applications in infrared optical systems.
Nucleotide Sequence of the Chromosomal
ampC
Gene of
Enterobacter aerogenes
Authors: Preston Karen E. , Radomski Christopher C. A. , Venezia Richard A. 
Published: July 2002

ABSTRACT

The AmpC β-lactamase gene and a small portion of the regulatory
ampR
sequence of
Enterobacter aerogenes
97B were cloned and sequenced. The β-lactamase had an isoelectric point of 8 and conferred cephalosporin and cephamycin resistance on the host. The sequence of the cloned gene is most closely related to those of the
ampC
genes of
E. cloacae
and
C. freundii
.
A Standardized Plaque Reduction Assay for Determination of Drug Susceptibilities of Cytomegalovirus Clinical Isolates
Authors: Landry Marie L. , Stanat Sylvia , Biron Karen , Brambilla Donald , Britt William , Jokela Janet , Chou Sunwen , Drew W. Lawrence , Erice Alejo , Gilliam Bruce , Lurain Nell , Manischewitz Jody , Miner Richard , Nokta Mostafa , Reichelderfer Patricia , Spector Stephen , Weinberg Adriana , Yen-Lieberman Belinda , Crumpacker Clyde ,   the AIDS Clinical Trials Group CMV Resistance Working Group
Published: July 2002

ABSTRACT
Twelve laboratories collaborated in formulating and testing a standardized plaque reduction assay for cytomegalovirus (CMV) cell-associated clinical isolates. Four characterized and plaque-purified CMV strains, as well as six coded clinical isolates obtained after antiviral therapy, were distributed and tested. Good agreement was obtained for four of the clinical isolates, but a broad distribution of results was obtained for two isolates. Analysis of these results indicates the problems associated with clinical isolates, including the large genetic variability and the highly cell-associated phenotype. This collaborative effort, by addressing these problems, represents a significant step toward the development of a standardized assay.
Effects of Atovaquone and Diospyrin-Based Drugs on the Cellular ATP of
Pneumocystis carinii
f. sp.
carinii
Authors: Cushion Melanie T. , Collins Margaret , Hazra Banasri , Kaneshiro Edna S. 
Published: July 2002

ABSTRACT

Atovaquone (also called Mepron, or 566C80) is a napthoquinone used for the treatment of infections caused by pathogens such as
Plasmodium
spp. and
Pneumocystis carinii
. The mechanism of action against the malarial parasite is the inhibition of dihydroorotate dehydrogenase (DHOD), a consequence of blocking electron transport by the drug. As an analog of ubiquinone (coenzyme Q [CoQ]), atovaquone irreversibly binds to the mitochondrial cytochrome
bc
1
complex; thus, electrons are not able to pass from dehydrogenase enzymes via CoQ to cytochrome
c
. Since DHOD is a critical enzyme in pyrimidine biosynthesis, and because the parasite cannot scavenge host pyrimidines, the drug is lethal to the organism. Oxygen consumption in
P. carinii
is inhibited by the drug; thus, electron transport has also been identified as the drug target in
P. carinii
. However, unlike
Plasmodium
DHOD,
P. carinii
DHOD is inhibited only at high atovaquone concentrations, suggesting that the organism may salvage host pyrimidines and that atovaquone exerts its primary effects on ATP biosynthesis. In the present study, the effect of atovaquone on ATP levels in
P. carinii
was measured directly from 1 to 6 h and then after 24, 48, and 72 h of exposure. The average 50% inhibitory concentration after 24 to 72 h of exposure was 1.5 μg/ml (4.2 μM). The kinetics of ATP depletion were in contrast to those of another family of naphthoquinone compounds, diospyrin and two of its derivatives. Whereas atovaquone reduced ATP levels within 1 h of exposure, the diospyrins required at least 48 h. After 72 h, the diospyrins were able to decrease ATP levels of
P. carinii
at nanomolar concentrations. These data indicate that although naphthoquinones inhibit the electron transport chain, the molecular targets in a given organism are likely to be distinct among members of this class of compounds.
SCH 56592, Amphotericin B, or Itraconazole Therapy of Experimental Murine Cerebral Phaeohyphomycosis Due to
Ramichloridium obovoideum
(“
Ramichloridium mackenziei
”)
Authors: Al-Abdely Hail M. , Najvar Laura , Bocanegra Rosie , Fothergill Annette , Loebenberg David , Rinaldi Michael G. , Graybill John R. 
Published: July 2002

ABSTRACT

Ramichloridium obovoideum
(“
Ramichloridium makenziei
”) is a rare cause of lethal cerebral phaeohyphomycosis. It has been, so far, geographically restricted to the Middle East. BALB/c mice were inoculated with two strains of
R. obovoideum
intracranially. Therapy with amphotericin B, itraconazole, or the investigational triazole SCH 56592 was conducted for 10 days. Half the mice were monitored for survival and half were killed for determination of the fungal load in brain tissue. Recipients of SCH 56592 had significantly prolonged survival and lower brain fungal burden, and this result was found for mice infected with both of the fungal strains tested. Itraconazole reduced the brain fungal load in mice infected with one strain but not the other, while amphotericin B had no effect on brain fungal concentrations. This study indicates a possible role of SCH 56592 in the treatment of the serious cerebral phaeohyphomycosis due to
R. obovoideum.
A Simple Screen for Murein Transglycosylase Inhibitors
Authors: Vollmer Waldemar , Höltje Joachim-Volker 
Published: July 2002

ABSTRACT
A simple assay for detection of compounds that bind to the active site in the transglycosylation domain of the essential bifunctional transglycosylase and transpeptidase penicillin-binding proteins (PBPs) is reported. The method is based on a competition with the specific transglycosylase inhibitor moenomycin. With moenomycin coupled to Affi-Gel beads, a simple filtration procedure allows the amount of labeled PBPs that bind to moenomycin beads in the presence of test substances to be determined. The PBPs can easily be labeled by the covalent binding of penicillin derivatives. Crude membrane extracts can be used as a source for the PBPs, and different kinds of labels for the penicillin-PBP complexes can be used. The assay can be adapted to high-throughput screens.
Comparison of High-Performance Liquid Chromatographic and Microbiological Methods for Determination of Voriconazole Levels in Plasma
Authors: Perea Sofia , Pennick Gennethel J. , Modak Asha , Fothergill Annette W. , Sutton Deanna A. , Sheehan Daniel J. , Rinaldi Michael G. 
Published: July 2002

ABSTRACTA new selective high-performance liquid chromatography (HPLC) method with UV detection for the determination of the investigational triazole voriconazole in human plasma by using acetonitrile precipitation followed by reverse-phase HPLC on a C18column was compared with a simple agar well diffusion bioassay method withCandida kefyrATCC 46764 as the assay organism. Pooled plasma was used to prepare standard and control samples for both methods. The results of analyses with spiked serum samples (run as unknowns) were concordant by the bioassay and HPLC methods, with expected values being obtained. HPLC demonstrated an improved precision (3.47 versus 12.12%) and accuracy (0.81 versus 1.28%) compared to those of the bioassay method. The range of linearity obtained by both methods (from 0.2 to 10 μg/ml for HPLC and from 0.25 to 20 μg/ml for the bioassay) includes the range of concentrations of voriconazole (from 1.2 to 4.7 μg/ml) which are considered clinically relevant. Although either methodology could be used for the monitoring of patient therapy, the smaller variability observed with HPLC compared to that observed with the bioassay favors the use of HPLC for pharmacokinetic studies.