PXD037413

PXD037413 is an original dataset announced via ProteomeXchange.

Title	Ligand binding and conformational dynamics of the E. coli nicotinamide nucleotide transhydrogenase revealed by hydrogen/deuterium exchange mass spectrometry
Description	Nicotinamide nucleotide transhydrogenases are integral membrane proteins that utilizes the proton motive force to reduce NADP+ to NADPH while converting NADH to NAD+. Atomic structures of various transhydrogenases in different ligand-bound states have become available, and it is clear that the molecular mechanism involves major conformational changes. Here we utilized hydrogen-deuterium-exchange mass spectrometry (HDX-MS) to map ligand binding sites and analyzed the structural dynamics of E. coli transhydrogenase. We found different allosteric effects on the protein depending on the bound ligand (NAD+, NADH, NADP+, NADPH). The binding of either NADP+ or NADPH to domain III had pronounced effects on the transmembrane helices comprising the proton-conducting channel in domain II. We also made use of cyclic ion mobility separation mass spectrometry (cyclic IMS-MS) to maximize coverage and sensitivity in the transmembrane domain, showing for the first time that this technique can be used for HDX-MS studies. Using cyclic IMS-MS, we increased sequence coverage from 68% to 73% in the transmembrane segments. Taken together, our results provide important new insights into the transhydrogenase reaction cycle and demonstrate the benefit of this new technique for HDX-MS to study ligand binding and conformational dynamics in membrane proteins.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_07:55:34.732.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Julian Langer
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2022-10-14 04:40:25	ID requested
1	2022-10-26 04:35:38	announced
⏵ 2	2023-11-14 07:55:35	announced	2023-11-14: Updated project metadata.

Z, ö, ller J, Hong S, Eisinger ML, Anderson M, Radloff M, Desch K, Gennis R, Langer JD, nicotinamide nucleotide transhydrogenase revealed by hydrogen/deuterium exchange mass spectrometry. Comput Struct Biotechnol J, 20():5430-5439(2022) [pubmed]

submitter keyword: channel opening,Membrane Protein, small ligand binding, HDX-MS, Cyclic IMS‑MS

Julian Langer
contact affiliation	Proteomics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
contact email	julian.langer@biophys.mpg.de
lab head
Julian Langer
contact affiliation	MPIs for Biophysics and Brain Research
contact email	julian.langer@biophys.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD037413
     1. Label: PRIDE project
     2. Name: Ligand binding and conformational dynamics of the E. coli nicotinamide nucleotide transhydrogenase revealed by hydrogen/deuterium exchange mass spectrometry