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991.
Amine Ghozlane Agnel Praveen Joseph Aurelie Bornot Alexandre G de Brevern 《Bioinformation》2009,3(9):367-369
Conversion of local structural state of a protein from an α-helix to a β-strand is usually associated with a major change in the
tertiary structure. Similar changes were observed during the self assembly of amyloidogenic proteins to form fibrils, which
are implicated in severe diseases conditions, e.g., Alzheimer disease. Studies have emphasized that certain protein sequence
fragments known as chameleon sequences do not have a strong preference for either helical or the extended conformations.
Surprisingly, the information on the local sequence neighborhood can be used to predict their secondary at a high accuracy
level. Here we report a large scale-analysis of chameleon sequences to estimate their propensities to be associated with
different local structural states such as α -helices, β-strands and coils. With the help of the propensity information derived
from the amino acid composition, we underline their complexity, as more than one quarter of them prefers coil state over to
the regular secondary structures. About half of them show preference for both α-helix and β-sheet conformations and either
of these two states is favored by the rest. 相似文献
992.
Hee-Bum?Yang Wing?Yee?Liu Won-Hee?Kang Molly?Jahn Byoung-Cheorl?KangEmail author 《Molecular breeding : new strategies in plant improvement》2009,24(4):433-446
In pepper, the TMV resistance locus L is syntenic to the tomato I2 and the potato R3 loci on chromosome 11. In this report, we identified pepper bacterial artificial chromosome (BAC) clones corresponding to
the I2 and R3 loci and developed L-linked markers using the BAC sequence information. A BAC library was screened using the tomato I2C-1 gene as a probe. The resulting clones were sorted further by PCR screening, sequencing, and genetic mapping. A linkage analysis
revealed that BAC clone 082F03 could be anchored to the target region near TG36 on chromosome 11. Using the 082F03 sequence,
more BAC clones were identified and a BAC contig spanning 224 kb was constructed. Gene prediction analysis showed that there
were at least three I2/R3 R gene analogs (RGAs) in the BAC contig. Three DNA markers closely linked (about 1.2 cM) to the L
4
gene were developed by using the BAC contig sequence. The single nucleotide polymorphism marker 087H3T7 developed in this
study was subjected to linkage analysis in L
4
- and L
3
-segregating populations together with previously developed markers. The 189D23M marker, which is known to co-segregate with
L
3
, was located on the opposite side of 087H3T7, about 0.7 cM away from L
4
. This supports the idea that L
3
and L
4
may be different genes closely linked within the region instead of different alleles at the same locus. Finally, use of flanking
markers in molecular breeding program for introgression of L
4
to elite germplasm against most aggressive tobamoviruses pathotype P1,2,3 is discussed. 相似文献
993.
994.
Chi‐Tai Chiang Wing‐Keung Chu Shu‐Er Chow Jan‐Kan Chen 《Journal of cellular physiology》2009,219(1):117-122
p63 belongs to a member of the tumor suppressor protein p53 family. Due to alternative promoter usage, two types of p63 proteins are produced. The ΔNp63 isoform lacks the N‐terminal transactivation domain and is thought to antagonize TAp63 and p53 in target gene regulation. ΔNp63 has been found to be overexpressed in numerous human squamous cell carcinomas, including nasopharyngeal carcinoma (NPC). However, the role of ΔNp63 overexpression in NPC pathogenesis has not been clear. In this study, we use a ΔNp63 overexpressing human NPC cell line (NPC‐076) to explore the possible roles of ΔNp63 in cell proliferation and cell‐cycle regulation. We found that the proliferation of NPC‐076 cell is greatly suppressed when the overexpressed ΔNp63 is silenced by specific ΔNp63 siRNA. Further studies show that ΔNp63 silencing results in the upregulation of CKIs, including p27kip1 and p57kip2 in both mRNA and protein levels. Cell‐cycle analysis shows that ΔNp63 silencing also results in an increased G1 phase cell and apoptotic cell population. Our findings indicate that ΔNp63 plays important roles in the regulation of NPC‐076 cell‐cycle progression, and may play a role in the maintenance of NPC‐076 tumor cell phenotype. J. Cell. Physiol. 219: 117–122, 2009. © 2008 Wiley‐Liss, Inc. 相似文献
995.
Jennifer S. Powers Rebecca A. Montgomery E. Carol Adair Francis Q. Brearley Saara J. DeWalt Camila T. Castanho Jerome Chave Erika Deinert Jörg U. Ganzhorn Matthew E. Gilbert José Antonio González-Iturbe Sarayudh Bunyavejchewin H. Ricardo Grau Kyle E. Harms Ankila Hiremath Silvia Iriarte-Vivar † Eric Manzane Alexandre A. de Oliveira Lourens Poorter Jean-Baptiste Ramanamanjato Carl Salk Amanda Varela George D. Weiblen Manuel T. Lerdau 《Journal of Ecology》2009,97(4):801-811
996.
Raymond W. Bourdeau Enrico Malito Alexandre Chenal Brian L. Bishop Mark W. Musch Mitch L. Villereal Eugene B. Chang Elise M. Mosser Richard F. Rest Wei-Jen Tang 《The Journal of biological chemistry》2009,284(21):14645-14656
Anthrolysin O (ALO) is a pore-forming, cholesterol-dependent cytolysin
(CDC) secreted by Bacillus anthracis, the etiologic agent for
anthrax. Growing evidence suggests the involvement of ALO in anthrax
pathogenesis. Here, we show that the apical application of ALO decreases the
barrier function of human polarized epithelial cells as well as increases
intracellular calcium and the internalization of the tight junction protein
occludin. Using pharmacological agents, we also found that barrier function
disruption requires increased intracellular calcium and protein degradation.
We also report a crystal structure of the soluble state of ALO. Based on our
analytical ultracentrifugation and light scattering studies, ALO exists as a
monomer. Our ALO structure provides the molecular basis as to how ALO is
locked in a monomeric state, in contrast to other CDCs that undergo
antiparallel dimerization or higher order oligomerization in solution. ALO has
four domains and is globally similar to perfringolysin O (PFO) and
intermedilysin (ILY), yet the highly conserved undecapeptide region in domain
4 (D4) adopts a completely different conformation in all three CDCs.
Consistent with the differences within D4 and at the D2-D4 interface, we found
that ALO D4 plays a key role in affecting the barrier function of C2BBE cells,
whereas PFO domain 4 cannot substitute for this role. Novel structural
elements and unique cellular functions of ALO revealed by our studies provide
new insight into the molecular basis for the diverse nature of the CDC
family.Cholesterol-dependent cytolysins
(CDCs)4 are a family
of pore-forming toxins from many organisms, including but not limited to the
genera Archanobacterium, Bacillus, Clostridium, Listeria, and
Streptococcus. Recently, work in vertebrates has revealed that CDCs
and membrane attack complex/perforin superfamily domain-containing proteins
share a similar fold, suggesting that vertebrates use a similar mechanism for
defense against infection (1,
2). A common feature of the CDC
family is the requirement of cholesterol in the membrane to form pores
(3). In addition to
cholesterol, certain members of the family also require a cellular receptor,
such as CD59 for the toxin ILY from Streptococcus intermedius
(4). The specific mechanism by
which CDCs form pores is not completely resolved; however, what is generally
known is that ring-shaped oligomerization at the cellular membrane is followed
by large conformational changes in each unit of the oligomer, resulting in the
insertion of a β-barrel into the cellular membrane
(5). Pore formation results in
a variety of downstream signaling effects, including but not limited to the
influx of Ca2+ into the cell
(6).A good deal is known about structures of the prepore conformation of CDCs.
The crystal structures of prepore PFO, from Clostridium perfringens,
and ILY have previously been elucidated
(7,
8). Each structure shows a
characteristic four-domain architecture, in which domain 4 (D4) is involved in
membrane recognition, domain 3 (D3) is involved in β-sheet insertion, and
domain 2 (D2) is the hinge region that undergoes a large conformational change
(9-11).
Nevertheless, despite the similarities, structural differences in D4
orientation and the conformation of a highly conserved segment named the
undecapeptide region confer functional differences to PFO and ILY
(8). Noting these differences,
we decided to explore the structure and function of another member of the CDC
family, anthrolysin O (ALO).ALO is secreted by Bacillus anthracis, the etiologic agent for
anthrax. ALO is chromosomally encoded by a gene whose regulation is poorly
understood, and it is highly homologous to other members of the CDC family
(12). ALO has been shown to
have hemolytic and cytolytic activity
(13,
14). Although clinical studies
have shown that B. anthracis is weakly hemolytic
(15), anthrax bacteria do
produce biologically relevant amounts of hemolytic ALO, although the levels of
expression are under complex regulation and are dependent on the culture media
and growth conditions (12,
13,
16). At lower concentrations,
ALO can disrupt cell signaling
(13,
14). Search for a cellular
receptor of ALO has lead to the conclusion that it is a TLR4 agonist
(17). However, it is not known
that ALO binds to TLR4 directly and, if so, whether ALO also binds other
cellular receptors.In addition to ALO, B. anthracis secrete ∼400 proteins, termed
the anthrax secretome (18). Of
those, two exotoxins, edema toxin (ET) and lethal toxin (LT) have been
characterized in greatest detail. ET raises intracellular cAMP to pathologic
levels, whereas LT impairs mitogenic and stress responses by inactivating
mitogen-activating protein kinase kinase
(19,
20). The complex interplay
between these two toxins on various aspects of host cellular functions have
been demonstrated
(20-25).
ALO could also work in conjunction with other anthrax virulence factors to
modulate their cellular toxicity. For example, ALO and LF together induce
macrophage apoptosis, whereas ALO and PLC play a redundant role in a murine
inhalation anthrax model (17,
26). Interplay among anthrax
secreted factors on cells relevant to anthrax infection is just beginning to
be understood. This network of interactions is vital to the molecular basis of
how anthrax bacteria interact with the hosts during anthrax infection.Anthrax infection initiates when B. anthracis spores enter the
host through one of three routes: cutaneous, inhalational, or gastrointestinal
(GI) (27,
28). All three routes of
infection can lead to systemic infection and are ultimately lethal. Different
from inhalational anthrax, spores are ingested and germinate on or within the
epithelium of the GI tract in GI anthrax
(29). This is primarily based
on pathological observations that primary lesions of the GI tract are found in
GI anthrax, whereas no primary lesions of the lung are found in inhalational
anthrax (29). Inhalational
anthrax is a disease of choice for biological weapons because of its high
infectivity and mortality
(30). The initiation of GI
anthrax requires much higher doses of spores than inhalational anthrax, and
the molecular basis for the initiation of GI anthrax remains elusive
(31).Since the primary function of GI epithelia is to control the flux of
material into the body, disruption of this barrier can lead to movement of
bacteria into the surrounding tissue
(32). The barrier is produced
by a matrix of transmembrane and membrane-associated proteins. These cell to
cell contacts, or tight junctions, are sometimes altered during bacterial
infection to specifically disrupt the barrier function of epithelial cells.
Using a functional model for the gut epithelium, human gut epithelial Caco-2
brush border expressor (C2BBE) cells, we report that ALO decreases the barrier
function of C2BBE cells through disruption of tight junctions. We also show
that ALO disruption of barrier function is dependent on epithelial cell
polarity. We also present the crystal structure of the soluble state of ALO
and compare it with the known structures of other CDCs. In addition, we show
that ALO exists primarily as a monomer, in contrast to its closely related
homologue PFO, which exists as a dimer. Finally, we used domain swapping to
examine the structural components that confer specificity of ALO to gut
epithelial cells. 相似文献
997.
Benjamin T. Goult Neil Bate Nicholas J. Anthis Kate L. Wegener Alexandre R. Gingras Bipin Patel Igor L. Barsukov Iain D. Campbell Gordon C. K. Roberts David R. Critchley 《The Journal of biological chemistry》2009,284(22):15097-15106
Talin is a large flexible rod-shaped protein that activates the integrin
family of cell adhesion molecules and couples them to cytoskeletal actin. It
exists in both globular and extended conformations, and an intramolecular
interaction between the N-terminal F3 FERM subdomain and the C-terminal part
of the talin rod contributes to an autoinhibited form of the molecule. Here,
we report the solution structure of the primary F3 binding domain within the
C-terminal region of the talin rod and use intermolecular nuclear Overhauser
effects to determine the structure of the complex. The rod domain (residues
1655–1822) is an amphipathic five-helix bundle; Tyr-377 of F3 docks into
a hydrophobic pocket at one end of the bundle, whereas a basic loop in F3
(residues 316–326) interacts with a cluster of acidic residues in the
middle of helix 4. Mutation of Glu-1770 abolishes binding. The rod domain
competes with β3-integrin tails for binding to F3, and the structure of
the complex suggests that the rod is also likely to sterically inhibit binding
of the FERM domain to the membrane.The cytoskeletal protein talin has emerged as a key player, both in
regulating the affinity of the integrin family of cell adhesion molecules for
ligand (1) and in coupling
integrins to the actin cytoskeleton
(2). Thus, depletion of talin
results in defects in integrin activation
(3), integrin signaling through
focal adhesion kinase, the maintenance of cell spreading, and the assembly of
focal adhesions in cultured cells
(4). In the whole organism,
studies on the single talin gene in worms
(5) and flies
(6) show that talin is
essential for a variety of integrin-mediated events that are crucial for
normal embryonic development. In vertebrates, there are two talin
genes, and mice carrying a talin1 null allele fail to complete
gastrulation (7).
Tissue-specific inactivation of talin1 results in an inability to activate
integrins in platelets (8,
9), defects in the
membrane-cytoskeletal interface in megakaryocytes
(10), and disruption of the
myotendinous junction in skeletal muscle
(11). In contrast, mice
homozygous for a talin2 gene trap allele have no phenotype, although
the allele may be hypomorphic
(12).Recent structural studies have provided substantial insights into the
molecular basis of talin action. Talin is composed of an N-terminal globular
head (∼50 kDa) linked to an extended flexible rod (∼220 kDa). The
talin head contains a
FERM2 domain (made up
of F1, F2, and F3 subdomains) preceded by a domain referred to here as F0
(2). Studies by Wegener et
al. (30) have shown how
the F3 FERM subdomain, which has a phosphotyrosine binding domain fold,
interacts with both the canonical NPXY motif and the
membrane-proximal helical region of the cytoplasmic tails of integrin
β-subunits (13). The
latter interaction apparently activates the integrin by disrupting the salt
bridge between the integrin α- and β-subunit tails that normally
keeps integrins locked in a low affinity state. The observation that the F0
region is also important in integrin activation
(14) may be explained by our
recent finding that F0 binds, albeit with low affinity,
Rap1-GTP,3 a known
activator of integrins (15,
16). The talin rod is made up
of a series of amphipathic α-helical bundles
(17–20)
and contains a second integrin binding site (IBS2)
(21), numerous binding sites
for the cytoskeletal protein vinculin
(22), at least two actin
binding sites (23), and a
C-terminal helix that is required for assembly of talin dimers
(20,
24).Both biochemical (25) and
cellular studies (16) suggest
that the integrin binding sites in full-length talin are masked, and both
phosphatidylinositol 4,5-bisphosphate (PIP2) and Rap1 have been implicated in
exposing these sites. It is well established that some members of the FERM
domain family of proteins are regulated by a head-tail interaction
(26); gel filtration,
sedimentation velocity, and electron microscopy studies all show that talin is
globular in low salt buffers, although it is more elongated (∼60 nm in
length) in high salt (27). By
contrast, the talin rod liberated from full-length talin by calpain-II
cleavage is elongated in both buffers, indicating that the head is required
for talin to adopt a more compact state. Direct evidence for an interaction
between the talin head and rod has recently emerged from NMR studies by Goksoy
et al. (28), who
demonstrated binding of 15N-labeled talin F3 to a talin rod
fragment spanning residues 1654–2344, an interaction that was confirmed
by surface plasmon resonance (Kd = 0.57 μm)
(28). Chemical shift data also
showed that this segment of the talin rod partially masked the binding site in
F3 for the membraneproximal helix of the β3-integrin tail
(28), directly implicating the
talin head-rod interaction in regulating the integrin binding activity of
talin. Goksoy et al.
(28) subdivided the F3 binding
site in this rod fragment into two sites with higher affinity
(Kd ∼3.6 μm; residues 1654–1848)
and lower affinity (Kd ∼78 μm; residues
1984–2344). Here, we define the rod domain boundaries and determine the
NMR structure of residues 1655–1822, a five-helix bundle. We further
show that this domain binds F3 predominantly via surface-exposed residues on
helix 4, with an affinity similar to the high affinity site reported by Goksoy
et al. (28). We also
report the structure of the complex between F3 and the rod domain and show
that the latter masks the known binding site in F3 for the β3-integrin
tail and is expected to inhibit the association of the talin FERM domain with
the membrane. 相似文献
998.
Alba Cenélia M. Silva Michelle Porto Marassi Mônica Mühlbauer Alexandre L. Lourenço Denise P. Carvalho Andrea C.F. Ferreira 《Life sciences》2009,84(19-20):673-677
AimsRetinoic acid is widely used in dermatological treatment and thyroid cancer management; however its possible side-effects on normal thyroid function remains unknown. We aimed to determine the effects of retinoic acid on thyroid function of adult female rats.Main methodsFemale Wistar rats were treated with all-trans-retinoic acid and 13-cis retinoic acid for 14 and 28 days. Then, rats were killed and thyroid function was evaluated.Key findingsSerum T4 and thyrotropin levels remained unchanged, while serum T3 increased in animals treated with all-trans-retinoic acid for 14 days. No changes were observed in hepatic or renal type 1 iodothyronine deiodinase (D1) activities, while thyroid D1 was higher in animals treated for 14 days with all-trans-retinoic acid, which could be related to the increased serum T3 levels. 13-cis retinoic acid increased thyroid iodide uptake after 28 days. These results show effects of retinoic acid treatment on these thyroid proteins: sodium/iodide symporter and deiodinase.SignificanceRetinoic acid is able to interfere with normal thyroid function, increasing thyroid type 1 deiodinase activity, serum T3 levels and sodium/iodide symporter function. However, the effects are time- and retinoic acid isomer-dependent. Since serum thyrotropin levels did not change in any group, the effects observed are probably mediated by a direct retinoic acid effect on the normal thyroid. 相似文献
999.
Erik Ahrné Alexandre Masselot Pierre‐Alain Binz Markus Müller Frederique Lisacek 《Proteomics》2009,9(6):1731-1736
Searching a spectral library for the identification of protein MS/MS data has proven to be a fast and accurate method, while yielding a high identification rate. We investigated the potential to increase peptide discovery rate, with little increase in computational time, by constructing a workflow based on a sequence search with Phenyx followed by a library search with SpectraST. Searching a consensus library compiled from the search results of the prior Phenyx search increased the number of confidently matched spectra by up to 156%. Additionally matched spectra by SpectraST included noisy spectra, spectra representing missed cleaved peptides as well as spectra from post‐translationally modified peptides. 相似文献
1000.
Supermatrix and supertree are two methods for constructing a phylogenetic tree by using multiple data sets. However, these methods are not a panacea, as conflicting signals between data sets can lead to misinterpret the evolutionary history of taxa. In particular, the supermatrix approach is expected to be misleading if the species-tree signal is not dominant after the combination of the data sets. Moreover, most current supertree methods suffer from two limitations: (i) they ignore or misinterpret secondary (non-dominant) phylogenetic signals of the different data sets; and (ii) the logical basis of node robustness measures is unclear.To overcome these limitations, we propose a new approach, called SuperTRI, which is based on the branch support analyses of the independent data sets, and where the reliability of the nodes is assessed using three measures: the supertree Bootstrap percentage and two other values calculated from the separate analyses: the mean branch support (mean Bootstrap percentage or mean posterior probability) and the reproducibility index.The SuperTRI approach is tested on a data matrix including seven genes for 82 taxa of the family Bovidae (Mammalia, Ruminantia), and the results are compared to those found with the supermatrix approach. The phylogenetic analyses of the supermatrix and independent data sets were done using four methods of tree reconstruction: Bayesian inference, maximum likelihood, and unweighted and weighted maximum parsimony. The results indicate, firstly, that the SuperTRI approach shows less sensitivity to the four phylogenetic methods, secondly, that it is more accurate to interpret the relationships among taxa, and thirdly, that interesting conclusions on introgression and radiation can be drawn from the comparisons between SuperTRI and supermatrix analyses. To cite this article: A. Ropiquet et al., C. R. Biologies 332 (2009). 相似文献