Looking for online definition of putative RNA-binding protein 11 in the Medical Dictionary? putative RNA-binding protein 11 explanation free. What is putative RNA-binding protein 11? Meaning of putative RNA-binding protein 11 medical term. What does putative RNA-binding protein 11 mean?

TY - JOUR. T1 - Definition of the Inhibitory Domain of Smooth Muscle Myosin Light Chain Kinase by Site-Directed Mutagenesis. AU - Ito, Masaaki. AU - Guerriero, Vince. AU - Chen, Xiaomin. AU - Hartshorne, David J.. PY - 1991/4/1. Y1 - 1991/4/1. N2 - Site-directed mutagenesis of smooth muscle myosin light chain kinase was applied to define its autoinhibitory domain. Mutants were all initiated at Leu-447 but contained varying lengths of C-terminal sequence. Those containing the complete C-terminal sequence to Glu-972 possessed kinase activities that were calmodulin-dependent. Removal of the putative inhibitory domain by truncation to Thr-778 resulted in generation of a constitutively active (calmodulin-independent) species. Thus, the inhibitory domain lies to the C-terminal side of Thr-778. Truncation to Lys-793 and to Trp-800 also resulted in constitutively active mutants, although the specific activity of the latter was less than the other mutants. None of the truncated mutants bound calmodulin. ...

Abstract. The use of recombinant peptides based upon the repeated amino acid sequences of Plasmodium has been proposed for malaria vaccines. By reducing homologies of such peptide vaccines to host proteins, the possibility of autoimmune complications may be reduced, and the effective immune response may be enhanced. The Wilbur and Lipman Wordsearch algorithm was used to identify homologous amino acid sequences between tandemly repeated Plasmodium amino acid sequences and the human and human viral sequences compiled in the National Biomedical Research Foundation database. Six published repetitive immunogenic amino acid sequences from the circumsporozoite (CS) antigen, ring-infected erythrocyte surface antigen (RESA), soluble (S) antigen, and falciparum interspersed repetitive antigen (FIRA) of P. falciparum, and the CS protein of P. vivax, were analyzed by computer. Matches of at least 4 amino acids were found for all sequences. In the database, 29 matches were found for human proteins and 26 matches

Divergence of transcription factor binding sites is considered to be an important source of regulatory evolution. The associations between transcription factor binding sites and phenotypic diversity have been investigated in many model organisms. However, the understanding of other factors that contribute to it is still limited. Recent studies have elucidated the effect of chromatin structure on molecular evolution of genomic DNA. Though the profound impact of nucleosome positions on gene regulation has been reported, their influence on transcriptional evolution is still less explored. With the availability of genome-wide nucleosome map in yeast species, it is thus desirable to investigate their impact on transcription factor binding site evolution. Here, we present a comprehensive analysis of the role of nucleosome positioning in the evolution of transcription factor binding sites. We compared the transcription factor binding site frequency in nucleosome occupied regions and nucleosome depleted regions

The gain and loss of functional transcription factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an evolutionary model to study binding-site turnover that uses multiple sequence alignments to assess the evolutionary constraint on individual binding sites, and to map gain and loss events along a phylogenetic tree. We apply this model to study the evolutionary dynamics of binding sites of the Drosophila melanogaster transcription factor Zeste, using genome-wide in vivo (ChIP-chip) binding data to identify functional Zeste binding sites, and the genome sequences of D. melanogaster, D. simulans, D. erecta, and D. yakuba to study their evolution. We estimate that more than 5% of functional Zeste binding sites in D. melanogaster were gained along the D. melanogaster lineage or lost along one of the other lineages. We find that Zeste-bound regions have a reduced rate of binding-site loss and an increased rate of binding

An accurate method based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been developed for quantitative analysis of calcitonin and insulin in different commercially available pharmaceutical products. Tryptic peptides derived from these polypeptides were chemically modified at their C-terminal lysine-residues with 2-methoxy-4,5-dihydro-imidazole (light tagging) as standard and deuterated 2-methoxy-4,5-dihydro-imidazole (heavy tagging) as internal standard (IS). The heavy modified tryptic peptides (4D-Lys tag), differed by four atomic mass units from the corresponding light labelled counterparts (4H-Lys tag). The normalized peak areas (the ratio between the light and heavy tagged peptides) were used to construct a standard curve to determine the concentration of the analytes. The concentrations of calcitonin and insulin content of the analyzed pharmaceutical products were accurately determined, and less than 5% error was obtained between the ...

Looking for online definition of cystic fibrosis transmembrane conductance regulator gene in the Medical Dictionary? cystic fibrosis transmembrane conductance regulator gene explanation free. What is cystic fibrosis transmembrane conductance regulator gene? Meaning of cystic fibrosis transmembrane conductance regulator gene medical term. What does cystic fibrosis transmembrane conductance regulator gene mean?

Looking for online definition of nonpolar amino acid in the Medical Dictionary? nonpolar amino acid explanation free. What is nonpolar amino acid? Meaning of nonpolar amino acid medical term. What does nonpolar amino acid mean?

TY - JOUR. T1 - Partial nucleotide sequence of the Murray Valley encephalitis virus genome. Comparison of the encoded polypeptides with yellow fever virus structural and non-structural proteins. AU - Dalgarno, Lynn. AU - Trent, Dennis W.. AU - Strauss, James H.. AU - Rice, Charles M.. PY - 1986/2/5. Y1 - 1986/2/5. N2 - The sequence of 5400 bases corresponding to the 5′-terminal half of the Murray Valley encephalitis virus genome has been determined. The genome contains a 5′ non-coding region of about 97 nucleotides, followed by a single continuous open reading frame that encodes the structural proteins followed by the non-structural proteins. Amino acid sequence homology between the Murray Valley encephalitis and yellow fever (Rice et al., 1985) polyproteins is 42% over the region sequenced. The start points of the various Murray Valley encephalitis virus-coded proteins have been assigned on the basis of this homology and a consistent set of potential proteolytic cleavage sites identified, ...

TY - JOUR. T1 - Mutations of the Walker B motif in the first nucleotide binding domain of multidrug resistance protein MRP1 prevent conformational maturation. AU - Cui, L.. AU - Hou, Y. X.. AU - Riordan, J. R.. AU - Chang, X. B.. PY - 2001/8/1. Y1 - 2001/8/1. N2 - ATP-binding cassette (ABC) transporters couple the binding and hydrolysis of ATP to the translocation of solutes across biological membranes. The so-called "Walker motifs" in each of the nucleotide binding domains (NBDs) of these proteins contribute directly to the binding and the catalytic site for the MgATP substrate. Hence mutagenesis of residues in these motifs may interfere with function. This is the case with the MRP1 multidrug transporter. However, interpretation of the effect of mutation in the Walker B motif of NBD1 (D792L/D793L) was confused by the fact that it prevented biosynthetic maturation of the protein. We have determined now that this latter effect is entirely due to the D792L substitution. This variant is unable to ...

BACKGROUND Sequence type 131 (ST131) is a predominant lineage among extraintestinal pathogenic Escherichia coli. It plays a major role in the worldwide dissemination of extended-spectrum β-lactamase (ESBL)-producing E. coli. The ST131 pandemic is mainly the result of clonal expansion of the single well-adapted subclone H30-Rx, which is acquired in hospitals more frequently than other ESBL-producing E. coli clones. AIM To develop a rapid method using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify ST131 for infection control purposes. METHODS Peak biomarkers of ST131 were identified from the mass spectrum profiles of 109 E. coli isolates (including 50 ST131 isolates). FINDINGS The models accurately identified ST131 isolates from mass spectrum profiles obtained with and without protein extraction. CONCLUSIONS The rapid identification of ST131 isolates with MALDI-TOF MS can be easily implemented in the laboratory, and could help to target

Proprotein convertase furin is responsible for the processing of a wide variety of precursors consisted of signal peptide, propeptide and mature peptide in mammal. Many precursors processed by furin have important physiological functions and can be recombinantly expressed in Pichia pastoris expression system for research, pharmaceutical and vaccine applications. However, it is not clear whether the furin cleavage sites between the propeptide and mature peptide can be properly processed in P. pastoris, bringing uncertainty for proper expression of the coding DNA sequences of furin precursors containing the propeptides and mature peptides. In this study, we evaluated the ability of P. pastoris to process furin cleavage sites and how to improve the cleavage efficiencies of furin cleavage sites in P. pastoris. The results showed that P. pastoris can process furin cleavage sites but the cleavage efficiencies are not high. Arg residue at position P1 or P4 in furin cleavage sites significantly affect cleavage

TY - JOUR. T1 - Molecular Cloning and Primary Structure of Rat Testes Metalloendopeptidase EC 3.4.24.15. AU - Pierotti, Adrian. AU - Glucksman, Marc J.. AU - Roberts, James L.. AU - Dong, Ke Wen. AU - Pierotti, Adrian. AU - Orlowski, Marian. PY - 1990/11/1. Y1 - 1990/11/1. N2 - The complete amino acid sequence of rat testes metalloendopeptidase (EC 3.4.24.15) was deduced from the nucleotide sequence of a cDNA clone isolated by screening a rat testes library with a polyclonal antibody raised against a homogeneous preparation of the rat testes enzyme. The correctness of the sequence was verified by N-terminal amino acid sequence analysis of the isolated enzyme and by partial amino acid sequence analysis of three tryptic peptides located near the N-terminus, the middle, and C-terminus of the native protein. The enzyme is composed of 645 amino acids with a molecular weight of 72 985. This value is close to that of the purified rat testes and brain enzyme as determined by polyacrylamide gel ...

TY - JOUR. T1 - Purification and amino acid sequence of kunitz-type protease inhibitor found in the hemocytes of horseshoe crab (Tachypleus tridentatus). AU - Nakamura, Takanori. AU - Hirai, Toshiaki. AU - Tokunaga, Fuminori. AU - Kawabata, Shun-Ichiro. AU - Iwanaga, Sadaaki. PY - 1987/1/1. Y1 - 1987/1/1. N2 - A low molecular weight protein protease inhibitor was purified from Japanese horseshoe crab (Tachypleus tridentatus) hemocytes. It consisted of a single polypeptide with a total of 61 amino acid residues. This protease inhibitor inhibited stoichiometrically the amidase activity of trypsin (K1=4.60×10-10 M), and also had inhibitory effects on α-chymotrypsin (K1=5.54×10-9M), elastase (K1=7.20×10-8 M), plasmin, and plasma kallikrein. However, it had no effect on T. tridentatus clotting enzyme and factor C, mammalian blood coagulation factors (activated protein C, factor Xa and α-thrombin), papain, and thermolysin. The complete amino acid sequence of this inhibitor was determined and its ...

TY - JOUR. T1 - Deletion mutation in the signal anchor domain activates cleavage of the influenza virus neuraminidase, a type II transmembrane protein. AU - Hogue, B. G.. AU - Nayak, D. P.. PY - 1994. Y1 - 1994. N2 - Influenza virus neuraminidase (NA) is a type II integral membrane protein with a long hydrophobic domain [29 amino acids (aa)] at the N terminus that functions as an uncleaved signal for translocation into the endoplasmic reticulum and anchors the protein in the membrane. The function of the transmembrane domain in intracellular transport was investigated by deletion mutagenesis. Expression of the mutated NA in eukaryotic cells and by in vitro translation in the presence of membranes showed that the deletion of eight amino acids (aa 28 to 35) from the carboxy end of the signal anchor domain resulted in cleavage, probably by the signal peptidase and secretion of NA into the culture medium. The mutant NA (N28-35) was present inside the cell predominantly as dimers, secreted as dimers, ...

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Genetic susceptibility to autoimmunity is frequently associated with specific MHC alleles. Diabetogenic MHC class II molecules, such as human HLA-DQ8 and mouse I-Ag7, typically have a small, uncharged amino acid residue at position 57 of their β chain (β57); this results in the absence of a salt bridge between β57 and Argα76, which is adjacent to the P9 pocket of the peptide-binding groove. However, the influence of Argα76 on the selection of the TCR repertoire remains unknown, particularly when the MHC molecule binds a peptide with a neutral amino acid residue at position P9. Here, we have shown that diabetogenic MHC class II molecules bound to a peptide with a neutral P9 residue primarily selected and expanded cells expressing TCRs bearing a negatively charged residue in the first segment of their complementarity determining region 3β. The crystal structure of one such TCR in complex with I-Ag7 bound to a peptide containing a neutral P9 residue revealed that a network of favorable ...

RNA Polymerase I Transcription Initiation / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase I Promoter Escape / RNA Polymerase III Transcription Initiation From Type 1 Promoter / B-WICH complex positively regulates rRNA expression / mRNA Capping / RNA polymerase II transcribes snRNA genes / FGFR2 alternative splicing / Estrogen-dependent gene expression / TP53 Regulates Transcription of DNA Repair Genes / RNA Pol II CTD phosphorylation and interaction with CE / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Transcriptional regulation by small RNAs / mRNA Splicing - Minor Pathway / Formation of the Early Elongation Complex / Formation of RNA Pol II elongation complex / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation / RNA ...

We describe the effect of nearest-neighbor sequence context on mismatch-dependent activation of hMSH2-hMSH6. Examination of the intrinsic sequences that occur around symmetric mismatched nucleotides suggests little if any effect of non-nearest-neighbor base pairs on hMSH2-hMSH6 mismatch recognition and ATPase activation (20), although longer-range effects have been reported (22). Although a sequence context effect is not novel in MMR (21), the underlying mechanism is unknown. Our studies have suggested that when a significant nearest-neighbor sequence context effect is manifest, 2 × 3′-purines enhanced, and 2 × 3′-pyrimidines reduced hMSH2-hMSH6 ATPase activation (kcat). A similar trend is observed for mismatch binding (KD), whereas an inverse effect was observed for the Tm of unbound mismatched oligonucleotides. Importantly, the KD and Tm do not accurately account for hMSH2-hMSH6 ATPase activation. Interestingly, the effect of sequence context on KD appears associated with alteration of ...

10) A base other than U at position 5 of the sense strand.(11) A base other than A at position 11 of the sense strand.(12) A base other than an A at position 1 of the sense strand.(13) A base other than an A at position 2 of the sense strand.(14) An A base at position 4 of the sense strand.(15) An A base at position 5 of the sense strand.(16) An A base at position 6 of the sense strand.(17) An A base at position 7 of the sense strand.(18) An A base at position 8 of the sense strand.(19) A base other than an A at position 9 of the sense strand.(20) A base other than an A at position 10 of the sense strand.(21) A base other than an A at position 11 of the sense strand.(22) A base other than an A at position 12 of the sense strand.(23) An A base at position 13 of the sense strand.(24) A base other than an A at position 14 of the sense strand.(25) An A base at position 15 of the sense strand(26) An A base at position 16 of the sense strand.(27) An A base at position 17 of the sense strand.(28) An A ...

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The chicken ovalbumin upstream promoter transcription factors (COUP-TFs) are members from the steroid/thyroid hormone receptor superfamily and function in transcriptional regulation of a multitude of genes. of the ovalbumin gene (Bagchi et al., 1987; Pastorcic et al., 1986; Wang et Procyanidin B3 inhibitor Mouse monoclonal to Human Albumin al., 1987). It was found to bind an element (COUP) between C90 and C70 within the ovalbumin promoter that is much like thyroid and estrogen response elements (Pastorcic et al., 1986). The COUP-TF has also been shown to bind cis-elements involved in positive transcription rules in the rat insulin II (Hwung et al., 1988; Hwung et al., 1988b), chicken VLDL II (Wijnholds et Procyanidin B3 inhibitor al., 1988), and human being apolipoprotein AI and CIII genes (Ladias and Karathanasis, 1991). It was also reported to bind to bad regulatory elements in the proopiomelanocortin (Drouin et al., 1989a; Drouin et al., 1989b) and HIV-1 (Cooney et al., 1991) promoters. The ...

RATIONALE: Regulatory DNA elements in the human genome play important roles in determining the transcriptional abundance and spatiotemporal gene expression during embryonic heart development and somatic cell reprogramming. It is not well known how chromatin marks in regulatory DNA elements are modulated to establish cell type-specific gene expression in the human heart. OBJECTIVE: We aimed to decipher the cell type-specific epigenetic signatures in regulatory DNA elements and how they modulate heart-specific gene expression. METHODS AND RESULTS: We profiled genome-wide transcriptional activity and a variety of epigenetic marks in the regulatory DNA elements using massive RNA-seq (n=12) and ChIP-seq (chromatin immunoprecipitation combined with high-throughput sequencing; n=84) in human endothelial cells (CD31(+)CD144(+)), cardiac progenitor cells (Sca-1(+)), fibroblasts (DDR2(+)), and their respective induced pluripotent stem cells. We uncovered 2 classes of regulatory DNA elements: class I was ...

The endogenous opioid enkephalin neuropeptides are mediators of pain perception and have been implicated in human addictions. The preproenkephalin gene and its mRNA have also provided many examples of tissue- and species-specific variations in mRNA structure produced through a variety of transcriptional and post-transcriptional mechanisms. Resultant differences in mRNA structure, in several cases, have impact on translation of enkephalin prepropeptide. The reports and discussion presented herein describe studies of the preproenkephalin gene and mRNA structure in the guinea pig, an animal that may have specific advantages for modeling the human endogenous opioid system. A guinea pig brain cDNA library was constructed and screened for clones of preproenkephalin and preprodynorphin, which were then sequenced. These studies confirmed the predicted mRNA structure that had been previously proposed based on homology with gene sequences and other methods. Multiple transcription initiation sites for each ...

TY - JOUR. T1 - Mutation of aromatic amino acid residues located at the amino- and carboxy-termini of Escherichia coli heat-stable enterotoxin Ip reduces the efficiency of the toxin to cross the outer membrane. AU - Yamanaka, Hiroyasu. AU - Okamoto, Keinosuke. PY - 2000/1/1. Y1 - 2000/1/1. N2 - Heat-stable enterotoxin Ip (STIp) of Escherichia coli is synthesized as a precursor form consisting of pre- (amino acid residues 1 to 19), pro- (amino acid residues 20 to 54) and mature (amino acid residues 55 to 72) regions. Mature STIp (bioactive STIp) is formed in the periplasmic space after the precursor is proteolytically processed and the mature STIp translocates across the outer membrane through the secretory system including TolC, an outer membrane protein of E. coli. However, it remains unknown how the mature STIp is recognized by this secretory system. In this study, we investigated the amino acid residues of STIp involved in its translocation across the outer membrane. We prepared mutant STIp ...

92118DNAArtificial SequenceA synthetic DNA fragment 1aaggagcgat cgccatgn 18210DNAArtificial SequenceA synthetic DNA fragment, wherein nnn is the first codon which is 3' to the start codon followed by the remainder of an open reading frame 2cgccatgnnn 10312DNAArtificial SequenceA synthetic DNA fragment 3nnnnnngtct tc 12410DNAArtificial SequenceA synthetic DNA fragment 4nnnngaagag 10513DNAArtificial SequenceA synthetic DNA fragment 5gcagcnnnnn nnn 13611DNAArtificial SequenceA synthetic DNA fragment 6nnnnngagac g 11711DNAArtificial SequenceA synthetic DNA fragment 7gccnnnnngg c 11814DNAArtificial SequenceA synthetic DNA fragment 8ggatgnnnnn nnnn 14911DNAArtificial SequenceA synthetic DNA fragment 9nnnnngagac c 111010DNAArtificial SequenceA synthetic DNA fragment 10gacgcnnnnn 101111DNAArtificial SequenceA synthetic DNA fragment 11ccnnnnnnng g 111211DNAArtificial SequenceA synthetic DNA fragment 12gcnnnnnnng c 111310DNAArtificial SequenceA synthetic DNA fragment 13nnnnngagac 101411DNAArtificial ...

GO Terms Descrition:, periodic partitioning by pair rule gene, central nervous system development, RNA polymerase II distal enhancer sequence-specific DNA binding, positive regulation of transcription from RNA polymerase II promoter, trunk segmentation, cell fate specification, RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription, regulation of transcription from RNA polymerase II promoter, blastoderm segmentation, negative regulation of transcription from RNA polymerase II promoter, regulation of transcription, DNA-templated, sequence-specific DNA binding transcription factor activity, nucleus, sequence-specific DNA binding, gonadal mesoderm development, segmentation, posterior head segmentation, germ cell migration ...

An assay based on the competitive polymerase chain reaction (PCR) was developed to quantify Glomus mosseae, an arbuscular mycorrhizal (AM) fungus, within plant roots. Using previously designed G. mosseae specific primers, a heterologous internal standard was constructed by amplifying Pseudomonas DNA under low stringency annealing conditions. Go-amplification of G. mosseae and internal standard DNA within leek root extracts provided accurate quantification of target DNA. Colonization of leek roots by G. mosseae was monitored in a comparative study by competitive PCR and microscopy, a conventional method of quantification. These two methods gave closely parallel data for G. mosseae colonization from three different inoculum levels over a 6 week period Results indicate that competitive PCR is a sensitive and accurate method of quantification. The major advantage of competitive PCR over microscopy is that it can quantify specific AM fungi. ...

The 72 kDa IE1 protein of human cytomegalovirus (HCMV) is one of a few viral regulatory proteins expressed immediately after infection of a host cell. Although it is now well-established that IE1 is a potent transcriptional activator of the human immunodeficiency virus (HIV) long terminal repeat (LTR), the identity of the nucleotide sequence responsive to IE1 remains elusive and the molecular mechanism of this interaction is not well-understood. We have constructed various LTR mutants and tested them for their ability to be activated by IE1 using transient transfection assays. Mutations in the NF-κB sites, of either a few changes in the nucleotide sequence or a deletion of the entire region, abrogated IE1-driven transactivation. Deletion of the Tat-responsive element (TAR) had no significant effect on reporter expression. Mutations in the Sp1 sites or the TATA box significantly lowered LTR activity, but this is probably due to an effect on the general transcription system, as these elements are also

The identification and study of the cis-regulatory elements that control gene expression are important areas of biological research, but few resources exist to facilitate large-scale bioinformatics studies of cis-regulation in metazoan species. Drosophila melanogaster, with its well-annotated genome, exceptional resources for comparative genomics and long history of experimental studies of transcriptional regulation, represents the ideal system for regulatory bioinformatics. We have merged two existing Drosophila resources, the REDfly database of cis-regulatory modules and the FlyReg database of transcription factor binding sites (TFBSs), into a single integrated database containing extensive annotation of empirically validated cis-regulatory modules and their constituent binding sites. With the enhanced functionality made possible through this integration of TFBS data into REDfly, together with additional improvements to the REDfly infrastructure, we have constructed a one-stop portal for ...

The long noncoding RNA, TINCR, functions as a competing endogenous RNA to regulate PDK1 expression by sponging miR-375 in gastric cancer Zhaoliang Chen,1 Hong Liu,1 Huili Yang,1 Yukai Gao,1 Gongwen Zhang,1 Jiaojiao Hu2 1Department of Oncology, Binzhou Central Hospital, Binzhou, Shandong, 2Department of Hematology, Zhongda Hospital, Southeast University, Nanjing, China Background: Accumulating evidence indicates that the long noncoding RNA, TINCR, plays a critical role in cancer progression and metastasis. However, the overall biological role and mechanisms of TINCR that were involved in human gastric cancer (GC) progression remain largely unknown.Methods: TINCR expression was measured in 56 paired tumor and adjacent nontumor tissue samples by real-time polymerase chain reaction (PCR). Insights of the mechanism of competitive endogenous RNAs (ceRNAs) were gained from bioinformatic analysis, luciferase assays. The effects of TINCR and miR-375 on GC cell apoptosis and proliferation were studied by RNA

Kunes S, Chu T, Chiu M, Zhang E. A C-terminal motif targets hedgehog to axons, coordinating assembly of the Drosophila eye and brain. Developmental Cell [Internet]. 2006;10 (5) :635-46.

The mitogen-activated protein kinase-activated protein kinase MK5 is a substrate of the mitogen-activated protein kinases p38, ERK3 and ERK4. Cell culture and animal studies have demonstrated that MK5 is involved in tumour suppression and promotion, embryogenesis, anxiety, cell motility and cell cycle regulation. In the present study, homology models of MK5 were used for molecular dynamics (MD) simulations of: (1) MK5 alone; (2) MK5 in complex with an inhibitor; and (3) MK5 in complex with the interaction partner p38α. The calculations showed that the inhibitor occupied the active site and disrupted the intramolecular network of amino acids. However, intramolecular interactions consistent with an inactive protein kinase fold were not formed. MD with p38α showed that not only the p38 docking region, but also amino acids in the activation segment, αH helix, P-loop, regulatory phosphorylation region and the C-terminal of MK5 may be involved in forming a very stable MK5-p38α complex, and that p38α

YRRM1 - Y Chromosome RNA Recognition Motif. Looking for abbreviations of YRRM1? It is Y Chromosome RNA Recognition Motif. Y Chromosome RNA Recognition Motif listed as YRRM1

Complete information for GSTCD gene (Protein Coding), Glutathione S-Transferase C-Terminal Domain Containing, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium

The C-type lectin-like receptor 2 (CLEC-2)activates platelets through Src and Syk tyrosine kinases via a single cytoplasmic YxxL motif known as a hem immunoreceptor tyrosine-based activation motif (hemITAM).Here, we demonstrate using sucrose gradient ultracentrifugation and methyl--cyclodextrin treatment that CLEC-2 translocates to lipid rafts upon ligand engagement and that translocation is essential for hemITAM phosphorylation and signal initiation. HemITAM phosphorylation, but not translocation, is also critically dependent on actin polymerization,Rac1 activation, and release of ADP and thromboxane A2 (TxA2). The role of ADP and TxA2 in mediating hosphorylation is dependent on ligand engagement and rac activation but is independent of platelet aggregation. In contrast,tyrosine phosphorylation of the GPVIFcR -chain ITAM, which has 2 YxxL motifs,is independent of actin polymerization and secondary mediators. These results reveal a unique series of proximal events in CLEC-2 phosphorylation ...

For three decades, sequence logos are the de facto standard for the visualization of sequence motifs in biology and bioinformatics. Reasons for this success story are their simplicity and clarity. The number of inferred and published motifs grows with the number of data sets and motif extraction algorithms. Hence, it becomes more and more important to perceive differences between motifs. However, motif differences are hard to detect from individual sequence logos in case of multiple motifs for one transcription factor, highly similar binding motifs of different transcription factors, or multiple motifs for one protein domain. Here, we present DiffLogo, a freely available, extensible, and user-friendly R package for visualizing motif differences. DiffLogo is capable of showing differences between DNA motifs as well as protein motifs in a pair-wise manner resulting in publication-ready figures. In case of more than two motifs, DiffLogo is capable of visualizing pair-wise differences in a tabular form.

The Gram-negative, intracellular bacterium Chlamydia trachomatis causes acute and chronic urogenital tract infection, potentially leading to infertility and ectopic pregnancy. The only partially characterized cytotoxin CT166 of serovar D exhibits a DXD motif, which is important for the enzymatic activity of many bacterial and mammalian type A glycosyltransferases, leading to the hypothesis that CT166 possess glycosyltransferase activity. CT166-expressing HeLa cells exhibit actin reorganization, including cell rounding, which has been attributed to the inhibition of the Rho-GTPases Rac/Cdc42. Exploiting the glycosylation-sensitive Ras(27H5) antibody, we here show that CT166 induces an epitope change in Ras, resulting in inhibited ERK and PI3K signaling and delayed cell cycle progression. Consistent with the hypothesis that these effects strictly depend on the DXD motif, CT166 with the mutated DXD motif causes neither Ras-ERK inhibition nor delayed cell cycle progression. In contrast, CT166 with the

A structured motif allows variable length gaps between several components, where each component is a simple motif, which allows either no gaps or only fixed length gaps. The motif can either be represented as a pattern or a profile (also called positional weight matrix). We propose an efficient algorithm, called SMOTIF, to solve the structured motif search problem, i.e., given one or more sequences and a structured motif, SMOTIF searches the sequences for all occurrences of the motif. Potential applications include searching for long terminal repeat (LTR) retrotransposons and composite regulatory binding sites in DNA sequences. SMOTIF can search for both pattern and profile motifs, and it is efficient in terms of both time and space; it outperforms SMARTFINDER, a state-of-the-art algorithm for structured motif search. Experimental results show that SMOTIF is about 7 times faster and consumes 100 times less memory than SMARTFINDER. It can effectively search for LTR retrotransposons and is well suited to

In this protocol, we explain how to run ab initio motif discovery in order to gather putative transcription factor binding motifs (TFBMs) from sets of genomic regions returned by ChIP-seq experiments. The protocol starts from a set of peak coordinates (genomic regions) which can be either downloaded from ChIP-seq databases, or produced by a peak-calling software tool. We provide a concise description of the successive steps to discover motifs, cluster the motifs returned by different motif discovery algorithms, and compare them with reference motif databases. The protocol is documented with detailed notes explaining the rationale underlying the choice of options. The interpretation of the results is illustrated with an example from the model plant Arabidopsis thaliana ...

The supernumerary subunit g is found in all mitochondrial ATP synthases. Most of the conserved amino acid residues are present in the membrane C-terminal part of the protein that contains a dimerization motif GXXXG. In yeast, alteration of this motif leads to the loss of subunit g and of supramolecular structures of the ATP synthase with concomitant appearance of anomalous mitochondrial morphologies. Disulfide bond formation involving an engineered cysteine in position 109 of subunit g and the endogenous cysteine 28 of subunit e promoted g + g, e + g, and e + e adducts, thus revealing the proximity in the mitochondrial membrane of several subunits e and g. Disulfide bond formation between two subunits g in mitochondria increased the stability of an oligomeric structure of the ATP synthase in digitonin extracts. These data suggest the participation of the dimerization motif of subunit g in the formation of supramolecular structures and is in favor of the existence of ATP synthase associations, in ...

Background Context-dependent transcription factor (TF) binding is one reason for differences in gene expression patterns between different cellular states. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identifies genome-wide TF binding sites for one particular context-the cells used in the experiment. But can such ChIP-seq data predict TF binding in other cellular contexts and is it possible to distinguish context-dependent from ubiquitous TF binding? Results We compared ChIP-seq data on TF binding for multiple TFs in two different cell types and found that on average only a third of ChIP-seq peak regions are common to both cell types. Expectedly, common peaks occur more frequently in certain genomic contexts, such as CpG-rich promoters, whereas chromatin differences characterize cell-type specific TF binding. We also find, however, that genotype differences between the cell types can explain differences in binding. Moreover, ChIP-seq signal intensity and peak ...

BayesPeak - Bayesian Analysis of ChIP-seq Data, This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.. ChIPpeakAnno - Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges.. Chipseq - A package for analyzing chipseq data. Tools for helping process short read data for chipseq experiments. ChIPseqR - ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.. ChIPsim - A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.. DESeq - Differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count ...

Mapping the chromosomal locations of transcription factors, nucleosomes, histone modifications, chromatin remodeling enzymes, chaperones, and polymerases is one of the key tasks of modern biology, as evidenced by the Encyclopedia of DNA Elements (ENCODE) Project. To this end, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is the standard methodology. Mapping such protein-DNA interactions in vivo using ChIP-seq presents multiple challenges not only in sample preparation and sequencing but also for computational analysis. Here, we present step-by-step guidelines for the computational analysis of ChIP-seq data. We address all the major steps in the analysis of ChIP-seq data: sequencing depth selection, quality checking, mapping, data normalization, assessment of reproducibility, peak calling, differential binding analysis, controlling the false discovery rate, peak annotation, visualization, and motif analysis. At each step in our guidelines we discuss some of the software

Institut National de la Sante et de la Recherche Medicale U124-IRCL, Lille, France. The BTB/POZ domain defines a newly characterized protein-protein interaction interface. It is highly conserved throughout metazoan evolution and generally found at the NH2 terminus of either actin-binding or, more commonly, nuclear DNA-binding proteins. By mediating protein binding in large aggregates, the BTB/POZ domain serves to organize higher order macromolecular complexes involved in ring canal formation or chromatin folding ...

Single nucleotide polymorphisms (SNPs) have been associated with many aspects of human development and disease, and many non-coding SNPs associated with disease risk are presumed to affect gene regulation. We have previously shown that SNPs within transcription factor binding sites can affect transcription factor binding in an allele-specific and heritable manner. However, such analysis has relied on prior whole-genome genotypes provided by large external projects such as HapMap and the 1000 Genomes Project. This requirement limits the study of allele-specific effects of SNPs in primary patient samples from diseases of interest, where complete genotypes are not readily available. In this study, we show that we are able to identify SNPs de novo and accurately from ChIP-seq data generated in the ENCODE Project. Our de novo identified SNPs from ChIP-seq data are highly concordant with published genotypes. Independent experimental verification of more than 100 sites estimates our false discovery rate at

The formyl peptide receptor (FPR) is a G-protein-coupled receptor (GPCR) that mediates chemotaxis and stimulates the mitogen-activated protein kinase (MAPK)/extracellular-signal-regulated kinase pathway. We have examined the functional effects of substitutions of a conserved aspartic acid residue in the second transmembrane domain (D71A) and of residues in the conserved NPXXY motif in the seventh transmembrane domain (N297A and Y301A). These mutated receptors, expressed in Chinese hamster ovary (CHO) cells, bind ligand with affinities similar to wild-type FPR, but the D71A mutant is uncoupled from G-protein [Miettinen, Mills, Gripentrog, Dratz, Granger and Jesaitis (1997) J. Immunol 159, 4045-4054]. In the present study, we show that both the D71A and N297A mutations resulted in defective endocytosis. The N297A substitution also prevented desensitization, as determined by intracellular calcium mobilization by sequential stimulation with ligand. In chemotaxis assays, the N297A mutation resulted ...

El etnònim "S(a)rd" pertany al substrat lingüístic pre-indoeuropeu. El nom fa la seva primera aparició en la estela de Nora, on la paraula Šrdn[18] testifica l'existència del nom quan van arribar per primera vegada els comerciants fenicis. D'acord amb el Timeu, un dels diàlegs de Plató, Sardenya i la seva gent, els "Sardonioi" (Σαρδονιοι), podrien haver estat nomenats en honor de Sardó (Σαρδώ), una llegendària dona nascuda a Sardes (Σάρδεις), capital de l'antic regne de Lidia en Anatòlia.[19][20] Pausanias i Sal·lusti diuen que era un heroi líbic i fill d'Hèrcules, reverenciat com Sardus Pater Babai ("Pare Sard" o "Pare dels Sards"), el qual va donar a l'illa el seu nom.[21] També se creu que els antics Sards foren associats amb els Sherden (šrdn en egipci), un dels Pobles del mar.[22][23][24][25] L'etnònim va ser després romanitzat com sardus (sarda en femení). ...

Application of Palladium-Mediated Diarylamine Synthesis and Directed Remote Metalation (DreM) in the Synthesis of Acridones, Anthranilates, Oxindoles and Dibenzo[b,f]azepinones. ...

Rabbit monoclonal antibody raised against a human INTS3 peptide using ARM Technology. A synthetic peptide of human INTS3 is used for rabbit immunization.Customer or Abnova will decide on the preferred peptide sequence. (H00065123-K) - Products - Abnova