Works (12)
Updated: August 29th, 2023 11:25
2014 journal article
Systems Biology of Lignin Biosynthesis in Populus trichocarpa: Heteromeric 4-Coumaric Acid:Coenzyme A Ligase Protein Complex Formation, Regulation, and Numerical Modeling
The Plant Cell, 26(3), 876–893.
MeSH headings : Coenzyme A Ligases / genetics; Coenzyme A Ligases / metabolism; Coumaric Acids / metabolism; Immunoprecipitation; Lignin / biosynthesis; Mass Spectrometry; Models, Biological; Populus / metabolism; Propionates; RNA, Messenger / genetics; Substrate Specificity; Systems Biology
TL;DR:
This work shows that 4CL, an enzyme in monolignol biosynthesis, is found as a heterotetrameric complex of two isoforms in Populus trichocarpa, where the two 4-coumaric acid:CoA ligase (4CL) isoforms, 4CL3 and 4CL5, interact in vivo and in vitro to form a heterosymmetric protein complex.
(via Semantic Scholar)
open access via www.plantcell.org (publisher PDF)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018
2013 journal article
Monolignol Pathway 4-Coumaric Acid: Coenzyme A Ligases in Populus trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of Coenzyme A Ligation Fluxes
PLANT PHYSIOLOGY, 161(3), 1501–1516.
MeSH headings : Allosteric Regulation / drug effects; Binding Sites; Biosynthetic Pathways / drug effects; Blotting, Western; Caffeic Acids / pharmacology; Coenzyme A / metabolism; Coenzyme A Ligases / antagonists & inhibitors; Coenzyme A Ligases / metabolism; Computer Simulation; Coumaric Acids / chemistry; Coumaric Acids / metabolism; Coumaric Acids / pharmacology; Kinetics; Lignin / biosynthesis; Lignin / chemistry; Phenylpropionates / metabolism; Phosphoproteins / metabolism; Phosphorylation / drug effects; Plant Extracts; Populus / drug effects; Populus / enzymology; Propionates; Proteomics; Recombinant Fusion Proteins / metabolism; Sequence Homology, Amino Acid; Substrate Specificity / drug effects; Xylem / drug effects; Xylem / metabolism
TL;DR:
Evidence is presented of two monolignol 4CLs, Ptr4CL3 and P tr4CL5, in Populus trichocarpa that act to mitigate the inhibition by caffeic acid to maintain a proper ligation flux and coenzyme A flux with novel specificity.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2013 journal article
Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa
Planta, 238(3), 487–497.
MeSH headings : Gene Expression Regulation, Plant / physiology; Mass Spectrometry; Phenylalanine Ammonia-Lyase / metabolism; Populus / enzymology; Populus / metabolism
TL;DR:
A greater functional significance of subgroup A PtrPALs for stem wood formation is indicated, and the role of gene post-transcriptional regulation is highlighted.
(via Semantic Scholar)
Sources: NC State University Libraries, ORCID, NC State University Libraries
Added: August 6, 2018
2012 journal article
Functional redundancy of the two 5-hydroxylases in monolignol biosynthesis of Populus trichocarpa: LC-MS/MS based protein quantification and metabolic flux analysis
PLANTA, 236(3), 795–808.
author keywords: Lignin; Syringyl lignin; Angiosperm; Kinetics; Subcellular localization
MeSH headings : Cloning, Molecular; Gene Expression Regulation, Enzymologic; Gene Expression Regulation, Plant; Hydroxylation; Kinetics; Lignin / analysis; Lignin / biosynthesis; Mixed Function Oxygenases / metabolism; Plants, Genetically Modified; Populus / metabolism; Xylem / enzymology; Yeasts / metabolism
TL;DR:
The combination of genetic analysis, absolute protein quantitation-based enzyme kinetics, homologous CPR specificity, SNP characterization, and ER localization provides a more rigorous basis for a comprehensive systems understanding of 5-hydroxylation in lignin biosynthesis.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2012 journal article
Peptide Production and Decay Rates Affect the Quantitative Accuracy of Protein Cleavage Isotope Dilution Mass Spectrometry (PC-IDMS)
Molecular & Cellular Proteomics, 11(9), 814–823.
MeSH headings : Indicator Dilution Techniques; Isotope Labeling; Mass Spectrometry; Peptide Biosynthesis; Peptides / analysis; Peptides / chemistry; Peptides / metabolism; Populus / enzymology; Populus / metabolism; Proteolysis; Xylem / enzymology
TL;DR:
It is concluded that the instability of peptides can often significantly bias the protein quantities measured in protein cleavage isotope dilution mass spectrometry-based assays and suggest peptide stability be made a priority when selecting peptides to use for quantification.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018
2011 journal article
Absolute quantification of free glutathione and cysteine in aquatic insects using isotope dilution and selected reaction monitoring
Analytical and Bioanalytical Chemistry, 402(1), 357–366.
Contributors: n, M. Poteat n, D. Buchwalter n & D. Muddiman n
author keywords: Glutathione; Cysteine; Selected reaction monitoring; Absolute quantification; Isotope dilution
MeSH headings : Animals; Aquatic Organisms / chemistry; Carbon Isotopes / analysis; Chromatography, High Pressure Liquid / methods; Cysteine / analysis; Glutathione / analysis; Indicator Dilution Techniques; Insecta / chemistry; Nitrogen Isotopes / analysis
TL;DR:
A simple and robust isotope dilution mass spectrometry-based assay was developed for the determination of free cysteine and glutathione in aquatic insects and was demonstrated to have a quantitative dynamic range spanning nearly three orders of magnitude.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref, ORCID
Added: August 6, 2018
2011 review
Capitalizing on the hydrophobic bias of electrospray ionization through chemical modification in mass spectrometry-based proteomics
[Review of ]. EXPERT REVIEW OF PROTEOMICS, 8(3), 317–323.
author keywords: ALiPHAT; electrospray ionization; hydrophobic tagging; mass spectrometry; quantification
MeSH headings : Humans; Hydrophobic and Hydrophilic Interactions; Proteomics / methods; Spectrometry, Mass, Electrospray Ionization / methods
TL;DR:
Improvements in targeted, mass spectrometry-based proteomic strategies are achieved by taking advantage of the mechanism of ESI through the use of hydrophobic chemical derivatization.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2011 journal article
Evaluation of Normalization Methods on GeLC-MS/MS Label-Free Spectral Counting Data to Correct for Variation during Proteomic Workflows
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 22(12), 2199–2208.
author keywords: Label-free; Proteomics; Mass spectrometry; Total spectral count normalization; Normalized spectral abundance factor; Quantification; Spectral counting; Significance test; Fold-change; GeLC-MS/MS; nanoLC-MS; Orbitrap XL
TL;DR:
The correlation between SpCs of the same proteins across the different data sets was investigated and it was reported that TSpC normalization and NSAF normalization yielded almost ideal slopes of unity for normalized SpC versus average normalized SpCs, while NSP did not afford effective corrections of the unnormalized data.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2011 journal article
Membrane protein complexes catalyze both 4-and 3-hydroxylation of cinnamic acid derivatives in monolignol biosynthesis
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108(52), 21253–21258.
MeSH headings : Carboxylic Ester Hydrolases / chemistry; Carboxylic Ester Hydrolases / metabolism; Chromatography, Liquid; Coumaric Acids; DNA Primers / genetics; Hydroxylation; Immunoprecipitation; Kinetics; Lignin / biosynthesis; Mass Spectrometry; Membrane Proteins / chemistry; Membrane Proteins / metabolism; Microscopy, Confocal; Molecular Structure; Multiprotein Complexes / chemistry; Multiprotein Complexes / metabolism; Phenols; Phenylpropionates; Plasmids / genetics; Populus / metabolism; Propionates; Trans-Cinnamate 4-Monooxygenase / chemistry; Trans-Cinnamate 4-Monooxygenase / metabolism; Xylem / metabolism; Yeasts
TL;DR:
Affinity purification-quantitative mass spectrometry, bimolecular fluorescence complementation, chemical cross-linking, and reciprocal coimmunoprecipitation provide further evidence for functional involvement of membrane protein complexes in monolignol biosynthesis.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2010 journal article
Utilizing Spectral Counting To Quantitatively Characterize Tandem Removal of Abundant Proteins (TRAP) in Human Plasma
ANALYTICAL CHEMISTRY, 82(24), 10179–10185.
MeSH headings : Biomarkers / analysis; Blood Proteins / analysis; Blood Proteins / isolation & purification; Humans
TL;DR:
The data demonstrate that this method, tandem removal of abundant proteins or TRAP, provides superior removal efficiency compared to traditional applications and improves the depth of proteome coverage in plasma.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2009 journal article
Coupling of a vented column with splitless nanoRPLC-ESI-MS for the improved separation and detection of brain natriuretic peptide-32 and its proteolytic peptides
Journal of Chromatography B, 877(10), 948–954.
author keywords: Vented column; BNP-32; Splitless nanoLC; Tryptic digestion
MeSH headings : Amino Acid Sequence; Brain Chemistry; Chromatography, Liquid / methods; Molecular Sequence Data; Natriuretic Peptide, Brain / chemistry; Natriuretic Peptide, Brain / isolation & purification; Natriuretic Peptide, Brain / pharmacokinetics; Spectrometry, Mass, Electrospray Ionization / methods
TL;DR:
It is demonstrated that the use of free cysteine as an alkylation quenching agent and a secondary digestion within the digestion scheme can provide targeted tryptic peptides with increased abundances, which will serve to further augment the detection of BNP-32 by LC-MS.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018
2009 journal article
Improving limits of detection for B-type natriuretic peptide using PC-IDMS: An application of the ALiPHAT strategy
ANALYST, 135(1), 36–41.
MeSH headings : Alkylating Agents / chemistry; Hydrophobic and Hydrophilic Interactions; Iodoacetamide / chemistry; Isotope Labeling; Limit of Detection; Natriuretic Peptide, Brain / analysis; Spectrometry, Mass, Electrospray Ionization / methods; Trypsin / metabolism
TL;DR:
Evaluated alkylation reagents for their utility in quantifying B-type Natriuretic Peptide, a low abundance cardiac biomarker, by protein cleavage isotope dilution mass spectrometry found a approximately 3.5-fold decrease in the detection limit for the best performing hydrophobic reagent, 2-iodo-N-octylacetamide.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
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