Mass spectrometry and proteomics Steven P Gygi* and Ruedi
... interest resulted in peptide fragments, which were identified by peptide mass mapping. Each 15N that was incorporated shifted the mass of any given peptide upwards, leading to a paired peak for each peptide. The authors measured protein expression of 42 high-abundance proteins derived from two pools ...
... interest resulted in peptide fragments, which were identified by peptide mass mapping. Each 15N that was incorporated shifted the mass of any given peptide upwards, leading to a paired peak for each peptide. The authors measured protein expression of 42 high-abundance proteins derived from two pools ...
Tsui, S, Dai, T, Warren, ST and Yen, P: Association of the mouse infertility factor DAZL1 with actively translating polyribosomes. Biology of Reproduction 62:1655-1660 (2000).
... the biological significance of the preferential binding observed in the in vitro assays has yet to be demonstrated. To delineate the regions required for RNA binding, a series of constructs with deletions in the RRM domain, the DAZ repeat region, or the C-terminal portion were generated (Fig. 2). Th ...
... the biological significance of the preferential binding observed in the in vitro assays has yet to be demonstrated. To delineate the regions required for RNA binding, a series of constructs with deletions in the RRM domain, the DAZ repeat region, or the C-terminal portion were generated (Fig. 2). Th ...
GYP5 - Genetics
... shown to be a GAP for Ypt1p (DE ANTONI et al. 2002), a Rab GTPase involved in ER to Golgi trafficking (BACON et al. 1989, SEGEV, 1991; for review see LAZAR et al. 1997). Gyl1p is a protein with sequence similarity to Gyp5 and has been shown to colocalize with Gyp5p (CHESNEAU et al. 2004). We show th ...
... shown to be a GAP for Ypt1p (DE ANTONI et al. 2002), a Rab GTPase involved in ER to Golgi trafficking (BACON et al. 1989, SEGEV, 1991; for review see LAZAR et al. 1997). Gyl1p is a protein with sequence similarity to Gyp5 and has been shown to colocalize with Gyp5p (CHESNEAU et al. 2004). We show th ...
The key to life at the atomic level
... nucleotide sequences on each of the strands. ATTGCCAT represents something completely different from GCGTATAG. Scientists realized that the sequence of nucleotides controls the sequence of amino acids in proteins. But the question remained: How? ...
... nucleotide sequences on each of the strands. ATTGCCAT represents something completely different from GCGTATAG. Scientists realized that the sequence of nucleotides controls the sequence of amino acids in proteins. But the question remained: How? ...
lecture 8
... TCP-1” or “TCP-1 Ring Complex”. TCP-1 was the first subunit of CCT to be characterized. It was found to be present within a hetero-oligomeric complex that contained 8 different (related) chaperonin subunits 8-fold symmetry (different than GroEL’s 7-fold) duplication of chaperonin subunits occurr ...
... TCP-1” or “TCP-1 Ring Complex”. TCP-1 was the first subunit of CCT to be characterized. It was found to be present within a hetero-oligomeric complex that contained 8 different (related) chaperonin subunits 8-fold symmetry (different than GroEL’s 7-fold) duplication of chaperonin subunits occurr ...
Comparative proteomics reveal characteristics of life
... and even without standardization more than 75% of the observed differences in protein expression remained (data not shown). Our analysis, therefore, is both reproducible and robust, and in the following we report the results based on correction toward actin. Of the 47 quantifiable proteins, 15 were ...
... and even without standardization more than 75% of the observed differences in protein expression remained (data not shown). Our analysis, therefore, is both reproducible and robust, and in the following we report the results based on correction toward actin. Of the 47 quantifiable proteins, 15 were ...
by David Holzman Unlike its twin
... downstream genes—which in one thoroughly studied case are the enzymes that make the amino acid tryptophan—the antiterminator helix comes together. This action masks some of the nucleotides that would normally fold into the terminator helix and permits transcription to proceed. Two types of attenuato ...
... downstream genes—which in one thoroughly studied case are the enzymes that make the amino acid tryptophan—the antiterminator helix comes together. This action masks some of the nucleotides that would normally fold into the terminator helix and permits transcription to proceed. Two types of attenuato ...
A number of antibiotics produced by different - J
... RNA synthesis is also sensitive to this antibiotic8,9). However, we found that the RNA polymerases of the five organisms used in this study were unaffected by thiolutin in vitro (Fig. 1 A-E), although they were very sensitive to the drug in vivo (see Table 1). We therefore suggest that, at least in ...
... RNA synthesis is also sensitive to this antibiotic8,9). However, we found that the RNA polymerases of the five organisms used in this study were unaffected by thiolutin in vitro (Fig. 1 A-E), although they were very sensitive to the drug in vivo (see Table 1). We therefore suggest that, at least in ...
REVIEWS
... deployed by cells is extremely low. For proteins, ‘proof-reading’ occurs at the level of transcription, translation, folding and assembly. To pass the final QC checkpoints, a protein must typically have reached a correctly folded conformation. This is generally the so-called ‘native’ conformation th ...
... deployed by cells is extremely low. For proteins, ‘proof-reading’ occurs at the level of transcription, translation, folding and assembly. To pass the final QC checkpoints, a protein must typically have reached a correctly folded conformation. This is generally the so-called ‘native’ conformation th ...
pdf file - The Department of Computer Science
... The first principles of the evolution of the triplet code (Trifonov 2004), suggested by the consensus evolutionary temporal order of amino acids are: (1) Abiotic start, (2) Primacy of thermostability, (3) Complementarity of codons and of early mRNA, (4) Processivity of codon acquirements, each havin ...
... The first principles of the evolution of the triplet code (Trifonov 2004), suggested by the consensus evolutionary temporal order of amino acids are: (1) Abiotic start, (2) Primacy of thermostability, (3) Complementarity of codons and of early mRNA, (4) Processivity of codon acquirements, each havin ...
The archaeal origins of the eukaryotic translational system
... segmental structure associated uniquely to one, two or all three of the phylodomains (Vishwanath et al. 2004) (Figure 3). Critically, the current analyses show that eukaryotic homologous proteins contain only the archaeal-specific blocks and no bacterial-specific blocks, with the possible but unclea ...
... segmental structure associated uniquely to one, two or all three of the phylodomains (Vishwanath et al. 2004) (Figure 3). Critically, the current analyses show that eukaryotic homologous proteins contain only the archaeal-specific blocks and no bacterial-specific blocks, with the possible but unclea ...
Plant nuclear proteomics inside the cell maestro
... structures containing nucleic acids: chromatin and the nuclear matrix [16]. The latter is a nonhistone structure that serves as a support for the genome and its activities. Calikowski et al. [17] initially characterized the Arabidopsis thaliana nuclear matrix by electron microscopy and MS. They obse ...
... structures containing nucleic acids: chromatin and the nuclear matrix [16]. The latter is a nonhistone structure that serves as a support for the genome and its activities. Calikowski et al. [17] initially characterized the Arabidopsis thaliana nuclear matrix by electron microscopy and MS. They obse ...
Transcription termination control in bacteria Tina M Henkin
... the RNA-binding activity of which is controlled by phosphorylation [26]. The structure of the RNA-binding domain of SacY, one of the regulatory proteins in this family, has been determined [27], and RNA binding by BglG is dependent on dimerization of the regulatory protein using a leucine zipper mot ...
... the RNA-binding activity of which is controlled by phosphorylation [26]. The structure of the RNA-binding domain of SacY, one of the regulatory proteins in this family, has been determined [27], and RNA binding by BglG is dependent on dimerization of the regulatory protein using a leucine zipper mot ...
Functional Anthology of Intrinsic Disorder. 1. Biological Processes
... view of intrinsic disorder.6 More detailed analysis of extended disordered proteins/regions revealed that they can be further divided into two groups, random coil-like and pre-molten globule-like conformations.7 Recently, more than 150 proteins have been identified as containing functional disordere ...
... view of intrinsic disorder.6 More detailed analysis of extended disordered proteins/regions revealed that they can be further divided into two groups, random coil-like and pre-molten globule-like conformations.7 Recently, more than 150 proteins have been identified as containing functional disordere ...
DNA in Action! A 3D Swarm-based Model of a Gene Regulatory
... Gene Complex 2: lacI The lacI gene, the second key module, is located downstream of the main lac complex (Fig. 1a). It likewise contains a promoter region, and produces proteins through the same action of RNA polymerase. The lacI protein product is known as a repressor, which has the ability to bind ...
... Gene Complex 2: lacI The lacI gene, the second key module, is located downstream of the main lac complex (Fig. 1a). It likewise contains a promoter region, and produces proteins through the same action of RNA polymerase. The lacI protein product is known as a repressor, which has the ability to bind ...
Chapter 17 (Oct 23, 27, 28)
... (a) An mRNA molecule is generally translated simultaneously by several ribosomes in clusters called polyribosomes. ...
... (a) An mRNA molecule is generally translated simultaneously by several ribosomes in clusters called polyribosomes. ...
Biochemistry - Elon University
... Cai et al. (2002) investigated the link between hyperglycemia, which is one of the diabetic risk factors thought to be associated with DCM’s pathogenesis, and cardiomyocyte apoptosis.17 This study confirmed increased apoptosis through a specific pathway of apoptosis (called the mitochondrial cytochr ...
... Cai et al. (2002) investigated the link between hyperglycemia, which is one of the diabetic risk factors thought to be associated with DCM’s pathogenesis, and cardiomyocyte apoptosis.17 This study confirmed increased apoptosis through a specific pathway of apoptosis (called the mitochondrial cytochr ...
Small-angle scattering studies of intrinsically disordered proteins
... precludes the oligomerization of N0 in vivo [ 69 **]. Using EOM, the authors simultaneously fitted one SAXS curve and four SANS curves measured at different contrast levels for the complex of N 0 with deuterated P protein. The additional information provided by the distinct contribution of the two p ...
... precludes the oligomerization of N0 in vivo [ 69 **]. Using EOM, the authors simultaneously fitted one SAXS curve and four SANS curves measured at different contrast levels for the complex of N 0 with deuterated P protein. The additional information provided by the distinct contribution of the two p ...
Plastid-Targeting Peptides from the
... other organisms, their homology with proteins involved in pathways specific to plastids, and their possession of a bipartite leader sequence consisting of a signal and transit peptide (Archibald et al. 2003). Three genes that encoded substantial Nterminal leaders but lacked obvious signal peptides w ...
... other organisms, their homology with proteins involved in pathways specific to plastids, and their possession of a bipartite leader sequence consisting of a signal and transit peptide (Archibald et al. 2003). Three genes that encoded substantial Nterminal leaders but lacked obvious signal peptides w ...
Life and Chemistry: Large Molecules
... Chemical signals such as hormones bind to proteins on the cell surface membrane. • The combination of attractions, repulsions, and interactions determines the right fit. ...
... Chemical signals such as hormones bind to proteins on the cell surface membrane. • The combination of attractions, repulsions, and interactions determines the right fit. ...
Post-translational Modifications
... 2. Quality Control in the Cytoplasm: C. Molecular Chaperones: Proteins that mediate correct fate of other polypeptides but are not part of the final structure. Fate includes folding, assembly, interaction with other cellular components, transport, or degradation. A. History: Molecular chaperones in ...
... 2. Quality Control in the Cytoplasm: C. Molecular Chaperones: Proteins that mediate correct fate of other polypeptides but are not part of the final structure. Fate includes folding, assembly, interaction with other cellular components, transport, or degradation. A. History: Molecular chaperones in ...
SDS-PAGE strongly overestimates the molecular
... coils for both standard and unknown proteins. Given the unusual amino acid composition of the carboxyterminal domain of H [3] and its extreme phosphate content [2,12] we do not know if the random coil requirement is really fulfilled. The latter two properties may, however, also influence the value f ...
... coils for both standard and unknown proteins. Given the unusual amino acid composition of the carboxyterminal domain of H [3] and its extreme phosphate content [2,12] we do not know if the random coil requirement is really fulfilled. The latter two properties may, however, also influence the value f ...
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.