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Robust analysis of the yeast proteome under 50 kDa by molecular-mass-based fractionation and top-down mass spectrometry.
Kellie JF, Catherman AD, Durbin KR, Tran JC, Tipton JD, Norris JL, Witkowski CE, Thomas PM, Kelleher NL
(2012) Anal Chem 84: 209-15
MeSH Terms: Chromatography, Liquid, Electrophoresis, Polyacrylamide Gel, Mass Spectrometry, Molecular Weight, Proteome, Saccharomyces cerevisiae Proteins, Tandem Mass Spectrometry
Show Abstract · Added August 17, 2016
As the process of top-down mass spectrometry continues to mature, we benchmark the next installment of an improving methodology that incorporates a tube-gel electrophoresis (TGE) device to separate intact proteins by molecular mass. Top-down proteomics is accomplished in a robust fashion to yield the identification of hundreds of unique proteins, many of which correspond to multiple protein forms. The TGE platform separates 0-50 kDa proteins extracted from the yeast proteome into 12 fractions prior to automated nanocapillary LC-MS/MS in technical triplicate. The process may be completed in less than 72 h. From this study, 530 unique proteins and 1103 distinct protein species were identified and characterized, thus representing the highest coverage to date of the Saccharomyces cerevisiae proteome using top-down proteomics. The work signifies a significant step in the maturation of proteomics based on direct measurement and fragmentation of intact proteins.
© 2011 American Chemical Society
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7 MeSH Terms
Albumin handling by renal tubular epithelial cells in a microfluidic bioreactor.
Ferrell N, Ricci KB, Groszek J, Marmerstein JT, Fissell WH
(2012) Biotechnol Bioeng 109: 797-803
MeSH Terms: Albumins, Animals, Bioreactors, Cells, Cultured, Chromatography, Gel, Electrophoresis, Polyacrylamide Gel, Endocytosis, Epithelial Cells, Kidney Tubules, Microfluidics, Molecular Weight, Opossums, Protein Transport, Proteolysis
Show Abstract · Added August 21, 2013
Epithelial cells in the proximal tubule of the kidney reclaim and metabolize protein from the glomerular filtrate. Proteinuria, an overabundance of protein in the urine, affects tubular cell function and is a major factor in the progression of chronic kidney disease. By developing experimental systems to study tubular protein handling in a setting that simulates some of the environmental conditions of the kidney tubule in vivo, we can better understand how microenviromental conditions affect cellular protein handling to determine if these conditions are relevant in disease. To this end, we used two in vitro microfluidic models to evaluate albumin handling by renal proximal tubule cells. For the first system, cells were grown in a microfluidic channel and perfused with physiological levels of shear stress to evaluate the effect of mechanical stress on protein uptake. In the second system, a porous membrane was used to separate an apical and basolateral compartment to evaluate the fate of protein following cellular metabolism. Opossum kidney (OK) epithelial cells were exposed to fluorescently labeled albumin, and cellular uptake was determined by measuring the fluorescence of cell lysates. Confocal fluorescence microscopy was used to compare uptake in cells grown under flow and static conditions. Albumin processed by the cells was examined by size exclusion chromatography (SEC) and SDS-PAGE. Results showed that cellular uptake and/or degradation was significantly increased in cells exposed to flow compared to static conditions. This was confirmed by confocal microscopy. Size exclusion chromatography and SDS-PAGE showed that albumin was broken down into small molecular weight fragments and excreted by the cells. No trace of intact albumin was detectable by either SEC or SDS-PAGE. These results indicate that fluid shear stress is an important factor mediating cellular protein handling, and the microfluidic bioreactor provides a novel tool to investigate this process.
Copyright © 2011 Wiley Periodicals, Inc.
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14 MeSH Terms
A face in the crowd: recognizing peptides through database search.
Eng JK, Searle BC, Clauser KR, Tabb DL
(2011) Mol Cell Proteomics 10: R111.009522
MeSH Terms: Algorithms, Amino Acid Sequence, Animals, Databases, Protein, Humans, Molecular Weight, Peptide Fragments, Protein Processing, Post-Translational, Proteome, Search Engine, Tandem Mass Spectrometry
Show Abstract · Added June 26, 2014
Peptide identification via tandem mass spectrometry sequence database searching is a key method in the array of tools available to the proteomics researcher. The ability to rapidly and sensitively acquire tandem mass spectrometry data and perform peptide and protein identifications has become a commonly used proteomics analysis technique because of advances in both instrumentation and software. Although many different tandem mass spectrometry database search tools are currently available from both academic and commercial sources, these algorithms share similar core elements while maintaining distinctive features. This review revisits the mechanism of sequence database searching and discusses how various parameter settings impact the underlying search.
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11 MeSH Terms
Application of small organic molecules reveals cooperative TGFβ and BMP regulation of mesothelial cell behaviors.
Cross EE, Thomason RT, Martinez M, Hopkins CR, Hong CC, Bader DM
(2011) ACS Chem Biol 6: 952-61
MeSH Terms: Bone Morphogenetic Proteins, Cell Differentiation, Cell Movement, Cells, Cultured, Epithelial Cells, Humans, Molecular Structure, Molecular Weight, Pyrazoles, Pyrimidines, Signal Transduction, Stereoisomerism, Structure-Activity Relationship, Transforming Growth Factor beta
Show Abstract · Added August 19, 2012
Epicardial development is a process during which epithelial sheet movement, single cell migration, and differentiation are coordinated to generate coronary arteries. Signaling cascades regulate the concurrent and complex nature of these three events. Through simple and highly reproducible assays, we identified small organic molecules that impact signaling pathways regulating these epicardial behaviors. Subsequent biochemical analyses confirmed the specificity of these reagents and revealed novel targets for the widely used dorsomorphin (DM) and LDN-193189 molecules. Using these newly characterized reagents, we show the broad regulation of epicardial cell differentiation, sheet movement, and single cell migration by Transforming Growth Factor β (TGFβ). With the DM analogue DMH1, a highly specific Bone Morphogenetic Protein (BMP) inhibitor, we demonstrate the cooperative yet exclusive role for BMP signaling in regulation of sheet migration. The action of DMH1 reveals that small organic molecules (SOM) can intervene on a single epicardial behavior while leaving other concurrent behaviors intact. All SOM data were confirmed by reciprocal experiments using growth factor addition and/or application of established non-SOM inhibitors. These compounds can be applied to cell lines or native proepicardial tissue. Taken together, these data establish the efficacy of chemical intervention for analysis of epicardial behaviors and provide novel reagents for analysis of epicardial development and repair.
3 Communities
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14 MeSH Terms
A new lysozyme from the eastern oyster, Crassostrea virginica, and a possible evolutionary pathway for i-type lysozymes in bivalves from host defense to digestion.
Xue Q, Hellberg ME, Schey KL, Itoh N, Eytan RI, Cooper RK, La Peyre JF
(2010) BMC Evol Biol 10: 213
MeSH Terms: Amino Acid Sequence, Animals, Cloning, Molecular, Crassostrea, DNA, Complementary, Evolution, Molecular, Molecular Sequence Data, Molecular Weight, Muramidase, Phylogeny, Selection, Genetic, Sequence Alignment, Sequence Analysis, DNA
Show Abstract · Added May 27, 2014
BACKGROUND - Lysozymes are enzymes that lyse bacterial cell walls, an activity widely used for host defense but also modified in some instances for digestion. The biochemical and evolutionary changes between these different functional forms has been well-studied in the c-type lysozymes of vertebrates, but less so in the i-type lysozymes prevalent in most invertebrate animals. Some bivalve molluscs possess both defensive and digestive lysozymes.
RESULTS - We report a third lysozyme from the oyster Crassostrea virginica, cv-lysozyme 3. The chemical properties of cv-lysozyme 3 (including molecular weight, isoelectric point, basic amino acid residue number, and predicted protease cutting sites) suggest it represents a transitional form between lysozymes used for digestion and immunity. The cv-lysozyme 3 protein inhibited the growth of bacteria (consistent with a defensive function), but semi-quantitative RT-PCR suggested the gene was expressed mainly in digestive glands. Purified cv-lysozyme 3 expressed maximum muramidase activity within a range of pH (7.0 and 8.0) and ionic strength (I = 0.005-0.01) unfavorable for either cv-lysozyme 1 or cv-lysozyme 2 activities. The topology of a phylogenetic analysis of cv-lysozyme 3 cDNA (full length 663 bp, encoding an open reading frame of 187 amino acids) is also consistent with a transitional condition, as cv-lysozyme 3 falls at the base of a monophyletic clade of bivalve lysozymes identified from digestive glands. Rates of nonsynonymous substitution are significantly high at the base of this clade, consistent with an episode of positive selection associated with the functional transition from defense to digestion.
CONCLUSION - The pattern of molecular evolution accompanying the shift from defensive to digestive function in the i-type lysozymes of bivalves parallels those seen for c-type lysozymes in mammals and suggests that the lysozyme paralogs that enhance the range of physiological conditions for lysozyme activity may provide stepping stones between defensive and digestive forms.
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13 MeSH Terms
Design parameters and sensitivity analysis of polymer-cladded porous silicon waveguides for small molecule detection.
Jiao Y, Weiss SM
(2010) Biosens Bioelectron 25: 1535-8
MeSH Terms: Biopolymers, Biosensing Techniques, Computer-Aided Design, Equipment Design, Equipment Failure Analysis, Molecular Weight, Polymers, Porosity, Refractometry, Reproducibility of Results, Sensitivity and Specificity, Silicon
Show Abstract · Added April 27, 2017
The relationship between the design parameters and small molecule detection sensitivity of porous silicon waveguides is theoretically and experimentally analyzed. Perturbation theory calculations suggest that the sensitivity asymptotically approaches infinity as the porosity of the waveguide approaches a critical porosity for a given mode and the resonant coupling angle of light into the waveguide approaches 90 degrees. Experimental measurements confirm the trend of the porosity-dependent sensitivity for multiple waveguide modes. Given the limitations of the available measurement apparatus that restricts the maximum coupling angle to 68 degrees, a high sensitivity of 120 degrees/RIU was demonstrated for the detection of 0.8 nm molecules attached inside a polymer-cladded nanoscale porous silicon waveguide. Optimized porous dielectric waveguides enable enhanced small molecule detection sensitivity due to their large available surface area for molecular binding.
Copyright 2009 Elsevier B.V. All rights reserved.
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12 MeSH Terms
On the use of Ripley's K-function and its derivatives to analyze domain size.
Kiskowski MA, Hancock JF, Kenworthy AK
(2009) Biophys J 97: 1095-103
MeSH Terms: Algorithms, Computer Simulation, Models, Chemical, Models, Molecular, Molecular Weight, Protein Conformation, Protein Structure, Tertiary, Proteins
Show Abstract · Added May 27, 2014
Ripley's K-, H-, and L-functions are used increasingly to identify clustering of proteins in membrane microdomains. In this approach, aggregation (or clustering) is identified if the average number of proteins within a distance r of another protein is statistically greater than that expected for a random distribution. However, it is not entirely clear how the function may be used to quantitatively determine the size of domains in which clustering occurs. Here, we evaluate the extent to which the domain radius can be determined by different interpretations of Ripley's K-statistic in a theoretical, idealized context. We also evaluate the measures for noisy experimental data and use Monte Carlo simulations to separate the effects of different types of experimental noise. We find that the radius of maximal aggregation approximates the domain radius, while identifying the domain boundary with the minimum of the derivative of H(r) is highly accurate in idealized conditions. The accuracy of both measures is impacted by the noise present in experimental data; for example, here, the presence of a large fraction of particles distributed as monomers and interdomain interactions. These findings help to delineate the limitations and potential of Ripley's K in real-life scenarios.
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8 MeSH Terms
EPR spectroscopy and electrospray ionization mass spectrometry reveal distinctive features of the iron site in leukocyte 12-lipoxygenase.
Rapp J, Xu S, Sharp AM, Griffith WP, Kim YW, Funk MO
(2009) Arch Biochem Biophys 490: 50-6
MeSH Terms: Amino Acid Sequence, Animals, Arachidonate 12-Lipoxygenase, Electron Spin Resonance Spectroscopy, Escherichia coli, Hydrogen-Ion Concentration, Iron, Leukocytes, Lipid Peroxides, Molecular Weight, Oxidation-Reduction, Recombinant Proteins, Spectrometry, Mass, Electrospray Ionization, Sus scrofa, Temperature, Transformation, Genetic
Show Abstract · Added April 14, 2017
The procedure for the expression and purification of recombinant porcine leukocyte 12-lipoxygenase using Escherichia coli [K.M. Richards, L.J. Marnett, Biochemistry 36 (1997) 6692-6699] was updated to make it possible to produce enough protein for physical measurements. Electrospray ionization tandem mass spectrometry confirmed the amino acid sequence. The redox properties of the cofactor iron site were examined by EPR spectroscopy at 25K following treatment with a variety of fatty acid hydroperoxides. Combination of the enzyme in a stoichiometric ratio with the hydroperoxides led to a g4.3 signal in EPR spectra instead of the g6 signal characteristic of similarly treated soybean lipoxygenase-1. Native 12-lipoxygenase was also subjected to electrospray ionization mass spectrometry. There was evidence for loss of the mass of an iron atom from the protein as the pH was lowered from 5 to 4. Native ions in these samples indicated that iron was lost without the protein completely unfolding.
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16 MeSH Terms
Protein aging: truncation of aquaporin 0 in human lens regions is a continuous age-dependent process.
Korlimbinis A, Berry Y, Thibault D, Schey KL, Truscott RJ
(2009) Exp Eye Res 88: 966-73
MeSH Terms: Aged, Aging, Aquaporins, Blotting, Western, Child, Preschool, Electrophoresis, Polyacrylamide Gel, Eye Proteins, Fetus, Humans, Lens, Crystalline, Middle Aged, Molecular Weight, Permeability, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Young Adult
Show Abstract · Added May 27, 2014
The human lens is ideal for the study of macromolecular aging because cells in the centre, along with their constituent proteins, are present for our entire lives. We examined the major membrane protein, aquaporin 0 (AQP0), in regions of the lens formed at different times during our lifespan, to determine if similar changes could be detected and if they were progressive. Membrane fractions from three concentric lens regions were examined by SDS-PAGE coupled with densitometry, and Western blotting, to assess the time course of truncation. The overall extent of modification was also examined by MALDI mass spectrometry of the undigested proteins. In all regions, AQP0 became progressively more truncated, specifically by the loss of a 2kDa intracellular C-terminal peptide. The proteolysis increased steadily in all regions such that half of the AQP0 in the barrier region (that part of the lens formed immediately after birth) had been cleaved by age 40-50. MALDI mass spectrometry revealed that in all regions, AQP0 not only was shortened, it also became progressively more heterogeneous with age. Since the lens interior is devoid of active enzymes, it is very likely that the cleavage of AQP0 is chemically induced. We speculate that the loss of this C-terminal peptide 'spacer' may allow occlusion of AQP0 pores on the cytoplasmic face of the fibre cell membranes. Once a significant proportion of AQP0 has been cleaved, this occlusion may contribute to the formation of the lens permeability barrier that develops at middle age.
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15 MeSH Terms
The E3 ubiquitin ligase WWP1 selectively targets HER4 and its proteolytically derived signaling isoforms for degradation.
Feng SM, Muraoka-Cook RS, Hunter D, Sandahl MA, Caskey LS, Miyazawa K, Atfi A, Earp HS
(2009) Mol Cell Biol 29: 892-906
MeSH Terms: Animals, COS Cells, Cell Line, Tumor, Cell Membrane, Cercopithecus aethiops, Enzyme Stability, ErbB Receptors, Gene Expression Regulation, Humans, Mice, Molecular Weight, Proteasome Endopeptidase Complex, Protein Binding, Protein Isoforms, Protein Processing, Post-Translational, Protein Structure, Tertiary, Protein Transport, RNA, Messenger, Receptor, ErbB-4, Signal Transduction, Solubility, Subcellular Fractions, Substrate Specificity, Ubiquitin-Protein Ligases, Ubiquitination
Show Abstract · Added March 5, 2014
In general, epidermal growth factor receptor family members stimulate cell proliferation. In contrast, at least one HER4 isoform, JM-a/Cyt1, inhibits cell growth after undergoing a two-step proteolytic cleavage that first produces a membrane-anchored 80-kDa fragment (m80(HER4)) and subsequently liberates a soluble 80-kDa fragment, s80(HER4). Here we report that s80(HER4) Cyt1 action increased the expression of WWP1 (for WW domain-containing protein 1), an E3 ubiquitin ligase, but not other members of the Nedd4 E3 ligase family. The HER4 Cyt1 isoform contains three proline-rich tyrosine (PY) WW binding motifs, while Cyt2 has only two. WWP1 binds to all three Cyt1 PY motifs; the interaction with PY2 found exclusively in Cyt1 was strongest. WWP1 ubiquitinated and caused the degradation of HER4 but not of EGFR, HER2, or HER3. The HER4-WWP1 interaction also accelerated WWP1 degradation. Membrane HER4 (full length and m80(HER4), the product of the first proteolytic cleavage) were the preferred targets of WWP1, correlating with the membrane localization of WWP1. Conversely s80(HER4), a poorer WWP1 substrate, was found in the cell nucleus, while WWP1 was not. Deletion of the C2 membrane association domain of WWP1 allowed more efficient s80(HER4) degradation, suggesting that WWP1 is normally part of a membrane complex that regulates HER4 membrane species levels, with a predilection for the growth-inhibitory Cyt1 isoform. Finally, WWP1 expression diminished HER4 biologic activity in MCF-7 cells. We previously showed that nuclear s80(HER4) is ubiquitinated and degraded by the anaphase-promoting complex, suggesting that HER4 ubiquitination within specific cellular compartments helps regulate the unique HER4 signaling capabilities.
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25 MeSH Terms