lecture 5
... evolutionary origin: the structural similarities could arise just from the physics and chemistry of proteins favoring certain packing arrangements and chain topologies. Class: secondary structure content and organization Murzin et al. J. Mol. Biol. 247, 536-540, 1995 ...
... evolutionary origin: the structural similarities could arise just from the physics and chemistry of proteins favoring certain packing arrangements and chain topologies. Class: secondary structure content and organization Murzin et al. J. Mol. Biol. 247, 536-540, 1995 ...
Table S6: Domains present in the primary network generated from
... typically between 205 to 258 amino acids in length. This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are about 220 amino acids in length. This family of proteins are functionally uncharacterised. This protein is found ...
... typically between 205 to 258 amino acids in length. This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are about 220 amino acids in length. This family of proteins are functionally uncharacterised. This protein is found ...
PDF
... anaerobic bacterium. D. turgidum and D. thermophilum together form the Dictyoglomi phylum. The two Dictyoglomus genomes are highly syntenic, and both are distantly related to Caldicellulosiruptor spp. D. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genom ...
... anaerobic bacterium. D. turgidum and D. thermophilum together form the Dictyoglomi phylum. The two Dictyoglomus genomes are highly syntenic, and both are distantly related to Caldicellulosiruptor spp. D. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genom ...
GmPep914, an Eight-Amino Acid Peptide Isolated
... increase in the extracellular pH of the media (Felix and Boller, 1995). An alkalinization assay was developed in the Ryan laboratory that has been a key to the purification of the defense peptides HypSys and AtPeps, as well as the peptide Rapid Alkalinization Factor (Pearce et al., 2001b), which is ...
... increase in the extracellular pH of the media (Felix and Boller, 1995). An alkalinization assay was developed in the Ryan laboratory that has been a key to the purification of the defense peptides HypSys and AtPeps, as well as the peptide Rapid Alkalinization Factor (Pearce et al., 2001b), which is ...
The role of IRES trans-acting factors in regulating translation initiation
... studied in this regard, and the data suggest that ITAFs remodel the structures of these two IRESs so that they attain the correct conformation for interaction with the 40S ribosomal subunit [27,32]. Thus the Bag-1 IRES requires the ITAF PCBP1 [poly(rC)-binding protein 1] (as an RNA chaperone) to bin ...
... studied in this regard, and the data suggest that ITAFs remodel the structures of these two IRESs so that they attain the correct conformation for interaction with the 40S ribosomal subunit [27,32]. Thus the Bag-1 IRES requires the ITAF PCBP1 [poly(rC)-binding protein 1] (as an RNA chaperone) to bin ...
SUPPLEMENTAL DATA FOR DUPLICATED SACCHAROMYCES
... There are conflicting reports for the location of PST2 and RFS1. In earlier studies, the green fluorescent protein (GFP)-fusion protein of PST2 localized to the cytoplasm in a punctuate pattern [5-7]. PST2 is predicted from its sequence to be located at ER. However, in a new study by Valencia-Burton ...
... There are conflicting reports for the location of PST2 and RFS1. In earlier studies, the green fluorescent protein (GFP)-fusion protein of PST2 localized to the cytoplasm in a punctuate pattern [5-7]. PST2 is predicted from its sequence to be located at ER. However, in a new study by Valencia-Burton ...
Formation and nuclear export of tRNA, rRNA and mRNA is regulated
... ACT1 mRNA (Fig. 3A) or of pre-U3, which contains a pre-mRNAlike intron in yeast. Thus, pre-mRNA splicing seems not to be affected by the rsp5-3 ts mutant. The level of the ACT1 mRNA was reduced in the rsp5-3 strain during incubation at 37 1C, but this decline was much slower than that seen for the p ...
... ACT1 mRNA (Fig. 3A) or of pre-U3, which contains a pre-mRNAlike intron in yeast. Thus, pre-mRNA splicing seems not to be affected by the rsp5-3 ts mutant. The level of the ACT1 mRNA was reduced in the rsp5-3 strain during incubation at 37 1C, but this decline was much slower than that seen for the p ...
Press Release
... led by Lars Steinmetz has turned this on its head. The researchers have shown that one end of the mRNA begins to decay while the other is still serving as a template for protein production. Thus, studying the decaying mRNA also provides a snapshot of how proteins are produced. The discovery was made ...
... led by Lars Steinmetz has turned this on its head. The researchers have shown that one end of the mRNA begins to decay while the other is still serving as a template for protein production. Thus, studying the decaying mRNA also provides a snapshot of how proteins are produced. The discovery was made ...
A novel EVI1 gene family, MEL1, lacking a PR domain (MEL1S) is
... EVI1 alternative transcripts.9 The genomic region of MDS1 is located around 300 kilobases (kb) upstream from the EVI1 gene, and the transcripts of MDS1/EVI1 were found in normal tissues including hematopoietic cells.10 Because EVI1 lacking the PR domain is overexpressed in leukemia cells with 3q26 a ...
... EVI1 alternative transcripts.9 The genomic region of MDS1 is located around 300 kilobases (kb) upstream from the EVI1 gene, and the transcripts of MDS1/EVI1 were found in normal tissues including hematopoietic cells.10 Because EVI1 lacking the PR domain is overexpressed in leukemia cells with 3q26 a ...
Investigating a Eukaryotic Genome
... any resulting colonies. Since the vector is treated with phosphatase, this background is usually very low. Sample data is provided in the following section. In the next lab session, students view their LB/ampicillin plates to determine if they obtained any colonies. Generally students have 10 – 100 ...
... any resulting colonies. Since the vector is treated with phosphatase, this background is usually very low. Sample data is provided in the following section. In the next lab session, students view their LB/ampicillin plates to determine if they obtained any colonies. Generally students have 10 – 100 ...
Function and specificity of 14-3-3 proteins in the regulation of
... tomato (Roberts and Bowles, 1999). The recent completion of the Arabidopsis genome project facilitated the identi®cation of up to 15 putative 14-3-3 genes, of which 12 are also represented as EST or cDNA clones (Rosenquist et al., 2001). An exon-based alignment enabled Wu et al. (1997) to classify A ...
... tomato (Roberts and Bowles, 1999). The recent completion of the Arabidopsis genome project facilitated the identi®cation of up to 15 putative 14-3-3 genes, of which 12 are also represented as EST or cDNA clones (Rosenquist et al., 2001). An exon-based alignment enabled Wu et al. (1997) to classify A ...
European Journal of Biochemistry
... the protein. The following lines of evidence indicate that the wparately digested with Hglll and G o R I . Plasmid DX/\ fragments PhoE* protein is norinally folded in thc outer membrane. ( a ) were analyzed on agarosc gels a n d the relevant fragment5 liere exAnalysis of the cell envelope protein pa ...
... the protein. The following lines of evidence indicate that the wparately digested with Hglll and G o R I . Plasmid DX/\ fragments PhoE* protein is norinally folded in thc outer membrane. ( a ) were analyzed on agarosc gels a n d the relevant fragment5 liere exAnalysis of the cell envelope protein pa ...
Sequence±structure±function studies of tRNA
... diverse class of S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases. The enzymes characterized to date include members of two unrelated superfamilies: `classical' Rossmann-fold-like (1,2) and SPOUT (3). The relatively small SPOUT superfamily includes only a few characterized RNAspeci®c en ...
... diverse class of S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases. The enzymes characterized to date include members of two unrelated superfamilies: `classical' Rossmann-fold-like (1,2) and SPOUT (3). The relatively small SPOUT superfamily includes only a few characterized RNAspeci®c en ...
NMR-driven secondary and tertiary structure model of Ca
... There are two X-ray crystal structures of Ca2+-loaded SCPs [12,13] and an NMR structure of Ca2+-calerythrin [14], a bacterial protein which shows SCP-like characteristics. Although the primary sequences of these three proteins are quite different (amino acid identities of 15%), the three structures ...
... There are two X-ray crystal structures of Ca2+-loaded SCPs [12,13] and an NMR structure of Ca2+-calerythrin [14], a bacterial protein which shows SCP-like characteristics. Although the primary sequences of these three proteins are quite different (amino acid identities of 15%), the three structures ...
Chapter 7: The New Genetics—Techniques for DNA Analysis
... double strand. But the probes, being composed of nucleotides, will also be invisible. To locate the probe after it binds to the DNA, it is necessary to engineer the probe so that it carries the biological equivalent of a light bulb. Two major types of light bulbs are used in molecular genetics. The ...
... double strand. But the probes, being composed of nucleotides, will also be invisible. To locate the probe after it binds to the DNA, it is necessary to engineer the probe so that it carries the biological equivalent of a light bulb. Two major types of light bulbs are used in molecular genetics. The ...
... answer using either glucose storage/release from glycogen, as regulated by hormones, or glycolysis or the TCA cycle, as regulated by energy sensing. Protein phosphorylation: Enzyme in pathways can be substrates for kinases. The phosphorylated form of the protein can be active or inactive. Dephosphor ...
Nomenclature for incompletely specified bases in nucleic acid
... sequences in DNA. For example, EcoRI and BamHI recognize the sequences 5'-GAATTC-3' and 5'-GGATCC-3' respectively. Nevertheless, a growing class of enzymes includes those that recognize series of derivative sequences, where two or more bases may be present at a particular position in the recognition ...
... sequences in DNA. For example, EcoRI and BamHI recognize the sequences 5'-GAATTC-3' and 5'-GGATCC-3' respectively. Nevertheless, a growing class of enzymes includes those that recognize series of derivative sequences, where two or more bases may be present at a particular position in the recognition ...
Characterization of new proteins found by analysis
... preferences for particular codon usage; the monopeptide score (MPS) related to amino acid composition; and the dipeptide score (DPS) related to the dipeptide usage. To calibrate the method, these scores were compared between a set of biologically characterized sequences and a set of ORFs extracted f ...
... preferences for particular codon usage; the monopeptide score (MPS) related to amino acid composition; and the dipeptide score (DPS) related to the dipeptide usage. To calibrate the method, these scores were compared between a set of biologically characterized sequences and a set of ORFs extracted f ...
Protein Folding and Expression
... The Brevibacillus Expression System II enables highly efficient production of target protein in secreted form. This system allows high yield of active proteins and is wellsuited for expression of eukaryotic proteins. The Brevibacillus system is nearly free of proteases, which facilitates production ...
... The Brevibacillus Expression System II enables highly efficient production of target protein in secreted form. This system allows high yield of active proteins and is wellsuited for expression of eukaryotic proteins. The Brevibacillus system is nearly free of proteases, which facilitates production ...
Finding Patterns in Protein Sequence and Structure
... • The human factor VIII gene (whose mutations cause hemophilia A) is spread over ~186,000 bp. It consists of 26 exons ranging in size from 69 to 3,106 bp, and its 25 introns range in size from 207 to 32,400 bp. The complete gene is thus ~9 kb of exon and ~177 kb of intron. • The biggest human gene y ...
... • The human factor VIII gene (whose mutations cause hemophilia A) is spread over ~186,000 bp. It consists of 26 exons ranging in size from 69 to 3,106 bp, and its 25 introns range in size from 207 to 32,400 bp. The complete gene is thus ~9 kb of exon and ~177 kb of intron. • The biggest human gene y ...
and paralogue-specific functions of acyl-CoA
... Abbreviations used: ACBD, acyl-CoA-binding domain; ACBP, acyl-CoA-binding protein; Acb1, Saccharomyces cerevisiae ACBP1; CARS, coherent anti-Stokes Raman scattering; DBI, diazepam-binding inhibitor; ECH, enoyl-CoA hydratase/isomerase; FAME, fatty acid methyl ester; GFP, green fluorescent protein; HN ...
... Abbreviations used: ACBD, acyl-CoA-binding domain; ACBP, acyl-CoA-binding protein; Acb1, Saccharomyces cerevisiae ACBP1; CARS, coherent anti-Stokes Raman scattering; DBI, diazepam-binding inhibitor; ECH, enoyl-CoA hydratase/isomerase; FAME, fatty acid methyl ester; GFP, green fluorescent protein; HN ...
Selection Vector for Direct Cloning of Proof Reading Polymerase
... The use of a blunt end restriction site which is destroyed as a result of incorporating a PCR fragment has also successfully been used [5]. Alternatively the vector can be engineered such that incorporation of the PCR-product affects a selection marker. Either the gene itself or its promoter is disr ...
... The use of a blunt end restriction site which is destroyed as a result of incorporating a PCR fragment has also successfully been used [5]. Alternatively the vector can be engineered such that incorporation of the PCR-product affects a selection marker. Either the gene itself or its promoter is disr ...
Large-scale identification of cytosolic mouse brain proteins by
... identified brain proteins by the use of prefractionation. In order to reduce the complexity of mouse brain proteome we applied chromatographic prefractionations, ionexchange and hydrophobic interaction chromatography, prior to 2-DE, followed by mass spectrometric identification (2-DE MALDI-MS). We a ...
... identified brain proteins by the use of prefractionation. In order to reduce the complexity of mouse brain proteome we applied chromatographic prefractionations, ionexchange and hydrophobic interaction chromatography, prior to 2-DE, followed by mass spectrometric identification (2-DE MALDI-MS). We a ...