PXD012939-2

PXD012939 is an original dataset announced via ProteomeXchange.

Title	Quantitative photo-crosslinking mass spectrometry reveals protein structure response to environmental changes
Description	Conformational changes of protein structures depend on their chemical and physical environment. Studying conformational changes depending on environmental parameters is notoriously difficult as many methods of structural biology are affected by parameters like temperature or pH. To make such conformational changes accessible to quantitative crosslinking mass spectrometry (QCLMS) approaches, crosslinking chemistry must be invariant to different conditions. We propose this can be achieved by photo-inducible crosslinkers, which are not influenced by changes in environmental parameters. Here, we introduce a workflow combining photo-crosslinking using 4,4’-azipentanoate (sulfo-SDA) with our recently developed data-independent acquisition (DIA)-QCLMS. In this study, we use this novel photo-DIA-QCLMS approach to quantify pH-dependent conformational changes in human serum albumin and cytochrome C. Both proteins show pH dependent conformational changes resulting in acidic and alkaline transitions. 93% and 95% unique residue pairs (URP) were quantifiable across triplicates for HSA and cytochrome C, respectively. Abundance changes of URPs and hence conformational changes of both proteins, were visualized using hierarchical clustering. For HSA we distinguished the N-F and the N-B form from the native conformation. Additionally, we observed for cytochrome C acidic and basic conformations. In conclusion, photo-DIA-QCLMS distinguished pH-dependent conformers of both proteins.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:53:40.726.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fränze Müller
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2019-03-04 00:39:09	ID requested
1	2019-07-01 05:52:39	announced
⏵ 2	2024-10-22 04:53:41	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: Data-independent acquisition, Structural dynamics, Human serum albumin, DIA-QCLMS,Quantitation, Xi, Cytochrome C, Spectronaut, Label-free, Mass spectrometry, Photo-crosslinking, Cross-linking, SDA

Juri Rappsilber
contact affiliation	1 Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany 2 Wellcome Centre for Cell Biology, School of Biologic Sciences, University of Edinburgh, Edinburgh
contact email	juri.rappsilber@tu-berlin.de
lab head
Fränze Müller
contact affiliation	TU Berlin
contact email	fraenze.mueller@tu-berlin.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD012939
     1. Label: PRIDE project
     2. Name: Quantitative photo-crosslinking mass spectrometry reveals protein structure response to environmental changes