PXD041269

PXD041269 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	PanoramaPublic
AnnounceDate	2023-12-02
AnnouncementXML	Submission_2023-12-02_23:42:22.329.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Matthew Tyl
SpeciesList	scientific name: Human herpesvirus 8 strain GK18; NCBI TaxID: 868565; scientific name: Homo sapiens; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-04-01 13:21:24	ID requested
⏵ 1	2023-12-02 23:42:22	announced

Dataset with its publication pending

submitter keyword: TPCA, IP, PRM, KSHV

Ileana Cristea
contact affiliation	Department of Molecular Biology, Princeton University
contact email	icristea@princeton.edu
lab head
Matthew Tyl
contact affiliation	Department of Molecular Biology, Princeton University
contact email	mtyl@princeton.edu
dataset submitter

Panorama Public dataset URI