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Proteomic Analysis of S-Palmitoylated Proteins in Ocular Lens Reveals Palmitoylation of AQP5 and MP20.
Wang Z, Schey KL
(2018) Invest Ophthalmol Vis Sci 59: 5648-5658
MeSH Terms: Animals, Aquaporin 5, Blotting, Western, Cattle, Chromatography, Liquid, Electrophoresis, Polyacrylamide Gel, Eye Proteins, Immunoblotting, Lens, Crystalline, Lipoylation, Membrane Proteins, Palmitates, Proteomics, Tandem Mass Spectrometry
Show Abstract · Added April 4, 2019
Purpose - The purpose of this study was to characterize the palmitoyl-proteome in lens fiber cells. S-palmitoylation is the most common form of protein S-acylation and the reversible nature of this modification functions as a molecular switch to regulate many biological processes. This modification could play important roles in regulating protein functions and protein-protein interactions in the lens.
Methods - The palmitoyl-proteome of bovine lens fiber cells was investigated by combining acyl-biotin exchange (ABE) chemistry and mass-spectrometry analysis. Due to the possibility of false-positive results from ABE experiment, a method was also developed for direct detection of palmitoylated peptides by mass spectrometry for validating palmitoylation of lens proteins MP20 and AQP5. Palmitoylation levels on AQP5 in different regions of the lens were quantified after iodoacetamide (IAA)-palmitate exchange.
Results - The ABE experiment identified 174 potential palmitoylated proteins. These proteins include 39 well-characterized palmitoylated proteins, 92 previously reported palmitoylated proteins in other tissues, and 43 newly identified potential palmitoylated proteins including two important transmembrane proteins in the lens, AQP5 and MP20. Further analysis by direct detection of palmitoylated peptides confirmed palmitoylation of AQP5 on C6 and palmitoylation of MP20 on C159. Palmitoylation of AQP5 was found to only occur in a narrow region of the inner lens cortex and does not occur in the lens epithelium, in the lens outer cortex, or in the lens nucleus.
Conclusions - AQP5 and MP20 are among 174 palmitoylated proteins found in bovine lens fiber cells. This modification to AQP5 and MP20 may play a role in their translocation from the cytoplasm to cell membranes during fiber cell differentiation.
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14 MeSH Terms
Structural Characterization of Methylenedianiline Regioisomers by Ion Mobility-Mass Spectrometry and Tandem Mass Spectrometry. 4. 3-Ring and 4-Ring Isomers.
Crescentini TM, Stow SM, Forsythe JG, May JC, McLean JA, Hercules DM
(2018) Anal Chem 90: 14453-14461
MeSH Terms: Aniline Compounds, Ion Mobility Spectrometry, Stereoisomerism, Tandem Mass Spectrometry
Show Abstract · Added December 17, 2018
Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) is used to characterize methylenedianiline (MDA) 3-ring and 4-ring species. Building on our previous MALDI-MS 2-ring MDA isomer study, here we compare 3-ring and 4-ring electrospray ionization (ESI) and MALDI results. In ESI, 3-ring and 4-ring MDAs each form a single [M + H] parent ion. However, in MALDI, each MDA multimer forms three unique precursor ions: [M + H], [M], and [M - H]. In this study, 3-ring and 4-ring MDA precursors are characterized to identify the unique fragment ions formed and their respective fragmentation pathways. In addition to the three possible precursors, the 3-ring and 4-ring species are higher-order oligomer precursors in polyurethane (PUR) production and thus provide additional insight into the polymeric behavior of these PUR hard block precursors. The combination of ion mobility-mass spectrometry (IM - MS) and tandem mass spectrometry (MS/MS) allow the structural characterization of these larger MDA multimers.
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4 MeSH Terms
Micro-Data-Independent Acquisition for High-Throughput Proteomics and Sensitive Peptide Mass Spectrum Identification.
Heaven MR, Cobbs AL, Nei YW, Gutierrez DB, Herren AW, Gunawardena HP, Caprioli RM, Norris JL
(2018) Anal Chem 90: 8905-8911
MeSH Terms: Algorithms, Chromatography, Liquid, Databases, Protein, Escherichia coli, Escherichia coli Proteins, HeLa Cells, High-Throughput Screening Assays, Humans, Peptides, Proteome, Proteomics, Software, Tandem Mass Spectrometry, Workflow
Show Abstract · Added August 27, 2018
State-of-the-art strategies for proteomics are not able to rapidly interrogate complex peptide mixtures in an untargeted manner with sensitive peptide and protein identification rates. We describe a data-independent acquisition (DIA) approach, microDIA (μDIA), that applies a novel tandem mass spectrometry (MS/MS) mass spectral deconvolution method to increase the specificity of tandem mass spectra acquired during proteomics experiments. Using the μDIA approach with a 10 min liquid chromatography gradient allowed detection of 3.1-fold more HeLa proteins than the results obtained from data-dependent acquisition (DDA) of the same samples. Additionally, we found the μDIA MS/MS deconvolution procedure is critical for resolving modified peptides with relatively small precursor mass shifts that cause the same peptide sequence in modified and unmodified forms to theoretically cofragment in the same raw MS/MS spectra. The μDIA workflow is implemented in the PROTALIZER software tool which fully automates tandem mass spectral deconvolution, queries every peptide with a library-free search algorithm against a user-defined protein database, and confidently identifies multiple peptides in a single tandem mass spectrum. We also benchmarked μDIA against DDA using a 90 min gradient analysis of HeLa and Escherichia coli peptides that were mixed in predefined quantitative ratios, and our results showed μDIA provided 24% more true positives at the same false positive rate.
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14 MeSH Terms
DehydroalanylGly, a new post translational modification resulting from the breakdown of glutathione.
Friedrich MG, Wang Z, Schey KL, Truscott RJW
(2018) Biochim Biophys Acta Gen Subj 1862: 907-913
MeSH Terms: Alanine, Amino Acid Sequence, Crystallins, Dipeptides, Glutathione, Glutathione Disulfide, Humans, Lens, Crystalline, Lysine, Middle Aged, Molecular Structure, Peptides, Protein Conformation, Protein Processing, Post-Translational, Proteins, Tandem Mass Spectrometry, Young Adult
Show Abstract · Added April 3, 2018
BACKGROUND - The human body contains numerous long-lived proteins which deteriorate with age, typically by racemisation, deamidation, crosslinking and truncation. Previously we elucidated one reaction responsible for age-related crosslinking, the spontaneous formation of dehydroalanine (DHA) intermediates from phosphoserine and cysteine. This resulted in non-disulphide covalent crosslinks. The current paper outlines a novel posttranslational modification (PTM) in human proteins, which involves the addition of dehydroalanylglycine (DHAGly) to Lys residues.
METHODS - Human lens digests were examined by mass spectrometry for the presence of (DHA)Gly (+144.0535 Da) adducts to Lys residues. Peptide model studies were undertaken to elucidate the mechanism of formation.
RESULTS - In the lens, this PTM was detected at 18 lysine sites in 7 proteins. Using model peptides, a pathway for its formation was found to involve initial formation of the glutathione degradation product, γ-Glu(DHA)Gly from oxidised glutathione (GSSG). Once the Lys adduct formed, the Glu residue was lost in a hydrolytic mechanism apparently catalysed by the ε-amino group of the Lys.
CONCLUSIONS - This discovery suggests that within cells, the functional groups of amino acids in proteins may be susceptible to modification by reactive metabolites derived from GSSG.
GENERAL SIGNIFICANCE - Our finding demonstrates a novel +144.0535 Da PTM arising from the breakdown of oxidised glutathione.
Copyright © 2018. Published by Elsevier B.V.
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Dietary Fatty Acids Control the Species of N-Acyl-Phosphatidylethanolamines Synthesized by Therapeutically Modified Bacteria in the Intestinal Tract.
Dosoky NS, Guo L, Chen Z, Feigley AV, Davies SS
(2018) ACS Infect Dis 4: 3-13
MeSH Terms: Acyltransferases, Animals, Bacteria, Biomarkers, Biosynthetic Pathways, Chromatography, Liquid, Diet, Fatty Acids, Gastrointestinal Microbiome, Lipid Metabolism, Liver, Male, Mice, Phosphatidylethanolamines, Tandem Mass Spectrometry, Temperature
Show Abstract · Added July 17, 2019
Engineering the gut microbiota to produce specific beneficial metabolites represents an important new potential strategy for treating chronic diseases. Our previous studies with bacteria engineered to produce N-acyl-phosphatidylethanolamines (NAPEs), the immediate precursors of the lipid satiety factors N-acyl-ethanolamides (NAEs), found that colonization of these bacteria inhibited development of obesity in C57BL/6J mice fed a high fat diet. Individual NAE species differ in their bioactivities. Intriguingly, colonization by our engineered bacteria resulted in increased hepatic N-stearoyl-ethanolamide (C18:0NAE) levels despite the apparent inability of these bacteria to biosynthesize its precursor N-stearoyl-phosphatidylethanolamine (C18:0NAPE) in vitro. We therefore sought to identify the factors that allowed C18:0NAPE biosynthesis by the engineered bacteria after colonization of the intestinal tract. We found that the species of NAPE biosynthesized by engineered bacteria depends on the species of dietary fatty acids available in the intestine, suggesting a simple method to fine-tune the therapeutic effects of modified microbiota.
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Prospective study of urinary prostaglandin E2 metabolite and pancreatic cancer risk.
Cui Y, Shu XO, Li HL, Yang G, Wen W, Gao YT, Cai Q, Rothman N, Yin HY, Lan Q, Xiang YB, Zheng W
(2017) Int J Cancer 141: 2423-2429
MeSH Terms: Adult, Aged, Body Mass Index, Case-Control Studies, China, Chromatography, Liquid, Cyclooxygenase 2, Female, Humans, Logistic Models, Male, Middle Aged, Odds Ratio, Pancreatic Neoplasms, Prospective Studies, Prostaglandins, Tandem Mass Spectrometry
Show Abstract · Added April 3, 2018
The cyclooxygenase 2 (COX-2) pathway is upregulated in many pancreatic cancer cells, and it is believed that carcinogenetic effects of COX-2 upregulation are largely through prostaglandin E2 (PGE2) overproduction. We tested this hypothesis by evaluating the association between urinary PGE2 metabolites (PGE-M), a biomarker of in vivo PGE2 overproduction, and pancreatic cancer risk. We conducted a case-control study with 722 subjects (239 cases and 483 controls) nested within two prospective cohort studies, the Shanghai Women's Health Study (SWHS) and Shanghai Men's Health Study (SMHS). Pre-diagnosis urine samples were measured for PGE-M using a liquid chromatography/tandem mass spectrometric method. Conditional logistic regression was used to estimate odds ratio (OR) and 95% confidence intervals (95%CI), with adjustment for potential confounders. Compared to those with the lowest urine level of PGE-M (the first quartile), individuals with higher urine levels of PGE-M had an increased risk of developing pancreatic cancer, with adjusted ORs (95%CI) of 1.63 (0.98-2.73), 1.55 (0.90-2.69) and 1.94 (1.07-3.51), for the second to the fourth quartile groups, respectively (p for trend = 0.054). This dose-response positive association was more evident among those who had BMI <25 kg/m than overweight individuals (p for interaction = 0.058). After excluding cases diagnosed in the first year of follow-up and their matched controls, this positive association persisted (p for trend = 0.037) and the interaction became statistically significant (p for interaction = 0.017). Our study adds additional evidence that the COX-2 pathway is involved in pancreatic carcinogenesis and suggests that urinary PGE-M may serve as a biomarker for predicting pancreatic cancer risk.
© 2017 UICC.
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MeSH Terms
Kidney function is associated with an altered protein composition of high-density lipoprotein.
Rubinow KB, Henderson CM, Robinson-Cohen C, Himmelfarb J, de Boer IH, Vaisar T, Kestenbaum B, Hoofnagle AN
(2017) Kidney Int 92: 1526-1535
MeSH Terms: Adult, African Americans, Aged, Chromatography, Liquid, Cohort Studies, Dyslipidemias, European Continental Ancestry Group, Female, Glomerular Filtration Rate, Humans, Lipoproteins, HDL, Male, Middle Aged, Proteomics, Renal Insufficiency, Chronic, Risk Factors, Tandem Mass Spectrometry
Show Abstract · Added September 19, 2017
Patients with chronic kidney disease (CKD) exhibit a myriad of metabolic derangements, including dyslipidemia characterized by low plasma concentrations of high-density lipoprotein (HDL)-associated cholesterol. However, the effects of kidney disease on HDL composition have not been comprehensively determined. Here we used a targeted mass spectrometric approach to quantify 38 proteins contained in the HDL particles within a CKD cohort of 509 participants with a broad range of estimated glomerular filtration rates (eGFRs) (CKD stages I-V, and a mean eGFR of 45.5 mL/min/1.73m). After adjusting for multiple testing, demographics, comorbidities, medications, and other characteristics, eGFR was significantly associated with differences in four HDL proteins. Compared to participants with an eGFR of 60 mL/min/1.73m or more, those with an eGFR under 15 mL/min/1.73m exhibited 1.89-fold higher retinol-binding protein 4 (95% confidence interval 1.34-2.67), 1.52-fold higher apolipoprotein C-III (1.25-1.84), 0.70-fold lower apolipoprotein L1 (0.55-0.92), and 0.64-fold lower vitronectin (0.48-0.85). Although the HDL apolipoprotein L1 was slightly lower among African Americans than among Caucasian individuals, the relationship to eGFR did not differ by race. After adjustment, no HDL-associated proteins associated with albuminuria. Thus, modest changes in the HDL proteome provide preliminary evidence for an association between HDL proteins and declining kidney function, but this needs to be replicated. Future analyses will determine if HDL proteomics is indeed a clinical predictor of declining kidney function or cardiovascular outcomes.
Copyright © 2017 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.
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Identification of Phosphorylation Codes for Arrestin Recruitment by G Protein-Coupled Receptors.
Zhou XE, He Y, de Waal PW, Gao X, Kang Y, Van Eps N, Yin Y, Pal K, Goswami D, White TA, Barty A, Latorraca NR, Chapman HN, Hubbell WL, Dror RO, Stevens RC, Cherezov V, Gurevich VV, Griffin PR, Ernst OP, Melcher K, Xu HE
(2017) Cell 170: 457-469.e13
MeSH Terms: Amino Acid Sequence, Animals, Arrestins, Chromatography, Liquid, Humans, Mice, Models, Molecular, Phosphorylation, Rats, Rhodopsin, Sequence Alignment, Tandem Mass Spectrometry, X-Rays
Show Abstract · Added March 14, 2018
G protein-coupled receptors (GPCRs) mediate diverse signaling in part through interaction with arrestins, whose binding promotes receptor internalization and signaling through G protein-independent pathways. High-affinity arrestin binding requires receptor phosphorylation, often at the receptor's C-terminal tail. Here, we report an X-ray free electron laser (XFEL) crystal structure of the rhodopsin-arrestin complex, in which the phosphorylated C terminus of rhodopsin forms an extended intermolecular β sheet with the N-terminal β strands of arrestin. Phosphorylation was detected at rhodopsin C-terminal tail residues T336 and S338. These two phospho-residues, together with E341, form an extensive network of electrostatic interactions with three positively charged pockets in arrestin in a mode that resembles binding of the phosphorylated vasopressin-2 receptor tail to β-arrestin-1. Based on these observations, we derived and validated a set of phosphorylation codes that serve as a common mechanism for phosphorylation-dependent recruitment of arrestins by GPCRs.
Copyright © 2017 Elsevier Inc. All rights reserved.
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13 MeSH Terms
Identification of Proteomic Features To Distinguish Benign Pulmonary Nodules from Lung Adenocarcinoma.
Codreanu SG, Hoeksema MD, Slebos RJC, Zimmerman LJ, Rahman SMJ, Li M, Chen SC, Chen H, Eisenberg R, Liebler DC, Massion PP
(2017) J Proteome Res 16: 3266-3276
MeSH Terms: 5-Lipoxygenase-Activating Proteins, Adenocarcinoma, Adenocarcinoma of Lung, Adult, Aged, Antigens, CD, Arachidonate 5-Lipoxygenase, Biomarkers, Tumor, CD11 Antigens, Cell Adhesion Molecules, Diagnosis, Differential, Female, GPI-Linked Proteins, Gene Expression Regulation, Neoplastic, Glucose Transporter Type 3, Humans, Integrin alpha Chains, Lung Neoplasms, Male, Middle Aged, Neoplasm Proteins, Proteomics, Respiratory Mucosa, Solitary Pulmonary Nodule, Tandem Mass Spectrometry, Tissue Array Analysis, Transcriptome
Show Abstract · Added January 29, 2018
We hypothesized that distinct protein expression features of benign and malignant pulmonary nodules may reveal novel candidate biomarkers for the early detection of lung cancer. We performed proteome profiling by liquid chromatography-tandem mass spectrometry to characterize 34 resected benign lung nodules, 24 untreated lung adenocarcinomas (ADCs), and biopsies of bronchial epithelium. Group comparisons identified 65 proteins that differentiate nodules from ADCs and normal bronchial epithelium and 66 proteins that differentiate ADCs from nodules and normal bronchial epithelium. We developed a multiplexed parallel reaction monitoring (PRM) assay to quantify a subset of 43 of these candidate biomarkers in an independent cohort of 20 benign nodules, 21 ADCs, and 20 normal bronchial biopsies. PRM analyses confirmed significant nodule-specific abundance of 10 proteins including ALOX5, ALOX5AP, CCL19, CILP1, COL5A2, ITGB2, ITGAX, PTPRE, S100A12, and SLC2A3 and significant ADC-specific abundance of CEACAM6, CRABP2, LAD1, PLOD2, and TMEM110-MUSTN1. Immunohistochemistry analyses for seven selected proteins performed on an independent set of tissue microarrays confirmed nodule-specific expression of ALOX5, ALOX5AP, ITGAX, and SLC2A3 and cancer-specific expression of CEACAM6. These studies illustrate the value of global and targeted proteomics in a systematic process to identify and qualify candidate biomarkers for noninvasive molecular diagnosis of lung cancer.
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27 MeSH Terms
Colorectal Cancer Cell Line Proteomes Are Representative of Primary Tumors and Predict Drug Sensitivity.
Wang J, Mouradov D, Wang X, Jorissen RN, Chambers MC, Zimmerman LJ, Vasaikar S, Love CG, Li S, Lowes K, Leuchowius KJ, Jousset H, Weinstock J, Yau C, Mariadason J, Shi Z, Ban Y, Chen X, Coffey RJC, Slebos RJC, Burgess AW, Liebler DC, Zhang B, Sieber OM
(2017) Gastroenterology 153: 1082-1095
MeSH Terms: Antineoplastic Agents, Biomarkers, Tumor, Cell Line, Tumor, Chromatography, Liquid, Colorectal Neoplasms, Databases, Protein, Dose-Response Relationship, Drug, Drug Screening Assays, Antitumor, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Humans, Mutation, Neoplasm Proteins, Patient Selection, Polymorphism, Single Nucleotide, Precision Medicine, Proteome, Proteomics, Signal Transduction, Stromal Cells, Tandem Mass Spectrometry, Transcriptome, Tumor Microenvironment
Show Abstract · Added July 17, 2017
BACKGROUND AND AIMS - Proteomics holds promise for individualizing cancer treatment. We analyzed to what extent the proteomic landscape of human colorectal cancer (CRC) is maintained in established CRC cell lines and the utility of proteomics for predicting therapeutic responses.
METHODS - Proteomic and transcriptomic analyses were performed on 44 CRC cell lines, compared against primary CRCs (n=95) and normal tissues (n=60), and integrated with genomic and drug sensitivity data.
RESULTS - Cell lines mirrored the proteomic aberrations of primary tumors, in particular for intrinsic programs. Tumor relationships of protein expression with DNA copy number aberrations and signatures of post-transcriptional regulation were recapitulated in cell lines. The 5 proteomic subtypes previously identified in tumors were represented among cell lines. Nonetheless, systematic differences between cell line and tumor proteomes were apparent, attributable to stroma, extrinsic signaling, and growth conditions. Contribution of tumor stroma obscured signatures of DNA mismatch repair identified in cell lines with a hypermutation phenotype. Global proteomic data showed improved utility for predicting both known drug-target relationships and overall drug sensitivity as compared with genomic or transcriptomic measurements. Inhibition of targetable proteins associated with drug responses further identified corresponding synergistic or antagonistic drug combinations. Our data provide evidence for CRC proteomic subtype-specific drug responses.
CONCLUSIONS - Proteomes of established CRC cell line are representative of primary tumors. Proteomic data tend to exhibit improved prediction of drug sensitivity as compared with genomic and transcriptomic profiles. Our integrative proteogenomic analysis highlights the potential of proteome profiling to inform personalized cancer medicine.
Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.
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23 MeSH Terms