Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Inhibition of fusidic acid resistance through restricting conformational flexibility in domain III of EF-G

ABSTRACT: HDX-MS was used to study the binding of FusB to EF-G variants.

INSTRUMENT(S):

ORGANISM(S): Staphylococcus Aureus

SUBMITTER: Antonio Calabrese

LAB HEAD: Antonio Calabrese

PROVIDER: PXD062993 | Pride | 2025-12-15

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	250123_EF-GFusB_t0_01.raw.zip	Raw
	250123_EF-G_FusB_t0-03.raw.zip	Raw
	250123_EF-G_FusB_t0_02.raw.zip	Raw
	250123_EF-G_FusB_t30m-01.raw.zip	Raw
	250123_EF-G_FusB_t30m-02.raw.zip	Raw

Items per page:

1 - 5 of 97

Publications

Inhibition of fusidic acid resistance through restricting conformational flexibility in domain III of EF-G.

Schindl Alexandra A Jones Megan E ME Ghimire Leela L Kalverda Arnout P AP Wildsmith Gemma G Calabrese Antonio N AN Tomlinson Jennifer H JH

Proceedings of the National Academy of Sciences of the United States of America 20251124 48

Fusidic acid (FA) is one of few remaining antibiotics active against Methicillin-resistant <i>Staphylococcus aureus</i>. FusB confers resistance to FA by rescuing the translocation factor Elongation Factor-G (EF-G) from FA-stalled ribosome complexes. FusB induces allosteric effects on dynamics in EF-G, causing significant changes in the conformational flexibility of domain III that result in an increase in a minor, more disordered state, overcoming the steric block induced by FA. We show that re ...[more]

PMID: 41284881

Similar Datasets

Mapping of a N-terminal alpha-helix domain required for human PINK1 stabilisation, Serine228 autophosphorylation and activation in cells

Project description:Comparative hydrogen deuterium exchange mass spectrometry of WT and I507A mutant for above titled manuscript.

2022-02-17 | PXD030382 | 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

Hydrogen-deuterium exchange mass spectrometry analysis of the CDK2-cyclin A-CDC25A complex

Project description:The cell division cycle 25 phosphatases CDC25A, B and C regulate cell cycle transitions by dephosphorylating residues in the conserved glycine-rich loop of cyclin-dependent protein kinases (CDKs) to activate CDK activity. Here, we present HDX-MS data to complement the cryogenic-electron microscopy (cryo-EM) structure of CDK2-cyclin A in complex with CDC25A, providing a detailed structural analysis of the overall complex architecture and key protein-protein interactions that underpin this 86 kDa complex. This work improves our understanding of the roles of CDC25 phosphatases in CDK regulation and may inform the development of CDC25-targeting anticancer strategies.

2024-05-29 | PXD050866 | Pride

Membranes prime the RapGEF EPAC1 to transduce cAMP signaling

Project description:EPAC1, a cAMP-activated GEF for Rap GTPases, is a major transducer of cAMP signaling in normal cells and a therapeutic target in cardiac diseases. The recent discovery that cAMP is compartmentalized in membrane-proximal nanodomains challenged the current model of EPAC1 activation in the cytosol. Here, we discover that anionic membranes are a major component of EPAC1 activation. We find that anionic membranes activate EPAC1 in the absence of cAMP, that they increase its affinity for cAMP by 2 orders of magnitude, and that they synergize with cAMP to yield maximal GEF activity. Thus, EPAC1 has four states that differ in their affinity for cAMP and GEF efficiency. In cells, where cytosolic cAMP is low, this implies that EPAC1 must be primed by membranes to bind cAMP. Examination of the inhibitory mechanism of the cardiomyocyte-active chemical CE3F4 in this new framework further reveals that it targets only only membrane- and cAMP-activated EPAC1. Together, our findings reformulate previous concepts of cAMP signaling to include a hitherto overlooked role of membranes through EPAC proteins, with important implications for drug discovery.

2023-04-07 | PXD040227 | 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

Investigating protein dynamics with millisecond precision using droplet microfluidic hydrogen/deuterium exchange

Project description:Hydrogen/deuterium exchange (HDX) methods for studying protein dynamics would benefit from millisecond-scale incubations to probe intrinsically disordered proteins, highly dynamic regions and conformation changes. Here we investigate droplet microfluidics for rapid mixing to trigger D2O labelling, uniform incubations and rapid droplet merging for acid quenching in advance of mass spectrometry. A surfactant-free merging approach combining expansion elements for synchronised droplet collision proved robust. The high diffusive flux of D2O and protons enable microsecond mixing to trigger and arrest D2O labelling, respectively, affording the possibility of single millisecond incubations. Millisecond droplet HDX processors were used to measure forward exchange and demonstrate that D2O labelling is the rate-limiting step, in essence defining 10 milliseconds as the minimum practical incubation time. With the ability to access millisecond time scales the fast dynamics of calmodulin, a model of calcium-triggered allostery with rapid conformational switching, was investigated. Calcium binding increases D2O accessibility to the linker region, reporting the flexibility which enables the scissor-like motion of calmodulin for capturing proteins. The millisecond precision of droplet microfluidic HDX paves the way to advance our understanding of protein structural dynamics.

2025-06-23 | PXD063880 | 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

Analysis of the PcrA-RNA polymerase complex reveals a helicase interaction motif and a role for PcrA/UvrD helicase in the suppression of R-loops

Project description:HDX-MS was used to study the binding of PcrA to RNA polymerase

2021-07-20 | PXD025332 | Pride

Hydrogen-deuterium exchange mass spectrometry of rotavirus NSP2/NSP5 biomolecular condensates

Project description:Biomolecular condensates selectively compartmentalise and organise biomolecules within the crowded cellular milieu, and are instrumental in some disease mechanisms, including aiding RNA virus replication. Upon infection, many RNA viruses form biomolecular condensates that are often referred to as viral factories. The assembly mechanism of these viral factories remains poorly defined, but involves transient, non-stoichiometric protein/RNA interactions, posing challenges for their characterisation. Here we present HDX-MS data of NSP2 and NSP5, in a biomolecular condensate to study the mechanism of condensate assembly.

2025-06-23 | PXD058097 | Pride