An Efficient Protocol for Identifying Separation-of-Function
... ABSTRACT Mutations that confer the loss of a single biochemical property (separation-of-function mutations) can often uncover a previously unknown role for a protein in a particular biological process. However, most mutations are identified based on loss-offunction phenotypes, which cannot differenti ...
... ABSTRACT Mutations that confer the loss of a single biochemical property (separation-of-function mutations) can often uncover a previously unknown role for a protein in a particular biological process. However, most mutations are identified based on loss-offunction phenotypes, which cannot differenti ...
Communication - Department of Molecular Physiology and Biophysics
... was overlaid by dystrophin fusion protein containing cysteinerich and C-terminal domains (16). This interaction was not detected in our experiments, probably because of the lower concentration of in vitro translated dystrophin in the overlay assay. Interaction of dystrophin with β-dystroglycan (one ...
... was overlaid by dystrophin fusion protein containing cysteinerich and C-terminal domains (16). This interaction was not detected in our experiments, probably because of the lower concentration of in vitro translated dystrophin in the overlay assay. Interaction of dystrophin with β-dystroglycan (one ...
Protein dynamics and proteolysis in plant vacuoles
... cleaved from the precursor and it enters the biosynthetic pathway (also called the secretion pathway). Large segments of the precursor correspond to the mature vacuolar protein. Precursors can contain more than one subunit of the mature protein (e.g. 2S and 11S storage proteins; Müntz, 1998) or eve ...
... cleaved from the precursor and it enters the biosynthetic pathway (also called the secretion pathway). Large segments of the precursor correspond to the mature vacuolar protein. Precursors can contain more than one subunit of the mature protein (e.g. 2S and 11S storage proteins; Müntz, 1998) or eve ...
Topology and Phosphorylation of Soybean Nodulin
... This phosphorylation is mediated by a Ca2+-dependent, calmodulin-independent protein kinase located in the peribacteroid membrane. Externally supplied acid phosphatase dephosphorylates this protein, but alkaline phosphatase does not. Based on its homology with several eukaryotic and prokaryotic chan ...
... This phosphorylation is mediated by a Ca2+-dependent, calmodulin-independent protein kinase located in the peribacteroid membrane. Externally supplied acid phosphatase dephosphorylates this protein, but alkaline phosphatase does not. Based on its homology with several eukaryotic and prokaryotic chan ...
GFP-labelled Rubisco and aspartate aminotransferase are present
... mGFP5(S65T) was ampli®ed by PCR using a forward primer that overlapped the ASP5 fragment and a reverse primer with an SstI site at the 5¢ end. These two fragments were joined via recombinant PCR, sequenced, and inserted into the binary vector. For the SS:CFP construct, a cDNA of the Pisum sativum Rb ...
... mGFP5(S65T) was ampli®ed by PCR using a forward primer that overlapped the ASP5 fragment and a reverse primer with an SstI site at the 5¢ end. These two fragments were joined via recombinant PCR, sequenced, and inserted into the binary vector. For the SS:CFP construct, a cDNA of the Pisum sativum Rb ...
UNIT 2. Structure and function of proteins.
... - Some of them show specific biological roles, but in other cases they are just part of the main structural and functional peptide. ...
... - Some of them show specific biological roles, but in other cases they are just part of the main structural and functional peptide. ...
2.3. Three-Dimensional structure and function of proteins.
... - Some of them show specific biological roles, but in other cases they are just part of the main structural and functional peptide. ...
... - Some of them show specific biological roles, but in other cases they are just part of the main structural and functional peptide. ...
a server for analyzing and predicting RNA
... protein–RNA complex. The output is a display of the sequence of each chain in the complex, with a label for each residue; ‘þ’ for residues that are within the specified distance cutoff and ‘’ for residues that do not have any atoms within the distance cutoff. The calculated RNA-binding residues are al ...
... protein–RNA complex. The output is a display of the sequence of each chain in the complex, with a label for each residue; ‘þ’ for residues that are within the specified distance cutoff and ‘’ for residues that do not have any atoms within the distance cutoff. The calculated RNA-binding residues are al ...
Protein splicing of PRP8 mini-inteins from species of the genus
... chrysogenum, P. expansum, P. vulpinum, and P. thomii. PCR amplifications were performed with oligonucleotides, allowing the detection of an intein sequence in an approximately 300-bp fragment of the prp8 gene encoding the conserved 3.2 region of the PRP8 protein. The presence of an intervening seque ...
... chrysogenum, P. expansum, P. vulpinum, and P. thomii. PCR amplifications were performed with oligonucleotides, allowing the detection of an intein sequence in an approximately 300-bp fragment of the prp8 gene encoding the conserved 3.2 region of the PRP8 protein. The presence of an intervening seque ...
Role of Streptococcus sanguinis sortase A in bacterial
... insertional inactivation (Figs. 1A,B) and used a differential display approach to demonstrate the enzymatic activity of SrtA against cell-associated proteins. In a comparison of strains ATCC 10556 and TR-56, at least 6 proteins were released from the 8 M urea extracted fraction of the srtAdeficient ...
... insertional inactivation (Figs. 1A,B) and used a differential display approach to demonstrate the enzymatic activity of SrtA against cell-associated proteins. In a comparison of strains ATCC 10556 and TR-56, at least 6 proteins were released from the 8 M urea extracted fraction of the srtAdeficient ...
Variations in amino acid composition in bacterial single stranded
... from three taxonomically distant species, Helicobacter pylori, (Epsilonproteobacteria), Escherichia coli (Gammaproteobacteria), and Streptomyces coelicolor (Actinobacteria). These species with solved SSB structures were selected since they possess 38 %, 50 % and 72 % GC ratio in their genomes, respe ...
... from three taxonomically distant species, Helicobacter pylori, (Epsilonproteobacteria), Escherichia coli (Gammaproteobacteria), and Streptomyces coelicolor (Actinobacteria). These species with solved SSB structures were selected since they possess 38 %, 50 % and 72 % GC ratio in their genomes, respe ...
PDF - Blood Journal
... with Ca⫹⫹ and ionophore A23187 are free of cytoskeletal components and are specifically enriched in glycosyl phosphatidylinositol (GPI)–anchored proteins, such as acetylcholinesterase (AChE) and decay accelerating factor (CD55).14 They are also enriched in the transmembrane protein complement recept ...
... with Ca⫹⫹ and ionophore A23187 are free of cytoskeletal components and are specifically enriched in glycosyl phosphatidylinositol (GPI)–anchored proteins, such as acetylcholinesterase (AChE) and decay accelerating factor (CD55).14 They are also enriched in the transmembrane protein complement recept ...
pdf
... separating the two strands (Fig. 3.1.10). The two strands are rewound at another active site, regenerating duplex DNA. c. Within the unwound region (bubble), the 3' terminus of the growing RNA chain is bound to its complement on the template strand via H-bonding. The DNA strand whose sequence is the ...
... separating the two strands (Fig. 3.1.10). The two strands are rewound at another active site, regenerating duplex DNA. c. Within the unwound region (bubble), the 3' terminus of the growing RNA chain is bound to its complement on the template strand via H-bonding. The DNA strand whose sequence is the ...
Full-Text PDF
... Alternative splicing of pre-mRNA is prevalent in mammalian genomes and acts as a mechanism to amplify genetic diversity by enabling the number of proteins arising from the genes to be increased by a factor of 10 times [4]. Alternative pre-mRNA splicing can also regulate protein expression in a cell- ...
... Alternative splicing of pre-mRNA is prevalent in mammalian genomes and acts as a mechanism to amplify genetic diversity by enabling the number of proteins arising from the genes to be increased by a factor of 10 times [4]. Alternative pre-mRNA splicing can also regulate protein expression in a cell- ...
RNA-based life forms
... transition to RNA might have been achieved. TNA consists of α-L-threofuranosyl sugars linked by 3´, 2´-phosphodiester bonds.9 The probability of TNA spontaneously forming from its components is much greater than that of RNA, as threose is one of just two aldotetroses, each of which has only four ste ...
... transition to RNA might have been achieved. TNA consists of α-L-threofuranosyl sugars linked by 3´, 2´-phosphodiester bonds.9 The probability of TNA spontaneously forming from its components is much greater than that of RNA, as threose is one of just two aldotetroses, each of which has only four ste ...
Cloning, Purification, and Partial Characterization of the
... large insertion (Fig. 1). Analysis of the insertion sequence and its integration site [5,6] clearly suggest that it is an intein. The intein is inserted in the middle of the Walker-A motif [7], a highly conserved motif which is found in all members of the AAA+ family of ATPases [8,9]. The sequence o ...
... large insertion (Fig. 1). Analysis of the insertion sequence and its integration site [5,6] clearly suggest that it is an intein. The intein is inserted in the middle of the Walker-A motif [7], a highly conserved motif which is found in all members of the AAA+ family of ATPases [8,9]. The sequence o ...
Interacting specificity of a histidine kinase and its cognate response
... sequence upstream of the prrA start codon in addition to the entire prrA gene. Since this additional DNA sequence does not contain a stop codon that lies in the same reading frame as the GAL4AD and prrA genes, the PrrA protein expressed from pPLAC (pGADT7 : : prrA) has an additional 28 amino acid re ...
... sequence upstream of the prrA start codon in addition to the entire prrA gene. Since this additional DNA sequence does not contain a stop codon that lies in the same reading frame as the GAL4AD and prrA genes, the PrrA protein expressed from pPLAC (pGADT7 : : prrA) has an additional 28 amino acid re ...
Lecture 10 Thurs 4-27-06
... 1. Adhesion to vascular endothelium is a key factor in pathogenicity and is dependent on the Plasmodium protein PfEMP1 and endothelial receptors including CD36. 2. Evidence that binding of IRBCs to CD36 on endothelial cells activates a signaling pathway important for cytoadherence (From Yipp, B. et ...
... 1. Adhesion to vascular endothelium is a key factor in pathogenicity and is dependent on the Plasmodium protein PfEMP1 and endothelial receptors including CD36. 2. Evidence that binding of IRBCs to CD36 on endothelial cells activates a signaling pathway important for cytoadherence (From Yipp, B. et ...
The DsbA Signal Sequence Directs Efficient
... methionine concentration of 90 mM for 15 s. For identification of polypeptides with or without their signal peptides, standards were prepared by labeling for 5 min in the presence or absence of azide, which allowed full incorporation of [35S]methionine. Labeling was terminated by addition of trichlo ...
... methionine concentration of 90 mM for 15 s. For identification of polypeptides with or without their signal peptides, standards were prepared by labeling for 5 min in the presence or absence of azide, which allowed full incorporation of [35S]methionine. Labeling was terminated by addition of trichlo ...
The protein import apparatus of chloroplasts
... indicate a common reeeptor for most of the bulk protein import or at least for the precursor proteins' listed above. which represent major chloroplast constituents of different localization. Though the influence of the synthetic peptides on the import pathway seems to be specific, it is not known wh ...
... indicate a common reeeptor for most of the bulk protein import or at least for the precursor proteins' listed above. which represent major chloroplast constituents of different localization. Though the influence of the synthetic peptides on the import pathway seems to be specific, it is not known wh ...
AA-tRNA - Studentportalen
... with G:C-base-pairs of fMet-tRNAi effectively selecting it over other tRNAs. •IF1 binding to the 30S and blocks the A site of the 30S preventing tRNA binding to the A site of 30S during initiation. •IF2 binds with high affinity to the 30S and to formylated tRNAs and effectively selects fMet-tRNAi ov ...
... with G:C-base-pairs of fMet-tRNAi effectively selecting it over other tRNAs. •IF1 binding to the 30S and blocks the A site of the 30S preventing tRNA binding to the A site of 30S during initiation. •IF2 binds with high affinity to the 30S and to formylated tRNAs and effectively selects fMet-tRNAi ov ...
Sequential steps in clathrin-mediated synaptic vesicle endocytosis
... average size is larger and the size variability is increased when compared with that of vesicles in wild-type controls [5,6]. Moreover, microinjection studies in the squid giant synapse [7] have shown that a peptide corresponding to the clathrin assembly domain of AP180 causes a marked depletion of ...
... average size is larger and the size variability is increased when compared with that of vesicles in wild-type controls [5,6]. Moreover, microinjection studies in the squid giant synapse [7] have shown that a peptide corresponding to the clathrin assembly domain of AP180 causes a marked depletion of ...
Molecular Components of the Bacterial Cytoskeleton
... protein polymer formation). The core structures of α- and β-tubulin are composed of two β-sheets surrounded by α-helices (Nogales et al. 1998b), making up two functional domains. The N-terminal of the two domains has a Rossmann fold similar to that of many ATPases, and it contains a GTP binding site ...
... protein polymer formation). The core structures of α- and β-tubulin are composed of two β-sheets surrounded by α-helices (Nogales et al. 1998b), making up two functional domains. The N-terminal of the two domains has a Rossmann fold similar to that of many ATPases, and it contains a GTP binding site ...
Not Every Disulfide Lasts Forever: Disulfide Bond
... the conformation in a way that exposes additional DNA binding residues. It results in a conformation that allows now the transcription factor to cooperatively interact with RNA polymerase (RNAp), an essential prerequisite to induce gene transcription. The major conformational changes that occur upon ...
... the conformation in a way that exposes additional DNA binding residues. It results in a conformation that allows now the transcription factor to cooperatively interact with RNA polymerase (RNAp), an essential prerequisite to induce gene transcription. The major conformational changes that occur upon ...
RiboMAX(TM) Large Scale RNA Production Systems
... reactions. The DNA template must be free of RNase. If the presence of RNase is suspected, treat the DNA with Proteinase K (100µg/ml) and SDS (0.5%) in 50mM Tris-HCl (pH 7.5), 5mM CaCl2 for 30 minutes at 37°C (6). Purify the DNA further by extraction with TE-saturated (pH 8.0) phenol:chloroform: isoa ...
... reactions. The DNA template must be free of RNase. If the presence of RNase is suspected, treat the DNA with Proteinase K (100µg/ml) and SDS (0.5%) in 50mM Tris-HCl (pH 7.5), 5mM CaCl2 for 30 minutes at 37°C (6). Purify the DNA further by extraction with TE-saturated (pH 8.0) phenol:chloroform: isoa ...
SR protein
SR proteins are a conserved family of proteins involved in RNA splicing. SR proteins are named because they contain a protein domain with long repeats of serine and arginine amino acid residues, whose standard abbreviations are ""S"" and ""R"" respectively. SR proteins are 50-300 amino acids in length and composed of two domains, the RNA recognition motif (RRM) region and the RS binding domain. SR proteins are more commonly found in the nucleus than the cytoplasm, but several SR proteins are known to shuttle between the nucleus and the cytoplasm.SR proteins were discovered in the 1990s in Drosophila and in amphibian oocytes, and later in humans. In general, metazoans appear to have SR proteins and unicellular organisms lack SR proteins.SR proteins are important in constitutive and alternative pre-mRNA splicing, mRNA export, genome stabilization, nonsense-mediated decay, and translation. SR proteins alternatively splice pre-mRNA by preferentially selecting different splice sites on the pre-mRNA strands to create multiple mRNA transcripts from one pre-mRNA transcript. Once splicing is complete the SR protein may or may not remain attached to help shuttle the mRNA strand out of the nucleus. As RNA Polymerase II is transcribing DNA into RNA, SR proteins attach to newly made pre-mRNA to prevent the pre-mRNA from binding to the coding DNA strand to increase genome stabilization. Topoisomerase I and SR proteins also interact to increase genome stabilization. SR proteins can control the concentrations of specific mRNA that is successfully translated into protein by selecting for nonsense-mediated decay codons during alternative splicing. SR proteins can alternatively splice NMD codons into its own mRNA transcript to auto-regulate the concentration of SR proteins. Through the mTOR pathway and interactions with polyribosomes, SR proteins can increase translation of mRNA.Ataxia telangiectasia, neurofibromatosis type 1, several cancers, HIV-1, and spinal muscular atrophy have all been linked to alternative splicing by SR proteins.