Protein-protein interaction networks (I): data preprocessing
... 2. It takes place in the nucleus, so many proteins are not in their native compartment. This could lead to both falsepositives and false-negatives. (i) False positives: Interactions that are falsely identified in the experiment. The reason is that even if two proteins potentially interact into the n ...
... 2. It takes place in the nucleus, so many proteins are not in their native compartment. This could lead to both falsepositives and false-negatives. (i) False positives: Interactions that are falsely identified in the experiment. The reason is that even if two proteins potentially interact into the n ...
Cis-elements of protein transport to the plant vacuoles
... motif recognized by proteins of the BP-80 family (or VSR, Paris et al., 1997). It is also present in the N-terminal propeptides of several potato proteinase inhibitors related to sporamin, linked to the NPI sequence (NPINLPS, Ishikawa et al., 1994). It could also be an indication that the receptor c ...
... motif recognized by proteins of the BP-80 family (or VSR, Paris et al., 1997). It is also present in the N-terminal propeptides of several potato proteinase inhibitors related to sporamin, linked to the NPI sequence (NPINLPS, Ishikawa et al., 1994). It could also be an indication that the receptor c ...
The Use of Multiple Transcription Starts Causes the Dual Targeting
... from chloroplasts (Fig. 4D). This result was confirmed by merging the red autofluorescence of chloroplasts (Fig. 4E, F). Cells in which a control construct, 35S-GFP, was introduced, exhibited green fluorescence from the nucleus and cytoplasm (Fig. 4B). These results strongly suggest that two PMDAR i ...
... from chloroplasts (Fig. 4D). This result was confirmed by merging the red autofluorescence of chloroplasts (Fig. 4E, F). Cells in which a control construct, 35S-GFP, was introduced, exhibited green fluorescence from the nucleus and cytoplasm (Fig. 4B). These results strongly suggest that two PMDAR i ...
ppt - Chair of Computational Biology
... repression of the positive transcription factors CLOCK and BMAL1 is maximal. There are many CKI sites on PER proteins, but the function of only a subset of these sites is known. c | One clear function of the phosphorylation of PER proteins is the regulation of protein stability. Phosphorylation of o ...
... repression of the positive transcription factors CLOCK and BMAL1 is maximal. There are many CKI sites on PER proteins, but the function of only a subset of these sites is known. c | One clear function of the phosphorylation of PER proteins is the regulation of protein stability. Phosphorylation of o ...
Drosophila C-terminal Binding Protein Functions as a Context
... Transcriptional repression plays a major role in segmentation gene expression that leads to proper body patterning during early Drosophila development (cf. Refs. 1 and 4). A number of different transcriptional repressors present in the early Drosophila embryo have been shown to encode sequence-speci ...
... Transcriptional repression plays a major role in segmentation gene expression that leads to proper body patterning during early Drosophila development (cf. Refs. 1 and 4). A number of different transcriptional repressors present in the early Drosophila embryo have been shown to encode sequence-speci ...
tethering redox proteins to the outer membrane in Neisseria and
... from the surface of the inner leaflet of the outer membrane. Hong et al. [18] showed that the Laz protein or a GST (glutathione transferase) fused to the signal peptide plus Nterminal LCR of Laz enables the globular azurin–GST to be surface-exposed in Neisseria (or indeed on expression in E. coli). ...
... from the surface of the inner leaflet of the outer membrane. Hong et al. [18] showed that the Laz protein or a GST (glutathione transferase) fused to the signal peptide plus Nterminal LCR of Laz enables the globular azurin–GST to be surface-exposed in Neisseria (or indeed on expression in E. coli). ...
Supplementary feeding of grazing sheep in South Africa
... essential nutrients to the microbes in the rumen. Where lambs received a medium quality roughage ad lib. the strategy increased roughage intake and enhanced animal performance by increasing liveweight gain, carcass weight, wool growth rate and altering fat depth. This research indicated that if ther ...
... essential nutrients to the microbes in the rumen. Where lambs received a medium quality roughage ad lib. the strategy increased roughage intake and enhanced animal performance by increasing liveweight gain, carcass weight, wool growth rate and altering fat depth. This research indicated that if ther ...
APG Phytochemical Database - American Pistachio Growers
... Amino Acid Building block for making proteins. (See Protein) Arginine maintains arteries flexible and enhances blood flow by boosting nitric oxide, a compound that relaxes blood vessels. ...
... Amino Acid Building block for making proteins. (See Protein) Arginine maintains arteries flexible and enhances blood flow by boosting nitric oxide, a compound that relaxes blood vessels. ...
The Generic Nature of Protein Folding and Misfolding
... The cellular levels of many chaperones are, for example, substantially increased during cellular stress, as their frequent designation as heat-shock proteins (Hsps) indicates (Pelham, 1986). Some molecular chaperones act to capture misfolded proteins, or even some types of aggregates, and provide th ...
... The cellular levels of many chaperones are, for example, substantially increased during cellular stress, as their frequent designation as heat-shock proteins (Hsps) indicates (Pelham, 1986). Some molecular chaperones act to capture misfolded proteins, or even some types of aggregates, and provide th ...
A tribute to Ko Shimamoto (1949–2013)
... A tribute to Ko Shimamoto (1949–2013) | 6757 complexity, but the connections identified by Ko’s group remain central to these models. The work of Hayama et al. (2003) demonstrated that activation of Hd3a transcription under short days was the photoperiodic output that led to early flowering. Thi ...
... A tribute to Ko Shimamoto (1949–2013) | 6757 complexity, but the connections identified by Ko’s group remain central to these models. The work of Hayama et al. (2003) demonstrated that activation of Hd3a transcription under short days was the photoperiodic output that led to early flowering. Thi ...
Endoplasmic reticulum stress in lung disease
... Inositol-requiring enzyme (IRE)1 is the oldest ER stress sensor in evolutionary terms (figure 1). Mammals possess two isoforms. IRE1α is the ubiquitous form found in all cells that possess an ER, while IRE1β is restricted to the cells of the gut and lung and appears to play a specific function in mu ...
... Inositol-requiring enzyme (IRE)1 is the oldest ER stress sensor in evolutionary terms (figure 1). Mammals possess two isoforms. IRE1α is the ubiquitous form found in all cells that possess an ER, while IRE1β is restricted to the cells of the gut and lung and appears to play a specific function in mu ...
Lipid–protein interactions probed by electron crystallography
... the eye lens, and like all other aquaporins, each monomer consists of six-transmembrane a-helices arranged as in a barrel forming a central pore for water (reviewed in [10,11]). Four AQP monomers assemble into tetramers although each monomer forms its own channel. It was suggested that tetramerizat ...
... the eye lens, and like all other aquaporins, each monomer consists of six-transmembrane a-helices arranged as in a barrel forming a central pore for water (reviewed in [10,11]). Four AQP monomers assemble into tetramers although each monomer forms its own channel. It was suggested that tetramerizat ...
Practical exercises INSA course: modelling integrated
... intensely studied for more than 50 years. The underlying regulatory system involves a complex interplay between metabolism, signaling by metabolites and proteins, and the regulation of gene expression, in the context of global constraints on cell physiology. In order to explain how the observed beha ...
... intensely studied for more than 50 years. The underlying regulatory system involves a complex interplay between metabolism, signaling by metabolites and proteins, and the regulation of gene expression, in the context of global constraints on cell physiology. In order to explain how the observed beha ...
Protein Folding at the Exit Tunnel
... cell compartments, secretion, and cotranslational insertion into membranes. The latter processes are neglected in this review, which focuses on the folding of cytosolic soluble proteins. The unfolded state. Protein folding and unfolding in the cell can occur either during or after protein biosynthes ...
... cell compartments, secretion, and cotranslational insertion into membranes. The latter processes are neglected in this review, which focuses on the folding of cytosolic soluble proteins. The unfolded state. Protein folding and unfolding in the cell can occur either during or after protein biosynthes ...
Nucleic Acid and Protein Quantitation Methods
... detection. For dsDNA, the common methods include Hoechst, and Invitrogen Quant-iT PicoGreen®, Broad Range, and High Sensitivity dsDNA kits. These dyes have different excitation/emission profiles (Table 1) which may be more or less convenient depending on the individual application. Hoechst can be le ...
... detection. For dsDNA, the common methods include Hoechst, and Invitrogen Quant-iT PicoGreen®, Broad Range, and High Sensitivity dsDNA kits. These dyes have different excitation/emission profiles (Table 1) which may be more or less convenient depending on the individual application. Hoechst can be le ...
Pseudogene function: regulation of gene expression
... A long held ostensible support for the absence of pseudogene function has been their usual apparent lack of sequence conservation. Protein-coding genes typically vary only slightly among orthologs and paralogs as a result of purifying selection*. This is a result of the fact that most proteins canno ...
... A long held ostensible support for the absence of pseudogene function has been their usual apparent lack of sequence conservation. Protein-coding genes typically vary only slightly among orthologs and paralogs as a result of purifying selection*. This is a result of the fact that most proteins canno ...
Cell and Molecular Biology
... Is a dynamic 3-dimensional structure that fills the cytoplasm, and is present in both eukaryotic and prokaryotic cells. The cytoskeleton acts as both muscle and skeleton, and plays a role in cell protection, cell motility (migration), cytokinesis, intracellular transport, cell division and the organ ...
... Is a dynamic 3-dimensional structure that fills the cytoplasm, and is present in both eukaryotic and prokaryotic cells. The cytoskeleton acts as both muscle and skeleton, and plays a role in cell protection, cell motility (migration), cytokinesis, intracellular transport, cell division and the organ ...
Functional Equivalence of Translation Factor eIF5B from Candida
... eIF5B of Saccharomyces cerevisiae Because the Nterminal region of eIF5B is not essential for its function, only the G-domain and C-terminal regions were cloned into the expression vector. The eIF5B gene of Arabidopsis thaliana was amplified from the cDNA library by PCR and the others were obtained f ...
... eIF5B of Saccharomyces cerevisiae Because the Nterminal region of eIF5B is not essential for its function, only the G-domain and C-terminal regions were cloned into the expression vector. The eIF5B gene of Arabidopsis thaliana was amplified from the cDNA library by PCR and the others were obtained f ...
Targeting of Proteins to Endoplasmic Reticulum
... sequences have been identified for RNA localization signals, and it is widely believed that the targeting process is likely to be more complex than first anticipated, with constant reorganization of the mRNAprotein complex en route to its final destination (for review, see Van de Bor and Davis, 2004 ...
... sequences have been identified for RNA localization signals, and it is widely believed that the targeting process is likely to be more complex than first anticipated, with constant reorganization of the mRNAprotein complex en route to its final destination (for review, see Van de Bor and Davis, 2004 ...
Mass Spectrometry in Viral Proteomics
... Two cleavage sites are accessible for the protein of interest alone (top, left), yielding fragments after limited digestion. In the complex with protein X, one site is protected (below, left), yielding fewer fragments. However, fragments from protein X are also produced. (right) A bar graph expressi ...
... Two cleavage sites are accessible for the protein of interest alone (top, left), yielding fragments after limited digestion. In the complex with protein X, one site is protected (below, left), yielding fewer fragments. However, fragments from protein X are also produced. (right) A bar graph expressi ...
Lecture 1 / WS 2007/08
... (a) illustrates the graph theoretic description for a simple pathway (catalysed by Mg2+-dependant enzymes). (b) In the most abstract approach all interacting metabolites are considered equally. The links between nodes represent reactions that interconvert one substrate into another. For many biologi ...
... (a) illustrates the graph theoretic description for a simple pathway (catalysed by Mg2+-dependant enzymes). (b) In the most abstract approach all interacting metabolites are considered equally. The links between nodes represent reactions that interconvert one substrate into another. For many biologi ...
PROTEIN SYNTHESIS: TRANSLATION AND
... subunits, each of which contains RNA and many proteins. With one exception, each protein is present in a single copy per ribosome, as is each RNA species. The composition of major ribosome types is shown in Table 17.1, and characteristics of their RNAs are given in Table 16.1. Ribosome architecture ...
... subunits, each of which contains RNA and many proteins. With one exception, each protein is present in a single copy per ribosome, as is each RNA species. The composition of major ribosome types is shown in Table 17.1, and characteristics of their RNAs are given in Table 16.1. Ribosome architecture ...
Phosphoproteomics as a tool to unravel plant
... Busconi 2001, Saijo et al. 2000) and overexpression of their genes enhances cold tolerance (Abbasi et al. 2004, ...
... Busconi 2001, Saijo et al. 2000) and overexpression of their genes enhances cold tolerance (Abbasi et al. 2004, ...
Intrinsically Disordered Linker and Plasma Membrane
... acid sequence. We constructed a gene in which the region encoding for the ID region (between amino acids 596 and 917) was replaced by a synthetic fragment of DNA that encoded a randomized version of the original amino acid sequence. The resulting ID linker thus shared with the native linker its diso ...
... acid sequence. We constructed a gene in which the region encoding for the ID region (between amino acids 596 and 917) was replaced by a synthetic fragment of DNA that encoded a randomized version of the original amino acid sequence. The resulting ID linker thus shared with the native linker its diso ...
Protein moonlighting
Protein moonlighting (or gene sharing) is a phenomenon by which a protein can perform more than one function. Ancestral moonlighting proteins originally possessed a single function but through evolution, acquired additional functions. Many proteins that moonlight are enzymes; others are receptors, ion channels or chaperones. The most common primary function of moonlighting proteins is enzymatic catalysis, but these enzymes have acquired secondary non-enzymatic roles. Some examples of functions of moonlighting proteins secondary to catalysis include signal transduction, transcriptional regulation, apoptosis, motility, and structural.Protein moonlighting may occur widely in nature. Protein moonlighting through gene sharing differs from the use of a single gene to generate different proteins by alternative RNA splicing, DNA rearrangement, or post-translational processing. It is also different from multifunctionality of the protein, in which the protein has multiple domains, each serving a different function. Protein moonlighting by gene sharing means that a gene may acquire and maintain a second function without gene duplication and without loss of the primary function. Such genes are under two or more entirely different selective constraints.Various techniques have been used to reveal moonlighting functions in proteins. The detection of a protein in unexpected locations within cells, cell types, or tissues may suggest that a protein has a moonlighting function. Furthermore, sequence or structure homology of a protein may be used to infer both primary function as well as secondary moonlighting functions of a protein.The most well-studied examples of gene sharing are crystallins. These proteins, when expressed at low levels in many tissues function as enzymes, but when expressed at high levels in eye tissue, become densely packed and thus form lenses. While the recognition of gene sharing is relatively recent—the term was coined in 1988, after crystallins in chickens and ducks were found to be identical to separately identified enzymes—recent studies have found many examples throughout the living world. Joram Piatigorsky has suggested that many or all proteins exhibit gene sharing to some extent, and that gene sharing is a key aspect of molecular evolution. The genes encoding crystallins must maintain sequences for catalytic function and transparency maintenance function.Inappropriate moonlighting is a contributing factor in some genetic diseases, and moonlighting provides a possible mechanism by which bacteria may become resistant to antibiotics.