Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effects of ATP binding on the conformational flexibility of proNGF

ABSTRACT: Nerve growth factor (NGF) is involved in the maintenance and growth of specific neuronal populations whereas its precursor, proNGF, shows opposite properties, like being involved in apoptosis. NGF/proNGF imbalance is linked to neurodegeneration. Here, we show that ATP binds to proNGF inducing an overall proNGF shape change, throughout a local conformational rearrangement of the flexible pro-peptide domain. This suggests a functional role for ATP in the modulation of proNGF/NGF physiological homeostasis.

INSTRUMENT(S): Synapt MS

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Antonio Calabrese

LAB HEAD: Antonio Calabrese

PROVIDER: PXD035625 | Pride | 2023-11-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Distinct conformational changes occur within the intrinsically unstructured pro-domain of pro-Nerve Growth Factor in the presence of ATP and Mg<sup>2</sup>.

Paoletti Francesca F Covaceuszach Sonia S Cassetta Alberto A Calabrese Antonio N AN Novak Urban U Konarev Petr P Grdadolnik Jože J Lamba Doriano D Golič Grdadolnik Simona S

Protein science : a publication of the Protein Society 20230201 2

Nerve growth factor (NGF), the prototypical neurotrophic factor, is involved in the maintenance and growth of specific neuronal populations, whereas its precursor, proNGF, is involved in neuronal apoptosis. Binding of NGF or proNGF to TrkA, p75<sup>NTR</sup> , and VP10p receptors triggers complex intracellular signaling pathways that can be modulated by endogenous small-molecule ligands. Here, we show by isothermal titration calorimetry and NMR that ATP binds to the intrinsically disordered pro- ...[more]

PMID: 36605018

Similar Datasets

HDX-MS data of BAM and SurA binding

Project description:We present HDX-MS data of the BAM:SurA complex to define the interaction sites for SurA on BAM and vice versa.

2022-07-12 | PXD030268 | Pride

Inter-domain dynamics in the chaperone SurA and multi-site binding to its unfolded outer membrane protein clients revealed by HDX-MS

Project description:We present HDX-MS data of apo-SurA, SurA in complex with OmpX, OmpF and a peptide with sequence WEYIPNV to define (1) interdomain dynamics in the periplasmic chaperone SurA, and (2) the binding site of OmpX, OmpF and WEYIPNV on SurA.

2020-05-22 | PXD017010 | Pride

Fusidic acid resistance through changes in the dynamics of EF-G

Project description:HDX-MS was used to study the binding of FusB to EF-G

2020-10-15 | PXD017491 | Pride

HDX-MS of NicA2 and a NicA2 variant with increased activity

Project description:Here we have used HDX-MS to investigate the change in structure/dynamics in NicA2 and a variant with increased activity (v321) that was generated using directed evolution

2023-11-16 | PXD037151 | Pride

Binding of a bovine ultralong CDRH3 to the SARS-CoV RBD

Project description:Here, we have used a SARS-naïve, bovine ultralong CDRH3 library to isolate a bovine paratope that engages the SARS-CoV and SARS-CoV-2 receptor-binding domain (RBD). This scFv (B9-scFv) neutralises viruses pseudo-typed with SARS-CoV Spike protein. Using differential hydrogen-deuterium exchange mass spectrometry and site-directed mutagenesis, we demonstrate that this CDRH3 recognises a conserved, cryptic epitope.

2023-03-11 | PXD032965 | Pride

Tension mediated mechanical activation and pocket delipidation lead to an analogous MscL channel state

Project description:We present HDX-MS data of WT and L89W TbMscL to interrogate the mechanism of molecular activation in this mechanosensitive channel.

2022-06-07 | PXD021983 | Pride

HDX-MS on secondary transporters

Project description:Secondary transporters undergo structural rearrangements to catalyze substrate translocation across the cell membrane – yet how such conformational changes happen within a lipid environment remains poorly understood. Here, we combine hydrogen-deuterium exchange mass spectrometry (HDX-MS) with molecular dynamics (MD) simulations to understand how lipids regulate the conformational dynamics of secondary transporters at the molecular level. Using the homologous transporters XylE, LacY and GlpT from Escherichia coli as model systems, we discover that conserved networks of charged residues act as molecular switches that drive the conformational transition between different states. We reveal that these molecular switches are regulated by interactions with surrounding phospholipids and show that phosphatidylethanolamine interferes with the formation of the conserved networks and favors an inward-facing state. Overall, this work provides insights into the importance of lipids in shaping the conformational landscape of an important class of transporters.

2018-10-16 | PXD011060 | Pride

HDX-MS of CSN-CRL2 complexes - Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome

Project description:Cullin-Ring E3 Ligases (CRLs) regulate a multitude of cellular pathways through specific substrate receptors. The COP9 signalosome (CSN) deactivates CRLs by removing NEDD8 (N8) from activated Cullins. The structure of stable CSN-CRL can be used to understand this mechanism of regulation. Here we present the first structures of the neddylated and deneddylated CSN-CRL2 complexes by combining single particle cryo-electron microscopy (cryo-EM) with chemical cross-linking mass spectrometry (MS). These structures reveal a conserved mechanism of CSN activation, consisting of conformational clamping of the CRL2 substrate by CSN2/CSN4, release of the catalytic CSN5/CSN6 heterodimer and finally activation of the CSN5 deneddylation machinery. Using hydrogen deuterium exchange-MS we show that CRL2 binding and conformational activation of CSN5/CSN6 occur in a neddylation-independent manner. The presence of NEDD8 is required to activate the CSN5 active site. Overall, by synergising cryo-EM with MS, we identified novel sensory regions of the CSN that mediate its stepwise activation mechanism and provide a framework for better understanding the regulatory mechanism of other Cullin family members.

2019-09-13 | PXD013001 | Pride

Distinct dynamics upon substrate and inhibitor binding to a secondary transporter

Project description:The bacterial sugar transporter XylE is a proton-coupled symporter from the Major Facilitator Family (MFS) that has been crystalized in multiple conformations, and with both substrate xylose and inhibitor glucose bound. However, this series of static pictures does not capture the coupling between ligand binding and conformational changes required for transport. Furthermore, the ability for the transporter to discriminate between substrate and inhibitor is puzzling in light of the similarity of the bound structures. Here, we combine differential HDX-MS with mutagenesis and MD simulations to dissect the molecular mechanism of transport in XylE. We show that protonation of D27 is a key event for conformational transition from outward-facing (OF) to inward-facing (IF). Strikingly, this transition only occurs in the presence of substrate xylose, while inhibitor glucose locks the transporter in the OF state. We corroborate our experimental findings with MD simulations by showing that D27 protonation in the presence of xylose, but not glucose, leads to unstable substrate binding, increased solvent accessibility, and correlated motions between the N- and C- lobes of the transporter, effectively setting the transporter up for the conformational transition. Overall, we demonstrate the unique ability of HDX-MS to distinguish between the conformational dynamics of inhibitor and substrate binding to XylE and propose that the allosteric coupling between ligand binding and protonation is a key step to initiate transport.

2021-03-23 | PXD018145 | Pride

Unravelling the mechanism of neurotensin recognition by neurotensin receptor 1

Project description:The conformational ensembles of G-protein coupled receptors (GPCRs) include inactive and active states. Spectroscopy techniques, including NMR, show that agonists, antagonists and other ligands shift the ensemble toward specific states depending on the pharmacological efficacy of the ligand. How receptors recognize ligands and the kinetic mechanism underlying this population shift is poorly understood. Here, we investigate the kinetic mechanism of neurotensin recognition by neurotensin receptor 1 (NTS1) using 19F-NMR, hydrogen-deuterium exchange mass spectrometry and stopped-flow fluorescence spectroscopy. Our results indicate slow-exchanging conformational heterogeneity on the extracellular surface of ligand-bound NTS1. Numerical analysis of the kinetic data of neurotensin binding to NTS1 shows that ligand recognition follows an induced fit mechanism, in which conformational changes occur after neurotensin binding. This approach is applicable to other GPCRs to provide insight into the kinetic regulation of ligand recognition by GPCRs.

2023-12-09 | PXD045464 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data