Biochemical analysis of PINK1 activation and ubiquitination signaling upon GTPP treatment
By onUbiquitinated proteins were enriched using Halo-m-DSK ubiquitin capture, and GFP-PINK1 complexes were isolated by IP, followed by SDS–PAGE and immunoblotting to assess PINK1 activation and downstream ubiquitination signaling upon GTPP treatment
Molecular dynamics flexible fitting output of mHsp60 models into in situ density maps
By onMDFF simulations were performed to evaluate how well atomic models of mHsp60 single rings in different nucleotide states fit the in situ subtomogram averaging density maps by RMSD-based assessment of model–map agreement.
Primary data associated with Figure 3–Figure Supplement 4 in doi: 10.1101/2022.04.25.489459
By onRaw immunoblotting data and tabular data for quantitation used to generate Figure 3–Figure Supplement 4 in doi: 10.1101/2022.04.25.489459 ("A Feed-forward Pathway Drives LRRK2 kinase Membrane Recruitment and Activation").
Primary data associated with doi: 10.1042/BCJ20220161 (Impact of 100 LRRK2 variants linked to Parkinson’s Disease on kinase activity and microtubule binding)
By onRaw immunoblotting data; tabular data for quantifications; numerical data for in vitro assays; immunofluorescence images; Prism files for statistical analysis.
Crystal structure of a substrate-trapping variant of PPM1H phosphatase
By onCrystal structure of a substrate-trapping variant of PPM1H phosphatase (as reported in 10.15252/embr.202152675) deposited in the Protein Data Bank with code 7L4I.
Structure of wild-type PPM1H phosphatase at 3.1 Angstrom resolution
By onStructure of wild-type PPM1H phosphatase at 3.1 Angstrom resolution (as reported in 10.15252/embr.202152675) deposited in the Protein Data Bank with code 7KPR.
Primary data associated with the manuscript “Genome-wide screen reveals Rab12 GTPase as 2 a critical activator of Parkinson’s disease-linked LRRK2 kinase” (2/3)
By onPrimary data associated with the manuscript, "Genome-wide screen reveals Rab12 GTPase as 2 a critical activator of Parkinson’s disease-linked LRRK2 kinase."
Proteomic data reported in doi.org/10.1073/pnas.2219953120 (Golgi-IP, a tool for multimodal analysis of Golgi molecular content)
By onProteomic data associated with doi.org/10.1073/pnas.2219953120 deposited in ProteomeXchange PRIDE repository with PID: PXD038046.
Primary data associated with the manuscript “Genome wide screen reveals Rab12 GTPase as a critical activator of pathogenic LRRK2 kinase” (doi: 10.1101/2023.02.17.529028)
By onPrimary data associated with the manuscript "Genome wide screen reveals Rab12 GTPase as a critical activator of pathogenic LRRK2 kinase"
Primary data associated with the manuscript “Parkinson’s VPS35[D620N] mutation induces LRRK2 mediated lysosomal association of RILPL1 and TMEM55B” (doi: 10.1101/2023.06.07.544051)
By onConfocal microscopy images, CellProfiler Excel files of Pearson's coefficients between TMEM55B/RILPL1 or pRab10/RILPL1 in R1441C MEF or VPS35 MEF cells as seen in doi: 10.1101/2023.06.07.544051.
Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function
By onRaw data files used for the manuscript "Glucocerebrosidase, a Parkinson´s disease-associated protein, is imported into mitochondria and regulates complex I assembly and function" https://www.researchsquare.com/article/rs-1521848/v1
Primary data associated with the manuscript “Golgi-IP, a novel tool for multimodal analysis of Golgi molecular content” (doi.org/10.1101/2022.11.22.517583)
By onRaw data files used for the manuscript "Golgi-IP, a novel tool for multimodal analysis of Golgi molecular content" (doi.org/10.1101/2022.11.22.517583).
Metabolomic and lipidomic data reported in doi.org/10.1073/pnas.2219953120 (Golgi-IP, a tool for multimodal analysis of Golgi molecular content)
By onMetabolomic and lipidomic data associated with doi.org/10.1073/pnas.2219953120 deposited in MetaboLights repository with identifier number MTBLS6511.
The GBA variant E326K is associated with alpha-synuclein aggregation and lipid droplet accumulation in human cell lines.
By onThe GBA variant E326K is associated with alpha-synuclein aggregation and lipid droplet accumulation in human cell lines (associated with publication 10.1101/2022.06.01.494130).
Crystal structure of Wild-Type PPM1H phosphatase
By onCrystal structure of WT PPM1H phosphatase (as reported in 10.15252/embr.202152675) deposited in the Protein Data Bank with code 7L4J.
Sex-specific microglial responses to glucocerebrosidase inhibition
By onMorpho-dynamic analysis occurring in primary cells derived from female and male mice in response to proinflammatory stimulations and glucocerebrosidase inhibition.
Axonal and somatodendritic proteomes of dopamine neurons in the mouse brain
By onDopamine (DA) neurons modulate neural circuits and behaviors via dopamine release from expansive, long range axonal projections. The elaborate cytoarchitecture of DA neurons is embedded within complex brain tissues, making it difficult to access the DA neuronal proteome using conventional methods. Here, we demonstrate APEX2 proximity labeling within genetically targeted neurons in the mouse brain, enabling subcellular proteomics with cell type-specificity. By combining APEX2 biotinylation with mass spectrometry, we mapped the somatodendritic and axonal proteomes of DA neurons. Our dataset reveals the proteomic architecture underlying axonal transport, dopamine transmission, and axonal metabolism in DA neurons. We find a significant enrichment of proteins encoded by Parkinson’s disease-linked genes in dopaminergic axons, including proteins with previously undescribed axonal localization. Our proteomic datasets comprise a significant resource for axonal and DA neuronal cell biology, while the methodology developed here will enable future studies of other neural cell types. This mass spectrometry proteomics dataset is a part of "Subcellular proteomics of dopamine neurons in the mouse brain" (Hobson et. al, 2022)
Structure of human ULK1 complex core (2:1:1 stoichiometry)
By onStructure of human ULK1 complex core (2:1:1 stoichiometry)
Structure of PPM1H phosphatase with manganese ions at the active site
By onStructure of PPM1H phosphatase with manganese ions at the active site (as reported in 10.15252/embr.202152675) deposited in the Protein Data Bank with code 7N0Z.
Structure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture
By onStructure of human ULK1 complex core (2:2:2 stoichiometry) in the PI3KC3-C1 mixture (Method: ELECTRON MICROSCOPY, Resolution: 5.85 Å, Aggregation State: PARTICLE, Reconstruction Method: SINGLE PARTICLE).
