Works Published in 2013
Displaying works 1 - 20 of 26 in total
Sorted by most recent date added to the index first, which may not be the same as publication date order.
2013 conference paper
A Quantitative Inspection of ESI Glucuronide Degradation
Presented at the 61st American Society for Mass Spectrometry Annual Conference, Minneapolis, MN.
Event: 61st American Society for Mass Spectrometry Annual Conference at Minneapolis, MN
Source: NC State University Libraries
Added: March 12, 2022
2013 conference paper
The North Carolina State University Mass Spectrometry Facility at the Cutting Edge of Scientific Research
Presented at the Workshop on Allergy and Inflammation, North Carolina State University, Raleigh, NC.
Event: Workshop on Allergy and Inflammation at North Carolina State University, Raleigh, NC
Source: NC State University Libraries
Added: August 13, 2021
2013 journal article
Characterization of phosphatidylcholine oxidation products by MALDI MS <inf>n</inf>
Analytical Chemistry, 85(23), 11410–11419.
Contributors: W. Stutts* , R. Menger*, A. Kiss*, R. Heeren * & R. Yost *
MeSH headings : Animals; Female; Oxidation-Reduction; Phosphatidylcholines / analysis; Phosphatidylcholines / metabolism; Rats; Rats, Sprague-Dawley; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / methods
TL;DR:
This work illustrates the enhanced selectivity afforded by MS(n) on the linear ion trap and develops a method for the identification of individual products of PC oxidation.
(via Semantic Scholar)
Source: ORCID
Added: May 20, 2021
2013 journal article
Dynamics of the Striped Bass (Morone saxatilis) Ovary Proteome Reveal a Complex Network of the Translasome
Journal of Proteome Research, 12(4), 1691–1699.
Contributors: B. Reading, V. Williams, R. Chapman*, T. Williams* & C. Sullivan
author keywords: ribosome; proteasome; translasome; ovary; reproduction; mass-spectrometry; support vector machines; teleost; fish
MeSH headings : Animals; Artificial Intelligence; Bass; Cluster Analysis; Female; Fish Proteins / genetics; Fish Proteins / metabolism; Gene Ontology; Mass Spectrometry / methods; Menstrual Cycle / physiology; Ovary / metabolism; Proteasome Endopeptidase Complex / metabolism; Proteome / metabolism; Ribosomes / genetics; Ribosomes / metabolism
TL;DR:
The striped bass ovary proteome is evaluated using label-free quantitative mass spectrometry and a novel machine learning analysis based on K-means clustering and support vector machines to suggest that protein synthesis and degradation are intimately linked.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(Web of Science)
Sources: ORCID, Crossref
Added: April 8, 2021
2013 journal article
Temporal Analysis of theMagnaporthe OryzaeProteome During Conidial Germination and Cyclic AMP (cAMP)-mediated Appressorium Formation
Molecular & Cellular Proteomics, 12(8), 2249–2265.
MeSH headings : Cyclic AMP / metabolism; Fungal Proteins / metabolism; Magnaporthe / growth & development; Magnaporthe / metabolism; Mitochondrial Proteins / metabolism; Peptide Hydrolases / metabolism; Proteome; Spores, Fungal / growth & development; Spores, Fungal / metabolism
TL;DR:
The data presented here provide the first comprehensive view of the M. oryzae proteome during early infection-related development and highlight biological processes important for pathogenicity.
(via Semantic Scholar)
www.mcponline.org (publisher PDF)
Sources: Crossref, ORCID
Added: January 18, 2021
2013 journal article
UDP-glucose Dehydrogenase Activity and Optimal Downstream Cellular Function Require Dynamic Reorganization at the Dimer-Dimer Subunit Interfaces
Journal of Biological Chemistry, 288(49), 35049–35057.
author keywords: Dehydrogenase; Enzyme Catalysis; Glycobiology; Hyaluronate; Prostate Cancer; Protein Conformation; Protein Dynamics; Cardiac Defects; Human UGDH; Hyaluronan
MeSH headings : Amino Acid Substitution; Enzyme Stability; HEK293 Cells; Humans; Kinetics; Models, Molecular; Mutagenesis, Site-Directed; Protein Interaction Domains and Motifs; Protein Multimerization; Protein Structure, Quaternary; Protein Subunits; Proteolysis; Thermodynamics; Uridine Diphosphate Glucose Dehydrogenase / chemistry; Uridine Diphosphate Glucose Dehydrogenase / genetics; Uridine Diphosphate Glucose Dehydrogenase / metabolism
TL;DR:
Comparison of kinetic and thermal stability parameters revealed structurally dependent properties consistent with a role for controlled assembly and disassembly of the hexamer in the regulation of UGDH, which support a model that requires an operational dimer-hexamer equilibrium to function efficiently and preserve regulated activity in the cell.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2013 journal article
Vinculin and metavinculin: Oligomerization and interactions with F-actin
FEBS Letters, 587(8), 1220–1229.
author keywords: Vinculin; Metavinculin; Actin; PIP2; Oligomerization
MeSH headings : Actin Cytoskeleton / chemistry; Actin Cytoskeleton / metabolism; Actins / chemistry; Actins / metabolism; Humans; Models, Molecular; Protein Binding; Protein Multimerization; Protein Structure, Tertiary; Vinculin / chemistry; Vinculin / genetics; Vinculin / metabolism
TL;DR:
Differences in these functions between vinculin and metavinculin provide key insights to the structure and function of these oligomers, and should guide further studies.
(via Semantic Scholar)
Source: ORCID
Added: December 10, 2019
2013 journal article
Combined computational design of a zinc-binding site and a protein-protein interaction: One open zinc coordination site was not a robust hotspot for de novo ubiquitin binding
Proteins: Structure, Function, and Bioinformatics, 81(7), 1245–1255.
author keywords: computational interface design; de novo; heterodimer; metal coordination; zinc binding; protein-protein interaction
MeSH headings : Alanine / chemistry; Binding Sites; Magnetic Resonance Spectroscopy; Mutagenesis; Protein Binding; Protein Interaction Maps; Ubiquitin / chemistry; Zinc / chemistry
TL;DR:
This study led us to conclude that 2/2 coordination arrangements or multiple‐zinc designs are more likely to promote high‐affinity protein interactions.
(via Semantic Scholar)
Sources: ORCID, Crossref
Added: December 10, 2019
2013 journal article
Combined computational design of a zinc-binding site and a protein-protein interaction: One open zinc coordination site was not a robust hotspot for de novo ubiquitin binding
Proteins, 81(9), 1678–1679.
Source: ORCID
Added: December 10, 2019
2013 journal article
Vinculin–actin interaction couples actin retrograde flow to focal adhesions, but is dispensable for focal adhesion growth
J Cell Biol, 202(1), 163–177.
MeSH headings : Actins / metabolism; Amino Acid Substitution; Animals; Cell Movement; Cloning, Molecular; Extracellular Matrix / metabolism; Fibroblasts / metabolism; Focal Adhesions / genetics; Focal Adhesions / metabolism; Green Fluorescent Proteins / metabolism; Mice; Mice, Inbred C57BL; Point Mutation; Protein Binding; Protein Interaction Mapping / methods; Protein Transport; Proteolysis; Pseudopodia / metabolism; Vinculin / genetics; Vinculin / metabolism
TL;DR:
Vinculin functions as a molecular clutch that organizes leading edge F-actin, generates traction, and promotes focal adhesion formation and turnover but not adhesion growth.
(via Semantic Scholar)
Source: ORCID
Added: December 10, 2019
2013 journal article
Synthesis, characterization and structural investigation of novel meso-pyridyl BODIPY–cobaloxime complexes
Dalton Transactions, 42(41), 14883.
TL;DR:
It is found that the synthesis of four boron-dipyrromethene (BODIPY) sensitized cobaloxime complexes as structural models of light-driven proton reduction catalysts produce sub-stoichiometric quantities of hydrogen under standard photon-driven hydrogen evolving conditions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(Web of Science)
Source: ORCID
Added: November 12, 2019
2013 journal article
Superexchange Contributions to Distance Dependence of Electron Transfer/Transport: Exchange and Electronic Coupling in Oligo(para-Phenylene)- and Oligo(2,5-Thiophene)-Bridged-Donor-Bridge Acceptor Biradical Complexes
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135(45), 17144–17154.
TL;DR:
The work provides a direct measurement of superexchange contributions to β, with no contribution from incoherent hopping, and offers unique insight into the intrinsic molecular factors that govern H(DA) and β, which are important for understanding the electronic origin of electron transfer and electron transport mediated by molecular bridges.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 journal article
Understanding the Role of Proteolytic Digestion on Discovery and Targeted Proteomic Measurements Using Liquid Chromatography Tandem Mass Spectrometry and Design of Experiments
JOURNAL OF PROTEOME RESEARCH, 12(12), 5820–5829.
author keywords: design of experiments; proteolytic digestion; LC-MS/MS; Populus trichocarpa
MeSH headings : Amino Acid Sequence; Animals; Cattle; Chromatography, Liquid / standards; Factor Analysis, Statistical; Hydrogen-Ion Concentration; Isotope Labeling; Molecular Sequence Annotation; Molecular Sequence Data; Peptide Fragments / chemistry; Peptide Fragments / isolation & purification; Plant Proteins / chemistry; Plant Proteins / isolation & purification; Populus / chemistry; Protein Stability; Proteolysis; Proteomics / methods; Proteomics / standards; Research Design; Swine; Tandem Mass Spectrometry / standards; Trypsin / chemistry; Xylem / chemistry
TL;DR:
The tryptic digest optimization described here has eliminated this previously observed peptide decay as well as provided a greater understanding and standardization for a common but critical sample treatment used across the field of proteomics.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 journal article
Lengthening the Intersubunit Linker of Procaspase 3 Leads to Constitutive Activation
BIOCHEMISTRY, 52(36), 6219–6231.
MeSH headings : Apoptosis / physiology; Caspase 3 / chemistry; Caspase 3 / genetics; Caspase 3 / metabolism; Caspase Inhibitors / pharmacology; Catalytic Domain; Enzyme Activation; Enzyme Precursors / chemistry; Models, Chemical; Models, Molecular; Molecular Dynamics Simulation; Protein Conformation; Protein Multimerization
TL;DR:
The data show that releasing the strain of the short IL is not sufficient to populate the active conformer of the native ensemble, and it is shown that increasing the length of the IL by introducing 3-5 alanines results in constitutively active procaspases.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2013 journal article
Mass Recalibration of FT-ICR Mass Spectrometry Imaging Data Using the Average Frequency Shift of Ambient Ions
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 24(7), 1137–1145.
author keywords: Mass spectrometry imaging; FT-ICR MS; Mass calibration; MALDESI; MMA
MeSH headings : Animals; Brain / anatomy & histology; Brain Chemistry; Calibration; Cyclotrons; Fourier Analysis; Infrared Rays; Ions; Mass Spectrometry / methods; Mass Spectrometry / statistics & numerical data; Mice; Molecular Imaging / methods; Molecular Imaging / statistics & numerical data; Spectrometry, Mass, Electrospray Ionization / methods; Spectrometry, Mass, Electrospray Ionization / statistics & numerical data; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / methods; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / statistics & numerical data
TL;DR:
A calibration method is applied based on the observed cyclotron frequency shift of ions found in the ambient laboratory environment, polydimethylcyclosiloxanes (PDMS) to achieve part per billion mass accuracy with relatively high precision for an infrared matrix-assisted laser desorption electrospray ionization (IR-MALDESI) MSI dataset.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 journal article
The role of T56 in controlling the flexibility of the distal histidine in dehaloperoxidase-hemoglobin from Amphitrite ornata
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834(10), 2020–2029.
author keywords: Enzyme kinetics; Catalytic efficiency; Hemichrome; Resonance Raman; Molecular dynamics
MeSH headings : Animals; Biocatalysis; Heme / chemistry; Hemoglobins / chemistry; Hemoglobins / genetics; Histidine / chemistry; Histidine / genetics; Iron / chemistry; Kinetics; Molecular Dynamics Simulation; Mutagenesis, Site-Directed; Peroxidases / chemistry; Peroxidases / genetics; Polychaeta / chemistry; Polychaeta / enzymology; Recombinant Proteins / chemistry; Recombinant Proteins / genetics; Spectroscopy, Fourier Transform Infrared; Spectrum Analysis, Raman; Thermodynamics; Threonine / chemistry; Threonine / genetics
TL;DR:
It is confirmed that subtle changes in the conformation of H55 affect the catalytic efficiency of DHP, and a balance of enzymatic rate and protein stability with respect to hemichrome formation appears to be optimum in wild type DHP (WT-DHP).
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2013 journal article
Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT): A Novel Glycan-Relative Quantification Strategy
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 24(9), 1376–1384.
author keywords: Glycomics; Hydrazide Reagents; Stable Isotope Labeling; Normalization; Hydrazone; Formation; Relative Quantification; N-Linked Glycans
MeSH headings : Chromatography, Reverse-Phase; Glycomics / methods; Glycoproteins / chemistry; Glycosylation; Humans; Isotope Labeling / methods; Mass Spectrometry / methods; Plasma / chemistry; Polysaccharides / analysis; Polysaccharides / isolation & purification
TL;DR:
The ability to spike in a glycoprotein and detect change at the glycan level validates both the sample preparation and data analysis strategy, making INLIGHT an invaluable relative quantification strategy for the field of glycomics.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 journal article
Factorial Experimental Designs Elucidate Significant Variables Affecting Data Acquisition on a Quadrupole Orbitrap Mass Spectrometer
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 24(10), 1501–1512.
author keywords: Design of experiments; Data dependent acquisition; Proteome coverage; Q Exactive; FTMS
MeSH headings : Models, Chemical; Proteome / analysis; Proteome / chemistry; Proteomics / methods; Research Design; Saccharomyces cerevisiae Proteins / analysis; Saccharomyces cerevisiae Proteins / chemistry; Tandem Mass Spectrometry / methods
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
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
Added: August 6, 2018
2013 journal article
Multi-peptide nLC-PC-IDMS-SRM-based Assay for the quantification of biomarkers in the chicken ovarian cancer model
METHODS, 61(3), 323–330.
author keywords: Proteomics; Quantification; Ovarian cancer; Chicken; Biomarkers
MeSH headings : Amino Acid Sequence; Animals; Biological Assay; Biomarkers, Tumor / analysis; Biomarkers, Tumor / blood; Biomarkers, Tumor / chemistry; Calibration; Carbon Isotopes; Chickens; Disease Models, Animal; Female; Humans; Indicator Dilution Techniques; Isotope Labeling; Molecular Sequence Data; Nitrogen Isotopes; Ovarian Neoplasms / chemistry; Ovarian Neoplasms / metabolism; Peptide Fragments / analysis; Prealbumin / analysis; Prealbumin / chemistry; Prealbumin / metabolism; Proteomics / methods; Proteomics / standards; Tandem Mass Spectrometry / methods; Tandem Mass Spectrometry / standards; Vitellogenins / analysis; Vitellogenins / blood; Vitellogenins / chemistry; alpha-Macroglobulins / analysis; alpha-Macroglobulins / chemistry; alpha-Macroglobulins / metabolism
TL;DR:
These data illustrate the successes and challenges of qualifying quantitative levels of proteins from an in-gel digestion sample preparation followed by LC-MS/MS (GeLC) label-free discovery-based approach to a targeted SRM-based quantitative assay in plasma and tissues.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018
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