PXD047098-1

PXD047098 is an original dataset announced via ProteomeXchange.

Title	Structural dynamics of Na+ and Ca 1 2+ interactions with full-size mammalian NCX
Description	NCX proteins (Na+/Ca2+ exchangers) are allosterically regulated by cytosolic Ca2+ and Na+ to feedback ion signaling in diverse cell types. The recently discovered cryo-EM structure of the cardiac NCX1.1 provided breakthrough information on the mammalian NCX structure, although the structure-dynamic basis of allosteric regulation remains unresolved. Here, we analyzed the apo, Ca2+-, and Na+ -bound species of the brain NCX1.4 variant using hydrogen-deuterium exchange mass spectrometry (HDX-MS) in conjunction with molecular dynamics (MD) simulations. We show that Ca2+ binding to the regulatory CBD domains dramatically rigidifies the intracellular regulatory loop (5L6) and promotes its interaction with the membrane. Either Na+ or Ca2+ stabilizes the intracellular portions of TM3, TM4, TM9, TM10, and their connecting loops (3L4 and 9L10), exposing a putative cation binding site for allosteric regulation. Either Ca2+ or Na+ rigidifies TMH2, encompassing the palmitoylation domain, and the neighboring two-helix TM1/TM6 bundle(governing the alternating access transitions) to control the ion transport rates. Collectively, our results uncovered important details of allosteric regulation in mammalian NCX, while highlighting structure-dynamic features of functional regions not resolved in the cryo-EM structure. The present outcomes provide useful clues toward resolving the structure-dynamic determinants of regulatory diversity in NCX isoform/splice variants.
HostingRepository	PRIDE
AnnounceDate	2024-04-17
AnnouncementXML	Submission_2024-04-16_23:07:31.318.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lukas Fojtik
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue
Instrument	Bruker Daltonics timsTOF series

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-20 05:44:08	ID requested
⏵ 1	2024-04-16 23:07:31	announced

10.1038/S42003-024-06159-9;

submitter keyword: NCX, Membrane proteins, molecule dynamics, Mass spectrometry, ion transporters

Petr Man
contact affiliation	Institute of Microbiology of the Czech Academy of Sciences, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic
contact email	pman@biomed.cas.cz
lab head
Lukas Fojtik
contact affiliation	Institute of Microbiology of the Czech Academy of Sciences, Division BioCeV, Prumyslova 595, 252 50 Vestec, Czech Republic
contact email	fojtikl@natur.cuni.cz
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD047098
     1. Label: PRIDE project
     2. Name: Structural dynamics of Na+ and Ca 1 2+ interactions with full-size mammalian NCX