Zecture #24
... cleavage of the leaving group and potential stabilization of the transition state. Chemically, this mechanism is much more reasonable than that put forth by Steitz and Moore. Steitz & Moore's (wrong) mechanism Refer to handout; figures taken from Science 289 from 2000. Models are all based on GAC, G ...
... cleavage of the leaving group and potential stabilization of the transition state. Chemically, this mechanism is much more reasonable than that put forth by Steitz and Moore. Steitz & Moore's (wrong) mechanism Refer to handout; figures taken from Science 289 from 2000. Models are all based on GAC, G ...
QPrEST™—isotope-labeled multipeptide standards for
... these peptides in the analysis can generate additional quantitative information, further increasing the reliability of the analysis. The ...
... these peptides in the analysis can generate additional quantitative information, further increasing the reliability of the analysis. The ...
Proteomic studies of the environmentally important methanotroph
... Incorrect matches often (but not always) result from use of low quality peptide MS/MS data to search the database Even high quality data can produce invalid identifications ...
... Incorrect matches often (but not always) result from use of low quality peptide MS/MS data to search the database Even high quality data can produce invalid identifications ...
Supplementary Information
... Motoyama A, Venable JD, Ruse CI and Yates JR, 3rd (2006) Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples. Anal Chem 78: 5109-5118 Motoyama A, Xu T, Ruse CI, Wohlschlegel JA and Yates JR, 3rd (2007) ...
... Motoyama A, Venable JD, Ruse CI and Yates JR, 3rd (2006) Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples. Anal Chem 78: 5109-5118 Motoyama A, Xu T, Ruse CI, Wohlschlegel JA and Yates JR, 3rd (2007) ...
Data Supplement
... Images for all westerns were obtained using the BIO-RAD Molecular Imager Gel Doc XR system and quantified using QuantityOne 1-D Analysis software (BIO-RAD). Values were then averaged for each time point and presented as ± sd. Statistical significance was determined (StatView) with Student’s unpaired ...
... Images for all westerns were obtained using the BIO-RAD Molecular Imager Gel Doc XR system and quantified using QuantityOne 1-D Analysis software (BIO-RAD). Values were then averaged for each time point and presented as ± sd. Statistical significance was determined (StatView) with Student’s unpaired ...
Antibody measurements in mice sera using recombinant CII peptides
... The sequence of the triple-helical segment of human CII was divided into 70 overlapping fragments, with the majority of them being 24 amino acids long. The N-terminal collagen like sequence covers fragments 1-3, while fragment 4 contains the proteolytic cleavage site. The mature CII sequence starts ...
... The sequence of the triple-helical segment of human CII was divided into 70 overlapping fragments, with the majority of them being 24 amino acids long. The N-terminal collagen like sequence covers fragments 1-3, while fragment 4 contains the proteolytic cleavage site. The mature CII sequence starts ...
(Affinity and SRM) assays for detection of potential biomarkers for
... developing them is very demanding and expensive. We have therefore developed assays for another technology. Mass spectrometry is a technology that identifies proteins based on their mass to charge ratio. Digesting a protein with an enzyme like Trypsin results in fragments of the protein called pepti ...
... developing them is very demanding and expensive. We have therefore developed assays for another technology. Mass spectrometry is a technology that identifies proteins based on their mass to charge ratio. Digesting a protein with an enzyme like Trypsin results in fragments of the protein called pepti ...
OCAM: A new tool for studying the oligomeric diversity of MscL
... sample migrates as two oligomeric species (oligomer a, oligomer b), while the C12E8 sample migrates as a single species (oligomer b). At a minimum, there are two possible scenarios to consider. If EcMscL is expressed as a mixture of two oligomers, the single C12E8 oligomer may be due to preferential ...
... sample migrates as two oligomeric species (oligomer a, oligomer b), while the C12E8 sample migrates as a single species (oligomer b). At a minimum, there are two possible scenarios to consider. If EcMscL is expressed as a mixture of two oligomers, the single C12E8 oligomer may be due to preferential ...
Purified Sp1 protein
... Buffer Contents: 2 µg of Purified Sp1 protein and Dilution Buffer AM1 (20 mM TrisCl (pH 8), 20% glycerol, 100 mM KCl, 1 mM DTT and 0.2 mM EDTA). Protein is supplied at 0.08 µg/µl in Dilution Buffer AM1. Background: Sp1 (specificity protein 1) is a human transcription factor involved in gene expressi ...
... Buffer Contents: 2 µg of Purified Sp1 protein and Dilution Buffer AM1 (20 mM TrisCl (pH 8), 20% glycerol, 100 mM KCl, 1 mM DTT and 0.2 mM EDTA). Protein is supplied at 0.08 µg/µl in Dilution Buffer AM1. Background: Sp1 (specificity protein 1) is a human transcription factor involved in gene expressi ...
Week 5 Assignment 1. Reverse Phase Arrays (RPA) involve printing
... A protein array with purified proteins printed on it belongs to which of the following categories of arrays when probed with serum samples containing autoantibodies? 0.5 points Forward Phase arrays Reverse phase arrays ...
... A protein array with purified proteins printed on it belongs to which of the following categories of arrays when probed with serum samples containing autoantibodies? 0.5 points Forward Phase arrays Reverse phase arrays ...
Document
... (2004) Folding of beta/alpha-unit scrambled forms of S. cerevisiae triosephosphate isomerase: Evidence for autonomy of substructure formation and plasticity of hydrophobic and hydrogen bonding interactions in the core of the (beta/alpha)8-barrel. Proteins : Structure, Function & Bioinformatics 55, 5 ...
... (2004) Folding of beta/alpha-unit scrambled forms of S. cerevisiae triosephosphate isomerase: Evidence for autonomy of substructure formation and plasticity of hydrophobic and hydrogen bonding interactions in the core of the (beta/alpha)8-barrel. Proteins : Structure, Function & Bioinformatics 55, 5 ...
Protein Degradation
... The 3 catalytic subunits are synthesized as pre-proteins. They are activated when the N-terminus is cleaved off, making threonine the N-terminal residue. Catalytic threonines are exposed at the lumenal surface. ...
... The 3 catalytic subunits are synthesized as pre-proteins. They are activated when the N-terminus is cleaved off, making threonine the N-terminal residue. Catalytic threonines are exposed at the lumenal surface. ...
Supplementary data 1,2,3,4,6,7,8,9 include N, Total (ProtScore)
... Conf, Sequence,Modifications for the identified proteins. The definitions of the table fields are described as follows: N is the rank of the specified protein relative to all other proteins in the list of detected proteins. Total (ProtScore) a measure of the total amount of evidence for a detected p ...
... Conf, Sequence,Modifications for the identified proteins. The definitions of the table fields are described as follows: N is the rank of the specified protein relative to all other proteins in the list of detected proteins. Total (ProtScore) a measure of the total amount of evidence for a detected p ...
A review of quantitative methods for proteomic studies
... considerable manual manipulation, however they provide the separation of several thousand soluble proteins with resolution as yet unequaled by other methods of protein separation. Two dimensional gels also provide visualization of samples with attendant advantages for comparison and record keeping. ...
... considerable manual manipulation, however they provide the separation of several thousand soluble proteins with resolution as yet unequaled by other methods of protein separation. Two dimensional gels also provide visualization of samples with attendant advantages for comparison and record keeping. ...
Supplementary Information (doc 34K)
... showed good discrimination between the predicted correct and incorrect peptide-spectrum assignments, and only peptides with charge states of +1, +2, and +3 were retained as confident identifications because the Peptide Prophet models were not a good fit to the data for charge states ≥ 4. Protein ide ...
... showed good discrimination between the predicted correct and incorrect peptide-spectrum assignments, and only peptides with charge states of +1, +2, and +3 were retained as confident identifications because the Peptide Prophet models were not a good fit to the data for charge states ≥ 4. Protein ide ...
Enzyme Biosinthess
... all short-lived proteins (i.e., half-lives < 2 h) contain 1 or more regions rich in proline, glutamate, serine, and threonine 4. N-terminal amino acid residue An N-terminal protein residue of ...
... all short-lived proteins (i.e., half-lives < 2 h) contain 1 or more regions rich in proline, glutamate, serine, and threonine 4. N-terminal amino acid residue An N-terminal protein residue of ...
A Mutation Inhibiting Protoplasmic Incompatibility in
... by pouring a suspension of microconidia from a strain of the opposite mating type. Preparation of cell-free extracts, chromatographic procedures, proteolytic activity and phenoloxidase (laccase) measurements. These procedures have been described previously (Boucherie et al., 1976). Drugs. Protease i ...
... by pouring a suspension of microconidia from a strain of the opposite mating type. Preparation of cell-free extracts, chromatographic procedures, proteolytic activity and phenoloxidase (laccase) measurements. These procedures have been described previously (Boucherie et al., 1976). Drugs. Protease i ...
Document
... Increased solubility of the hydrolyzed protein is usually due to increase in the number of small peptides, and the corresponding increase in the ionizable amino and carboxyl groups Hydrolysis processes needs to be controlled to improve solubility Hydrolysates can expose hydrophobic peptides wh ...
... Increased solubility of the hydrolyzed protein is usually due to increase in the number of small peptides, and the corresponding increase in the ionizable amino and carboxyl groups Hydrolysis processes needs to be controlled to improve solubility Hydrolysates can expose hydrophobic peptides wh ...
Activity-based probes that target diverse cysteine protease families
... To assess probe labeling of endogenous caspases, cytosolic extracts from the neuroblastoma cell line SHSY5Y were treated with cytochrome c and dATP to initiate caspase-9 activation and subsequent activation of caspase-3 and caspase-7 (ref. 21). Treatment of cell extracts with either bVAD-FMK or bEVD ...
... To assess probe labeling of endogenous caspases, cytosolic extracts from the neuroblastoma cell line SHSY5Y were treated with cytochrome c and dATP to initiate caspase-9 activation and subsequent activation of caspase-3 and caspase-7 (ref. 21). Treatment of cell extracts with either bVAD-FMK or bEVD ...
THERAPUETIC DISCOVERY BY MODELLING
... offers a way to speed up discovery time and reduce costs, but such techniques have typically had low accuracy and need high resolution structures. We will capitalise on advances in computational protein structure prediction and protein docking to improve accuracy of target-based in silico compound s ...
... offers a way to speed up discovery time and reduce costs, but such techniques have typically had low accuracy and need high resolution structures. We will capitalise on advances in computational protein structure prediction and protein docking to improve accuracy of target-based in silico compound s ...
nLC-nESI-MS
... spectrometry (nLC-nESI-MS/MS). The extracted tryptic peptides were analyzed on an Agilent 6520 Q-TOF mass spectrometer with an HPLC Chip Cube source (Agilent Technologies). The chip consisted of a 40-nL enrichment column (Zorbax 300SB-C18, 5 µm pore size) and a 43-mm separation column (Zorbax 300SB- ...
... spectrometry (nLC-nESI-MS/MS). The extracted tryptic peptides were analyzed on an Agilent 6520 Q-TOF mass spectrometer with an HPLC Chip Cube source (Agilent Technologies). The chip consisted of a 40-nL enrichment column (Zorbax 300SB-C18, 5 µm pore size) and a 43-mm separation column (Zorbax 300SB- ...
An Introduction to Proteomics
... • Offer a high-throughput technique for proteome analysis. • These small plates are able to hold many different samples at a time. • Current research is ongoing in an attempt to interface array methodologies with Mass Spectrometry at ORNL. ...
... • Offer a high-throughput technique for proteome analysis. • These small plates are able to hold many different samples at a time. • Current research is ongoing in an attempt to interface array methodologies with Mass Spectrometry at ORNL. ...