Proteomics

Dataset Information

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Nanodiscs-based proteomics to identify lipid-interacting proteins in yeast


ABSTRACT: Many soluble proteins interact with membranes to perform important biological functions, including signal transduction, regulation, transport, trafficking and biogenesis. Despite their importance, these protein-membrane interactions are difficult to characterize due to their often-transient nature as well as phospholipids’ poor solubility in aqueous solution. Here, we employ nanodiscs – small, water-soluble patches of lipid bilayer encircled with amphipathic scaffold proteins – along with quantitative proteomics to identify lipid-binding proteins in S. cerevisiae. Using nanodiscs reconstituted with yeast total lipid extracts or only phosphatidylethanolamine (PE-nanodiscs), we capture several known membrane-interacting proteins, including the Rab GTPases Sec4 and Ypt1, which play key roles in vesicle trafficking. Utilizing PE-nanodiscs enriched with phosphatidic acid (PEPA-nanodiscs), we specifically capture a member of the Hsp40/J-protein family, Caj1, whose function has recently been linked to membrane protein quality control. We show that Caj1 interaction with liposomes containing PA is modulated by pH and PE lipids, and depends on two patches of positively charged residues near the C-terminus of the protein. The protein Caj1 is the first example of an Hsp40/J-domain protein with affinity for membranes and phosphatidic acid lipid specificity. These findings highlight the utility of the nanodisc system to identify and characterize protein-lipid interactions that may not be evident using other methods.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: John Young  

LAB HEAD: Franck Duong

PROVIDER: PXD027992 | Pride | 2021-12-30

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
Caj1_Supp_File_1_June_17_FINAL.xlsx Xlsx
Nd-PEPA_rep2.RAW Raw
Nd-PE_rep2.RAW Raw
Nd-Yeast_rep1.RAW Raw
Nd-Yeast_rep2.RAW Raw
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Publications

Nanodisc-Based Proteomics Identify Caj1 as an Hsp40 with Affinity for Phosphatidic Acid Lipids.

Zhang Xiao X XX   Young John William JW   Foster Leonard J LJ   Duong Franck F  

Journal of proteome research 20210914 10


Many soluble proteins interact with membranes to perform important biological functions, including signal transduction, regulation, transport, trafficking, and biogenesis. Despite their importance, these protein-membrane interactions are difficult to characterize due to their often-transient nature as well as phospholipids' poor solubility in aqueous solution. Here, we employ nanodiscs-small, water-soluble patches of a lipid bilayer encircled with amphipathic scaffold proteins-along with quantit  ...[more]

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