PXD055402

PXD055402 is an original dataset announced via ProteomeXchange.

Title	An alkyne-containing isoprenoid analogue based on a farnesyl diphosphate scaffold is a biologically functional universal probe for proteomic analysis
Description	Prenylation consists of the modification of proteins with either farnesyl diphosphate (FPP) or geranylgeranyl diphosphate (GGPP) at a cysteine near the C-terminus of target proteins to generate thioether-linked lipidated proteins. Given the widespread involvement of prenylation in protein localization, membrane trafficking, and cellular signaling, dysregulation of prenylation and prenylated proteins have been implicated in the pathogenesis of numerous diseases. In recent work, metabolic labeling with alkyne-containing isoprenoid analogues including C15AlkOPP has been used to identify prenylated proteins and track their levels in different diseases. Here, a systematic study of the impact of isoprenoid length on proteins labeled with these probes was performed. First docking experiments were used to examine how lipid length might impact prenyltransferase selectivity. Next, chemical synthesis was used to generate two new analogues, C15hAlkOPP and C20AlkOPP, bringing the total number of compounds to four used in this study. Enzyme kinetics were used to evaluate these molecules as substrates for prenyltransferases in vitro. In cellulo metabolic labeling, enrichment and proteomic analysis were performed, resulting in the labeling of 8 proteins for C10AlkOPP (lipid length = 12 atoms), 70 proteins for C15AlkOPP (lipid length = 16 atoms), 41 proteins for C15hAlkOPP (lipid length = 17 atoms) and 7 proteins for C20AlkOPP (lipid length = 20 atoms). While C10AlkOPP was the most selective for farnesylated proteins and C20AlkOPP was most selective for geranylgeranylated proteins, the number of proteins identified using those probes was relatively small. In contrast, C15AlkOPP labeled the most proteins including representatives from all classes of prenylated proteins. Functional analysis of these analogues demonstrated that C15AlkOPP was particularly well suited for biological studies since it was efficiently incorporated in cellulo, was able to confer correct plasma membrane localization of H-Ras protein and complement the effects of GGPP depletion in macrophages to yield correct cell polarization and filopodia. Collectively, these results indicate that C15AlkOPP is a biologically functional, universal probe for metabolic labeling experiments that has minimal effects on cellular physiology.
HostingRepository	PRIDE
AnnounceDate	2025-04-08
AnnouncementXML	Submission_2025-04-07_19:12:34.483.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Shelby Auger
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	farnesylated residue; TMT6plex-126 reporter+balance reagent acylated residue; geranylgeranylated residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-30 16:01:07	ID requested
⏵ 1	2025-04-07 19:12:35	announced

10.1021/acs.biochem.4c00558;

Auger SA, Pedersen JS, Maity S, Sprague-Getsy AM, Lorimer EL, Koehn OJ, Krauklis SA, Berns B, Murphy KM, Hussain J, Thao P, Bernhagen K, Justyna K, Sundaresan AP, McKim DB, Williams CL, Hougland JL, Li L, Distefano MD, An Alkyne-Containing Isoprenoid Analogue Based on a Farnesyl Diphosphate Scaffold Is a Biologically Functional Universal Probe for Proteomic Analysis. Biochemistry, 64(1):138-155(2025) [pubmed]

submitter keyword: Prenylation, Prenylomics, Chemical Probes, Post-Translational Modifications

Distefano, Mark
contact affiliation	University of Minnesota
contact email	diste001@umn.edu
lab head
Shelby Auger
contact affiliation	University of Minnesota
contact email	auger054@umn.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD055402
     1. Label: PRIDE project
     2. Name: An alkyne-containing isoprenoid analogue based on a farnesyl diphosphate scaffold is a biologically functional universal probe for proteomic analysis