BIOINFORMATICS ORIGINAL PAPER Going from where to why—interpretable prediction of protein subcellular localization
... localization. However, in many cases only one or two of feature types were included in one predictor. In our study, we included numerous types of features and properties. First, we make use of sequence-derived features. These include amino acid composition, normalized amino acid composition and pseu ...
... localization. However, in many cases only one or two of feature types were included in one predictor. In our study, we included numerous types of features and properties. First, we make use of sequence-derived features. These include amino acid composition, normalized amino acid composition and pseu ...
The Ribosome, rRNA and mRNA (3.1)
... The large ribosomal subunit catalyzes peptide bond formation and binds initiation, termination, and elongation factors. We have determined the crystal structure of the large ribosomal subunit from Haloarcula marismortui at 2.4 angstrom resolution, and it includes 2833 of the subunit's 3045 nucleotid ...
... The large ribosomal subunit catalyzes peptide bond formation and binds initiation, termination, and elongation factors. We have determined the crystal structure of the large ribosomal subunit from Haloarcula marismortui at 2.4 angstrom resolution, and it includes 2833 of the subunit's 3045 nucleotid ...
Recombinant N-terminal Nucleotide
... the mdr2 and mdr3 ones, such sequences being rare due to the high similarity in primary structure of the three proteins (40). To fulfill all these conditions, Asn-395 and Ser-643 were chosen, respectively, as N-terminal and C-terminal ends for NBD1 (named NBD1– 643); the corresponding cDNA was prepa ...
... the mdr2 and mdr3 ones, such sequences being rare due to the high similarity in primary structure of the three proteins (40). To fulfill all these conditions, Asn-395 and Ser-643 were chosen, respectively, as N-terminal and C-terminal ends for NBD1 (named NBD1– 643); the corresponding cDNA was prepa ...
Going from where to why—interpretable
... localization. However, in many cases only one or two of feature types were included in one predictor. In our study, we included numerous types of features and properties. First, we make use of sequence-derived features. These include amino acid composition, normalized amino acid composition and pseu ...
... localization. However, in many cases only one or two of feature types were included in one predictor. In our study, we included numerous types of features and properties. First, we make use of sequence-derived features. These include amino acid composition, normalized amino acid composition and pseu ...
Protein phosphorylation in bacterial signal transduction
... were first discovered in Eukarya and later in Bacteria. Since it is very unlikely that the genes encoding these kinases arrived to almost all bacterial genomes by horizontal transfer from Eukarya, we would like to argue here that the name “eukaryotic type kinases” is somewhat misleading. Hanks kinase ...
... were first discovered in Eukarya and later in Bacteria. Since it is very unlikely that the genes encoding these kinases arrived to almost all bacterial genomes by horizontal transfer from Eukarya, we would like to argue here that the name “eukaryotic type kinases” is somewhat misleading. Hanks kinase ...
Intrinsic Disorder in Cell-signaling and Cancer
... signaling proteins (AfCS), eukaryotic proteins from SWISS-PROT (EU_SW) and non-homologous protein segments with well-defined (ordered) 3D structure (O_PDB_S25). PONDR VL-XT predicts $ 30 consecutive disordered residues for 79(^ 5)%, 66(^ 6)%, 47(^ 4)% and 13(^ 4)% of the proteins from HCAP, AfCS, EU ...
... signaling proteins (AfCS), eukaryotic proteins from SWISS-PROT (EU_SW) and non-homologous protein segments with well-defined (ordered) 3D structure (O_PDB_S25). PONDR VL-XT predicts $ 30 consecutive disordered residues for 79(^ 5)%, 66(^ 6)%, 47(^ 4)% and 13(^ 4)% of the proteins from HCAP, AfCS, EU ...
Supplementary Notes - Word file
... allow for repair of the DNA, or if the damage is too severe, apoptosis. ING2 recognition of the H3-triMeK4 mark on these actively transcribed genes can stabilize a repressive HDAC1 complex acutely at these genes, leading to deacetylation and transcriptional inactivation. By focusing HDAC1 repressor ...
... allow for repair of the DNA, or if the damage is too severe, apoptosis. ING2 recognition of the H3-triMeK4 mark on these actively transcribed genes can stabilize a repressive HDAC1 complex acutely at these genes, leading to deacetylation and transcriptional inactivation. By focusing HDAC1 repressor ...
The CS2 fimbrial antigen from escherichia coli, purification
... viz. CS1, CS2 and CS3 [5,6]. The CFA2 antigens are, like the CFA1, plasmid-encoded [7,8]. However, the expression of the CS1 and CS2 is highly dependent on the serotype and biotype of the host strain. The same plasmid codes for CS1 and CS2 in an O6:H16 biotype A strain and for the CS2 and CS3 in 06 ...
... viz. CS1, CS2 and CS3 [5,6]. The CFA2 antigens are, like the CFA1, plasmid-encoded [7,8]. However, the expression of the CS1 and CS2 is highly dependent on the serotype and biotype of the host strain. The same plasmid codes for CS1 and CS2 in an O6:H16 biotype A strain and for the CS2 and CS3 in 06 ...
Slide 1
... Structural Levels of Proteins • Primary – amino acid sequence • Secondary – alpha helices or beta pleated ...
... Structural Levels of Proteins • Primary – amino acid sequence • Secondary – alpha helices or beta pleated ...
NMR Experiments studies
... Isotope-labeling of proteins (IV) Site-specific labeling • Add labeled amino acids to non-labeled media. • Assuming that the amino acid is not metabolized, all residues corresponding to that amino acid will be labeled in the protein. • Technique is interesting when structural or dynamic information ...
... Isotope-labeling of proteins (IV) Site-specific labeling • Add labeled amino acids to non-labeled media. • Assuming that the amino acid is not metabolized, all residues corresponding to that amino acid will be labeled in the protein. • Technique is interesting when structural or dynamic information ...
Methods S2.
... inhibitor, KK271, the protein complex was concentrated to about 20 mg/ml and subjected to the crystallization screening with the sitting drop vapor diffusion method. The crystals of the MDM2-KK271 complex appeared after several days at 4oC in 0.2 M ammonium nitrate, 20% (w/v) PEG 3350 forming hexago ...
... inhibitor, KK271, the protein complex was concentrated to about 20 mg/ml and subjected to the crystallization screening with the sitting drop vapor diffusion method. The crystals of the MDM2-KK271 complex appeared after several days at 4oC in 0.2 M ammonium nitrate, 20% (w/v) PEG 3350 forming hexago ...
MD Simulations of the P53 oncoprotein structure
... ---top(a) Res{His273}DNA{P(DG395)} ---bottom(b) Res{His273}DNA{P(DT394)} While constructing the p53DNA distance diagrams in Figure 3 (mouW) and 5 (mouM), we estimated the distance distributions between the corresponding residue heavy atoms (from the N- to CO- ends) and two DNA phosphorus atoms P( ...
... ---top(a) Res{His273}DNA{P(DG395)} ---bottom(b) Res{His273}DNA{P(DT394)} While constructing the p53DNA distance diagrams in Figure 3 (mouW) and 5 (mouM), we estimated the distance distributions between the corresponding residue heavy atoms (from the N- to CO- ends) and two DNA phosphorus atoms P( ...
Regulation of Protein Degradation
... have very limited cleavage site specificities and produce detectable protein products. Although several of the proteasome cleaving activities can be related to the four classes of proteinase through the use of class-specific inhibitors and peptide substrates, none of the proteasome subunits shares a ...
... have very limited cleavage site specificities and produce detectable protein products. Although several of the proteasome cleaving activities can be related to the four classes of proteinase through the use of class-specific inhibitors and peptide substrates, none of the proteasome subunits shares a ...
N-Terminal Intramolecularly Conserved Histidines of Three Domains
... full-length luciferase cDNA (4037 bp) has an open reading frame (ORF) of 3723 bp and encodes the 136 994 Da luciferase molecule (5). The ORF (Figure 1) contains an N-terminal sequence of 111 amino acids, which is homologous to the N-terminal region of the substrate-binding protein, LBP. This is foll ...
... full-length luciferase cDNA (4037 bp) has an open reading frame (ORF) of 3723 bp and encodes the 136 994 Da luciferase molecule (5). The ORF (Figure 1) contains an N-terminal sequence of 111 amino acids, which is homologous to the N-terminal region of the substrate-binding protein, LBP. This is foll ...
paper - General Guide To Personal and Societies Web Space at
... the basis of potential incorporation into proteins. A reasonable starting point was homoallylglycine (Hag) since its in ViVo incorporation by methionine auxotrophic Escherichia coli is known.4 Hoveyda-Grubbs second generation catalyst 17 was selected since it is phosphine free and therefore more lik ...
... the basis of potential incorporation into proteins. A reasonable starting point was homoallylglycine (Hag) since its in ViVo incorporation by methionine auxotrophic Escherichia coli is known.4 Hoveyda-Grubbs second generation catalyst 17 was selected since it is phosphine free and therefore more lik ...
Identification of surface proteins in Enterococcus - UiO
... has so far not been possible to link virulence to one or very few key gene products. Since virulence depends on the ability to colonize the GI tract and interact with host cells and proteins in the GI tract, secreted proteins and proteins located on the cell surface are thought to be important. One ...
... has so far not been possible to link virulence to one or very few key gene products. Since virulence depends on the ability to colonize the GI tract and interact with host cells and proteins in the GI tract, secreted proteins and proteins located on the cell surface are thought to be important. One ...
Chapter 4.32
... traverses the endoplasmic reticulum (ER) and Golgi compartments. In N-glycosylation, a preformed oligosaccharide moiety is transferred en bloc from a long-chain isoprenoid lipid (dolichol) onto the specific N-glycosylation site via an N-glycosidic linkage to the asparagine (Asn) residue of a nascent ...
... traverses the endoplasmic reticulum (ER) and Golgi compartments. In N-glycosylation, a preformed oligosaccharide moiety is transferred en bloc from a long-chain isoprenoid lipid (dolichol) onto the specific N-glycosylation site via an N-glycosidic linkage to the asparagine (Asn) residue of a nascent ...
Lab 6
... which the acyl group is the acetyl group. Such reactions are called acetylation reactions. These reactions involve the transfer of an acetyl acyl group to an oxygen atom (i.e., the substitution of an acetyl group for an H atom bonded to oxygen). When alcohols or phenols are acylated, the products ar ...
... which the acyl group is the acetyl group. Such reactions are called acetylation reactions. These reactions involve the transfer of an acetyl acyl group to an oxygen atom (i.e., the substitution of an acetyl group for an H atom bonded to oxygen). When alcohols or phenols are acylated, the products ar ...
Exploring Proteins - Weber State University
... • Immunoglobulins (antibodies) can be utilized as powerful analytical tools in biochemistry • An antibody (Immunoglobulin, Ig) is a complex protein formed by an animal in response to the presence of a foreign substance (most often foreign proteins). • An antibody usually exhibits specific and high ...
... • Immunoglobulins (antibodies) can be utilized as powerful analytical tools in biochemistry • An antibody (Immunoglobulin, Ig) is a complex protein formed by an animal in response to the presence of a foreign substance (most often foreign proteins). • An antibody usually exhibits specific and high ...
The proteome of Saccharomyces cerevisiae mitochondria
... of the known mitochondrial proteins. Several more proteins are likely candidates for a dual localization (36, 37). (v) We synthesized a number of the proteins, which had been localized to other compartments or had not been localized so far, in rabbit reticulocyte lysate in the presence of [35S]methi ...
... of the known mitochondrial proteins. Several more proteins are likely candidates for a dual localization (36, 37). (v) We synthesized a number of the proteins, which had been localized to other compartments or had not been localized so far, in rabbit reticulocyte lysate in the presence of [35S]methi ...
Protein synthesis meets ABC ATPases: new roles for Rli1/ABCE1
... catalysed by several translation factors. The fundamental reactions of protein synthesis, such as mRNA decoding, peptide bond formation and tRNA translocation, follow the same basic principles in prokaryotes and eukaryotes. However, some steps are quite different and require a larger set of factors ...
... catalysed by several translation factors. The fundamental reactions of protein synthesis, such as mRNA decoding, peptide bond formation and tRNA translocation, follow the same basic principles in prokaryotes and eukaryotes. However, some steps are quite different and require a larger set of factors ...
SIRT3 - Safic-Alcan Italia
... is the third member of the mammalian sirtuin family. The SIRT3 gene encodes the protein SIRT3, which exhibits NAD+-dependent deacetylase activity. SIRT3 is a member of the sirtuin family of proteins, homologs to the yeast Sir2 protein. Members of the sirtuin family are characterized by a sirtuin c ...
... is the third member of the mammalian sirtuin family. The SIRT3 gene encodes the protein SIRT3, which exhibits NAD+-dependent deacetylase activity. SIRT3 is a member of the sirtuin family of proteins, homologs to the yeast Sir2 protein. Members of the sirtuin family are characterized by a sirtuin c ...
Unicellular Eukaryotes to Humans Protein Arginine
... nuclear extracts (69). However, the first genes encoding protein arginine methyltransferases (PRMTs) were identified only a decade ago (29, 37, 54). Since this important discovery, the study of protein arginine methylation has been a rapidly expanding field, and PRMT-encoding genes have been identif ...
... nuclear extracts (69). However, the first genes encoding protein arginine methyltransferases (PRMTs) were identified only a decade ago (29, 37, 54). Since this important discovery, the study of protein arginine methylation has been a rapidly expanding field, and PRMT-encoding genes have been identif ...
Amino Acids, Peptides and Proteins
... 2. Approximate pKa of amino acid ionizable groups and their ionization state at different pH’s. ...
... 2. Approximate pKa of amino acid ionizable groups and their ionization state at different pH’s. ...
Protein Posttranslational Modifications: The Chemistry of Proteome
... rium Pseudomonas aeruginosa exhibits more than 60 such pathways.[6] The enzymes dedicated to protein phosphorylation are among the largest class of PTM enzymes. This superfamily of protein kinases have been termed the kinome, with over 500 members in the human kinome.[7] If these acted on average on ...
... rium Pseudomonas aeruginosa exhibits more than 60 such pathways.[6] The enzymes dedicated to protein phosphorylation are among the largest class of PTM enzymes. This superfamily of protein kinases have been termed the kinome, with over 500 members in the human kinome.[7] If these acted on average on ...
Acetylation
Acetylation (or in IUPAC nomenclature ethanoylation) describes a reaction that introduces an acetyl functional group into a chemical compound. (Deacetylation is the removal of the acetyl group.)Acetylation refers to the process of introducing an acetyl group (resulting in an acetoxy group) into a compound, namely the substitution of an acetyl group for an active hydrogen atom. A reaction involving the replacement of the hydrogen atom of a hydroxyl group with an acetyl group (CH3 CO) yields a specific ester, the acetate. Acetic anhydride is commonly used as an acetylating agent reacting with free hydroxyl groups. For example, it is used in the synthesis of aspirin and heroin.