Primary data associated with doi: 10.7554/eLife.67900 (Pathogenic LRRK2 control of primary cilia and Hedgehog signaling in neurons and astrocytes of mouse brain)on
Immunofluorescence microscopy images, raw immunoblotting data and tabular data used to generate graphs shown in all figures.
Primary data associated with doi: 10.15252/embr.202152675 (Structural basis for the specificity of PPM1H phosphatase for Rab GTPases. EMBO Rep. 2021 Nov 4;22(11):e52675)on
Raw immunoblotting data; Scans of Coomassie-stained SDS-PAGE gels; Tabular data for quantifications; List of cross-links with distances; Numerical data for in vitro assays; Data files from Astra Software analysis.
Mass spectrometry proteomic data supporting the PPM1H/Rab8A crosslinking study described in doi: 10.15252/embr.202152675on
Mass spectrometry proteomic data supporting the PPM1H/Rab8A crosslinking study described in doi: 10.15252/embr.202152675, deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD026367
Plasmid for bacterial expression of human PPM1H (H153D); contains TEV protease site for removal of 6His tag.
Preprint: The authors develop a novel approach for deriving the time-varying functional connectivity of cortical networks and show this information encodes rapid fluctuations in behavioral state.
Review: Several mutations of genes that encode proteins localized at the endoplasmic reticulum membrane contact sites result in familial neurodegenerative diseases. Here, the authors provide an overview of such diseases, with a specific focus on proteins that directly or indirectly impact lipid transport.
Published: This study investigated the relationship between neuronal activity and interneuronal transfer of α-synuclein, a Parkinson-associated protein, and elucidated mechanisms underlying this relationship.
Genetic variations in GBA1 and LRRK2 genes: Biochemical and clinical consequences in Parkinson diseaseon
Review: This review compares GBA1 and LRRK2-associated PD, and highlights possible genotype-phenotype associations for GBA1 and LRRK2 separately, based on biochemical consequences of single variants.
Review: This paper highlights new findings related to LRRK2-mediated phosphorylation of Rab GTPases and their consequences.
Python script used to generate the heatmap representation of identified LRRK1 phosphosites reported in doi: 10.1042/BCJ20220308on
Python script used to generate the heatmap representation of identified high-confident LRRK1 phosphosites reported in doi: 10.1042/BCJ20220308. It contains the data used for analysis as well as the necessary FASTA sequences for mapping of phosphosite positions on peptides to the original protein sequence.
Protocol for Data Independent Acquisition – Mass spectrometry analysis – a DIA-based Organelle Proteomicson
This protocol details a Data Independent Acquisition (DIA)-based mass spectrometry (MS) data acquisition method for proteomic profiling of the Golgi, including a description of how to construct the nano Liquid chromatography and DIA MS methods and a Data Dependent Acquisition (DDA) strategy to generate deep spectral libraries for searching the DIA data.
Raw 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: 10.1101/2022.04.25.489459 (A Feed-forward Pathway Drives LRRK2 kinase Membrane Recruitment and Apparent Activation)on
Raw immunoblotting data; tabular data for quantifications; immunofluorescence images.
Primary data associated with doi: 10.1042/BCJ20220308 (PKC isoforms activate LRRK1 kinase by phosphorylating conserved residues (Ser1064, Ser1074 and Thr1075) within the CORB GTPase domain)on
Raw immunoblotting data; immunofluorescence microscopy images; tabular data for quantification; autoradiograph films; scans of Coomassie-stained protein gels; Prism files with statistical analysis.
Primary data associated with doi: 10.1042/BCJ20220161 (Impact of 100 LRRK2 variants linked to Parkinson’s Disease on kinase activity and microtubule binding)on
Raw immunoblotting data; tabular data for quantifications; numerical data for in vitro assays; immunofluorescence images; Prism files for statistical analysis.
This protocol describes how Golgi, isolated from cells by GolgiTAG immunoprecipitation (IP) (as described in dx.doi.org/10.17504/protocols.io.6qpvrdjrogmk/v1), can be prepared and imaged using TEM. This protocol can also be used to image any organelles isolated using various organelle-IP protocols that are available.
Immunofluorescence imaging of cells expressing GolgiTAG (TMEM115-3HA) or HA-tagged non-Golgi annotated proteinson
This method that can be used to verify the correct localisation of HA-tagged Golgi proteins (like TMEM115-3HA, or GolgiTAG), by assessing their colocalisation with known Golgi markers such as GM130, GOLGIN97 and ACBD3 or can be used to assess if HA-tagged, non-Golgi annotated proteins transiently expressed in cells localise at the Golgi.
This protocol describes an immunoblotting method to assess efficient enrichment of Golgi proteins in Golgi immunoprecipitation products compared to whole cell lysates and the purity of the immunoprecipitated Golgi by monitoring the expression of other organelles’ markers. This method can also be used to verify the expression of GolgiTAG (TMEM115-3HA) in cells.
This protocol details how to generate stable cell lines using a retrovirus system (can also be used for lentivirus systems) and includes the production of retroviruses encoding the transgene of interest in HEK293FT and the subsequent transduction of the cell line that is intended to stably express the protein of interest.
Crystal structure of WT PPM1H phosphatase (as reported in 10.15252/embr.202152675) deposited in the Protein Data Bank with code 7L4J.