PXD041152-1

PXD041152 is an original dataset announced via ProteomeXchange.

Title	Tapioca – A Novel Platform for Prediction Of Protein-Protein Interaction Dynamics Identifies NUCKS1 as a Broad-Spectrum Herpesvirus Proviral Factor
Description	Understanding protein-protein interaction (PPI) network dynamics is key to understanding nominal and perturbed cell states. Here, we develop a new machine learning framework called Tapioca that allows for the study of PPIs in dynamics contexts at a global scale in ex/in vivo conditions. Furthermore, we optimized the thermal denaturation and lysis conditions used in the thermal proximity coaggregation (TPCA) methodology, one of the types of data Tapioca can use to make predictions. Using this optimized protocol and Tapioca, we investigated the temporal dynamics of reactivation from latency of the oncogenic gammaherpesvirus Kaposi’s sarcoma-associated herpesvirus (KSHV), identifying the host protein NUCKS1 as a factor promoting KSHV genome replication during lytic infection. Integrating this dataset with published TPCA datasets from the alphaherpesvirus herpes simplex virus type-1 (HSV-1) and the betaherpesvirus human cytomegalovirus (HCMV), we determined NUCKS1 to have a proviral role across all three herpesvirus subfamilies.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_12:56:58.439.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD041152
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Tavis Reed
SpeciesList	scientific name: Human herpesvirus 8 strain GK18; NCBI TaxID: 868565; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-27 21:38:07	ID requested
⏵ 1	2025-05-06 12:56:59	announced

10.6019/PXD041152;

Reed TJ, Tyl MD, Tadych A, Troyanskaya OG, Cristea IM, Tapioca: a platform for predicting de novo protein-protein interactions in dynamic contexts. Nat Methods, 21(3):488-500(2024) [pubmed]

10.1038/s41592-024-02179-9;

submitter keyword: Human, KSHV, Herpesvirus, Thermal Proximity Coaggregation

Ileana M.
contact affiliation	Princeton University, Department of Molecular Biology
contact email	icristea@princeton.edu
lab head
Tavis Reed
contact affiliation	Princeton University
contact email	tjreed@princeton.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/2025/05/PXD041152

PRIDE project URI

• PRIDE
  1. PXD041152
     1. Label: PRIDE project
     2. Name: Tapioca – A Novel Platform for Prediction Of Protein-Protein Interaction Dynamics Identifies NUCKS1 as a Broad-Spectrum Herpesvirus Proviral Factor