Exploration of the genetic diversity of WU polyomavirus (WUV) has been limited in terms of the specimen numbers and particularly the sizes of the genomic fragments analyzed. Using whole-genome sequencing of 48 WUV strains collected in four continents over a 5-year period and 16 publicly available whole-genome sequences, we identified three main WUV clades and five subtypes, provisionally termed Ia, Ib, Ic, II, IIIa, and IIIb. Overall nucleotide variation was low (0 to 1.2%). The discriminatory power of the previous VP2 fragment typing method was found to be limited, and a new, larger genotyping region within the VP2/1 interface was proposed.In 2007, two new human polyomaviruses isolated from respiratory samples of pediatric patients suffering from respiratory disease were discovered, with one being KI polyomavirus (KIV) (2) and the other being WU polyomavirus (WUV) (8).WU polyomavirus shares most of the genomic characteristics of other polyomaviruses, with a noncoding control region (NCCR) separating the early and late coding regions on opposite strands. However, unlike for JCV and BKV, but similar to what was observed for KIV, a late-region-residing agnoprotein gene has not been identified in WUV (8).Despite being frequently detected in respiratory samples of ill patients, no distinct disease associations have so far been conclusively identified for WUV (1, 2, 4, 8, 10, 27). There have been some suggestions that sequence variation plays a role in disease severity and pathogenesis in other polyomaviruses (6, 24). Unfortunately, due to the early nature of research into WUV, there has been a dearth of available complete genomic sequences.In this study, we set out to investigate a large sample set of whole WUV genomes from diverse geographical, temporal, and clinical origins. Incorporating existing WUV genomes with this data set allowed us to investigate global WUV genomic diversity, to characterize the WUV genome, and to propose a new robust typing scheme. 相似文献
To investigate whether accelerated hand bone mineral density (BMD) loss is associated with progressive joint damage in hands and feet in the first year of rheumatoid arthritis (RA) and whether it is an independent predictor of subsequent progressive total joint damage after 4 years.
Methods
In 256 recent-onset RA patients, baseline and 1-year hand BMD was measured in metacarpals 2-4 by digital X-ray radiogrammetry. Joint damage in hands and feet were scored in random order according to the Sharp-van der Heijde method at baseline and yearly up to 4 years.
Results
68% of the patients had accelerated hand BMD loss (>-0.003 g/cm2) in the first year of RA. Hand BMD loss was associated with progressive joint damage after 1 year both in hands and feet with odds ratios (OR) (95% confidence intervals [CI]) of 5.3 (1.3-20.9) and 3.1 (1.0-9.7). In univariate analysis, hand BMD loss in the first year was a predictor of subsequent progressive total joint damage after 4 years with an OR (95% CI) of 3.1 (1.3-7.6). Multivariate analysis showed that only progressive joint damage in the first year and anti-citrullinated protein antibody positivity were independent predictors of long-term progressive joint damage.
Conclusions
In the first year of RA, accelerated hand BMD loss is associated with progressive joint damage in both hands and feet. Hand BMD loss in the first year of recent-onset RA predicts subsequent progressive total joint damage, however not independent of progressive joint damage in the first year. 相似文献
We present crystal structures of the calcium-free E2 state of the sarcoplasmic reticulum Ca2+ -ATPase, stabilized by the inhibitor thapsigargin and the ATP analog AMPPCP. The structures allow us to describe the ATP binding site in a modulatory mode uncoupled from the Asp351 phosphorylation site. The Glu439 side chain interacts with AMPPCP via an Mg2+ ion in accordance with previous Fe2+ -cleavage studies implicating this residue in the ATPase cycle and in magnesium binding. Functional data on Ca2+ mediated activation indicate that the crystallized state represents an initial stage of ATP modulated deprotonation of E2, preceding the binding of Ca2+ ions in the membrane from the cytoplasmic side. We propose a mechanism of Ca2+ activation of phosphorylation leading directly from the compact E2-ATP form to the Ca2E1-ATP state. In addition, a role of Glu439 in ATP modulation of other steps of the functional cycle is suggested. 相似文献
An analysis of the binding of the 8-O-N-tert-butoxycarbonyl-12-aminododecanoyl derivative of 8-O-debutanoylthapsigargin to the target molecule, the SERCA pump, has revealed the importance of the length and flexibility of the side chain attached to O-8. Based on the analysis a series of analogues to the 2-unsubstituted analogue trilobolide has been constructed and shown to be equipotent with thapsigargin as SERCA inhibitors. Only the 12-Boc-aminododecaonoyl derivative, however, was found to be apoptotic. 相似文献
We have determined the structure of the sarco(endo)plasmic reticulum
Ca2+-ATPase (SERCA) in an E2·Pi-like form
stabilized as a complex with , an
ATP analog, adenosine 5′-(β,γ-methylene)triphosphate
(AMPPCP), and cyclopiazonic acid (CPA). The structure determined at 2.5Å
resolution leads to a significantly revised model of CPA binding when compared
with earlier reports. It shows that a divalent metal ion is required for CPA
binding through coordination of the tetramic acid moiety at a characteristic
kink of the M1 helix found in all P-type ATPase structures, which is expected
to be part of the cytoplasmic cation access pathway. Our model is consistent
with the biochemical data on CPA function and provides new measures in
structure-based drug design targeting Ca2+-ATPases, e.g.
from pathogens. We also present an extended structural basis of ATP modulation
pinpointing key residues at or near the ATP binding site. A structural
comparison to the Na+,K+-ATPase reveals that the
Phe93 side chain occupies the equivalent binding pocket of the CPA
site in SERCA, suggesting an important role of this residue in stabilization
of the potassium-occluded E2 state of Na+,K+-ATPase.The Ca2+-ATPase from sarco(endo)plasmic reticulum of rabbit
skeletal muscle
(SERCA,5 isoform 1a)
is a thoroughly studied member of the P-type ATPase family
(1). SERCA possesses 10
transmembrane helices (M1 through M10) with both the N terminus and the C
terminus facing the cytoplasmic side and three cytoplasmic domains, inserted
in loops between M2 and M3 (A-domain) and between M4 and M5 (P- and N-domain)
(2). The enzyme mediates the
uptake of Ca2+ ions into the lumen of the sarcoplasmic reticulum
(SR) after their release into the cytoplasm through calcium release channels
during muscle contraction (3).
SERCA, plasma membrane Ca2+-ATPase, and a third, Golgi-located
secretory pathway Ca2+-ATPase are important factors in calcium and
manganese homeostasis, transport, signaling, and regulation
(4,
5).Crystal structures of all major states in the reaction cycle of SERCA have
been determined. These include the Ca2E1·ATP
state (6,
7) with high affinity
Ca2+ binding sites accessible from the cytoplasmic side of the SR
membrane, the calcium-occluded
transition state (6), the open
E2P state with luminal facing ion binding sites that have low affinity for
Ca2+ and high affinity for protons
(8) and the proton-occluded
H2–3E2[ATP] state with a bound modulatory ATP
(9). This considerable amount
of structural information has turned the Ca2+-ATPase into a
valuable model system for studies on structural rearrangements that take place
during the catalytic cycle of P-type ATPases. SERCA is considered a promising
drug target in medical research, with a particular focus on prostate cancer
and infectious diseases. Several compounds have already been shown to bind and
inhibit SERCA by stabilizing the enzyme in a particular conformational state.
Thapsigargin (TG), cyclopiazonic acid (CPA), and 2,5-di-(tert-butyl)
hydroquinone (BHQ) stabilize an E2-like state, and 1,3-dibromo-2,4,6-tri
(methylisothiouronium)benzene stabilizes an E1-P-like conformation
(10–13).
CPA is a toxic indole tetramic acid first isolated from Penicillium
cyclopium (14) and later
found to be produced by Aspergillus versicolor and Aspergillus
flavus. Like TG, CPA specifically binds to and inhibits SERCA with
nanomolar affinity (15).
Indeed, CPA is widely used in biochemical and physiological studies on
Ca2+ signaling and muscle function, where it causes Ca2+
store depletion due to specific inhibition of Ca2+ reuptake by
SERCA. CPA and TG were originally proposed to bind to similar sites on SERCA
(16), but recent crystal
structures have shown a distinct site of interaction
(17,
18). Despite these structural
insights, a previously demonstrated magnesium dependence of CPA binding
(19) remained unexplained, and
opposing CPA binding modes were observed (see below).Tetramic acids are synthesized naturally, and more than 150 natural
derivatives have been isolated from bacterial and fungal species (reviewed in
Ref. 20). Tetramic acids
possessing a 3-acyl group have the ability to chelate divalent metal ions. For
instance, tenuazonic acid from the fungus Phoma sorghina has been
shown to form complexes with Ca2+ and Mg2+
(21), as well as heavier
metals such as Cu(II), Ni(II), and Fe(III)
(22).Previously published crystallographic structures of the SERCA·CPA
complex (PDB ID 2O9J and 2EAS) demonstrated that CPA binds within the proposed
calcium access channel of SERCA. However, the structures did not reveal a role
for magnesium, and the orientation of CPA within this binding site differed in
the two studies (17,
18). To address these
ambiguities, we have determined the crystal structure of SERCA in complex with
, AMPPCP (an ATP analog), and
Mn2+·CPA. The structure reveals novel insight into CPA
binding, which we find to be mediated by a divalent cation, as demonstrated by
means of the anomalous scattering properties of Mn2+. Further and
improved refinement using previously deposited data (PDB ID 2O9J and 2OA0), in
light of our new findings, also revealed a strong plausibility for a magnesium
ion bound at this site. Furthermore, we find a new configuration of the bound
AMPPCP nucleotide, addressing the modulatory role of ATP binding to the
E2·Pi occluded conformation of SERCA. 相似文献
Thapsigargin (Tg), a specific inhibitor of sarco/endoplasmic Ca2+-ATPases (SERCA), binds with high affinity to the E2 conformation of these ATPases. SERCA inhibition leads to elevated calcium levels in the cytoplasm, which in turn induces apoptosis. We present x-ray crystallographic and intrinsic fluorescence data to show how Tg and chemical analogs of the compound with modified or removed side chains bind to isolated SERCA 1a membranes. This occurs by uptake via the membrane lipid followed by insertion into a resident intramembranous binding site with few adaptative changes. Our binding data indicate that a balanced hydrophobicity and accurate positioning of the side chains, provided by the central guaianolide ring structure, defines a pharmacophore of Tg that governs both high affinity and access to the protein-binding site. Tg analogs substituted with long linkers at O-8 extend from the binding site between transmembrane segments to the putative N-terminal Ca2+ entry pathway. The long chain analogs provide a rational basis for the localization of the linker, the presence of which is necessary for enabling prostate-specific antigen to cleave peptide-conjugated prodrugs targeting SERCA of cancer cells (Denmeade, S. R., Jakobsen, C. M., Janssen, S., Khan, S. R., Garrett, E. S., Lilja, H., Christensen, S. B., and Isaacs, J. T. (2003) J. Natl. Cancer Inst. 95, 990–1000). Our study demonstrates the usefulness of a simple in vitro system to test and direct development toward the formulation of new Tg derivatives with improved properties for SERCA targeting. Finally, we propose that the Tg binding pocket may be a regulatory site that, for example, is sensitive to cholesterol. 相似文献
Tuftsin (Thr‐Lys‐Pro‐Arg) is a natural immunomodulating peptide found to stimulate phagocytosis in macrophages/microglia. Tuftsin binds to the receptor neuropilin‐1 (Nrp1) on the surface of cells. Nrp1 is a single‐pass transmembrane protein, but its intracellular C‐terminal domain is too small to signal independently. Instead, it associates with a variety of coreceptors. Despite its long history, the pathway through which tuftsin signals has not been described. To investigate this question, we employed various inhibitors to Nrp1's coreceptors to determine which route is responsible for tuftsin signaling. We use the inhibitor EG00229, which prevents tuftsin binding to Nrp1 on the surface of microglia and reverses the anti‐inflammatory M2 shift induced by tuftsin. Furthermore, we demonstrate that blockade of transforming growth factor beta (TGFβ) signaling via TβR1 disrupts the M2 shift similar to EG00229. We report that tuftsin promotes Smad3 phosphorylation and reduces Akt phosphorylation. Taken together, our data show that tuftsin signals through Nrp1 and the canonical TGFβ signaling pathway.
Receptor for activated C-kinase 1 (RACK1) serves as a scaffolding protein in numerous signaling pathways involving kinases and membrane-bound receptors from different cellular compartments. It exists simultaneously as a cytosolic free form and as a ribosome-bound protein. As part of the 40S ribosomal subunit, it triggers translational regulation by establishing a direct link between protein kinase C and the protein synthesis machinery. It has been suggested that RACK1 could recruit other signaling molecules onto the ribosome, providing a signal-specific modulation of the translational process. RACK1 is able to dimerize both in vitro and in vivo. This homodimer formation has been observed in several processes including the regulation of the N-methyl-d-aspartate receptor by the Fyn kinase in the brain and the oxygen-independent degradation of hypoxia-inducible factor 1. The functional relevance of this dimerization is, however, still unclear and the question of a possible dimerization of the ribosome-bound protein is still pending. Here, we report the first structure of a RACK1 homodimer, as determined from two independent crystal forms of the Saccharomyces cerevisiae RACK1 protein (also known as Asc1p) at 2.9 and 3.9 Å resolution. The structure reveals an atypical mode of dimerization where monomers intertwine on blade 4, thus exposing a novel surface of the protein to potential interacting partners. We discuss the significance of the dimer structure for RACK1 function. 相似文献
The serpin plasminogen activator inhibitor-1 (PAI-1) is a crucial regulator in fibrinolysis and tissue remodeling. PAI-1 has been associated with several pathological conditions and is a validated prognostic marker in human cancers. However, structural information about the native inhibitory form of PAI-1 has been elusive because of its inherent conformational instability and rapid conversion to a latent, inactive structure. Here we report the crystal structure of PAI-1 W175F at 2.3 Å resolution as the first model of the metastable native molecule. Structural comparison with a quadruple mutant (14-1B) previously used as representative of the active state uncovered key differences. The most striking differences occur near the region that houses three of the four mutations in the 14-1B PAI-1 structure. Prominent changes are localized within a loop connecting β-strand 3A with the F helix, in which a previously observed 310-helix is absent in the new structure. Notably these structural changes are found near the binding site for the cofactor vitronectin. Because vitronectin is the only known physiological regulator of PAI-1 that slows down the latency conversion, the structure of this region is important. Furthermore, the previously identified chloride-binding site close to the F-helix is absent from the present structure and likely to be artifactual, because of its dependence on the 14-1B mutations. Instead we found a different chlorine-binding site that is likely to be present in wild type PAI-1 and that more satisfactorily accounts for the chlorine stabilizing effect on PAI-1. 相似文献