Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mitochondria cross-linking mass spectrometry

ABSTRACT: We performed cross-linking mass spectrometry experiments on intact mitochondria isolated from mouse heart in two conditions, native-state and high-salt treatment to disrupt electrostatic interactions. Both conditions were provided in biological replicates.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Heart

SUBMITTER: Fan Liu

LAB HEAD: Albert J.R. Heck

PROVIDER: PXD006816 | Pride | 2017-12-11

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	F1_Agilent6_20160920_FL_mito_3_DR_SCX_f24.raw	Raw
	F1_Agilent6_20160920_FL_mito_3_DR_SCX_f25.raw	Raw
	F1_Agilent6_20160920_FL_mito_3_DR_SCX_f26.raw	Raw
	F1_Agilent6_20160920_FL_mito_3_DR_SCX_f27.raw	Raw
	F1_Agilent6_20160920_FL_mito_3_DR_SCX_f28.raw	Raw

Items per page:

1 - 5 of 88

Publications

The interactome of intact mitochondria by cross-linking mass spectrometry provides evidence for coexisting respiratory supercomplexes.

Liu Fan F Lössl Philip P Rabbitts Beverley M BM Balaban Robert S RS Heck Albert J R AJR

Molecular & cellular proteomics : MCP 20171208 2

Mitochondria exert an immense amount of cytophysiological functions, but the structural basis of most of these processes is still poorly understood. Here we use cross-linking mass spectrometry to probe the organization of proteins in native mouse heart mitochondria. Our approach provides the largest survey of mitochondrial protein interactions reported so far. In total, we identify 3,322 unique residue-to-residue contacts involving half of the mitochondrial proteome detected by bottom-up proteom ...[more]

PMID: 29222160

Similar Datasets

cross-linking mass spectrometry of synaptosome

Project description:Cross-linking mass spectrometry data of synaptosome and microsome fractions of mouse cerebellum and hippocampus.

2020-12-03 | PXD010317 | Pride

The cochaperone CHIP marks Hsp70- and Hsp90-bound substrates for degradation through a very flexible mechanism

Project description:Some molecular chaperones are involved not only in assisting the folding of proteins but also, given appropriate conditions, in their degradation. This is the case of Hsp70 and Hsp90, which direct their bound substrate to degradation through ubiquitination in concert with the cochaperone CHIP –an E3 ligase. We have generated complexes between the chaperone (Hsp70 or Hsp90), the cochaperone CHIP and, as substrate, a p53 variant containing the GST protein (p53-TMGST). The two ternary complexes (Hsp70:p53-TMGST:CHIP and Hsp90:p53-TMGST:CHIP) ubiquitinate the substrate, and this is done with a higher efficiency than in the absence of the chaperones. The 3D structures of the two complexes, obtained using a combination of cryoelectron microscopy and crosslinking mass spectrometry, show the substrate located between the chaperone and the cochaperone, which suggests an ubiquitination mechanism. Both complexes are extremely flexible, which is crucial for the ubiquitination process.

2019-03-07 | PXD009756 | Pride

Cross-linking mass spectrometry of synapses purified from mouse brain

Project description:cross-linking experiments of three biologically independent replicates of hippocampal synaptosomes.

2020-12-03 | PXD015160 | Pride

Normal respiratory chain capacity and physiology in mice with severely reduced levels of mitochondrial respirasomes; Cross-linking of intact mitochondria

Project description:The mammalian oxidative phosphorylation (OXPHOS) system in the inner mitochondrial membrane comprises respiratory chain complexes I-IV (CI-CIV) and ATP synthase. Together, these protein complexes harvest metabolic energy to generate ATP, the cellular energy currency. The inner mitochondrial membrane is abundant in OXPHOS complexes and CI, CIII and CIV exhibit specific protein-protein interactions to form stable supercomplex assemblies, exemplified by the respirasome (CI-CIII2-CIV). Respirasomes are conserved in evolution, and as well documented by biochemical and structural methods. However, their physiological roles are much debated, despite a substantial literature suggesting their importance in facilitating catalysis and regulating turnover in response to metabolic demand. To investigate the in vivo role of respirasomes, we deleted a short conserved, charged loop in the UQCRC1 subunit of CIII that contacts CI. The resulting homozygous knock-in mice show profoundly decreased levels of respirasomes on blue native polyacrylamide gel electrophoresis (BN-PAGE) and complexome profiling proteomics analyses of different tissues, although the individual complexes appear unaffected. In vivo The spatial organization of respirasomes in vivo was altered in knock-in mice as shown by cross-linking experiments on intact mitochondria. Surprisingly, the mutant mice are healthy, with normal respiratory chain capacity and normal exercise tolerance. Therefore, respirasomes are dispensable for OXPHOS function in vivo.

2023-03-11 | PXD031345 | Pride

Cross-linking of the Endolysosomal System Reveals Potential Flotillin Structures and Cargo

Project description:Lysosomes are well-established as the main cellular organelles for the degradation of macromolecules and emerging as regulatory centers of metabolism. They are of crucial importance for cellular homeostasis, which is exemplified by a plethora of disorders related to alterations in lysosomal function. In this context, protein complexes play a decisive role, regulating not only metabolic lysosomal processes but also lysosome biogenesis, transport, and interaction with other organelles. Using cross-linking mass spectrometry, we analyzed lysosomes and early endosomes. Based on the identification of 5,376 cross-links, we investigated protein-protein interactions and structures of lysosome- and endosome-related proteins. In particular, we present evidence for a tetrameric assembly of the lysosomal hydrolase PPT1 and a heterodimeric structure of FLOT1/FLOT2 at lysosomes and early endosomes. For FLOT1-/FLOT2-positive early endosomes, we identified >300 proteins presenting putative cargo, and confirmed several substrates for flotillin-dependent endocytosis, including the latrophilin family of adhesion G protein-coupled receptors.

2022-10-22 | PXD030532 | Pride

Reverse-phase liquid chromatography (RPLC) in Combination with Tip-Based Strong Cation Exchange (SCX-Tip) Fractionation, ReST, an Alternative Approach for Cross-linked Peptides analysis

Project description:Chemical cross-linking in combination with mass spectrometry (XL-MS) has emerged as a useful method for structural elucidation of proteins and protein complexes. Efficient enrichment procedures are necessary to analyze cross-linked products due to their relatively low abundance. Currently, strong cation exchange chromatography (SCX), size exclusion chromatography (SEC), and affinity tag-based enrichment are among the widely used enrichment strategies. Herein, we present a two-dimensional enrichment strategy combining basic RPLC (bRPLC) fractionation and tip-based SCX (SCX-Tip) enrichment, termed ReST method, for the characterization of cross-linked peptides. We revealed the unbiased separation effects of the bRPLC in the cross-linked peptide fractionation. We optimized the enrichment conditions of SCX-Tip for cross-linked peptides using well-designed cross-linked peptides. Taking advantage of the high resolution of bRPLC fractionation and the high enrichment efficiency of SCX-Tip, we were able to identify 43.6% more cross-links than the conventional SCX approach. The presented ReST approach is an effective fractionation method for XL-MS analysis, and could be beneficial for protoeme-scale protein-protein interaction studies. Moreover, more stringent data filtering was proposed in order to achieve the high confidence of cross-linked peptide identification.

2022-06-16 | PXD023817 | Pride

The catalytic activity of TCPTP is auto-regulated by its intrinsically disordered tail and activated by Integrin alpha-1

Project description:T-Cell Protein Tyrosine Phosphatase (TCPTP, PTPN2) is a non-receptor type protein tyrosine phosphatase that is ubiquitously expressed in human cells. TCPTP is a critical component of a variety of key signaling pathways that are directly associated with the formation of cancer and inflammation. Thus, understanding the molecular mechanism of TCPTP activation and regulation is essential for the development of TCPTP therapeutics. Under basal conditions, TCPTP is largely inactive, although how this is achieved is poorly understood. Thus, in this study we used Intra and inter molecular CX-MS analysis to reveal molecular mechanism of TCPTP activity regulation, our both intra- and inter- molecular CX-MS analysis result shows that the C-terminal intrinsically disordered tail of TCPTP directly bind on the surface of catalytic domain and function as autoinhibitory element to control the TCPTP catalytic activity.

2021-11-10 | PXD029256 | Pride

Spatial, Quantitative and Functional Deconstruction of Virus and Host Protein Interactions Inside Intact Cytomegalovirus Particles

Project description:Viral infections involve packaging of the viral genome and proteins into virions. Knowing virion composition and structure is critical to understand viral pathogenesis. However, an integrated picture of virion proteome organization of large viruses, such as Herpesviruses, is lacking. Here we use cross-linking mass spectrometry to derive a spatially resolved structural interactome of intact human cytomegalovirus virions. We capture interactions of 82 host and 33 viral proteins, allowing us to de novo allocate them into distinct virion-layers and identify several host proteins as constitutive virion components recruited via specific protein interactions. The abundant viral protein pp150 forms domain-specific interactions with all virion layers and scaffolds numerous viral and host proteins such as PP1 phosphatase and 14-3-3 proteins, which are incorporated via nearby short linear motifs in pp150’s C-terminus. PP1 recruitment antagonizes 14-3-3 proteins and is pivotal during early and late viral replication steps. Collectively, this study gives a spatial and quantitative inventory of the system-wide organization and functional relevance of protein interactions inside native herpesvirus particles.

2023-06-14 | PXD031911 | Pride

Cross-linking mass spectrometry of the CCAN and CCAN-Cenp-A complexes

Project description:Here we performed a cross-linking mass spectrometry analysis of the inner kinethocore complex CCAN and of the complex associated with a CenpA-nucleosome (CCAN-CenpA)from budding yeast. These experiments validated the cryo-EM structure of both complexes and provided additional structural insights on the complex organization.

2019-08-20 | PXD013769 | Pride

In-cell structures of a conserved supramolecular array at the mitochondria-cytoskeleton interface in mammalian sperm

Project description:Mitochondria-cytoskeleton interactions modulate cellular physiology by regulating mitochondrial transport, positioning, and immobilization. However, there is very little structural information defining mitochondria-cytoskeleton interfaces in any cell type. Here, we use cryo-focused ion beam milling-enabled cryo-electron tomography to image mammalian sperm, where mitochondria wrap around the ciliary cytoskeleton. We find that mitochondria are tethered to their neighbors through inter-mitochondrial linkers and are anchored to the cytoskeleton through ordered arrays on the outer mitochondrial membrane. We use subtomogram averaging to resolve in-cell structures of these arrays from three mammalian species, revealing they are conserved across species despite variations in mitochondrial dimensions and cristae organization. We find that the arrays consist of boat-shaped particles anchored on a network of membrane pores whose arrangement and dimensions are consistent with voltage dependent anion channels. Proteomics and in-cell cross-linking mass spectrometry suggest that the conserved arrays are composed of glycerol kinase-like proteins. Ordered supramolecular assemblies may serve to stabilize similar contact sites in other cell types where mitochondria need to be immobilized in specific subcellular environments, such as in muscles and neurons.

2021-10-29 | PXD025562 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data