PXD015435

PXD015435 is an original dataset announced via ProteomeXchange.

Title	Mass spectrometry study of formaldehyde cross-linking of structured proteins
Description	Formaldehyde is a widely used fixative in biology and medicine. The current chemical model for formaldehyde cross-linking of proteins is the formation of a methylene bridge that incorporates one carbon atom into the link. Here, we present mass spectrometry data that largely refute this model. Instead, our data show that cross-linking of structured proteins mainly involves a reaction that incorporates two carbon atoms into the link. Under MS/MS fragmentation, the link cleaves symmetrically to yield unusual fragments with a modification of one carbon atom. We apply this new understanding of the underlying cross-linking chemistry to the structural approach of cross-linking coupled to mass spectrometry. First, we cross-linked a mixture of purified proteins with formaldehyde. Our new analysis readily identified tens of cross-links from these proteins, which fit well with their atomic structures. We then perform in-situ cross-linking of human cells in culture. We identified 469 intra-protein and 90 inter-protein cross-links, which also fit well with available atomic structures. Interestingly, many of these cross-links could not be mapped onto a known structure and thus provide new structural insights. We highlight an example in which formaldehyde cross-links localize the binding site of βNAC on the ribosome. We also find several interactions of actin with auxiliary proteins. Our findings not only expand our understanding of formaldehyde reactivity and toxicity, but also clearly demonstrate how to use this potent reagent for structural studies.
HostingRepository	PRIDE
AnnounceDate	2020-06-25
AnnouncementXML	Submission_2020-06-24_23:09:56.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nir Kalisman
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-09-12 08:40:35	ID requested
⏵ 1	2020-06-24 23:09:57	announced

Tayri-Wilk T, Slavin M, Zamel J, Blass A, Cohen S, Motzik A, Sun X, Shalev DE, Ram O, Kalisman N, Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins. Nat Commun, 11(1):3128(2020) [pubmed]

submitter keyword: Cross-linking coupled to mass spectrometry, XL-MS, Actin, Nascent polypeptide-associated complex, Structural biology

Nir Kalisman
contact affiliation	Dept. of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
contact email	nirka@mail.huji.ac.il
lab head
Nir Kalisman
contact affiliation	Dept. of Biological Chemistry, The Hebrew University of Jerusalem
contact email	nirka@mail.huji.ac.il
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/2020/06/PXD015435

PRIDE project URI

• PRIDE
  1. PXD015435
     1. Label: PRIDE project
     2. Name: Mass spectrometry study of formaldehyde cross-linking of structured proteins