Catalog

ASAP is committed to accelerating the pace of discovery and informing a path to a cure for Parkinson’s disease through collaboration, research-enabling resources, and data sharing. We’ve created this catalog to showcase the research outputs and tools developed by ASAP-funded programs.

Article

ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA-dependent STING signaling

Published: Mutations in VPS13C cause early onset, autosomal recessive PD. VPS13C encodes a lipid transfer protein that is localized to ER-endosome/lysosome contact sites. The authors demonstrate that depletion of VPS13C causes an accumulation of lysosomes and activated STING, suggesting a link between ER-lysosome lipid transfer and innate immune activation. View original preprint.

Protocol

Cell culture on EM grids and fluorescence microscopy imaging

This protocol describes the general procedure of seeding mammalian cells on EM grids and confocal fluorescence microscopy imaging of grids for subsequent cryo-tomography experiments, performed.

Protocol

Regular maintenance of human pluripotent stem cells

This protocol describes the regular maintenance and passaging human iPSCs.

Article

Mitoguardin-2–mediated lipid transfer preserves mitochondrial morphology and lipid droplet formation

Published: Lipid transport at membrane contact sites is a critical biological process. The authors identify mitoguardin-2, a mitochondrial protein that functions as a lipid transporter at contact sites between the ER and/or lipid droplets. They show that mitoguardin-2 transfers glycerophospholipids between membranes in vitro.

Lab Resource

mCh-Miro1(∆TM)-SspB

mCh-Miro1(∆TM)-SspB plasmid has a deletion of transmembrane domain and is used for improved light inducible dimer assay.
 

Protocol

RNA isolation and qRT-PCR

This protocol describes the RNA isolation from cultured cells and quantitative RT PCR.

Protocol

siRNA-mediated knockdown of TFE3

This protocol details siRNA-mediated knockdown of TFE3.

Protocol

Transfection and protein over-expression

This protocol provides the details for how to transfect and harvest 3X-FLAG-SHIP164Δ901-1099.

Lab Resource

VPS13C^halo∆1235-1748

Express VPS13C truncation mutant in mammalian cells (VPS13C^halo∆1235-1748).

Protocol

Surface protein biotinylation

This protocol describes surface protein labeling with biotin using EZ-Link Sulfo-NHSLC-Biotin. This chemical reacts with primary amines such as lysine but does not permeate cell membranes because of the charge. Thus, it only biotinylates surface proteins.

Protocol

Subtomogram averaging and classification

This protocol describes the procedure of subtomogram averaging and 3D classification of VPS13C rod-shaped densities inside cryotomograms of mammalian cells. Sub-tomogram averaging package i3 was used for 3D alignment and classification.

Article

In situ architecture of the lipid transport protein VPS13C at ER-lysosomes membrane contacts

Publication: Loss-of-function mutations in VPS13C are responsible for rare cases of familial early onset Parkinson’s disease. Using cryo-ET, the authors provide in-situ evidence for a bridge-model of VPS13 in lipid transport. View the original preprint.

Protocol

Crystallization, data collection and structure solution of PxP-VAB

Protocol lists the steps to obtain PxP(Mcp1ct)-VABct crystals, X-ray diffraction data acquisition and obtaining the structure solution using molecular replacement with a model generated by AlphaFold2.