bluuebunny/crossref_metadata_2025_split huggingface dataset:
MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison
Authors: Ortiz Angel R. , Strauss Charlie E.M. , Olmea Osvaldo 
Published: October 2002

AbstractAdvances in structural genomics and protein structure prediction require the design of automatic, fast, objective, and well benchmarked methods capable of comparing and assessing the similarity of low‐resolution three‐dimensional structures, via experimental or theoretical approaches. Here, a new method for sequence‐independent structural alignment is presented that allows comparison of an experimental protein structure with an arbitrary low‐resolution protein tertiary model. The heuristic algorithm is given and then used to show that it can describe random structural alignments of proteins with different folds with good accuracy by an extreme value distribution. From this observation, a structural similarity score between two proteins or two different conformations of the same protein is derived from the likelihood of obtaining a given structural alignment by chance. The performance of the derived score is then compared with well established, consensus manual‐based scores and data sets. We found that the new approach correlates better than other tools with the gold standard provided by a human evaluator. Timings indicate that the algorithm is fast enough for routine use with large databases of protein models. Overall, our results indicate that the new program (MAMMOTH) will be a good tool for protein structure comparisons in structural genomics applications. MAMMOTH is available from our web site at http://physbio.mssm.edu/∼ortizg/.
A statistically derived parameterization for the collagen triple‐helix
Authors: Rainey Jan K. , Goh M. Cynthia 
Published: October 2002

AbstractThe triple‐helix is a unique secondary structural motif found primarily within the collagens. In collagen, it is a homo‐ or hetero‐tripeptide with a repeating primary sequence of (Gly‐X‐Y)n, displaying characteristic peptide backbone dihedral angles. Studies of bulk collagen fibrils indicate that the triple‐helix must be a highly repetitive secondary structure, with very specific constraints. Primary sequence analysis shows that most collagen molecules are primarily triple‐helical; however, no high‐resolution structure of any entire protein is yet available. Given the drastic morphological differences in self‐assembled collagen structures with subtle changes in assembly conditions, a detailed knowledge of the relative locations of charged and sterically bulky residues in collagen is desirable. Its repetitive primary sequence and highly conserved secondary structure make collagen, and the triple‐helix in general, an ideal candidate for a general parameterization for prediction of residue locations and for the use of a helical wheel in the prediction of residue orientation. Herein, a statistical analysis of the currently available high‐resolution X‐ray crystal structures of model triple‐helical peptides is performed to produce an experimentally based parameter set for predicting peptide backbone and Cβ atom locations for the triple‐helix. Unlike existing homology models, this allows easy prediction of an entire triple‐helix structure based on all existing high‐resolution triple‐helix structures, rather than only on a single structure or on idealized parameters. Furthermore, regional differences based on the helical propensity of residues may be readily incorporated. The parameter set is validated in terms of the predicted bond lengths, backbone dihedral angles, and interchain hydrogen bonding.
Prediction of the disulfide‐bonding state of cysteines in proteins at 88% accuracy
Authors: Martelli Pier Luigi , Fariselli Piero , Malaguti Luca , Casadio Rita 
Published: October 2002

AbstractThe task of predicting the cysteine‐bonding state in proteins starting from the residue chain is addressed by implementing a new hybrid system that combines a neural network and a hidden Markov model (hidden neural network). Training is performed using 4136 cysteine‐containing segments extracted from 969 nonhomologous proteins of well‐resolved three‐dimensional structure. After a 20‐fold cross‐validation procedure, the efficiency of the prediction scores as high as 88% and 84%, when measured on cysteine and protein basis, respectively. These results outperform previously described methods for the same task.
Structural‐based mutational analysis of d‐aminoacylase from Alcaligenes faecalis DA1
Authors: Hsu Cheng‐Sheng , Lai Wen‐Lin , Chang Wei‐Wei , Liaw Shwu‐Huey , Tsai Ying‐Chieh 
Published: October 2002

Abstractd‐Aminoacylase is an attractive candidate for commercial production of d‐amino acids through its catalysis in the zinc‐assistant hydrolysis of N‐acyl‐d‐amino acids. We report here the cloning, expression, and structural‐based mutation of the d‐aminoacylase from Alcaligenes faecalis DA1. A 1,007‐bp PCR product amplified with degenerate primers, was used to isolate a 4‐kb genomic fragment, encoding a 484‐residue d‐aminoacylase. The enzyme amino‐terminal segment shared significant homology within a variety of enzymes including urease. The structural fold was predicted by 3D‐PSSM to be similar to urease and dihydroorotase, which have grouped into a novel α/β‐barrel amidohydrolase superfamily with a virtually indistinguishable binuclear metal centers containing six ligands, four histidines, one aspartate, and one carboxylated lysine. Three histidines, His‐67, His‐69, and His‐250, putative metal ligands in d‐aminoacylase, have been mutated previously, the remaining histidine (His‐220) and aspartate (Asp‐366) Asp‐65, and four cysteines were then characterized. Substitution of Asp‐65, Cys‐96, His‐220, and Asp‐366 with alanine abolished the enzyme activity. The H220A mutant bound approximately half the normal complement of zinc ion as did H250N. However, the C96A mutant showed little zinc‐binding ability, revealing that Cys‐96 may replace the carboxylated lysine to serve as a bridging ligand. According to the urease structure, the conserved amino‐terminal segment including Asp‐65 may be responsible for structural stabilization.
13C CP/MAS NMR study on structural heterogeneity in Bombyx mori silk fiber and their generation by stretching
Authors: Asakura Tetsuo , Yao Juming 
Published: October 2002

AbstractIt is important to resolve the structure of Bombyx mori silk fibroin before spinning (silk I) and after spinning (silk II), and the mechanism of the structural transition during fiber formation in developing new silk‐like fiber. The silk I structure has been recently resolved by 13C solid‐state NMR as a “repeated β‐turn type II structure.” Here, we used 13C solid‐state NMR to clarify the heterogeneous structure of the natural fiber from Bombyx mori silk fibroin in the silk II form. Interestingly, the 13C CP/MAS NMR revealed a broad and asymmetric peak for the Ala Cβ carbon. The relative proportions of the various heterogeneous components were determined from their relative peak intensities after line shape deconvolution. Namely, for 56% crystalline fraction (mainly repeated Ala‐Gly‐Ser‐Gly‐Ala‐Gly sequences), 18% distorted β‐turn, 13% β‐sheet (parallel Ala residues), and 25% β‐sheet (alternating Ala residues). The remaining fraction of 44% amorphous Tyr‐rich region, 22% in both distorted β‐turn and distorted β‐sheet. Such a heterogeneous structure including distorted β‐turn can be observed for the peptides (AG)n (n > 9 ). The structural change from silk I to silk II occurs exclusively for the sequence (Ala‐Gly‐Ser‐Gly‐Ala‐Gly)n in B. mori silk fibroin. The generation of the heterogeneous structure can be studied by change in the Ala Cβ peak of 13C CP/MAS NMR spectra of the silk fibroin samples with different stretching ratios.
Intestinal Nematode Infection Ameliorates Experimental Colitis in Mice
Authors: Khan W. I. , Blennerhasset P. A. , Varghese A. K. , Chowdhury S. K. , Omsted P. , Deng Y. , Collins S. M. 
Published: October 2002

ABSTRACTEpidemiological studies suggest that inflammatory bowel disease (IBD) is common in developed countries and rare in countries where intestinal nematode infections are common. T cells are critical in many immune responses, including those associated with IBD and nematode infection. Among the distinct T helper (Th) cell subsets, Th1-type immune response is predominantly associated with Crohn's disease, while many nematode infections generate a strong Th2 response. The reciprocal cross regulation between Th1 and Th2 cells suggests that generation of a Th2 response by nematodes could prevent or reduce the effects of Th1-mediated diseases. In the present study, we investigated the effect of polarizing the immune response toward the Th2 type, using intestinal nematode infection, on subsequent experimental colitis. Mice were infected with the intestinal nematodeTrichinella spiralisand allowed to recover before colitis was induced with dinitrobenzene sulfonic acid. The mice were sacrificed postcolitis to assess colonic damage macroscopically, histologically, and by myeloperoxidase (MPO) activity and Th cytokines. Prior nematode infection reduced the severity of colitis both macroscopically and histologically together with a decreased mortality and was correlated with a down-regulation of MPO activity, Th1-type cytokine expression in colonic tissue, and emergence of a Th2-type immune response. These results indicate a protective role of nematode infection in Th1 cell-driven inflammation and prompt consideration of a novel therapeutic strategy in IBD based on immunological distraction.
Characterization of the
Pasteurella multocida hgbA
Gene Encoding a Hemoglobin-Binding Protein
Authors: Bosch Montserrat , Garrido M. Elena , Llagostera Montserrat , Pérez de Rozas Ana M. , Badiola Ignacio , Barbé Jordi 
Published: October 2002

ABSTRACT

Reverse transcriptase PCR analyses have demonstrated that open reading frames (ORFs) PM0298, PM0299, and PM0300 of the animal pathogen
Pasteurella multocida
constitute a single transcriptional unit. By cloning and overexpression studies in
Escherichia coli
cells, the product of ORF PM0300 was shown to bind hemoglobin in vitro; this ORF was therefore designated
hgbA.
In vitro and in vivo quantitative assays demonstrated that the
P. multocida hgbA
mutant bound hemoglobin to the same extent as the wild-type strain, although the adsorption kinetics was slightly slower for the
hgbA
cells. In agreement with this, the virulence of
P. multocida hgbA
cells was not affected, suggesting that other functional hemoglobin receptor proteins must be present in this organism. On the other hand,
P. multocida
mutants defective in PM0298 and PM0299 could be isolated only when a plasmid containing an intact copy of the gene was present in the cells, suggesting that these genes are essential for the viability of this bacterial pathogen. By adapting the recombinase-based expression technology in vivo to
P. multocida
, we also demonstrated that the transcriptional PM0298-PM0299-
hgbA
unit is iron regulated and that its expression is triggered in the first 2 h following infection in a mouse model. Furthermore, hybridization experiments showed that the
hgbA
gene is widespread in
P. multocida
strains regardless of their serotype or the animal from which they were isolated.
Nitric Oxide Limits the Expansion of Antigen-Specific T Cells in Mice Infected with the Microfilariae ofBrugia pahangi
Authors: O'Connor Richard A. , Devaney Eileen 
Published: October 2002

ABSTRACTInfection of BALB/c mice with the microfilariae (Mf) of the filarial nematodeBrugia pahangiresults in an antigen-specific proliferative defect that is induced by high levels of NO. Using carboxyfluorescein diacetate succinimydl ester and cell surface labeling, it was possible to identify a population of antigen-specific T cells from Mf-infected BALB/c mice that expressed particularly high levels of CD4 (CD4hi). These cells proliferated in culture only when inducible NO synthase was inhibited and accounted for almost all of the antigen-specific proliferative response under those conditions. CD4hicells also expressed high levels of CD44, consistent with their status as activated T cells. A similar population of CD4hicells was observed in cultures from Mf-infected gamma interferon receptor knockout (IFN-γR−/−) mice. Terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling staining revealed that the CD4+T cells from Mf-infected wild-type mice were preferentially susceptible to apoptosis compared to CD4+T cells from IFN-γR−/−mice. These studies suggest that the expansion of antigen-specific T cells in Mf-infected mice is limited by NO.
Acquisition of Mn(II) in Addition to Fe(II) Is Required for Full Virulence of
Salmonella enterica
Serovar Typhimurium
Authors: Boyer E. , Bergevin I. , Malo D. , Gros P. , Cellier M. F. M. 
Published: October 2002

ABSTRACT

The roles of the genes
feoB
(ABC ferrous iron transporter),
mntH
(proton-dependent manganese transporter), and
sitABCD
(putative ABC iron and/or manganese transporter) in
Salmonella
pathogenicity were investigated by using mutant strains deficient in one, two, or three transporters. Our results indicated that
sitABCD
encodes an important transporter of Mn(II) and Fe(II) which is required for full virulence in susceptible animals (
Nramp1
−/−
) and for replication inside
Nramp1
−/−
macrophages in vitro. The
mntH sitABCD
double mutant (mutant MS) showed minimal Mn(II) uptake and increased sensitivity to H
2
O
2
and to the divalent metal chelator 2,2′-dipyridyl (DP) and was defective for replication in macrophages. In vivo MS appeared to be as virulent as the
sitABCD
mutant in
Nramp1
−/−
animals. The ferrous iron transporter Feo was required for full virulence in 129/Sv
Nramp1
−/−
mice, and infection with multiple mutants lacking FeoB was not fatal. The
sitABCD feoB
mutant (mutant SF) and the
mntH sitABCD feoB
mutant (mutant MSF) showed minimal Fe(II) uptake and were slightly impaired for replication in susceptible macrophages. MSF showed reduced growth in minimal medium deficient in divalent cations. The role of the
mntH
gene, which is homologous to mammalian
Nramp
genes, was also investigated after overexpression in the double mutant MS. MntH preferred Mn(II) over Fe(II) and could suppress MS sensitivity to H
2
O
2
and to DP, and it also improved the intracellular survival in
Nramp1
−/−
macrophages. This study indicates that acquisition of Mn(II), in addition to Fe(II), is required for intracellular survival and replication of
Salmonella enterica
serovar Typhimurium in macrophages in vitro and for virulence in vivo.
The Transcriptional Regulator AlgR Is Essential for
Pseudomonas aeruginosa
Pathogenesis
Authors: Lizewski Stephen E. , Lundberg Derek S. , Schurr Michael J. 
Published: October 2002

ABSTRACT

Chronic
Pseudomonas aeruginosa
lung infection is the major cause of morbidity and mortality in cystic fibrosis (CF) patients. One
P. aeruginosa
virulence factor unique to CF isolates is overproduction of alginate, phenotypically termed mucoidy. Mucoidy is the result of increased transcription from the
algD
gene and is activated by the transcriptional regulator AlgR. Mutations in
algR
result in a nonmucoid phenotype and loss of twitching motility. Additionally, AlgR controls transcription of
algC
, encoding a dual-function enzyme necessary for both lipopolysaccharide (LPS) and alginate production. Therefore, to determine the effect of
algR
on
P. aeruginosa
virulence, an
algR
mutant was examined for sensitivity to reactive oxygen intermediates, killing by phagocytes, systemic virulence, and the ability to maintain a murine lung infection. We found that
P. aeruginosa
PAO700 (
algR
::Gm
r
) was less lethal than PAO1, as tested in an acute septicemia infection mouse model, and was cleared more efficiently in a mouse pneumonia model. Additionally, the
algR
mutant (PAO700) was more sensitive to hypochlorite. However, PAO700 was more resistant to hydrogen peroxide and killed less readily in an acellular myeloperoxidase assay than PAO1. There was little difference in killing between PAO1 and PAO700 with macrophage-like J774 cells and human polymorhonuclear leukocytes. Two-dimensional gel analysis of
P. aeruginosa algR
mutant and wild-type protein extracts revealed 47 differentially regulated proteins, suggesting that AlgR plays both a positive role and a negative role in gene expression. Together, these results imply that AlgR is necessary for virulence and regulates genes in addition to the genes associated with alginate and LPS production and pilus function.
Characterization of the Gene Encoding the Major Secreted Lysophospholipase A of
Legionella pneumophila
and Its Role in Detoxification of Lysophosphatidylcholine
Authors: Flieger Antje , Neumeister Birgid , Cianciotto Nicholas P. 
Published: October 2002

ABSTRACT

We previously showed that
Legionella pneumophila
secretes, via its type II secretion system, phospholipase A activities that are distinguished by their specificity for certain phospholipids. In this study, we identified and characterized
plaA
, a gene encoding a phospholipase A that cleaves fatty acids from lysophospholipids. The
plaA
gene encoded a 309-amino-acid protein (PlaA) which had homology to a group of lipolytic enzymes containing the catalytic signature GDSL. In
Escherichia coli
, the cloned gene conferred trypsin-resistant hydrolysis of lysophosphatidylcholine and lysophosphatidylglycerol. An
L. pneumophila plaA
mutant was generated by allelic exchange. Although the mutant grew normally in standard buffered yeast extract broth, its culture supernatants lost greater than 80% of their ability to release fatty acids from lysophosphatidylcholine and lysophosphatidylglycerol, implying that PlaA is the major secreted lysophospholipase A of
L. pneumophila
. The mutant's reduced lipolytic activity was confirmed by growth on egg yolk agar and thin layer chromatography and was complemented by reintroduction of an intact copy of
plaA
. Overexpression of
plaA
completely protected
L. pneumophila
from the toxic effects of lysophosphatidylcholine, suggesting a role for PlaA in bacterial detoxification of lysophospholipids. The
plaA
mutant grew like the wild type in U937 cell macrophages and
Hartmannella vermiformis
amoebae, indicating that PlaA is not essential for intracellular infection of
L. pneumophila
. In the course of characterizing
plaA
, we discovered that wild-type legionellae secrete a phospholipid cholesterol acyltransferase activity, highlighting the spectrum of lipolytic enzymes produced by
L. pneumophila
.
Infection Stage-Dependent Modulation of Macrophage Activation inTrypanosoma congolense-Resistant and -Susceptible Mice
Authors: Noël Wim , Hassanzadeh Gholamreza , Raes Geert , Namangala Boniface , Daems Inge , Brys Lea , Brombacher Frank , Baetselier Patrick De , Beschin Alain 
Published: October 2002

ABSTRACTThe contribution of cytokines and chemokines to resistance and susceptibility to African trypanosomiasis remains controversial. In the present study, the levels of type I and type II cytokines and of the MCP-1 chemokine were compared during the early and late stages ofTrypanosoma congolenseinfection in susceptible BALB/c and resistant C57BL/6 mice. Moreover, the status of macrophage activation was compared in these animals by analyzing the inducible nitric oxide synthase-arginase balance, tumor necrosis factor secretion, and expression of the FIZZ1 and YM genes. Data show that changing from a predominant type I cytokine environment in the early stage of infection to a predominant type II cytokine environment and an enhanced MCP-1 secretion in the late stage of infection correlates with resistance toT. congolense. Concomitantly, macrophage activation evolves from a classical to a predominant alternative phenotype. We further confirmed that the simultaneous occurrence of type I/type II cytokines in the early stage of infection in susceptible BALB/c mice, reflected by the presence of macrophages exhibiting a mixed classical/alternative activation phenotype, is associated with uncontrolled parasite growth and early death. Interleukin-4 (IL-4) and IL-13 signaling did not influence the susceptibility of BALB/c mice toT. congolenseinfection and interestingly were not the main trigger to alternative macrophage activation. InT. congolense-resistant C57BL/6 mice, our results corroborated the induction of FIZZ1 and YM gene expressions with the alternative pathway of macrophage activation. In susceptible BALB/c mice, however, YM but not FIZZ1 induction reflected the emergence of alternatively activated macrophages. Hence, the FIZZ1 and YM genes may be useful markers to discriminate between distinct populations of alternatively activated macrophages.
Interleukin-10 (IL-10) in Experimental Visceral Leishmaniasis and IL-10 Receptor Blockade as Immunotherapy
Authors: Murray Henry W. , Lu Christina M. , Mauze Smita , Freeman Sherry , Moreira Andre L. , Kaplan Gilla , Coffman Robert L. 
Published: October 2002

ABSTRACTInterleukin-10 (IL-10) is thought to promote intracellular infection, including human visceral leishmaniasis, by disabling Th1 cell-type responses and/or deactivating parasitized tissue macrophages. To develop a rationale for IL-10 inhibition as treatment in visceral infection, Th1 cytokine-driven responses were characterized inLeishmania donovani-infected BALB/c mice in which IL-10 was absent or overexpressed or its receptor (IL-10R) was blockaded. IL-10 knockout and normal mice treated prophylactically with anti-IL-10R demonstrated accelerated granuloma assembly and rapid parasite killing without untoward tissue inflammation; IL-12 and gamma interferon mRNA expression, inducible nitric oxide synthase reactivity, and responsiveness to antimony chemotherapy were also enhanced in knockout mice. In IL-10 transgenic mice, parasite replication was unrestrained, and except for antimony responsiveness, measured Th1 cell-dependent events were all initially impaired. Despite subsequent granuloma assembly, high-level infection persisted, and antimony-treated transgenic mice also relapsed. In normal mice with established infection, anti-IL-10R treatment was remarkably active, inducing near-cure by itself and synergism with antimony. IL-10's deactivating effects regulate outcome in experimental visceral leishmaniasis, and IL-10R blockade represents a potential immuno- and/or immunochemotherapeutic approach in this infection.