Simultaneous Quantification of Protein Expression and Modifications by Top-down Targeted Proteomics: A Case of the Sarcomeric Subproteome

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Highlights

• •A new strategy for simultaneous quantification of protein expression and modification.
• •This top-down LC/MS-based method shows high reproducibility and high throughput.
• •Quantification at the intact protein level with results comparable to Western blot.
• •This top-down proteomics method is applicable to different species and tissues.

     

Effects of Size and Geographical Origin on Atlantic salmon,Salmo salar,Mucin O-Glycan Repertoire

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Highlights

• •Atlantic salmon O-glycome expanded to 169 structures in three epithelia.
• •Low interindividual variation amongst all populations and geographical regions.
• •Small variations in glycosylation between geographical locations and fish size.
• •Prominent fucosylation in gastrointestinal mucins from Tasmanian fish.

     

Metabolic,Anti-apoptotic and Immune Evasion Strategies of Primary Human Myeloma Cells Indicate Adaptations to Hypoxia*

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Highlights

• •In-depth proteome profiling of primary human myeloma cells
• •Characteristics of myeloma cells are related to hypoxic bone marrow conditions
• •Myeloma cells show specific immune evasion strategies
• •Metabolic adaptations involve tumor and stroma cells

     

Characterization of the Prion Protein in Human Urine

The presence of the prion protein (PrP) in normal human urine is controversial and currently inconclusive. This issue has taken a special relevance because prion infectivity has been demonstrated in urine of animals carrying experimental or naturally occurring prion diseases, but the actual presence and tissue origin of the infectious prion have not been determined. We used immunoprecipitation, one- and two-dimensional electrophoresis, and mass spectrometry to prove definitely the presence of PrP in human urine and its post-translational modifications. We show that urinary PrP (uPrP) is truncated mainly at residue 112 but also at other residues up to 122. This truncation makes uPrP undetectable with some commonly used antibodies to PrP. uPrP is glycosylated and carries an anchor which, at variance with that of cellular PrP, lacks the inositol-associated phospholipid moiety, indicating that uPrP is probably shed from the cell surface. The detailed characterization of uPrP reported here definitely proves the presence of PrP in human urine and will help determine the origin of prion infectivity in urine.     

Apolipoprotein A1 Forms 5/5 and 5/4 Antiparallel Dimers in Human High-density Lipoprotein

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Highlights

• •Zero-length chemical cross-linking of APOA1 peptides in HDL.
• •Cross-links match antiparallel isomers of APOA dimers in molecular modeling.
• •Identical MS/MS spectra of native and synthetic cross-linked peptides.
• •First biochemical evidence of LL5/5 and LL5/4 isomers in human HDL.

     

Quantitative Multiplex Substrate Profiling of Peptidases by Mass Spectrometry

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Highlights

• •Quantitative substrate profiling method for characterizing peptidase specificity.
• •Applicable to both purified peptidases and peptidases in complex biological samples.
• •TMT labeling improves throughput, accuracy and reproducibility of the assay.
• •Design of fluorescent probes to monitor peptidase activity based on substrate data.

     

重组人SHH蛋白N端在HEK293T细胞中的分泌表达与鉴定

目的:获得有活性的Sonic Hedgehog(SHH)蛋白N端结构域蛋白纯品,该结构域是SHH蛋白与受体结合结构域,可用作抗原,用于研制抗SHH的中和抗体。方法:应用PCR技术从商业化人Shh基因中分别扩增该基因5'端591和600 bp的片段,并插入真核表达载体pL293,分别在HEK293T细胞中进行瞬时分泌表达,通过His标签纯化后获得SHH-591和SHH-600蛋白纯品,SDS-PAGE和Western印迹对表达产物进行分析,并通过ELISA进行结合活性鉴定。结果:构建了重组表达载体pL293-Shh-N591和pL293-Shh-N600,酶切鉴定和测序证实含有目的基因片段,真核瞬时表达产物均在相对分子质量约20×103处可见与预期相符的条带,该条带可被His标签抗体所识别;纯化获得了SHH-591-His和SHH-600-His蛋白纯品;ELISA结合实验结果显示SHH-591-His和SHH-600-His均能与抗His标签抗体结合,而SHH-591-His与SHH中和抗体的结合能力更强。结论:获得了真核表达的SHH-N蛋白SHH-591-His,可用于下一步中和抗体药物的筛选和后续研究。     

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.

     

Dex-ras1 and Serum- and Glucocorticoid-inducible Protein Kinase 1: Regulation of Expression by Dexamethasone in HEK293 Cells

The molecular and cellular basis of the psychotropic actions of adrenal corticosteroids is poorly understood. Previously, we reported that modulation of large conductance Ca²⁺-activated potassium channel (BK-channel) function by glucocorticoids can be recapitulated in human embryonic kidney293 (HEK293) cells (J Physiol 537:57, 2001). In the present paper, we examined the effect of dexamethasone on the expression of candidate mediator proteins of glucocorticoid action, dex-ras1 and serum and glucocorticoid inducible protein kinase 1 (SGK), in HEK293 cells. Dex-ras1 mRNA was readily detectable under basal conditions however, no changes of dex-ras1 mRNA expression occurred upon exposure to 100 nM of dexamethasone for 2 h. In contrast, a 2.5-fold increase of SGK mRNA was found under similar conditions. Total levels of cellular SGK protein were unaltered upon exposure to dexamethasone, but a marked increase of SGK in a Triton-X100 insoluble fraction was observed. BK-channel α-subunits could not be co-immunoprecipitated with SGK. In summary, SGK, but not dex-ras1, mRNA is rapidly induced by glucocorticoid stimulation in HEK293 cells. However, there appears to be no direct protein-protein interaction between SGK and BK-channel α-subunits. Presented to mark the 70th birthday of Professor George Fink. Special issue article in honor of George Fink.     

Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains

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Highlights

• •Quantitative changes in global proteome and ubiquitinome in Huntington's disease.
• •Differential ubiquitination of wild-type and mutant Htt in mice brain.
• •Enriched pathways include vesicle transport and mRNA processing.
• •Correlation between protein and diGly site fold changes.

     

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.