PXD021393

PXD021393 is an original dataset announced via ProteomeXchange.

Title	Multivalent lipid targeting by the calcium-independent C2A domain of Slp-4/granuphilin
Description	Synaptotagmin-like protein 4 (Slp-4), also known as granuphilin, is a Rab effector responsible for docking insulin secretory vesicles to the plasma membrane prior to exocytosis. Slp-4 binds vesicular Rab proteins via an N-terminal Slp homology (SHD) domain, interacts with plasma membrane SNARE complex proteins via a central linker region, and contains tandem C-terminal C2 domains (C2A and C2B) with affinity for phosphatidylinositol-(4,5)-bisphosphate (PIP2). Its C2A domain has previously been shown to bind PIP2 or its soluble analogues with low micromolar affinity; however, the domain docks with low nanomolar apparent affinity to PIP2 in lipid vesicles that also contain background anionic lipids such as phosphatidylserine (PS). Here we show using a combination of computational and experimental approaches that this high-affinity membrane interaction arises from concerted interaction at multiple sites on the C2A domain. In addition to the previously identified, PIP2-selective lysine cluster, a larger cationic surface surrounding the cluster contributes substantially to the affinity for physiologically relevant lipid compositions. While mutations at the PIP2-selective site decreases affinity for PIP2, multiple mutations are needed to decrease binding to physiologically relevant lipid compositions. Docking and molecular dynamics simulations indicate several conformationally flexible loops that contribute to the nonspecific cationic surface. In addition, we identify and characterize a covalently modified variant in the bacterially expressed protein, which arises through reactivity of the PIP2-binding lysine cluster with endogenous bacterial compounds and has a low membrane affinity. Overall, multivalent lipid binding by the Slp-4 C2A domain provides selective recognition and high affinity docking of large dense-core secretory vesicles to the plasma membrane.
HostingRepository	PRIDE
AnnounceDate	2024-10-08
AnnouncementXML	Submission_2024-10-08_11:18:46.693.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cole Michel
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	6520A Quadrupole Time-of-Flight LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2020-09-10 01:38:09	ID requested
⏵ 1	2024-10-08 11:18:47	announced

10.1074/jbc.ra120.014618;

Alnaas AA, Watson-Siriboe A, Tran S, Negussie M, Henderson JA, Osterberg JR, Chon NL, Harrott BM, Oviedo J, Lyakhova T, Michel C, Reisdorph N, Reisdorph R, Shearn CT, Lin H, Knight JD, Multivalent lipid targeting by the calcium-independent C2A domain of synaptotagmin-like protein 4/granuphilin. J Biol Chem, 296():100159(2021) [pubmed]

submitter keyword: granuphilin,Intact Protein, phosphogluconate, LCMS

Cole Robert Michel
contact affiliation	Residorph Lab, Mass Spectrometry Core - Skaggs School of Pharmacy, University of Colorado - Anschutz Medical Campus
contact email	cole.michel@cuanschutz.edu
lab head
Cole Michel
contact affiliation	Univeristy of Colorado - Skaggs School of Pharmacy
contact email	cole.michel@cuanschutz.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/12/PXD021393

PRIDE project URI

• PRIDE
  1. PXD021393
     1. Label: PRIDE project
     2. Name: Multivalent lipid targeting by the calcium-independent C2A domain of Slp-4/granuphilin