Protein digestion and mass spectrometry analysis protocol
By Emma Sherrell onThis protocol details a protocol for the trypsin digestion of PI3KC3-C1 and subsequent analysis of digested peptides using LC-MS/MS.
Plasmid construction protocol
By Emma Sherrell onThis protocol details plasmid construction in general terms for the insertion of genes into the pCAG mammalian expression vector.
Preparing mitochondrial samples for immunoblot analysis
By Emma Sherrell onProtocol for preparation of mitochondrial samples for immunoblot analysis.
Molecular dynamics simulations
By Emma Sherrell onThis protocol details molecular dynamics simulations of PI3KC3-C1 on a lipid membrane.
HPLC analysis of nucleotides
By Emma Sherrell onIon-pair reversed phase HPLC analysis of the nucleotide bound to PI3KC3-C1.
Electrospray ionization analysis of eluted nucleotides
By Emma Sherrell onThis protocol describes the denaturation of PI3KC3-C1, and subsequent analysis of eluted nucleotides by electrospray ionization mass spec.
Cryo-EM sample preparation for PI3KC3-C1~RAB1A complex
By Emma Sherrell onThis protocol details cryo-EM sample preparation for PI3KC3-C1~RAB1A complex.
Jensen_etal_2022_molecular_dynamics_simulation_data_2
By Emma Sherrell onFull molecular dynamics simulation data set accompanying Jensen et al, 2022, containing (i) representative coordinates and measurements described therein, (ii) simulation trajectories, and (iii) GROMACS input files.
Structural pathway for class III PI 3-kinase activation by the myristoylated GTP-binding pseudokinase VPS15
By Emma Sherrell onPreprint: The class III phosphatidylinositol (PI) 3-kinase complexes I and II (PI3KC3-C1 and -C2) are central to the initiation of macroautophagy and endosomal maturation, respectively. These results provide a pathway of general mechanism for PI3KC3 activation in autophagy and endosome biogenesis and a roadmap for their pharmacological upregulation.
Cell culture
By Emma Sherrell onThis protocol describes routine cell culture maintenance as described in Adriaenssens & Nguyen et al., 2023 (BioRxiv).
Plasmid construction and Gibson cloning
By Emma Sherrell onThis protocol describes plasmid construction as described in Adriaenssens & Nguyen et al., 2023 (BioRxiv).
Control of mitophagy initiation and progression by the TBK1 adaptors NAP1 and SINTBAD
By Emma Sherrell onPreprint: The authors'results thus define NAP1 and SINTBAD as cargo receptor rheostats, elevating the threshold for mitophagy initiation by OPTN while promoting the progression of the pathway once set in motion by supporting NDP52. These findings shed light on the cellular strategy to prevent pathway hyperactivity while still ensuring efficient progression.
Temporal landscape of mitochondrial proteostasis governed by the UPRmt_NGS data_Part 2
By Emma Sherrell onPart 2 of NGS data associated with Uoselis et al., 2023.
Temporal landscape of mitochondrial proteostasis governed by the UPRmt_NGS data_Part 1
By Emma Sherrell onNGS data associated with Uoselis et al., 2023.
Temporal landscape of mitochondrial proteostasis governed by the UPRmt
By Emma Sherrell onThis study defines the network of proteostasis mediated by the UPRmt and highlights the value of functional proteomics in decoding stressed proteomes.
Immunofluorescence assay (IFA)
By Emma Sherrell onProtocol for performing an immunofluorescence assay with fixed HeLa cells.
qRT-PCR sample preparation
By Emma Sherrell onProtocol for qRT-PCR sample preparation for analysis using a RotorGeneQ machine (Qiagen).
Analyzing oxygen consumption of isolated mitochondria using the Seahorse XFe96 analyzer
By Emma Sherrell onProtocol for analyzing oxygen consumption of isolated mitochondria using the Seahorse XFe96 analyzer.
Analyzing cellular ATP levels
By Emma Sherrell onProtocol for analysis of cellular ATP levels using the Promega Mitochondrial ToxGlo Kit.
