PXD016529

PXD016529 is an original dataset announced via ProteomeXchange.

Title	Nucleolin uses its RBD2 domain to recognize long-loop G-Quadruplexes from human minisatellite CEB25
Description	We investigated herein the interaction between nucleolin (NCL) and a set of G4 sequences derived from the CEB25 human minisatellite which adopt a parallel topology while differing by the length of the central loop (from 9nt to1nt). It is revealed that NCL strongly binds to long-loop (9-5 nt) G4 whilst interacting weakly with the shorter variants (loop < 3nt). Photocrosslinking experiments using 5-bromouracil (BrdU) modified sequences further confirmed the loop-length dependency thereby indicating that the CEB25-WT (9nt) is the best G4 substrate. Quantitative proteomic analysis (LC-MS/MS) of the photocrosslinking product(s) obtained with NCL bound to this sequence enabled the identification of one contact site within the 9nt loop. The protein fragment identified is located in the helix of the RBD2 domain of NCL, shedding light on the role of this structural element in the G4-loop recognition. Then, the ability of a panel of benchmark G4 ligands to prevent the NCL/G4 interaction was explored. It was found that only the most potent ligand PhenDC3 is able to inhibit NCL binding, thereby suggesting that the terminal guanine quartet is also a strong determinant of G4 recognition, putatively through interaction with the RGG domain. This study puts forward the molecular mechanism by which NCL recognizes G4-containing long loops and leads to propose a model implying a concerted action of RBD2 and RGG domains to achieve specific G4 recognition via a dual loop-quartet interaction.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:01:09.685.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Valentin SABATET
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-29 03:02:44	ID requested
1	2020-03-19 08:31:37	announced
2	2020-03-24 08:00:43	announced	2020-03-24: Updated publication reference for PubMed record(s): 32191439.
⏵ 3	2024-10-22 05:01:11	announced	2024-10-22: Updated project metadata.

10.1021/acs.biochem.9b01094;

Saha A, Duchambon P, Masson V, Loew D, Bombard S, Teulade-Fichou MP, Nucleolin Discriminates Drastically between Long-Loop and Short-Loop Quadruplexes. Biochemistry, 59(12):1261-1272(2020) [pubmed]

submitter keyword: RNA binding domain, G4-ligands, proteomics, G-Quadruplex, RGG domain, photo-crosslinking,Nucleolin, long loop

Damarys Loew
contact affiliation	Head of the Curie Institute Mass Spectrometry Platform
contact email	damarys.loew@curie.fr
lab head
Valentin SABATET
contact affiliation	Curie Institute
contact email	valentin.sabatet@curie.fr
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/2020/03/PXD016529

PRIDE project URI

• PRIDE
  1. PXD016529
     1. Label: PRIDE project
     2. Name: Nucleolin uses its RBD2 domain to recognize long-loop G-Quadruplexes from human minisatellite CEB25