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Protein Binding (0):
Recent article
Protein Binding
Abstract
We have discovered that other cellular stressors are integrated with glucocorticoid signaling through a new hormone-independent phosphorylation site, Ser134, on the human glucocorticoid receptor (GR). Ser134 phosphorylation is induced by a variety of stress-activating stimuli in a p38 mitogen-activa...
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PMID: 21930780
PDF is available here.
PDF is available here.
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Abstract
We studied allelic variants of the V(H)2-5 inferred germ line forms of the HIV-1 gp41 bNAb 2F5 for their antigen binding affinities to gp41 linear peptide and conformational protein antigens. Both V(H)2-5 2F5 inferred germ line variants bound to gp41 peptides and protein, including the fusion interm...
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PMID: 21917975
PDF is available here.
PDF is available here.
Human Molecular Genetics (20)21 2011
Abstract
We previously found that loss-of-function mutations in the transcription factor GLIS2, a putative vertebrate ortholog of Drosophila Ci, cause nephronophthisis type 7 in humans and mice. Kidney tubular cells in Glis2-knockout mice acquire mesenchymal phenotype, but the cellular mechanisms of this tra...
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PMID: 21816948
PDF is available here.
PDF is available here.
Abstract
We developed a nuclear magnetic resonance approach that enabled direct detection of structural elements within the intact leader (712-nucleotide dimer) that are critical for genome packaging. Residues spanning the gag start codon (AUG) form a hairpin in the monomeric leader and base pair with residu...
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PMID: 21998393
PDF is available here.
PDF is available here.
Abstract
We found that the core ER-lumenal domain (cLD) of yeast Ire1 binds to unfolded proteins in yeast cells and to peptides primarily composed of basic and hydrophobic residues in vitro. Mutation of amino acid side chains exposed in a putative peptide-binding groove of Ire1 cLD impaired peptide binding....
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PMID: 21852455
PDF is available here.
PDF is available here.
Abstract
We determined the high-resolution crystal structures of the EV71 3C(pro)/rupintrivir complex, showing that although rupintrivir interacts with EV71 3C(pro) similarly to HRV 3C(pro), the C terminus of the inhibitor cannot accommodate the leaving-group pockets of EV71 3C(pro). Our structures reveal th...
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PMID: 21813612
PDF is available here.
PDF is available here.
Abstract
Saccharopine dehydrogenase catalyzes the NAD-dependent oxidative deamination of saccharopine to l-lysine and α-ketoglutarate. Lysine 99 is within hydrogen-bond distance to the α-carboxylate of the lysine substrate and D319 is in the vicinity of the carboxamide side chain of NADH. Both are conserved...
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PMID: 21819960
PDF is available here.
PDF is available here.
Abstract
We have studied the composition of complexes that copurify with Spb4 tagged by tandem affinity purification (TAP-tagged Spb4). These complexes contain mainly the 27SB pre-rRNAs and about 50 ribosome biogenesis proteins, primarily components of early pre-60S ribosomal particles. To a lesser extent, s...
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PMID: 21825077
PDF is available here.
PDF is available here.
Abstract
We show that homozygous disruption of PHD-1 (PHD-1(-/-)) could facilitate HIF-1α-mediated cardioprotection in ischemia/reperfused (I/R) myocardium. Wild-type (WT) and PHD-1(-/-) mice were randomized into WT time-matched control (TMC), PHD-1(-/-) TMC (PHD1TMC), WT I/R, and PHD-1(-/-) I/R (PHD1IR). I...
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PMID: 21083501
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1813)10 2011
Abstract
We report here for the first time that Parcs/Gpn3 plays a critical role in the nuclear accumulation of RNAP II, and we propose that this function explains the relative importance of Parcs/Gpn3 in cell proliferation. Intriguingly, at least some tumorigenic mammary cells have evolved mechanisms that a...
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PMID: 21782856
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)10 2011
Abstract
The structural basis of the extreme pH dependence of oxygen binding to Root effect Hbs is a long-standing puzzle in the field of protein chemistry. A previously unappreciated role of steric factors in the Root effect was revealed by a comparison of pH effects on oxygenation and oxida...
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PMID: 21745602
PDF is available here.
PDF is available here.
Abstract
The heat of lysozyme adsorption on mesostructured cellular foam (MCF) silica was measured using flow microcalorimetry (FMC) to investigate the influence of a neutral salt, sodium sulfate. At concentrations up to 0.5 M sodium sulfate, a complex initial exotherm was followed by an endotherm. Protein su...
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PMID: 21835415
PDF is available here.
PDF is available here.
Abstract
We purified each individual NEAT domain of IsdX2 as a GST fusion and analyzed the specific function of each domain as it relates to heme acquisition and transport. NEAT domains 1, 3, 4, and 5 all bind heme, with domain 5 having the highest affinity. All NEATs associate with hemoglobin, but only NEAT...
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PMID: 21808055
PDF is available here.
PDF is available here.
Abstract
We report that arginine methylation weakens the affinity of PABPN1 for transportin. Recombinant, unmethylated PABPN1 binds more strongly to transportin than its methylated counterpart from mammalian tissue, and in vitro methylation reduces the affinity. Transportin and RNA compete for binding to PAB...
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PMID: 21808065
PDF is available here.
PDF is available here.
Abstract
We determined the crystal structure of the catalytic domain of MMP-2 in complex with APP-IP. We found that APP-IP in the complex is indeed embedded into the substrate-binding cleft of the catalytic domain in the N to C direction opposite that of substrate. With the crystal structure, it was first cl...
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PMID: 21813640
PDF is available here.
PDF is available here.
Abstract
We demonstrated in vitro and in vivo phosphorylation of RanBP1 by Plk1 as well as the importance of phosphorylation of RanBP1 in the interaction between Plk1 and Ran during early mitosis. Both phosphorylation-defective and N-terminal deletion mutant constructs of RanBP1 disrupted the interaction wit...
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PMID: 21813642
PDF is available here.
PDF is available here.
Abstract
We show that KLHL7 forms a dimer, assembles with Cul3 through its BTB and BACK domains, and exerts E3 activity. Lys-48-linked but not Lys-63-linked polyubiquitin chain co-localized with KLHL7, which increased upon proteasome inhibition suggesting that KLHL7 mediates protein degradation via UPS. An a...
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PMID: 21828050
PDF is available here.
PDF is available here.
Abstract
We show that the properties of B. anthracis Mn-NrdF and Fe-NrdF are in general similar for interaction with NrdE and NrdI. Intriguingly, the enzyme activity of Mn-NrdF was approximately an order of magnitude higher than that of Fe-NrdF in the presence of the class Ib-specific physiological reductant...
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PMID: 21832039
PDF is available here.
PDF is available here.
Abstract
We show that labile S4 complexes rearrange into stable complexes within a few minutes at 42 °C, with longer coincubation leading to an increased population of stable complexes. In contrast, prefolding the rRNA has a smaller effect on stable S4 binding. Experiments with minimal rRNA fragments show...
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PMID: 21821049
PDF is available here.
PDF is available here.
Abstract
We show that C0 and C1 can each bind to the same two distinctly different positions on F-actin. One position aligns well with the previously reported binding site that clashes with the binding of myosin to actin, but would force tropomyosin into an "on" position that exposes myosin binding sites alo...
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PMID: 21821050
PDF is available here.
PDF is available here.
Abstract
We identify a previously unknown target of POA as the ribosomal protein S1 (RpsA), a vital protein involved in protein translation and the ribosome-sparing process of trans-translation. Three PZA-resistant clinical isolates without pncA mutation harbored RpsA mutations. RpsA overexpression conferred...
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PMID: 21835980
PDF is available here.
PDF is available here.
Abstract
We report that TAF1B, a subunit of human Pol I basal transcription factor SL1, is structurally related to TFIIB/TFIIB-like proteins, through predicted amino-terminal zinc ribbon and cyclin-like fold domains. SL1, essential for Pol I recruitment to the ribosomal RNA gene promoter, also has an essenti...
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PMID: 21921199
PDF is available here.
PDF is available here.
Abstract
We report that the histone acetyltransferase (HAT), p300, specifically acetylates BTas both in vivo and in vitro. Further studies demonstrated that BTas acetylation markedly enhances its transactivation activity. Mutagenesis analysis identified three lysines at positions 66, 109 and 110 in BTas that...
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PMID: 21813148
PDF is available here.
PDF is available here.
Abstract
We show that CUP employs multiple mechanisms to repress the expression of target mRNAs. In addition to inducing translational repression, CUP maintains mRNA targets in a repressed state by promoting their deadenylation and protects deadenylated mRNAs from further degradation. Translational repressio...
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PMID: 21937713
PDF is available here.
PDF is available here.
Abstract
We show that CLIP (cytoplasmic linker protein)-associated protein (CLASP), originally identified as a MT plus end-binding protein, displays both plus end-binding and lattice-binding activities in nerve growth cones, and reveal that the two MT-binding activities regulate axon growth in an opposing ma...
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PMID: 21937714
PDF is available here.
PDF is available here.
Abstract
We show that a LIM domain protein, Espinas (Esn), binds to an intracellular juxtamembrane domain of Flamingo (Fmi), and that this Fmi-Esn interplay elicits repulsion between dendritic branches of Drosophila sensory neurons. In wild-type larvae, branches of the same class IV dendritic arborization ne...
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PMID: 21937715
PDF is available here.
PDF is available here.
Biomacromolecules (12)9 2011
Abstract
We propose substrate-independent modification for creating a protein-repellent surface based on dopamine-melanin anchoring layer used for subsequent binding of poly(ethylene oxide) (PEO) from melt. We verified that the dopamine-melanin layer can be formed on literally any substrate and could serve a...
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PMID: 21823677
PDF is available here.
PDF is available here.
Abstract
We characterized an E-box motif (RBE1) within the core promoter that was previously implicated in both transcriptional activation and repression. We show that RBE1 is a binding site for the RBF-2 transcription factor complex (USF1, USF2, and TFII-I), previously shown to bind an upstream viral elemen...
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PMID: 21813151
PDF is available here.
PDF is available here.
Abstract
We recently characterized the interaction between the intraviral domains of envelope glycoproteins (Gn and Gc) and ribonucleoprotein (RNP) of Puumala and Tula hantaviruses (genus Hantavirus, family Bunyaviridae). Herein we report a direct interaction between spike-forming glycoprotein and nucleic ac...
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PMID: 21807393
PDF is available here.
PDF is available here.
Abstract
One of the fundamental questions of enzymology is how catalytic power is derived. This review focuses on recent developments in the structure--function relationships of chorismate-utilizing enzymes involved in siderophore biosynthesis to provide insight into the biocatalysis of pericyclic reactions....
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PMID: 21823653
PDF is available here.
PDF is available here.
Abstract
We report the development of an in vitro assay for the enzyme and the discovery of a cell-permeable CPAF zymogen-based peptide inhibitor with nanomolar inhibitory affinity. Treating C. trachomatis-infected HeLa cells with this inhibitor prevented CPAF cleavage of the intermediate filament vimentin a...
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PMID: 21830778
PDF is available here.
PDF is available here.
Abstract
Background. The complement system is tightly controlled by several regulators. Two of these, factor H (FH) and C4b-binding protein (C4BP), can be acquired by pathogens conveying resistance to complement attack. The aim of the study was to characterize the FH binding molecule of Candida albicans, a...
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PMID: 21844307
PDF is available here.
PDF is available here.
Abstract
We have shown previously that deficiency of another peptidyl prolyl isomerase, FK506 binding protein 12/12.6, alters endothelial NO synthase phosphorylation and causes endothelial dysfunction and hypertension. Endothelial NO synthase contains the Pin1 binding sequence at (p)serine 116-proline 117 an...
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PMID: 21810655
PDF is available here.
PDF is available here.
Abstract
We examine the distribution, interactions and functions of the maternal planar cell polarity core protein Vangl2 and the apical-basal complex component aPKC. We show that Vangl2 is distributed in animally enriched islands in the subcortical cytoplasm in full-grown oocytes, where it interacts with a...
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PMID: 21813572
PDF is available here.
PDF is available here.
Abstract
We show that Act D and CHX reduced glucocorticoid binding, GR turnover and impaired GR nuclear translocation. We performed the same experiments in different thymocyte subpopulations of Balb/c mice. At the highest dose tested, actinomycin D and cycloheximide abolished glucocorticoid-induced cell deat...
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PMID: 21569845
PDF is available here.
PDF is available here.
Abstract
Junctional adhesion molecules are transmembrane proteins that belong to the immunoglobulin superfamily. In addition to their localization in close proximity to the tight junctions in endothelial and epithelial cells, junctional adhesion molecules are also expressed in circulating cel...
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PMID: 21254840
PDF is available here.
PDF is available here.
Molecular BioSystems (7)9 2011
Abstract
We resolved cytoplasmic and membrane-associated complexes from hESCs and characterised their composition, stoichiometry, and dynamics by denaturing SDS-PAGE. The reliability of the fractionation was examined by western blot analysis of membrane and cytosolic markers. MALDI TOF/TOF mass spectrometry...
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PMID: 21727978
PDF is available here.
PDF is available here.
Molecular BioSystems (7)9 2011
Abstract
We developed an integrated proteomic platform with the combination of 2-D native/SDS-PAGE-based proteomics with co-immunoprecipitation, far-Western blotting, His-tag affinity purification and functional analysis, and used it to investigate the E. coli cytosolic complexome. A total of 24 distinct het...
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PMID: 21717022
PDF is available here.
PDF is available here.
Mucosal Immunology (4)5 2011
Abstract
We summarize recent findings regarding normal functions of NOD2 and discuss the mechanisms by which NOD2 polymorphisms associated with Crohn's disease lead to intestinal inflammation....
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PMID: 21750585
PDF is available here.
PDF is available here.
Abstract
Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) has been shown to modulate multiple cellular processes, including apoptosis. The aim of this study was to assess the effects of HCV NS5A on apoptosis induced by Toll-like receptor (TLR) 4 ligand, lipopolysaccharide (LPS)....
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PMID: 21844306
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)10 2011
Abstract
We therefore examined the interaction of peptides corresponding to either AS1 or AS2 of four different, well-characterized HAMP domains with several membrane model systems. The proteins included an Archaeoglobus fulgidus protein (Af1503), the Escherichia coli osmosensor EnvZ(Ec), the E. coli nitrate...
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PMID: 21763270
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)10 2011
Abstract
The interaction of the extra-membranous domain of tetrameric inwardly rectifying Kir2.1 ion channels (Kir2.1NC(4)) with the membrane associated guanylate kinase protein PSD-95 has been studied using Transmission Electron Microscopy in negative stain. Three types of complexes were observed in electron...
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PMID: 21756874
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1809)9 2011
Abstract
We review chromatin-associated signals that are recognized by remodelers. It is discussed how these regulate the remodeling reaction via changing the nucleosome substrate/product binding affinity or the catalytic translocation rate. Finally, we address the question of how chromatin remodelers operat...
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PMID: 21704204
PDF is available here.
PDF is available here.
Abstract
We have examined the in vivo amyloid reactivity of seven heparin-binding peptides by using single photon emission and X-ray computed tomographic imaging, microautoradiography, and tissue biodistribution measurements. All of the peptides bound amyloid deposits within 1 h post-injection, but the exten...
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PMID: 21807994
PDF is available here.
PDF is available here.
Abstract
We use sortase-mediated transpeptidation, a technique that allows placement of a variety of probes on a polypeptide backbone, to monitor the behavior of labeled functional dectin-1 in live cells with and without fungal challenge. Installation of probes on dectin-1 by sortagging permitted highly spec...
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PMID: 21825168
PDF is available here.
PDF is available here.
Abstract
We evaluated the direct-contact and respiratory-droplet transmissibility in ferrets of representative swine influenza viruses of different lineages obtained through a 13-y surveillance program in southern China. Whereas all viruses studied were transmitted by direct contact with varying efficiency,...
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PMID: 21825167
PDF is available here.
PDF is available here.
Abstract
We show here that DNA binding to the DNA-gate of gyrase and wrapping of DNA around the C-terminal domains of GyrA induces a narrowing of the N-gate. This half-closed state prepares capture of a T-segment in the upper cavity of gyrase. Subsequent N-gate closure upon binding of ATP then poises the rea...
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PMID: 21817063
PDF is available here.
PDF is available here.
Abstract
We determined the structure of the hydrophilic domain. Here we report the crystal structure of the Esherichia coli complex I membrane domain at 3.0 Å resolution. It includes six subunits, NuoL, NuoM, NuoN, NuoA, NuoJ and NuoK, with 55 transmembrane helices. The fold of the homologous antiporter-l...
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PMID: 21822288
PDF is available here.
PDF is available here.
Abstract
A large-scale similarity search investigation has been carried out on 266 well-defined compound activity classes extracted from the ChEMBL database. The analysis was performed using two widely applied two-dimensional (2D) fingerprints that mark opposite ends of the current performanc...
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PMID: 21728295
PDF is available here.
PDF is available here.
Abstract
We sought to develop an appropriate method to examine large sets of GPCR ligand information for both screening collection enhancement and hit expansion. To this end, we have implemented a modified version of BDACCS that removes highly correlated descriptors (rBDACCS). To test the hypothesis that a s...
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PMID: 21761904
PDF is available here.
PDF is available here.
Abstract
We report the crystal structure of a motor domain dimer in complex with its tail domain at 2.2 angstroms and compare it with a structure of the motor domain alone at 2.7 angstroms. These structures indicate that neither an induced conformational change nor steric blocking is the cause of inhibition....
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PMID: 21836017
PDF is available here.
PDF is available here.
Abstract
We found that KIF1A, an axonal transporter of synaptic vesicles, interacts with the domain encoded by the HSN2 exon. In parallel to this screen, we performed genome-wide homozygosity mapping in a consanguineous Afghan family affected by HSANII and identified a unique region of homozygosity located o...
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PMID: 21820098
PDF is available here.
PDF is available here.
Journal of Cell Science (124)Pt 16 2011
Abstract
We provide novel insights into the roles of the CB2 splice variants, CB2(SH3+) and CB2(SH3-), and their substrate, Cdc42, in regulating gephyrin clustering at GABAergic synapses. Transfection of Myc-tagged CB2(SH3+) and CB2(SH3-) into cultured neurons revealed strong, but distinct, effects promoting...
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PMID: 21807943
PDF is available here.
PDF is available here.
Abstract
We identified cartilage acidic protein-1B as a key molecule for lateral olfactory tract (LOT) formation and named it LOT usher substance (LOTUS). We further identified Nogo receptor-1 (NgR1) as a LOTUS-binding protein. NgR1 is a receptor of myelin-derived axon growth inhibitors, such as Nogo, which...
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PMID: 21817055
PDF is available here.
PDF is available here.
Journal of Cell Biology (194)3 2011
Abstract
We address this issue using yeast mitochondria and the multispan protein Ugo1. Using a specific insertion assay and analysis by native gel electrophoresis, we show that the import receptor Tom70, but not its partner Tom20, is involved in the initial recognition of the Ugo1 precursor. Surprisingly, t...
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PMID: 21825074
PDF is available here.
PDF is available here.
Abstract
We evaluated four docking tools-MOE2009, Glide 5.5, QXP-Flo+0802, and Autodock 4.0-for their ability to simulate complexes between these enzymes and RNA oligomers. To validate our results, we analyzed the docking results with respect to the known key interactions between the protein and the nucleoti...
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PMID: 21120556
PDF is available here.
PDF is available here.
Abstract
We first show using deletion analysis and in vivo infection, that InlK is a bona fide virulence factor, poorly expressed in vitro and well expressed in vivo, and that it is anchored to the bacterial surface by sortase A. We then demonstrate by a yeast two hybrid screen using InlK as a bait, validate...
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PMID: 21829365
PDF is available here.
PDF is available here.
Abstract
Measurement of drug concentrations in biological samples is of utmost importance in many research areas. The information about the amount of drug in a biological sample can be given as either total concentration, which ignores the interaction of the drug with the sample matrix, or as...
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PMID: 21827273
PDF is available here.
PDF is available here.
Abstract
Peroxynitrite (ONOO-) besides its toxic possesses regulatory action that includes the modulation of oxygen binding properties of blood. The aim of this work was to estimate ONOO- effect on the haemoglobin oxygen affinity (HOA) in vitro in presence of different partial pressure of car...
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PMID: 21961310
PDF is available here.
PDF is available here.
Ukrainskij biokhimicheskij zhurnal/Ukrayins'kij biokhimichnij zhurnal/Ukrainian biochemical journal (82)6 2011
Abstract
The paper presents new information about the carbohydrate structures of 39-days chicken's fibronectin. It is found out that chicken fibronectin contains mainly biantennary N-glycans with a core fucose and fucosylated O-glycans. It is shown that N-glycans of chicken fibronectin are poorly sialated, si...
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PMID: 21805863
PDF is available here.
PDF is available here.