bluuebunny/crossref_metadata_2025_split huggingface dataset:
Importance of secondary structural specificity determinants in protein folding: Insertion of a native β‐sheet sequence into an α‐helical coiled‐coil
Authors: Kwok Stanley C. , Mant Colin T. , Hodges Robert S. 
Published: July 2002

AbstractTo examine how a short secondary structural element derived from a native protein folds when in a different protein environment, we inserted an 11‐residue β‐sheet segment (cassette) from human immunoglobulin fold, Fab new, into an α‐helical coiled‐coil host protein (cassette holder). This de novo design protein model, the structural cassette mutagenesis (SCM) model, allows us to study protein folding principles involving both short‐ and long‐range interactions that affect secondary structure stability and conformation. In this study, we address whether the insertion of this β‐sheet cassette into the α‐helical coiled‐coil protein would result in conformational change nucleated by the long‐range tertiary stabilization of the coiled‐coil, therefore overriding the local propensity of the cassette to form β‐sheet, observed in its native immunoglobulin fold. The results showed that not only did the nucleating helices of the coiled‐coil on either end of the cassette fail to nucleate the β‐sheet cassette to fold with an α‐helical conformation, but also the entire chimeric protein became a random coil. We identified two determinants in this cassette that prevented coiled‐coil formation: (1) a tandem dipeptide NN motif at the N‐terminal of the β‐sheet cassette, and (2) the hydrophilic Ser residue, which would be buried in the hydrophobic core if the coiled‐coil structure were to fold. By amino acid substitution of these helix disruptive residues, that is, either the replacement of the NN motif with high helical propensity Ala residues or the substitution of Ser with Leu to enhance hydrophobicity, we were able to convert the random coil chimeric protein into a fully folded α‐helical coiled‐coil. We hypothesized that this NN motif is a “secondary structural specificity determinant” which is very selective for one type of secondary structure and may prevent neighboring residues from adopting an alternate protein fold. These sequences with secondary structural specificity determinants have very strong local propensity to fold into a specific secondary structure and may affect overall protein folding by acting as a folding initiation site.
Genomic‐scale comparison of sequence‐ and structure‐based methods of function prediction: Does structure provide additional insight?
Authors: Fetrow Jacquelyn S. , Siew Naomi , Di Gennaro Jeannine A. , Martinez‐Yamout Maria , Dyson H. Jane , Skolnick Jeffrey 
Published: July 2002

AbstractA function annotation method using the sequence‐to‐structure‐to‐function paradigm is applied to the identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method identifies 27 sequences as potential disulfide oxidoreductases. All previously known thioredoxins, glutaredoxins, and disulfide isomerases are correctly identified. Three of the 27 predictions are probable false‐positives. Three novel predictions, which subsequently have been experimentally validated, are presented. Two additional novel predictions suggest a disulfide oxidoreductase regulatory mechanism for two subunits (OST3 and OST6) of the yeast oligosaccharyltransferase complex. Based on homology, this prediction can be extended to a potential tumor suppressor gene, N33, in humans, whose biochemical function was not previously known. Attempts to obtain a folded, active N33 construct to test the prediction were unsuccessful. The results show that structure prediction coupled with biochemically relevant structural motifs is a powerful method for the function annotation of genome sequences and can provide more detailed, robust predictions than function prediction methods that rely on sequence comparison alone.
Residual Stress Measurement in a Ceramic-Metallic Graded Material
Authors: Hill Michael R. , Lin Wei-Yan 
Published: July 2002

Abstract
This paper presents experimental measurements of the through-thickness distribution of residual stress in a ceramic-metallic functionally graded material (FGM). It further presents an error analysis and optimization of the residual stress measurement technique. Measurements are made in a seven-layered plate with a base of commercially pure titanium and successive layers containing an increasing proportion of titanium-boride, reaching 85% titanium-boride in the final layer. The compliance method is employed to determine residual stress, where a slot is introduced using wire electric-discharge machining and strain release is measured as a function of increasing slot depth. Strain release measurements are used with a back-calculation scheme, based on finite element simulation, to provide residual stresses in the FGM. The analysis is complicated by the variation of material properties in the FGM, but tractable due to the flexibility of the finite element method. The Monte Carlo approach is used for error analysis and a method is described for optimization of the functional form assumed for the residual stresses. The magnitude and variation of the resulting residual stress distributions and several aspects of the error analyses are discussed.
Dynamic Response Predictions for a Mistuned Industrial Turbomachinery
Rotor Using Reduced-Order Modeling
Authors: Bladh R. , Pierre C. , Castanier M. P. , Kruse M. J. 
Published: July 2002

Abstract
This paper explores the effects of random blade mistuning on the dynamics of an advanced industrial compressor rotor, using a component-mode-based reduced-order model formulation for tuned and mistuned bladed disks. The technique uses modal data obtained from finite element models to create computationally inexpensive models of mistuned bladed disks in a systematic manner. Both free and forced responses of the rotor are considered, and the obtained results are compared with “benchmark” finite element solutions. A brief statistical study is presented, in which Weibull distributions are shown to yield reliable estimates of forced response statistics. Moreover, a simple method is presented for computing natural frequencies of noninteger harmonics, using conventional cyclic symmetry finite element analysis. This procedure enables quantification of frequency veering data relevant to the assessment of mistuning sensitivity (e.g., veering curvatures), and it may provide a tool for quantifying structural interblade coupling in finite element rotor models of arbitrary complexity and size. The mistuned forced response amplitudes and stresses are found to vary considerably with mistuning strength and the degree of structural coupling between the blades. In general, this work demonstrates how reduced order modeling and Weibull estimates of the forced response statistics combine to facilitate thorough investigations of the mistuning sensitivity of industrial turbomachinery rotors.
Long-wavelength infrared detectors based on strained InAs–Ga1−xInxSb type-II superlattices
Authors: Mailhiot C. , Smith D. L. 
Published: July 2002

We demonstrate that infrared detectors made from strained type-II superlattices consisting of III–V semiconductors can have favorable properties for long-wavelength (λc &gt;10 μm) detection applications. We specifically consider InAs–Ga1−x Inx Sb strained-layer superlattices with x≊0.4 . This is a type-II superlattice where the conduction-band minimum of InAs is lower in energy than the valence-band maximum of Ga1−x Inx Sb. Electrons are localized in the InAs layers while holes are localized in the Ga1−x Inx Sb layers. Generally, in a type-II superlattice such as InAs–GaSb, large absorption coefficients cannot be achieved at the small values of band gap necessary for long-wavelength detection because the localization of electrons and holes in adjacent layers leads to small optical matrix elements. Therefore, small band gaps and large optical matrix elements appear to be two mutually exclusive requirements in the InAs–GaSb superlattice. Here, we show that it is possible to obtain large optical absorption coefficients at the values of band gap required for long-wavelength detection by taking advantage of internal lattice-mismatch induced strains present in InAs–Ga1−x Inx Sb superlattices.
This feature eliminates the principal difficulty associated with type-II superlattices as candidate materials for long-wavelength detection applications. In fact, the near-threshold optical absorption coefficient of the InAs–Ga0.6 In0.4 Sb strained-layer superlattice is found to be as large as that of conventional Hg1−x Cdx Te alloys in the λc ≊ 10–12 μm region. Moreover, the electron effective mass of the InAs–Ga0.6 In0.4 Sb strained-layer superlattice is found to be nearly isotropic and much larger (m*super/m ≊0.05 at λc ≊10 μm) than that of the Hg1−x Cdx Te alloy. This value of the electron effective mass is a favorable feature of the InAs–Ga0.6 In0.4 Sb strained-layer superlattice since it is large enough to lead to small diode tunneling currents, yet it is small enough to lead to large mobilities and diffusivities. As a result, leakage currents are expected to be much less of a problem in infrared detector diodes based on InAs–Ga0.6 In0.4 Sb strained-layer superlattices than they are in conventional Hg1−x Cdx Te-based infrared detectors. Overall, InAs–Ga1−x Inx Sb strained-layer superlattices are expected to have superior materials properties for long-wavelength detection than the Hg1−x Cdx Te alloy.
Clinical Correlates of Antifungal Macrodilution Susceptibility Test Results for Non-AIDS Patients with Severe
Candida
Infections Treated with Fluconazole
Authors: Lee Sai-Cheong , Fung Chang-Phone , Huang Jen-Seng , Tsai Chi-Jen , Chen Kuo-Su , Chen Huang-Yang , Lee Ning , See Lai-Chu , Shieh Wen-Ben 
Published: July 2002

ABSTRACT

Although the clinical correlates of the reference antifungal susceptibility test results in hematogenous and deep-seated
Candida
infection are still controversial, we evaluated the clinical correlates of this test in deep-seated
Candida
infections in non-AIDS patients. Thirty-two non-AIDS patients with hematogenous or deep-seated
Candida
infections were treated with intravenous fluconazole (400 mg a day), and the clinical outcomes were evaluated. Coexisting bacterial infections were treated with appropriate antibiotics, superinfection or reinfection was excluded, inadequate fluconazole therapy was avoided, and essential surgical intervention was performed. The MICs of fluconazole for these 32
Candida
isolates were determined according to the M27-A procedure approved by the National Committee on Clinical Laboratory Standards. MICs were interpreted as susceptible (≤8 μg/ml), dose-dependent susceptible (16 to 32 μg/ml), and resistant (≥64 μg/ml) according to the criteria of the M27-A standard. The success rates were 79% (19 of 24; 95% confidence interval [CI], 59 to 93%) in the susceptible category, 66% (4 of 6; 95% CI, 19 to 95%) in the dose-dependent susceptible category, and 0% (0 of 2; 95% CI, 0 to 84%) in the resistant category. We conclude that the clinical correlation of the reference antifungal susceptibility test results is high in hematogenous and deep-seated
Candida
infections.
Engineering the Specificity of Antibacterial Fluoroquinolones: Benzenesulfonamide Modifications at C-7 of Ciprofloxacin Change Its Primary Target in
Streptococcus pneumoniae
from Topoisomerase IV to Gyrase
Authors: Alovero Fabiana L. , Pan Xiao-Su , Morris Julia E. , Manzo Ruben H. , Fisher L. Mark 
Published: July 2002

ABSTRACT

We have examined the antipneumococcal mechanisms of a series of novel fluoroquinolones that are identical to ciprofloxacin except for the addition of a benzenesulfonylamido group to the C-7 piperazinyl ring. A number of these derivatives displayed enhanced activity against
Streptococcus pneumoniae
strain 7785, including compound NSFQ-105, bearing a 4-(4-aminophenylsulfonyl)-1-piperazinyl group at C-7, which exhibited an MIC of 0.06 to 0.125 μg/ml compared with a ciprofloxacin MIC of 1 μg/ml. Several complementary approaches established that unlike the case for ciprofloxacin (which targets topoisomerase IV), the increased potency of NSFQ-105 was associated with a target preference for gyrase: (i)
parC
mutants of strain 7785 that were resistant to ciprofloxacin remained susceptible to NSFQ-105, whereas by contrast, mutants bearing a quinolone resistance mutation in
gyrA
were four- to eightfold more resistant to NSFQ-105 (MIC of 0.5 μg/ml) but susceptible to ciprofloxacin; (ii) NSFQ-105 selected first-step
gyrA
mutants (MICs of 0.5 μg/ml) encoding Ser-81-to-Phe or -Tyr mutations, whereas ciprofloxacin selects
parC
mutants; and (iii) NSFQ-105 was at least eightfold more effective than ciprofloxacin at inhibiting DNA supercoiling by
S. pneumoniae
gyrase in vitro but was fourfold less active against topoisomerase IV. These data show unequivocally that the C-7 substituent determines not only the potency but also the target preference of fluoroquinolones. The importance of the C-7 substituent in drug-enzyme contacts demonstrated here supports one key postulate of the Shen model of quinolone action.
The Macrolide-Lincosamide-Streptogramin B Resistance Determinant from
Clostridium difficile
630 Contains Two
erm
(B) Genes
Authors: Farrow Kylie A. , Lyras Dena , Rood Julian I. 
Published: July 2002

ABSTRACT

The ErmB macrolide-lincosamide-streptogramin B (MLS) resistance determinant from
Clostridium difficile
630 contains two copies of an
erm
(B) gene, separated by a 1.34-kb direct repeat also found in an Erm(B) determinant from
Clostridium perfringens
. In addition, both
erm
(B) genes are flanked by variants of the direct repeat sequence. This genetic arrangement is novel for an ErmB MLS resistance determinant.
In Vitro Activity of ABT-773, a New Ketolide, against Recent Clinical Isolates of
Streptococcus pneumoniae
,
Haemophilus influenzae
, and
Moraxella catarrhalis
Authors: Brueggemann Angela B. , Doern Gary V. , Huynh Holly K. , Wingert Elizabeth M. , Rhomberg Paul R. 
Published: July 2002

ABSTRACT

The in vitro activity of ABT-773 was evaluated against
Streptococcus pneumoniae
,
Haemophilus influenzae
, and
Moraxella catarrhalis
isolates. ABT-773 was the most active antimicrobial tested against
S. pneumoniae
. ABT-773 and azithromycin were equivalent in activity against
H. influenzae
and
M. catarrhalis
and more active than either clarithromycin or erythromycin.
Carrier-Mediated Delivery of 9-(2-Phosphonylmethoxyethyl)Adenine to Parenchymal Liver Cells: a Novel Therapeutic Approach for Hepatitis B
Authors: de Vrueh Remco L. A. , Rump Erik T. , van de Bilt Erika , van Veghel Richard , Balzarini Jan , Biessen Erik A. L. , van Berkel Theo J. C. , Bijsterbosch Martin K. 
Published: July 2002

ABSTRACT

Our aim is to selectively deliver 9-(2-phosphonylmethoxyethyl)adenine (PMEA) to parenchymal liver cells, the primary site of hepatitis B virus (HBV) infection. Selective delivery is necessary because PMEA, which is effective against HBV in vitro, is hardly taken up by the liver in vivo. Lactosylated reconstituted high-density lipoprotein (LacNeoHDL), a lipid particle that is specifically internalized by parenchymal liver cells via the asialoglycoprotein receptor, was used as the carrier. PMEA could be incorporated into the lipid moiety of LacNeoHDL by attaching, via an acid-labile bond, lithocholic acid-3α-oleate to the drug. The uptake of the lipophilic prodrug (PMEA-LO) by the liver was substantially increased after incorporation into LacNeoHDL. Thirty minutes after injection of [
3
H]PMEA-LO-loaded LacNeoHDL into rats, the liver contained 68.9% ± 7.7% of the dose (free [
3
H]PMEA, <5%). Concomitantly, the uptake by the kidney was reduced to <2% of the dose (free [
3
H]PMEA, >45%). The hepatic uptake of PMEA-LO-loaded LacNeoHDL occurred mainly by parenchymal cells (88.5% ± 8.2% of the hepatic uptake). Moreover, asialofetuin inhibited the liver association by >75%, indicating uptake via the asialoglycoprotein receptor. The acid-labile linkage in PMEA-LO, designed to release PMEA during lysosomal processing of the prodrug-loaded carrier, was stable at physiological pH but was hydrolyzed at lysosomal pH (half-life, 60 to 70 min). Finally, subcellular fractionation indicates that the released PMEA is translocated to the cytosol, where it is converted into its active diphosphorylated metabolite. In conclusion, lipophilic modification and incorporation of PMEA into LacNeoHDL improves the biological fate of the drug and may lead to an enhanced therapeutic efficacy against chronic hepatitis B.
In Vivo Pharmacodynamic Activities of Two Glycylcyclines (GAR-936 and WAY 152,288) against Various Gram-Positive and Gram-Negative Bacteria
Authors: van Ogtrop M. L. , Andes D. , Stamstad T. J. , Conklin B. , Weiss W. J. , Craig W. A. , Vesga O. 
Published: July 2002

ABSTRACT

The in vivo pharmacodynamic activities of two glycylcyclines (GAR-936 and WAY 152,288) were assessed in an experimental murine thigh infection model in neutropenic mice. Mice were infected with one of several strains of
Streptococcus pneumoniae
,
Staphylococcus aureus
,
Escherichia coli
, or
Klebsiella pneumoniae
. Most infections were treated with a twice-daily dosing schedule, with administration of 0.75 to 192 mg of GAR-936 or WAY 152,288 per kg of body weight. A maximum-effect dose-response model was used to calculate the dose that produced a net bacteriostatic effect over 24 h of therapy. This dose was called the bacteriostatic dose. More extensive dosing studies were performed with
S. pneumoniae
1199,
E. coli
ATCC 25922, and
K. pneumoniae
ATCC 43816, with doses being given as one, two, four, or eight equal doses over a period of 24 h. The dosing schedules were designed in order to minimize the interrelationship between the various pharmacokinetic and pharmacodynamic parameters studied. These parameters were time above 0.03 to 32 times the MIC, area under the concentration-time curve (AUC), and maximum concentration of drug in serum (
C
max
). The bacteriostatic dose remained essentially the same, irrespective of the dosing frequency, for
S. pneumoniae
1199 (0.3 to 0.9 mg/kg/day). For
E. coli
ATCC 25922 and
K. pneumoniae
ATCC 43816, however, more frequent dosing led to lower bacteriostatic doses. Pharmacokinetic studies demonstrated dose-dependent elimination half-lives of 1.05 to 2.34 and 1.65 to 3.36 h and serum protein bindings of 59 and 71% for GAR-936 and WAY 152,288, respectively. GAR-936 and WAY 152,288 were similarly effective against the microorganisms studied, with small differences in maximum effect and 50% effective dose. The glycylcyclines were also similarly effective against tetracycline-sensitive and tetracycline-resistant bacteria. Time above a certain factor (range, 0.5 to 4 times) of the MIC was a better predictor of in vivo efficacy than
C
max
or AUC for most organism-drug combinations. The results demonstrate that in order to achieve 80% maximum efficacy, the concentration of unbound drug in serum should be maintained above the MIC for at least 50% of the time for GAR-936 and for at least 75% of the time for WAY 152,288. The results of these experiments will aid in the rational design of dose-finding studies for these glycylcyclines in humans.
Effect of Azithromycin plus Rifampin versus Amoxicillin Alone on Eradication and Inflammation in the Chronic Course of
Chlamydia pneumoniae
Pneumonitis in Mice
Authors: Bin Xie Xiao , Wolf Katerina , Schaffner Thomas , Malinverni Raffaele 
Published: July 2002

ABSTRACT

The effects of treatment with azithromycin plus rifampin (A+R), amoxicillin (A), or placebo (P) on the chronic course of experimental
Chlamydia pneumoniae
pneumonitis in mice were assessed by culture, PCR, and immunocytochemistry as well as by degree of inflammation in lung tissue. Eradication of the pathogen was significantly more frequent and inflammation in tissue was significantly reduced after treatment with A+R compared to after treatment with A or P. Combination therapy with azithromycin plus rifampin showed favorable effects in the chronic course of
C. pneumoniae
pneumonitis.
BMS-284756 in Experimental Cephalosporin-Resistant Pneumococcal Meningitis
Authors: Rodriguez-Cerrato Violeta , Ghaffar Faryal , Saavedra Jesus , Michelow Ian C. , Hardy Robert D. , Iglehart Janie , Olsen Kurt , McCracken George H. 
Published: July 2002

ABSTRACT

BMS-284756 is a novel des-fluoro(6) quinolone with a broad antimicrobial activity, including
Streptococcus pneumoniae
. The purpose of this study was to evaluate the pharmacodynamic profile and effectiveness of BMS-284756 for therapy of experimental meningitis caused by penicillin- and cephalosporin-resistant
S. pneumoniae
(CRSP). Meningitis was induced in rabbits by intracisternal inoculation of CRSP. BMS-284756 was given intravenously 16 h after intracisternal inoculation in single doses of 2.5 (
n
= 5 animals), 5 (
n
= 6), 10 (
n
= 6), 20 (
n
= 8), and 30 mg/kg (
n
= 6), in two doses of 10 mg/kg each separated by 5 h (
n
= 4), and as a 20-mg/kg dose followed 5 h later by 10 mg/kg (
n
= 5). The MICs and MBCs of BMS-284756, ceftriaxone, and vancomycin were 0.06 and 0.06, 4 and 4, and 0.25 and 0.25 μg/ml, respectively. After single doses of 10, 20, and 30 mg/kg, the maximum concentrations in cerebrospinal fluid (CSF) (mean ± standard deviation) were 0.32 ± 0.12, 0.81 ± 0.38, and 1.08 ± 0.43 μg/ml, respectively; the elimination half-life in CSF was 4.5 to 6.3 h. The CSF bacterial killing rates (BKR) at 5 h of the single-dose regimens of 10, 20 and 30 mg/kg were −0.84 ± 0.48, −1.09 ± 0.32, and −1.35 ± 0.05 Δlog
10
CFU/ml/h. The BKR
0–5
of the divided regimens (10 mg/kg twice and 20 mg/kg followed by 10 mg/kg) was −0.82 ± 0.52 and −1.24 ± 0.34 Δlog
10
CFU/ml/h, respectively. The BKR
0–5
of the combined therapy with vancomycin and ceftriaxone was −1.09 ± 0.39 Δlog
10
CFU/ml/h. The penetration of BMS-284756 into purulent CSF relative to plasma was 14 to 25%. The bactericidal effect of BMS-284756 in CSF was concentration dependent. BMS-284756 at 30 mg/kg as a single or divided dose was as effective as standard therapy with vancomycin and ceftriaxone.
Analysis of Antimalarial Synergy between Bestatin and Endoprotease Inhibitors Using Statistical Response-Surface Modelling
Authors: Gavigan Clare S. , Machado Stella G. , Dalton John P. , Bell Angus 
Published: July 2002

ABSTRACT

The pathway of hemoglobin degradation by erythrocytic stages of the human malarial parasite
Plasmodium falciparum
involves initial cleavages of globin chains, catalyzed by several endoproteases, followed by liberation of amino acids from the resulting peptides, probably by aminopeptidases. This pathway is considered a promising chemotherapeutic target, especially in view of the antimalarial synergy observed between inhibitors of aspartyl and cysteine endoproteases. We have applied response-surface modelling to assess antimalarial interactions between endoprotease and aminopeptidase inhibitors using cultured
P. falciparum
parasites. The synergies observed were consistent with a combined role of endoproteases and aminopeptidases in hemoglobin catabolism in this organism. As synergies between antimicrobial agents are often inferred without proper statistical analysis, the model used may be widely applied in studies of antimicrobial drug interactions.
Synergistic Activities of Gatifloxacin in Combination with Other Antimicrobial Agents against
Pseudomonas aeruginosa
and Related Species
Authors: Gradelski Elizabeth , Valera Lourdes , Bonner Daniel , Fung-Tomc Joan 
Published: July 2002

ABSTRACT

Drug combinations have been used to treat serious infections caused by
Pseudomonas, Burkholderia, Stenotrophomonas
, and
Acinetobacter
. In this study, the combined drug effects of gatifloxacin (GAT) and nonquinolones were determined by time-kill analysis at clinically achievable drug concentrations. Synergy (≥2 log
10
-enhanced killing at 24 h) was observed with GAT plus amikacin or a β-lactam against 50 to 75% of strains, including strains nonsusceptible to one or both drugs.