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Surveyance of apparent proteome unfolding curves via thiol labelling

ABSTRACT: Census of apparent proteome unfolding curves following urea denaturation in cell lysate using thiol reactivity probe tetraphenylethene maleimide (TPE-MI).

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Dezerae Cox

LAB HEAD: Danny M. Hatters

PROVIDER: PXD022640 | Pride | 2022-05-19

REPOSITORIES: Pride

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			Action	DRS
	180309_DezeraeC_DC074-DC086.msf	Msf
	180309_DezeraeC_DC074-DC086.pdResult	Other
	180309_DezeraeC_DC074.raw	Raw
	180309_DezeraeC_DC075.raw	Raw
	180309_DezeraeC_DC076.raw	Raw

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Publications

Hidden information on protein function in censuses of proteome foldedness.

Cox Dezerae D Ang Ching-Seng CS Nillegoda Nadinath B NB Reid Gavin E GE Hatters Danny M DM

Nature communications 20220414 1

Methods that assay protein foldedness with proteomics have generated censuses of apparent protein folding stabilities in biological milieu. However, different censuses poorly correlate with each other. Here, we show that the reason for this is that methods targeting foldedness through monitoring amino acid sidechain reactivity also detect changes in conformation and ligand binding, which can be a substantial fraction of the data. We show that the reactivity of only one quarter of cysteine or met ...[more]

PMID: 35422070

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Surveyance of apparent proteome unfolding curves via thiol labelling under HSP70 inhibition

Project description:Census of apparent proteome unfolding curves following urea denaturation in cell lysate derived from control of VER155008-treated N2a cells using thiol reactivity probe tetraphenylethene maleimide (TPE-MI).

2022-05-20 | PXD030567 | Pride

TPE-MI reveals proteome remodelling in response to cellular stimuli

Project description:Census of apparent proteome conformation in response to stimuli using thiol reactivity probe tetraphenylethene maleimide (TPE-MI).

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Project description:Census of apparent chaperone-client interaction using thiol reactivity probe tetraphenylethene maleimide (TPE-MI).

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A thiol probe for measuring unfolded protein load and proteostasis in cells

Project description:When proteostasis becomes unbalanced, unfolded proteins accumulate and can aggregate. However, probes quantifying proteostasis imbalance are lacking. We report a dye, tetraphenylethene maleimide (TPE-MI) that can measure unfolded protein load.TPE-MI fluorescence is enhanced upon reaction with cellular proteomes under conditions promoting accumulation of unfolded proteins and, via proteomic analysis, can track which proteins expose more cysteine residues under stress.

2018-10-24 | PXD006527 | Pride

affy_rose_2012_06: RhDiF1 knockdown

Project description:affy_rose_2012_06 - affy_rose_2012_06 - - Study of rose perfume by comparing a wild-tpe rose with one in which the expression of a scent gene has been altered.-Study of rose perfume by comparing a wild-tpe rose with one in which the expression of a scent gene has been altered. 8 arrays - rose; normal vs rnai mutant comparaison

2013-09-12 | E-GEOD-45236 | biostudies-arrayexpress

Spontaneous Unfolding-Refolding of Fibronectin Type III Domains Assayed by Thiol Exchange: THERMODYNAMIC STABILITY CORRELATES WITH RATES OF UNFOLDING RATHER THAN FOLDING.

Project description:Globular proteins are not permanently folded but spontaneously unfold and refold on time scales that can span orders of magnitude for different proteins. A longstanding debate in the protein-folding field is whether unfolding rates or folding rates correlate to the stability of a protein. In the present study, we have determined the unfolding and folding kinetics of 10 FNIII domains. FNIII domains are one of the most common protein folds and are present in 2% of animal proteins. FNIII domains are ideal for this study because they have an identical seven-strand β-sandwich structure, but they vary widely in sequence and thermodynamic stability. We assayed thermodynamic stability of each domain by equilibrium denaturation in urea. We then assayed the kinetics of domain opening and closing by a technique known as thiol exchange. For this we introduced a buried Cys at the identical location in each FNIII domain and measured the kinetics of labeling with DTNB over a range of urea concentrations. A global fit of the kinetics data gave the kinetics of spontaneous unfolding and refolding in zero urea. We found that the folding rates were relatively similar, ∼0.1-1 s-1, for the different domains. The unfolding rates varied widely and correlated with thermodynamic stability. Our study is the first to address this question using a set of domains that are structurally homologous but evolved with widely varying sequence identity and thermodynamic stability. These data add new evidence that thermodynamic stability correlates primarily with unfolding rate rather than folding rate. The study also has implications for the question of whether opening of FNIII domains contributes to the stretching of fibronectin matrix fibrils.

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Molecular basis of TPE-OLD [methylation]

Project description:Among epigenetic modifiers, telomeres, represent attractive modulators of the genome in part through position effects. Telomere Position Effect – Over Long Distances (TPE-OLD) modulates genes expression by changes in telomeric-dependent long-distance loops, with a reach of 10Mb from the telomeres. However, TPE-OLD remain poorly defined. We used cells with controlled telomere length combined to a genome wide approach revealing its transcriptome and methylome. We identified a common cis element that behaved as an insulator/ enhancer. By using reporter assays integrating this element, we disclosed additional trans partners further validated by in silico data. Exploiting our cellular model we observed the depletion of one candidate (RBPJ) at TPE-OLD associated loci concomitant to telomere shortening. Therefore, we conclude that TPE-OLD is orchestrated by Alu-like elements acting as enhancers in association with RBPJ. We propose that TPE-OLD functions by the coordinated action of newly evolved enhancers; an associated protein RBPJ and telomere length to produce an adapted response to external stimuli (i.e., Aging)

2023-01-05 | GSE213427 | GEO

Molecular basis of TPE-OLD [RNA-seq]

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affy_rose_2012_06: RhDiF1 knockdown

2013-09-12 | GSE45236 | GEO

Gene Expression of Breast Cancer Cell Lines Across Biomaterial Platforms

Project description:2 Breast Cancer Cell lines were seeded onto TCPS, on 2D PEG-PC gels, and encapsulated in 3D PEG-Maleimide gels as single cells or spheroids to determine transcript level changes based on culture platform

2017-03-01 | GSE93562 | GEO

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