identification of potential protein binding sites in 4e

... RB144, consists of 144 proteins, all solved before 2006, with 4304 binding and 27932 non -binding residues RB109 is a smaller set of 109 RNA -binding protein chains extracted from the PDB in 2004, which ... for identification of RNA-interacting residue in proteins Genome Informatics 2004, 15:105-116 Terribilini M, Lee J, Yan C, Jernigan R, Honavar V, Dobbs D: Prediction of RNA -binding sites in proteins ... predicting RNAbinding sites in proteins Nucleic Acids Res 2007 Kumar M, Gromiha M, Raghava G: Prediction of RNA binding sites in a protein using SVM and PSSM profile Proteins 2007, 1(71):189-194

Ngày tải lên: 02/11/2022, 10:39

... percent area stained that exceeded background staining C) Anti-OPH Western blot of COS-7 and COS-7-OPH lystates containing 90 μg of total protein D) Cell lysates containing 120 μg of protein were separated ... understanding of OPH remains elusive Nevertheless, the acetylation of the N-terminal α-amine group of proteins is the most common post-translational modification in eukaryotic proteins yet, little ... supernatant collected Protein concentrations were determined with the BCA kit using the manufacturer’s instructions n-PAGE esterase activity profiles Cell lysates containing 120 μg of protein were mixed

Ngày tải lên: 05/11/2020, 01:08

... MYB DNA -binding domain N-terminal myb-domain 1 B3 domain, DNA binding domain and single AP2/ERF domain S1F binding site, NLS and a putative DNA binding helix Two zinc -binding sites, Cys3HisCys2HisCys ... domains GROWTH-REGULATING FACTOR HB-other 1 Homeobox domain HD-ZIP HD-ZIP protein, N terminus HSF Heat stress transcription factors, DNA binding C-terminal domains 1 LOB domain zinc finger domains, ... B-box zinc finger Dof DNA binding with one finger EIL Ethylene insensitive ERF AP2 domain Auxin response factor BRI1-EMS-SUPPRESSOR 15 24 39 FAR1 G2-like 7 Homeodomain-like, GLK proteins belonging

Ngày tải lên: 27/05/2020, 00:39

... numbers in parentheses refer to the number of RNA editing sites in which editing occurred at the second position in a codon) (Fig 3) Most RNA editing sites exist in the protein- coding regions and often ... corresponding amino acid alterations In addition to 16 silent editing sites, there were 239 sites that resulted in corresponding codon Fig The distribution of editing sites and editing frequencies in ... chloroplast genes of Ginkgo biloba a The distribution of editing sites in the chloroplast genes of Ginkgo biloba b The editing frequencies of Ginkgo biloba chloroplast genes Editing frequency is indicated

Ngày tải lên: 27/05/2020, 00:53

... experiments of each gene pair as its confidence score In addition, we also include protein- protein interactions from mass spectrometry data [Ewing et al., 2007] Protein Domain-Domain Interaction Proteins ... Gene context Protein phosphorylation Protein- Protein Interactions and Genetic Interactions Experimental human protein- protein interactions were collected from diverse databases, including, NCBI, ... data source of Protein Phophorylation, PhosphoPOINT [Yang et al., 2008], also provides 4,195 phospho-proteins, 518 serine/threonine/tyrosine kinases, and their corresponding protein interactions

Ngày tải lên: 18/10/2022, 08:40

... method for detecting oxygen binding in proteins Internal cavities in proteins are important structural elements that may produce functional motions1, such as drug and ligand binding2 and conformational ... cavities, as well as the binding and egress of O2, suggesting that the channel consisting of helices D, E, G, H, and J could be the potential gateway for ligand binding to the protein Due to strong paramagnetic ... crevices and cavities of proteins, which have the potential for ligand binding By using gas-pressure NMR and MD simulation, we investigate O2 accessibility to the protein interior for the cavity-enlarged

Ngày tải lên: 24/11/2022, 17:49

... for the Retrieval of Interacting Genes/Proteins for protein- protein interaction network analysis Results: Upregulation of proteins involved in innate immunity (LCN2), cell signalling (CALM) and ... overexpression of proteins involved in TNF-α signalling (CPNE1) and B cell survival (PRDX3) Moreover, neutrophil gelatinase-associated lipocalin was upregulated in saliva and tears in pSS Consistently, ... pathways of the adaptive immune response in saliva, of cellular component assembly for saliva EVs, and of metabolism and protein folding in tears in pSS patients Conclusions: LC-MS of saliva

Ngày tải lên: 04/12/2022, 10:35

... transport proteins Table Statistics of all retrieved FAD binding proteins with FAD and non-FAD binding sites Number of FAD binding Non-FAD proteins sites binding sites FAD binding in electron ... identifying FAD binding sites in electron transport proteins We used a set of 55 FAD binding proteins as the training data set and six FAD binding proteins in electron transport proteins as an independent ... composition of interacting and noninteracting FAD binding sites by computing the occurrence frequency of amino acids in these sites Regarding the interacting FAD binding sites, the amino acids

Ngày tải lên: 04/12/2022, 15:52

... The protein device is a system of synthetic scaffold and scaffold -binding proteins composed of modular transac- tivating, protein- protein interaction, DNA -binding, and non DNA -binding protein ... create a system of interacting fusion proteins (b) The binding and unbinding of the ligands and their correspond- ing protein- protein interaction (PPI) domains generates eight different bound scaffold ... The fusion proteins are created from transactivating, DNA -binding, non-DNA binding, and pro- teinprotein interaction domains along with the corresponding peptide ligands These domains cre- ate

Ngày tải lên: 02/10/2024, 01:37

... distinct binding sites lying close together (separated by a distance on the order of 100 bp or less), instead interpreting such cases as a single, incorrectly located binding site Such cases of ... demonstrate this by analyzing GABP binding over a 2-Mbp segment of human chromosome 19 In our analysis of DosR binding, we found 24 distinct binding sites distributed over 18 regions, of which 15 regions ... several instances of very closely spaced binding sites For example, we identify two binding sites upstream of Rv1737c that are separated by only 40 bp, and we identify two binding sites upstream of

Ngày tải lên: 09/08/2014, 20:21

... numbers in the Rosaceae family Physical mapping of rDNA sites by FISH has been performed in several genera of the Rosaceae family, but very few species have been examined within each of ... analysis in. .. twelve for 25S rDNA in decaploid F iturupensis do not fit an origination model involving a simple combination of an octoploid and a diploid In such an origin, the decaploid ... rDNA sites The presence of four 5S and fifteen 25S rDNA sites suggests that the decaploid cytotype for CFRA 110 of the F virginiana subsp platypetala originated from doubling of an interspecific

Ngày tải lên: 11/08/2014, 11:21

... identification of the in vivo RIN -binding sites in the putative promoters of several ripening-induced genes through ChIPbased analyses using ripening tomato fruit In addition, we screened novel RIN -binding ... analyses Binding of RIN to the novel CArG-box sites in vivo and in vitro To examine the binding of RIN to the CArG-box sites within the cloned fragments, we monitored their enrichment levels in the ... identify the RIN -binding sequences within the enriched regions, the binding of RIN to the CArG-box sequences in the promoters of LeACS2, LeACS4, TBG4, LeEXP1, LeMAN4 and RIN were examined by in vitro

Ngày tải lên: 11/08/2014, 11:21

... EBNA1 binding sites in chromosome 11 and MAP3K7IP2 promoter region TodetermineifsomeoftheEBNA1ChIP-Seqsites were bound directly by EBNA1, we assayed the ability of purified EBNA1 protein DNA binding ... Exami- nation of EBNA1 binding sites in these translocated Figure 6 shRNA depletion of EBNA1 causes a loss of transcription of several genes with EBNA1 binding sites. A) Western blot showing EBNA1 ... viral binding sites, sug- gesting that some of these sites are indirectly bound by EBNA1. EBNA1 also bound close to the transcriptional start sites of a large number of cellular genes, including

Ngày tải lên: 12/08/2014, 01:22

... pattern in interphase nuclei in low DAPI-stained euchromatic regions (arrows in Figure 3, J). Strong clustering of AluI-satellite arrays was observed in the intercalary heterochromatin on four ... located in subterminal, intercalary and centromeric regions of plant chromosomes. The majori ty of typical plant satellite arrays are several megabases in size [15]. In c ontrast, arra ys of minisatellites ... 3J). Using minisatellites as probes, similarities in the chro- mosome distribution patterns were preferentially observed in the intercalary heterochromatin and for some minisatellites in terminal

Ngày tải lên: 12/08/2014, 03:21

... article Identification of amino acid residues involved in substrate specificity of plant acyl-ACP thioesterases using a bioinformatics-guided approach Kimberly M Mayer1,2 and John Shanklin*1 Address: ... found to have more 16:1 in the medium than the M141T variant (data not shown) Variants containing arginine, leucine, or isoleucine produced amounts of 16:1 similar to the threonine variant and were ... californica) in canola allowed the commercial production of a genetically engineered oil crop containing large amounts of laurate [5] while expression of a thioesterase from Garcinia mangostana in canola

Ngày tải lên: 12/08/2014, 05:20

... factor binding sites) fall into two general categories One approach is to employ a training set of transcription factor binding sites and a scoring scheme to evaluate predictions [2-8] The scoring ... Crp Binding Site Motif and Generation of Weaker Versions Crp Binding Site Motif and Generation of Weaker Versions The logo in panel A indicates the Crp motif used to scan for Crp binding sites ... statistically incorporate any sites other than the best found binding site in each intergenic region In another three pairs of runs we ran PhyloScan, permitting it to consider multiple sites within an intergenic...

Ngày tải lên: 12/08/2014, 17:20

... investigation of protein- DNA interactions in Drosophila Results Identification of Su(Hw) in vivo binding locations We have used ChIP-array to investigate the in vivo binding of the Su(Hw) protein in a ... the in vivo Su(Hw) binding sites It is interesting to compare our set of endogenous Su(Hw) sites with the gypsy insulator The 340 bp gypsy insulator contains a cluster of 12 Su(Hw) binding sites ... identified Su(Hw) binding sites Analysis of these endogenous Su(Hw) binding sites allowed considerable expansion of the Su(Hw) consensus binding sequence The existing Su(Hw) binding consensus was...

Ngày tải lên: 14/08/2014, 08:20

... 2003) These two proteins are members of the S100 Calcium -binding protein family They function as inhibitors of casein kinases I and II that are essential for phosphorylation of various molecules ... TOFTOF/MS 107 3.4 Validation of haptoglobin-α2 subunit using PS20 immunocapture proteinChip analysis 112 3.5 Validation of haptoglobin-α2 subunit as potential protein ... Confirmation of identification of ceruloplasmin and haptoglobin using 2-DE followed by Western blotting analysis 138 Figure 4.13 Western blotting analysis of ceruloplasmin and haptoglobin in cyst...

Ngày tải lên: 12/09/2015, 08:19

... diffusing too quickly away from the cell wall Surfacebased carbohydrate binding sites of weak affinity are well known (e.g in lectins and haemagglutinin) where Carbohydrate binding sites in Candida ... Carbohydrate binding sites in Candida exoglucanase Fig Key properties of the +1 subsite of Exg (A) Subsite binding energies based on published kinetic data for Exg-catalysed hydrolysis of b-1,3-linked ... structure of Exg involving an oligosaccharide and provides an insight into the enzyme’s mechanism of action in the C albicans cell wall Finally, the unexpected discovery of an isolated binding site...

Ngày tải lên: 15/03/2014, 23:20

... e.g a discharge or incident resulting in potential effects on natural ecosystems in the vicinity of the release point or incident; ongoing effects on people in the vicinity of a site due to impacts ... pollution incident resulting in harm to the health of members of the public over a wide area due to contamination of drinking water supplies; accident resulting in death or serious injury to ... the identification of potential risks for the environment and human health arising from hydrocarbons operations involving hydraulic fracturing in Europe Overview of hydraulic fracturing in Europe...

Ngày tải lên: 23/03/2014, 00:20