bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contributions of the interdomain loop, amino terminus, and subunit interface to the ligand‐facilitated dimerization of neurophysin: Crystal structures and mutation studies of bovine neurophysin‐I
Authors: Li Xintian , Lee Hunjoong , Wu Jin , Breslow Esther 
Published: December 2006

AbstractCurrent evidence indicates that the ligand‐facilitated dimerization of neurophysin is mediated in part by dimerization‐induced changes at the hormone binding site of the unliganded state that increase ligand affinity. To elucidate other contributory factors, we investigated the potential role of neurophysin's short interdomain loop (residues 55–59), particularly the effects of loop residue mutation and of deleting amino‐terminal residues 1–6, which interact with the loop and adjacent residues 53–54. The neurophysin studied was bovine neurophysin‐I, necessitating determination of the crystal structures of des 1–6 bovine neurophysin‐I in unliganded and liganded dimeric states, as well as the structure of its liganded Q58V mutant, in which peptide was bound with unexpectedly increased affinity. Increases in dimerization constant associated with selected loop residue mutations and with deletion of residues 1–6, together with structural data, provided evidence that dimerization of unliganded neurophysin‐I is constrained by hydrogen bonding of the side chains of Gln58, Ser56, and Gln55 and by amino terminus interactions, loss or alteration of these hydrogen bonds, and probable loss of amino terminus interactions, contributing to the increased dimerization of the liganded state. An additional intersubunit hydrogen bond from residue 81, present only in the liganded state, was demonstrated as the largest single effect of ligand binding directly on the subunit interface. Comparison of bovine neurophysins I and II indicates broadly similar mechanisms for both, with the exception in neurophysin II of the absence of Gln55 side chain hydrogen bonds in the unliganded state and a more firmly established loss of amino terminus interactions in the liganded state. Evidence is presented that loop status modulates dimerization via long‐range effects on neurophysin conformation involving neighboring Phe22 as a key intermediary.
Atomic‐resolution crystal structure of thioredoxin from the acidophilic bacterium Acetobacter aceti
Authors: Starks Courtney M. , Francois Julie A. , MacArthur Kelly M. , Heard Brittney Z. , Kappock T. Joseph 
Published: December 2006

AbstractThe crystal structure of thioredoxin (AaTrx) from the acetic acid bacterium Acetobacter aceti was determined at 1 Å resolution. This is currently the highest resolution crystal structure available for any thioredoxin. Thioredoxins facilitate thiol‐disulfide exchange, a process that is expected to be slow at the low pH values encountered in the A. aceti cytoplasm. Despite the apparent need to function at low pH, neither the active site nor the surface charge distribution of AaTrx is notably different from that of Escherichia coli thioredoxin. Apparently the ancestral thioredoxin was sufficiently stable for use in A. aceti or the need to interact with multiple targets constrained the variation of surface residues. The AaTrx structure presented here provides a clear view of all ionizable protein moieties and waters, a first step in understanding how thiol‐disulfide exchange might occur in a low pH cytoplasm, and is a basis for biophysical studies of the mechanism of acid‐mediated unfolding. The high resolution of this structure should be useful for computational studies of thioredoxin function, protein structure and dynamics, and side‐chain ionization.
Human lysosomal DNase IIα contains two requisite PLD‐signature (HxK) motifs: Evidence for a pseudodimeric structure of the active enzyme species
Authors: Schäfer Patrick , Cymerman Iwona A. , Bujnicki Janusz M. , Meiss Gregor 
Published: December 2006

AbstractLysosomal DNase IIα is essential for DNA waste removal and auxiliary apoptotic DNA fragmentation in higher eukaryotes. Despite the key role of this enzyme, little is known about its structure–function relationships. Here, mutational and biochemical analyses were used to characterize human DNase IIα variants expressed in mammalian cells. The resulting data strongly support the hypothesis that the enzyme is a monomeric phospholipase D–family member with a pseudodimeric protein fold. According to our results, DNase IIα contains two requisite PLD‐signature motifs (113HTK115 and 295HSK297) in the N‐ and C‐terminal subdomains, respectively, that together form a single active site. Based on these data, we present an experimentally validated structural model of DNase IIα.
Studying multisite binary and ternary protein interactions by global analysis of isothermal titration calorimetry data in SEDPHAT: Application to adaptor protein complexes in cell signaling
Authors: Houtman Jon C.D. , Brown Patrick H. , Bowden Brent , Yamaguchi Hiroshi , Appella Ettore , Samelson Lawrence E. , Schuck Peter 
Published: December 2006

AbstractMultisite interactions and the formation of ternary or higher‐order protein complexes are ubiquitous features of protein interactions. Cooperativity between different ligands is a hallmark for information transfer, and is frequently critical for the biological function. We describe a new computational platform for the global analysis of isothermal titration calorimetry (ITC) data for the study of binary and ternary multisite interactions, implemented as part of the public domain multimethod analysis software SEDPHAT. The global analysis of titrations performed in different orientations was explored, and the potential for unraveling cooperativity parameters in multisite interactions was assessed in theory and experiment. To demonstrate the practical potential and limitations of global analyses of ITC titrations for the study of cooperative multiprotein interactions, we have examined the interactions of three proteins that are critical for signal transduction after T‐cell activation, LAT, Grb2, and Sos1. We have shown previously that multivalent interactions between these three molecules promote the assembly of large multiprotein complexes important for T‐cell receptor activation. By global analysis of the heats of binding observed in sets of ITC injections in different orientations, which allowed us to follow the formation of binary and ternary complexes, we observed negative and positive cooperativity that may be important to control the pathway of assembly and disassembly of adaptor protein particles.
Methodology for Determining the Variance of the Taylor Factor: Application in Fe-3%Si
Authors: Przybyla Craig P. , Adams Brent L. , Miles Michael P. 
Published: December 2006

AbstractA method is proposed to determine the variance of an arbitrary material property based on the statistics of the texture of polycrystalline materials for a specified volume. This method is applied to determine the variance of the Taylor factor (i.e., measure of plastic deformation in crystal plasticity) and is compared to a random sampling method. The results from the random sampling method correlated well with the statistical variance relationship when the magnitude of the variance was greater than that of the numerical errors observed in the statistical calculation. An empirical relation was also shown to model the results, and the constants for this relationship were determined for pseudo-three-dimensional Fe-3%Si. Implementation of the statistical variance relationship in true three-dimensional microstructures is not limited by material opacity, since it depends only on the two-point pair correlation functions. The connection between the variance of the R-value and variance of the Taylor factor is considered. Although only a weak connection was found, it was observed that relatively small variations in the Taylor factor yield large variances in the R-value.
Amodiaquine and Artemether-Lumefantrine Select Distinct Alleles of the
Plasmodium falciparum mdr1
Gene in Tanzanian Children Treated for Uncomplicated Malaria
Authors: Humphreys G. S. , Merinopoulos I. , Ahmed J. , Whitty C. J. M. , Mutabingwa T. K. , Sutherland C. J. , Hallett R. L. 
Published: December 2006

ABSTRACT

The artemisinin-based combination therapies artemether-lumefantrine (AL) and amodiaquine (AQ) plus artesunate have been adopted for treatment of
Plasmodium falciparum
malaria in many African countries. Molecular markers of parasite resistance suitable for surveillance have not been established for any of the component drugs in either of these combinations. We assessed
P. falciparum mdr1
(Pf
mdr1
) alleles present in 300 Tanzanian children presenting with uncomplicated falciparum malaria, who were enrolled in a clinical trial of antimalarial therapy. Pf
mdr1
genotype analysis was also performed with isolates from 182 children who failed AQ monotherapy and 54 children who failed AL treatment. Pf
mdr1
alleles 86Y, 184Y, and 1246Y were more common among treatment failures in the AQ group than among pretreatment infections. The converse was found in the AL-treated group. Children presenting with the 86Y/184Y/1246Y Pf
mdr1
haplotype and treated with AQ were significantly more likely to retain this haplotype if they were parasite positive during posttreatment follow-up than were children treated with AL (odds ratio, 33.25; 95% confidence interval, 4.17 to 1441;
P
, <0.001). We conclude that AL and AQ exert opposite within-host selective effects on the Pf
mdr1
gene of
P. falciparum
.
In Vitro Activities of Tigecycline and Eight Other Antimicrobials against Different
Nocardia
Species Identified by Molecular Methods
Authors: Cercenado Emilia , Marín Mercedes , Sánchez-Martínez Mónica , Cuevas Oscar , Martínez-Alarcón José , Bouza Emilio 
Published: December 2006

ABSTRACT

The in vitro activities of tigecycline and other antimicrobials against 51 isolates of
Nocardia
spp. were evaluated. MIC
90
s and MIC ranges were as follows: tigecycline, 4 and ≤0.06 to 8 mg/liter, respectively; minocycline, 2 and ≤0.06 to 2 mg/liter, respectively; linezolid, 1 and ≤0.06 to 2 mg/liter, respectively; moxifloxacin, 2 and ≤0.06 to >64 mg/liter, respectively; ertapenem, 32 and ≤0.06->64 mg/liter, respectively; imipenem, 2 and ≤0.06 to >64 mg/liter, respectively; meropenem, 8 and ≤0.06 to >64 mg/liter, respectively; amikacin, 1 and ≤0.06 to 32 mg/liter, respectively; and trimethoprim-sulfamethoxazole, 1/19 and ≤0.5/9.5 to >2/38 mg/liter, respectively.
Similar Trends of Pyrimethamine Resistance-Associated Mutations in
Plasmodium vivax
and
P. falciparum
Authors: Alam Mohammad Tauqeer , Bora Hema , Bharti Praveen K. , Saifi Muheet A. , Das Manoj K. , Dev Vas , Kumar Ashwani , Singh Neeru , Dash Aditya P. , Das Brahmananda , Wajihullah  , Sharma Yagya D. 
Published: December 2006

ABSTRACT

The antifolate drugs sulfadoxine and pyrimethamine are commonly used to treat
Plasmodium falciparum
malaria. However, they can also affect the
Plasmodium vivax
parasite if it coexists with
P. falciparum
, as both species have common drug targets. Resistance to the antifolate drugs arises due to point mutations in the target enzymes of the respective parasite. To assess the cross-species impact of antifolate drug treatment, we describe here the dihydrofolate reductase (DHFR) mutations among field isolates of
P. vivax
and
P. falciparum
. The overall DHFR mutation rate for
P. vivax
was lower than that for
P. falciparum
. However, both species of
Plasmodium
followed similar trends of DHFR mutations. Similar to
P. falciparum
, the DHFR mutation rate of
P. vivax
also varied from region to region. It was lower in
P. vivax
-dominant regions but higher in the
P. falciparum
-dominated areas and highest where antifolates are used as the first line of antimalarial treatment. In conclusion, the antifolate treatment of falciparum malaria is proportionately affecting the DHFR mutations of
P. vivax
, suggesting that the drug should be used with caution to minimize the development of cross-species resistance in the field.
Pretreatment with Empty Liposomes Attenuates the Immunopathology of Invasive Pulmonary Aspergillosis in Corticosteroid-Immunosuppressed Mice
Authors: Lewis Russell E. , Chamilos Georgios , Prince Randall A. , Kontoyiannis Dimitrios P. 
Published: December 2006

ABSTRACT
In a nonneutropenic murine model of invasive pulmonary aspergillosis, pretreatment with empty liposomes (E-lipo) was nearly as effective as 10 mg/kg of body weight liposomal amphotericin B and superior to 1 mg/kg amphotericin B deoxycholate. The beneficial immunomodulatory properties of E-lipo appear to compensate for their lack of direct antifungal activity.
Salivaricin A2 and the Novel Lantibiotic Salivaricin B Are Encoded at Adjacent Loci on a 190-Kilobase Transmissible Megaplasmid in the Oral Probiotic Strain
Streptococcus salivarius
K12
Authors: Hyink Otto , Wescombe Philip A. , Upton Mathew , Ragland Nancy , Burton Jeremy P. , Tagg John R. 
Published: December 2006

ABSTRACT

The commercial probiotic
Streptococcus salivarius
strain K12 is the prototype of those
S. salivarius
strains that are the most strongly inhibitory in a standardized test of streptococcal bacteriocin production and has been shown to produce the 2,368-Da salivaricin A2 (SalA2) and the 2,740-Da salivaricin B (SboB) lantibiotics. The previously uncharacterized SboB belongs to the type AII class of lantibiotic bacteriocins and is encoded by an eight-gene cluster. The genetic loci encoding SalA2 and SboB in strain K12 have been fully characterized and are localized to nearly adjacent sites on pSsal-K12, a 190-kb megaplasmid. Of 61 strongly inhibitory strains of
S. salivarius
, 19 (31%) were positive for the
sboB
structural gene. All but one (strain NR) of these 19 strains were also positive for
salA2
, and in each of these cases of double positivity, the two loci were separated by fewer than 10 kb. This is the first report of a single streptococcus strain producing two distinct lantibiotics.
Two Complex, Adenovirus-Based Vaccines That Together Induce Immune Responses to All Four Dengue Virus Serotypes
Authors: Holman David H. , Wang Danher , Raviprakash Kanakatte , Raja Nicholas U. , Luo Min , Zhang Jianghui , Porter Kevin R. , Dong John Y. 
Published: December 2006

ABSTRACT
Dengue virus infections can cause hemorrhagic fever, shock, encephalitis, and even death. Worldwide, approximately 2.5 billion people live in dengue-infested regions with about 100 million new cases each year, although many of these infections are believed to be silent. There are four antigenically distinct serotypes of dengue virus; thus, immunity from one serotype will not cross-protect from infection with the other three. The difficulties that hamper vaccine development include requirements of the natural conformation of the envelope glycoprotein to induce neutralizing immune responses and the necessity of presenting antigens of all four serotypes. Currently, the only way to meet these requirements is to use a mixture of four serotypes of live attenuated dengue viruses, but safety remains a major problem. In this study, we have developed the basis for a tetravalent dengue vaccine using a novel complex adenovirus platform that is capable of expressing multiple antigens de novo. This dengue vaccine is constructed as a pair of vectors that each expresses the premembrane and envelope genes of two different dengue virus serotypes. Upon vaccination, the vaccine expressed high levels of the dengue virus antigens in cells to mimic a natural infection and induced both humoral and cellular immune responses against multiple serotypes of dengue virus in an animal model. Further analyses show the humoral responses were indeed neutralizing against all four serotypes. Our studies demonstrate the concept of mimicking infections to induce immune responses by synthesizing dengue virus membrane antigens de novo and the feasibility of developing an effective tetravalent dengue vaccine by vector-mediated expression of glycoproteins of the four serotypes.
Experimental
Fasciola hepatica
Infection Alters Responses to Tests Used for Diagnosis of Bovine Tuberculosis
Authors: Flynn Robin J. , Mannion Celine , Golden Olwen , Hacariz Orcun , Mulcahy Grace 
Published: December 2006

ABSTRACT

Fasciola hepatica
is a prevalent helminth parasite of livestock. Infection results in polarization of the host's immune response and generation of type 2 helper (Th2) immune responses, which are known to be inhibitory to Th1 responses. Bovine tuberculosis (BTB) is a bacterial disease of economic and zoonotic importance. Control polices for this disease rely on extensive annual testing and a test-and-slaughter policy. The correct diagnosis of BTB relies on cell-mediated immune responses. We established a model of coinfection of
F. hepatica
and
Mycobacterium bovis
BCG to examine the impact of helminth infection on correct diagnosis. We found the predictive capacity of tests to be compromised in coinfected animals and that
F. hepatica
infection altered macrophage function. Interleukin-4 and gamma interferon expression in whole-blood lymphocytes restimulated in vitro with
M. bovis
antigen was also altered in coinfected animals. These results raise the question of whether
F. hepatica
infection can affect the predictive capacity of tests for the diagnosis of BTB and possibly also influence susceptibility to BTB and other bacterial diseases. Further studies on the interplay between helminth infection and BTB are warranted.
Interference of Components of the Phosphoenolpyruvate Phosphotransferase System with the Central Virulence Gene Regulator PrfA ofListeria monocytogenes
Authors: Mertins Sonja , Joseph Biju , Goetz Monika , Ecke Regina , Seidel Gerald , Sprehe Mareen , Hillen Wolfgang , Goebel Werner , Müller-Altrock Stefanie 
Published: December 2006

ABSTRACTAnalysis ofListeria monocytogenes ptsH,hprK, andccpAmutants defective in carbon catabolite repression (CCR) control revealed significant alterations in the expression of PrfA-dependent genes. ThehprKmutant showed high up-regulation of PrfA-dependent virulence genes upon growth in glucose-containing medium whereas expression of these genes was even slightly down-regulated in theccpAmutant compared to the wild-type strain. TheptsHmutant could only grow in a rich culture medium, and here the PrfA-dependent genes were up-regulated as in thehprKmutant. As expected, HPr-Ser-P was not produced in thehprKandptsHmutants and synthesized at a similar level in theccpAmutant as in the wild-type strain. However, no direct correlation was found between the level of HPr-Ser-P or HPr-His-P and PrfA activity whenL. monocytogeneswas grown in minimal medium with different phosphotransferase system (PTS) carbohydrates. Comparison of the transcript profiles of thehprKandccpAmutants with that of the wild-type strain indicates that the up-regulation of the PrfA-dependent virulence genes in thehprKmutant correlates with the down-regulation of genes known to be controlled by the efficiency of PTS-mediated glucose transport. Furthermore, growth in the presence of the non-PTS substrate glycerol results in high PrfA activity. These data suggest that it is not the component(s) of the CCR or the common PTS pathway but, rather, the component(s) of subsequent steps that seem to be involved in the modulation of PrfA activity.
Regulation of Rugosity and Biofilm Formation in
Vibrio cholerae
: Comparison of VpsT and VpsR Regulons and Epistasis Analysis of
vpsT
,
vpsR
, and
hapR
Authors: Beyhan Sinem , Bilecen Kivanc , Salama Sofie R. , Casper-Lindley Catharina , Yildiz Fitnat H. 
Published: December 2006

ABSTRACT

Vibrio cholerae
undergoes phenotypic variation that generates two
morphologically different variants, termed smooth and rugose. The transcriptional profiles of the two variants differ greatly, and many of the differentially regulated genes are controlled by a complex regulatory circuitry that includes the transcriptional regulators VpsR, VpsT, and HapR. In this study, we identified the VpsT regulon and
compared the VpsT and VpsR regulons to elucidate the contribution of each positive regulator to the rugose variant transcriptional profile and associated phenotypes. We have found that although the VpsT and VpsR regulons are very similar, the magnitude of the gene regulation accomplished by each regulator is different. We also determined that
cdgA
, which encodes a GGDEF domain protein, is partially responsible for the altered
vps
gene expression between the
vpsT
and
vpsR
mutants. Analysis of epistatic
relationships among
hapR
,
vpsT
, and
vpsR
with respect to a whole-genome expression profile, colony morphology, and biofilm formation revealed that
vpsR
is epistatic to
hapR
and
vpsT
. Expression of virulence genes was increased in a
vpsR hapR
double mutant relative to a
hapR
mutant, suggesting that VpsR negatively regulates
virulence gene expression in the
hapR
mutant. These results show that a complex regulatory interplay among VpsT, VpsR, HapR, and GGDEF/EAL family proteins controls transcription of the genes required for
Vibrio
polysaccharide and virulence factor production in
V.
cholerae
.
Role for the Nonessential N Terminus of FtsN in Divisome Assembly
Authors: Goehring Nathan W. , Robichon Carine , Beckwith Jon 
Published: December 2006

ABSTRACT

FtsN, the last essential protein in the cell division localization hierarchy in
Escherichia coli
, has several peculiar characteristics, suggesting that it has a unique role in the division process despite the fact that it is conserved in only a subset of bacteria. In addition to suppressing temperature-sensitive mutations in
ftsA
,
ftsK
,
ftsQ
, and
ftsI
, overexpression of FtsN can compensate for a complete lack of FtsK in the cell. We examined the requirements for this phenomenon. We found that the N-terminal terminal region (cytoplasmic and transmembrane domains) is critical for suppression, while the C-terminal murein-binding domain is dispensable. Our results further suggest that FtsN and FtsK act cooperatively to stabilize the divisome.
Genomic Structure and Phylogeny of the Plant Pathogen
Ralstonia solanacearum
Inferred from Gene Distribution Analysis
Authors: Guidot Alice , Prior Philippe , Schoenfeld Jens , Carrère Sébastien , Genin Stéphane , Boucher Christian 
Published: December 2006

ABSTRACT

In the present study, we investigated the gene distribution among strains of the highly polymorphic plant pathogenic β-proteobacterium
Ralstonia solanacearum
, paying particular attention to the status of known or candidate pathogenicity genes. Based on the use of comparative genomic hybridization on a pangenomic microarray for the GMI1000 reference strain, we have defined the conditions that allowed comparison of the repertoires of genes among a collection of 18 strains that are representative of the biodiversity of the
R. solanacearum
species. This identified a list of 2,690 core genes present in all tested strains. As a corollary, a list of 2,338 variable genes within the
R. solanacearum
species has been defined. The hierarchical clustering based on the distribution of variable genes is fully consistent with the phylotype classification that was previously defined from the nucleotide sequence analysis of four genes. The presence of numerous pathogenicity-related genes in the core genome indicates that
R. solanacearum
is an ancestral pathogen. The results establish the long coevolution of the two replicons that constitute the bacterial genome. We also demonstrate the clustering of variable genes in genomic islands. Most genomic islands are included in regions with an alternative codon usage, suggesting that they originate from acquisition of foreign genes through lateral gene transfers. Other genomic islands correspond to genes that have the same base composition as core genes, suggesting that they either might be ancestral genes lost by deletion in certain strains or might originate from horizontal gene transfers.