Discovery of a Human Testis-specific Protein Complex TEX101-DPEP3 and Selection of Its Disrupting Antibodies

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Highlights

• •Quantitative co-IP-MS approach to discover the human TEX101 interactome.
• •Validation of the human testis-specific protein complex TEX101-DPEP3.
• •Development of a hybrid immunoassay to screen for disruptors of TEX101-DPEP3 complex.

     

Quantification of Dynamic Protein Interactions and Phosphorylation in LPS Signaling Pathway by SWATH-MS

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Highlights

• •Intensive investigation of dynamic interactions in MyD88, TRAF6, and NEMO complexes.
• •Mechanistic insights into IRAKs proteins' assembly.
• •A signal amplification mechanism for MyD99-denpendent TLR signaling disclosed by stoichiometry of complexes.
• •Quantitative measurement of multiple phosphorylation sites on the key components in TLR signaling pathway.

     

Assembly of the β4-Integrin Interactome Based on Proximal Biotinylation in the Presence and Absence of Heterodimerization,

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Highlights

• •This study reports the first proteomic characterization of a type II hemidesmosomal complex.
• •This study characterizes the interactome of β4-integrin in the presence and absence of α6-integrin in a simple epithelial cell model.
• •The assembly of the β4-integrin interacting complex was largely independent of α6-integrin expression.

     

Proteomic Profiling of Human Prostate Cancer-associated Fibroblasts (CAF) Reveals LOXL2-dependent Regulation of the Tumor Microenvironment

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Highlights

• •Quantitative (phoshpo)proteome of primary cell cultures of patient-matched prostate CAF and NPF.
• •Key CAF-associated proteins validated using orthogonal methodologies.
• •LOXL2 inhibitors D-penicillamine and PXS-S2A impaired CAF migration and ECM alignment.
• •Pre-treatment with LOXL2 inhibitors impaired migratory capacity of RWPE-2 cells in co-culture.

     

Identification of Novel Protein Targets of Dimethyl Fumarate Modification in Neurons and Astrocytes Reveals Actions Independent of Nrf2 Stabilization

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Highlights

• •Dimethyl fumarate covalently modifies cysteine residues in neurons and astrocytes.
• •Cofilin-1, tubulin and collapsin response mediator protein 2 (CRMP2) are targets.
• •DMF-modified cofilin-1 reduces actin-severing ability, preserving filamentous actin.

     

Quantitative Proteomics of the Mitotic Chromosome Scaffold Reveals the Association of BAZ1B with Chromosomal Axes,

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Highlights

• •Quantitative proteomics of mitotic chromosome scaffold isolated from chicken DT40 cells.
• •BAZ1B identified in the isolated mitotic chromosome scaffold localizes to mitotic chromosome axes.
• •BAZ1B knockout caused prophase delay because of altered chromosome condensation timing and impaired mitosis progression.
• •BAZ1B knockout did not affect prometaphase chromosome structure.

     

ScCobB2-mediated Lysine Desuccinylation Regulates Protein Biosynthesis and Carbon Metabolism in Streptomyces coelicolor,

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Highlights

• •Identification of the first evolutionary divergent sirtuin ScCobB2 in bacteria.
• •Implementing a global quantitative succinylome between ΔScCobB2 and WT cells.
• •ScCobB2 regulates S. coelicolor protein biosynthesis and carbon metabolism pathways.
• •The divergent sirtuin enzymes are prevalent in other groups of Actinobacteria.

     

A Combined N-terminomics and Shotgun Proteomics Approach to Investigate the Responses of Human Cells to Rapamycin and Zinc at the Mitochondrial Level

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Highlights

• •Rapamycin and zinc induce moderate but significant mitochondrial proteome changes.
• •The mitochondrial proteins processing system is robust under subtoxic conditions.
• •Rapamycin and zinc perturb the mitochondrial proteins processing system.
• •Rapamycin and zinc perturb the mitochondrial proteins homeostasis.

     

Spatiotemporal Changes of the Phagosomal Proteome in Dendritic Cells in Response to LPS Stimulation*

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Highlights

• •Characterization of the phagosomal proteome comparing resting and LPS-treated BMDCs.
• •Label-free quantification determined 2843 phagosomal proteins.
• •Reduced recruitment of hydrolases and V-ATPase to phagosomes of LPS-treated cells.
• •Increased recruitment of antigen cross-presentation molecules to these phagosomes.

     

Vascular Endothelial Receptor Tyrosine Phosphatase: Identification of Novel Substrates Related to Junctions and a Ternary Complex with EPHB4 and TIE2,

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Highlights

• •Identification of the substrates profile of the endothelial phosphatase VE-PTP.
• •A large fraction of VE-PTP substrate candidates (29%) is cell junction related.
• •Tie-2 and EPHB are substrates which associate as ternary complex with VE-PTP.

     

HLA-DO Modulates the Diversity of the MHC-II Self-peptidome

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Highlights

• •MHC-II-bound peptide repertoires from DO-sufficient and DO-deficient cells.
• •Fewer unique peptides and core epitopes were presented in the absence of DO.
• •Immunopeptidome differences appeared to result from reduced DM editing.
• •DO-dependent self-epitopes elicited CD4 T cell responses in mice.

     

Comprehensive Analysis of Individual Variation in the Urinary Proteome Revealed Significant Gender Differences

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Highlights

• •Comprehensive analysis of inter-individual variation of normal urinary proteome.
• •Significant gender differences were observed.
• •Proteins increased in female urine are enriched in immunological pathways.
• •Estimated reference intervals of proteins as the baseline for biomarker discovery.

     

Reductive Stress Selectively Disrupts Collagen Homeostasis and Modifies Growth Factor-independent Signaling Through the MAPK/Akt Pathway in Human Dermal Fibroblasts

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Highlights

• •Changes to the proteome of skin fibroblasts subjected to reductive stress have been quantitated.
• •Only a small set of proteins is selectively diminished upon exposure to reductants.
• •Collagens (COL1A2 and COL6A2) emerge as sentinels of reductive stress.
• •Reductive stress triggers receptor-independent Akt phosphorylation at Ser473.

     

psims - A Declarative Writer for mzML and mzIdentML for Python

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Highlights

• •Incrementally build mzML 1.1, and mzIdentML 1.2 files in Python over a file stream.
• •Traverse controlled vocabularies using common mapping patterns.
• •Generate byte offset index as the document streams.
• •Manage referential integrity on-the-fly.

     

Phytoplasma-induced Changes in the Acetylome and Succinylome of Paulownia tomentosa Provide Evidence for Involvement of Acetylated Proteins in Witches' Broom Disease

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Highlights

• •Quantitative global proteome, acetylome and succinylome of phytoplasma-infected Paulownia tomentosa seedlings.
• •Acetylation may be more important than succinylation in response to phytoplasma infection.
• •Acetylation modified the activities of POR and RuBisCO.
• •Possible model to elucidate the molecular mechanism responses to PaWB from proteome and PTMs.

     

High-throughput Identification of FLT3 Wild-type and Mutant Kinase Substrate Preferences and Application to Design of Sensitive In Vitro Kinase Assay Substrates

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Highlights

• •Developed a data processing pipeline to format phosphopeptide identifications.
• •Identified the preferred substrate motif for FLT3 and mutant kinases.
• •Designed and validated a panel of pan-FTL3 artificial substrates.
• •Monitored FLT3 and mutant kinase activity through FAStide phosphorylation.

     

Sample Preparation Scale-Up for Deep N-glycomic Analysis of Human Serum by Capillary Electrophoresis and CE-ESI-MS*

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Highlights

• •Efficient sample preparation workflow for deep N-glycomics analysis from serum.
• •Temperature gradient denaturing protocol to prevent protein precipitation.
• •Decrease of free sugar content in serum enhanced PNGase F digestion efficiency.
• •Modified evaporative labeling method increased fluorophore labeling yield.

     

Insulin Induces Microtubule Stabilization and Regulates the Microtubule Plus-end Tracking Protein Network in Adipocytes

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Highlights

• •Insulin Affects the Phosphorylation of G2L1, MARK2, CLIP2, EB1, AGAP3, and CKAP5.
• •Insulin Increases CLASP2 +TIP Density and Decreases CLASP2 +TIP Velocity.
• •Insulin Stimulates CLASP2 and G2L1 Trailing Along Microtubules.
• •Insulin Stimulates α-Tubulin Acetylation at Lysine 40 and Microtubule Stabilization.

     

A Systems-level Characterization of the Differentiation of Human Embryonic Stem Cells into Mesenchymal Stem Cells,

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Highlights

• •Integrative multi-omics study characterizing the differentiation from hESCs into hMSCs.
• •Set of high confidence genes important in hESC to hMSC differentiation defined.
• •Two distinct expression waves of HOX genes and a AGO2-to-AGO3 switch in gene silencing identified.
• •AHNAK hypothesized as a defining factor in MSC biology.