PXD004971

PXD004971 is an original dataset announced via ProteomeXchange.

Title	Carbene Footprinting Accurately Maps Binding Sites in Protein-Ligand and Protein-Protein Interactions
Description	Specific interactions between proteins and their binding partners are fundamental to life processes. Differential protein footprinting using a new and efficient, photo-activated aryltrifluromethylcarbene probe together with mass spectrometry has been employed to identify protein-ligand and protein-protein interaction sites. In a model protein-small molecule system, the location of a penta-N-acetylchitopentaose carbohydrate substrate was accurately mapped to the binding cleft of lysozyme. As a fine detail, footprinting revealed disruption of an intramolecular hydrogen-bond network within lysozyme, which is known to be associated with substrate binding. In a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5, and a diubiquitin substrate were located to different functional domains thus clarifying uncertainties from an X-ray crystal structure of USP5. The much improved properties of this bespoke diazirine probe make differential carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_03:08:49.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lucio Manzi
SpeciesList	scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ FT

Revision	Datetime	Status	ChangeLog Entry
0	2016-09-14 08:07:58	ID requested
1	2016-12-21 04:52:31	announced
⏵ 2	2017-10-24 03:08:50	announced	Updated project metadata.

Manzi L, Barrow AS, Scott D, Layfield R, Wright TG, Moses JE, Oldham NJ, Carbene footprinting accurately maps binding sites in protein-ligand and protein-protein interactions. Nat Commun, 7():13288(2016) [pubmed]

curator keyword: Biological

submitter keyword: Covalent labelling, carbene footprinting, USP5, lysozyme

Neil J. Oldham
contact affiliation	School of Chemistry, University of Nottingham, Nottingham, UK
contact email	neil.oldham@nottingham.ac.uk
lab head
Lucio Manzi
contact affiliation	University of Nottingham
contact email	pcxlm5@nottingham.ac.uk
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/2016/12/PXD004971

PRIDE project URI

• PRIDE
  1. PXD004971
     1. Label: PRIDE project
     2. Name: Carbene Footprinting Accurately Maps Binding Sites in Protein-Ligand and Protein-Protein Interactions