PXD027725

PXD027725 is an original dataset announced via ProteomeXchange.

Title	Mapping the peptide binding groove of MHC class I
Description	An essential element of adaptive immunity is the selective binding of peptide antigens by major histocompatibility complex (MHC) class I proteins and their presentation to cytotoxic T lymphocytes on the cell surface. Using native mass spectrometry, we here analyze the binding of peptides to an empty disulfide-stabilized HLA-A*02:01 molecule. This novel approach allows us to examine the binding properties of diverse peptides. The unique stability of our MHC class I even enables us to determine the binding affinity of complexes, which are suboptimally loaded with truncated or charge-reduced peptides. Notably, a unique erucamide adduct decouples affinity analysis from peptide identity alleviating issues usually attributed to clustering. We discovered that two anchor positions at the binding surface between MHC and peptide can be stabilized independently and further analyze the contribution of other peptidic amino acids on the binding. We propose this as an alternative, likely universally applicable method to artificial prediction tools to estimate the binding strength of peptides to MHC class I complexes quickly and efficiently. This newly described MHC class I-peptide binding affinity quantitation represents a much needed orthogonal, confirmatory approach to existing computational affinity predictions and has the potential to eliminate binding affinity biases and thus accelerate drug discovery in infectious diseases autoimmunity, vaccine design, and cancer immunotherapy.
HostingRepository	PRIDE
AnnounceDate	2022-05-31
AnnouncementXML	Submission_2022-05-31_02:34:46.035.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Janine-Denise Kopicki
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q-Tof Ultima

Revision	Datetime	Status	ChangeLog Entry
0	2021-08-05 08:58:24	ID requested
⏵ 1	2022-05-31 02:34:46	announced

Dataset with its publication pending

submitter keyword: human, MHC class I, HLA-A, peptide-binding, native MS

Charlotte Uetrecht
contact affiliation	Leibniz Institute for Experimental Virology (HPI), Germany; Centre for Structural Systems Biology, Germany; 5European XFEL GmbH, Germany.
contact email	charlotte.uetrecht@xfel.eu
lab head
Janine-Denise Kopicki
contact affiliation	Leibniz Institute for Experimental Virology (HPI)
contact email	janine.kopicki@leibniz-hpi.de
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/2022/05/PXD027725

PRIDE project URI

• PRIDE
  1. PXD027725
     1. Label: PRIDE project
     2. Name: Mapping the peptide binding groove of MHC class I