Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Peptidisc-based Survey of the Plasma Membrane Proteome of a Mammalian Cell

ABSTRACT: The low abundance and hydrophobicity of plasma membrane proteome relative to soluble proteins makes it difficult to characterize. Here, we apply the peptidisc membrane mimetic to purify the cell membrane proteome. We used HeLa cells as a reference to establish the method, and compared the plasma membrane proteomes between Pancreatic cancer cell Panc-1 and hPSC.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Zhiyu Zhao

LAB HEAD: Dr Franck Duong

PROVIDER: PXD041913 | Pride | 2023-10-24

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20220316_UVPD_CDS_DuongF_HeLa-Lib-His-Nspr3.raw	Raw
	20220422_UVPD_CDS_DuongF_HeLa-Lib-His-Nspr4.raw	Raw
	HeLa-Lib-His-Nspr3.index	Other
	HeLa-Lib-His-Nspr4.index	Other
	allPeptides.txt	Txt

Items per page:

1 - 5 of 14

Publications

A Peptidisc-Based Survey of the Plasma Membrane Proteome of a Mammalian Cell.

Zhao Zhiyu Z Khurana Arshdeep A Antony Frank F Young John W JW Hewton Keeley G KG Brough Zora Z Zhong Tianshuang T Parker Seth J SJ Duong van Hoa Franck F

Molecular & cellular proteomics : MCP 20230607 8

Membrane proteins play critical roles at the cell surface and their misfunction is a hallmark of many human diseases. A precise evaluation of the plasma membrane proteome is therefore essential for cell biology and for discovering novel biomarkers and therapeutic targets. However, the low abundance of this proteome relative to soluble proteins makes it difficult to characterize, even with the most advanced proteomics technologies. Here, we apply the peptidisc membrane mimetic to purify the cell ...[more]

PMID: 37295717

Similar Datasets

A Peptidisc-based Survey of the Plasma Membrane Proteome of a Mammalian Cell

Project description:The low abundance and hydrophobicity of plasma membrane proteome relative to soluble proteins makes it difficult to characterize. Here, we apply the peptidisc membrane mimetic to purify the cell membrane proteome. We used HeLa cells as a reference to establish the method, and compared the plasma membrane proteomes between Pancreatic cancer cell Panc-1 and hPSC.

2023-10-24 | PXD039990 | Pride

Development of a Method Combining Peptidiscs and Proteomics to Identify, Stabilize and Purify a Detergent-Sensitive Membrane Protein Assembly

Project description:The peptidisc membrane mimetic enables global reconstitution of the bacterial membrane proteome into water-soluble detergent-free particles, termed peptidisc libraries. We present here a method that combines peptidisc libraries and chromosomal-level gene tagging technology with affinity purification and mass spectrometry (AP/MS) to stabilize and identify fragile membrane protein complexes that exist at native expression levels. This method circumvents common artifacts caused by bait protein overproduction and protein complex dissociation due to lengthy exposure to detergents during protein isolation. Using the E. coli Sec system as a case study, we identify an expanded version of the translocon, termed the HMD complex, consisting of 9 different integral membrane subunits. This complex is stable in peptidiscs but dissociates in detergent. Guided by this native-level proteomic information, we design and validate a procedure that enables purification of the HMD complex with minimal protein dissociation. These results highlight the utility of peptidiscs and AP/MS to discover and stabilize fragile membrane protein assemblies.

2022-06-09 | PXD032315 | Pride

A Simple Method to Isolate and Characterize a Bacterial Outer Membrane Proteome by Bottom-Up Mass Spectrometry

Project description:The outer membrane of gram-negative bacteria plays a critical role in protecting the cell against external stressors, including antibiotics. Given its importance to the resistance mechanisms, the outer membrane is a prime target for antimicrobial drug discovery. To facilitate discovery efforts, however, a precise characterization of the outer membrane protein content – or the "outer membrane proteome" - and possible variations during bacterial resistance, is important. This information is necessary to understand how bacteria interact with their host organism during infection. However, proteomic-based investigations of the bacterial outer membrane remain technically challenging, given this cell compartment's lower abundance and high hydrophobicity. We report here a simple but efficacious enrichment of the bacterial outer membrane proteome for downstream characterization by mass spectrometry. We start with a dual detergent approach to preferentially solubilize the outer membrane, followed by reconstitution in peptidisc library to isolate and purify the entire outer membrane proteome at once. Our method identifies 71 outer membrane proteins (OMPs), including 26 integral -barrels and 26 lipoproteins; many of which are present with high-intensity and peptide number values, indicative of a high abundance in the library sample. Given this enrichment, the method may be useful for comparing outer membrane proteomes. We also show that the library can also be employed for downstream protein binding assays.

2023-03-11 | PXD036749 | Pride

A peptidisc-based AP/MS approach to explore the interactome of the bacterial Sec translocon

Project description:We recently presented the peptidisc membrane mimetic for the global reconstitution of membrane proteomes into water-soluble detergent-free particles, termed peptidisc library. We here develop a method that combines the peptidisc library with affinity pulldown and mass spectrometry (AP/MS) to explore the membrane interactome at native expression level, which minimizes artifacts due to protein overproduction or exposure to detergents. Using the Sec translocon as a case study, we identify an expanded holo-translocon complex, termed the HMD complex, which consists of 9 different membrane subunits - SecYEG, SecDFyajC, YidC, plus YfgM and PpiD. This super-complex can be biochemically isolated in peptidisc but not in detergent. We also detect associations of the HMD complex with the outer membrane Bam complex and we discover a novel unannotated inner membrane protein named YibN. This interactome analysis at native expression level points out the membrane complexes that are dissociated in detergent, yet stable enough to be captured in peptidiscs. We believe this information is critical for the design of biochemical procedures that will enable their successful purification.

2023-03-22 | PXD018866 | Pride

Cell-surface proteomics identifies differences in signalling and adhesion protein expression between naive and primed human pluripotent stem cells

Project description:Naive and primed human pluripotent stem cells (hPSC) provide valuable models to study cellular and molecular developmental processes. The lack of detailed information about cell-surface protein expression in these two pluripotent cell types prevents an understanding of how the cells communicate and interact with their microenvironments. Here, we used plasma membrane profiling to directly measure cell-surface protein expression in naive and primed hPSC. This unbiased approach quantified over 1700 plasma membrane proteins including those involved in cell adhesion, signalling and cell interactions. Notably, multiple cytokine receptors upstream of JAK-STAT signalling were more abundant in naive hPSC. In addition, functional experiments showed that FOLR1 and SUSD2 proteins are highly expressed at the cell surface in naive hPSC but are not required to establish human naive pluripotency. This study provides a comprehensive stem cell proteomic resource that uncovers differences in signalling pathway activity and has identified new markers to define human pluripotent states.

2020-04-17 | PXD015359 | Pride

Functionalized Peptidisc Scaffolds Enable Affinity Purification of the Membrane Proteome

Project description:We reconstituted the total E. coli membrane proteome into His-tagged peptidiscs. We then performed an affinity purification to enrich the bona fide membrane proteome away from soluble contaminants which co-sediment with cellular membranes after cell lysis. As a case study, we employ this method to survey changes to the membrane proteome caused by altered gene expression.

2022-04-11 | PXD017242 | Pride

Plasma Membrane Integrity Signaling

Project description:Plasma Membrane Integrity Signaling

| PRJNA701242 | ENA

Expression profiling of NM1 KO and WT mice

Project description:Plasma membrane tension is an important feature that determines the cell shape and influences processes such as cell motility, spreading, endocytosis and exocytosis. Unconventional class 1 myosins are potent regulators of plasma membrane tension because they physically link the plasma membrane with the adjacent cytoskeleton. We identified nuclear myosin 1 (NM1) - a putative nuclear isoform of myosin 1c (Myo1c) - as a new player in the field. Although having specific nuclear function, we show that NM1 localizes preferentially to the plasma membrane. Deletion of NM1 causes more than 50% increase in the elasticity of the plasma membrane around the actin cytoskeleton as measured by atomic force microscopy. This higher elasticity of NM1 knock-out cells leads to 25% higher resistance to short-term hypotonic environment and rapid cell swelling. In contrary, overexpression of NM1 in WT cells leads to additional 30% reduction of their survival. We have brought evidence that NM1 has a direct functional role in the cytoplasm as a dynamic linker between the cell membrane and the underlying cytoskeleton, regulating the degree of effective plasma membrane tension. We used tissues from NM1 WT and KO mice with highest expression of NM1, lungs and heart (3 replicates each) and skin fibroblast derived from each mice (2 replicates each)

2015-12-05 | E-GEOD-75709 | biostudies-arrayexpress

Discovery of plasma membrane associated RNAs through APEX-seq

Project description:In addition to nucleic acids, a variety of biomolecules have been found on the plasma membrane. Whereas, researchers have realized that RNA has the ability to bind to membrane vesicles in vitro and connect to the plasma membrane of the cell. Hence, the combination of high-throughput sequencing and in suit labelling methods provides approaches for large-scale identification of subcellular RNAs. Here, we applied the recently published method APEX-seq, and identified 75 plasma membrane-associated RNAs, of which lncRNA PMAR72 is located around the membrane. In addition, we observed that PMAR72 was concentrated into foci in specific membrane areas. Our findings will provide some new evidence to elaborate the relationship between RNA and the plasma membrane of mammalian cells.

2021-05-25 | GSE166725 | GEO

Expression profiling of NM1 KO and WT mice

2015-12-05 | GSE75709 | GEO