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HDX-MS of VDR-RXR in complex with ZK168281

ABSTRACT: Characterization of the interaction between the full nuclear receptor VDR-RXR heterodimer and VDR antagonist ZK168281

INSTRUMENT(S): Synapt MS

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Anna Belorusova

LAB HEAD: Tomas Leek

PROVIDER: PXD019810 | Pride | 2020-12-16

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	20180904_VDR_RXR_D3_0sec.zip	Other
	20180904_VDR_RXR_D3_1800sec.zip	Other
	20180904_VDR_RXR_D3_180sec.zip	Other
	20180904_VDR_RXR_D3_30sec.zip	Other
	20180904_VDR_RXR_D3_600sec.zip	Other

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1 - 5 of 27

Publications

Cytosolic sequestration of the vitamin D receptor as a therapeutic option for vitamin D-induced hypercalcemia.

Rovito Daniela D Belorusova Anna Y AY Chalhoub Sandra S Rerra Anna-Isavella AI Guiot Elvire E Molin Arnaud A Linglart Agnès A Rochel Natacha N Laverny Gilles G Metzger Daniel D

Nature communications 20201207 1

The bioactive vitamin D3, 1α,25(OH)2D3, plays a central role in calcium homeostasis by controlling the activity of the vitamin D receptor (VDR) in various tissues. Hypercalcemia secondary to high circulating levels of vitamin D3 leads to hypercalciuria, nephrocalcinosis and renal dysfunctions. Current therapeutic strategies aim at limiting calcium intake, absorption and resorption, or 1α,25(OH)2D3 synthesis, but are poorly efficie ...[more]

PMID: 33288743

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Structural Premise of Selective Deubiquitinase USP30 Inhibition by Small-Molecule Benzosulfonamides

Project description:Dampening functional levels of the mitochondrial deubiquitylating enzyme USP30 has been suggested as an effective therapeutic strategy against neurodegenerative disorders such as Parkinson’s Disease. USP30 inhibition may counteract the deleterious effects of impaired turnover of damaged mitochondria which is inherent to both familial and sporadic forms of the disease. Small-molecule inhibitors targeting USP30 are currently in development, but little is known about their precise nature of binding to the protein. We have integrated biochemical and structural approaches to gain novel mechanistic insights into USP30 inhibition by a small-molecule benzosulfonamide containing compound, 39. Activity-based protein profiling (ABPP) mass spectrometry confirmed target engagement, the high selectivity, and potency of 39 for USP30 against 49 other deubiquitylating enzymes in a neuroblastoma cell line. In vitro characterization of 39 enzyme kinetics infers slow and tight binding behavior, which is comparable with features of covalent modification of USP30. Finally, we blended hydrogen-deuterium exchange mass spectrometry and computational docking to elucidate the molecular architecture and geometry of USP30 complex formation with 39, identifying structural rearrangements at the cleft of the USP30 thumb and palm subdomains. These studies suggest that 39 binds to the thumb-palm cleft that guides the ubiquitin C-terminus into the active site, thereby preventing ubiquitin binding and isopeptide bond cleavage, and confirming its importance in the inhibitory process. Our data will pave the way for the design and development of next-generation inhibitors targeting USP30 and associated deubiquitinylases.

2023-10-24 | PXD041582 | Pride

Engineering and exploiting synthetic allostery of NanoLuc luciferase

Project description:The ability to endow constitutively active proteins with synthetic allostery is a central objective of Synthetic Biology, mostly focused on the creation of protein biosensors – artificial sensing proteins with easily quantifiable outputs. Here we hypothesize that circular permutation of proteins increases the probability of functional coupling of new N- and C- terminal sequences with the active center of the protein through increased local structural disorder. We test this by constructing a synthetically allosteric version of circular permutated NanoLuc luciferase, activated through ligand-induced intramolecular non-covalent cyclisation. The developed biosensors cover a range of emission wavelengths and display sensitivity as low as 50 pM and dynamic range as high as 16-fold and could quantify their cognate ligand in human fluids such as saliva, serum and lysed blood. We apply hydrogen exchange kinetic mass spectrometry to analyze time resolved structural changes in the developed biosensors and observed ligand-mediated folding of newly created termini. While a large study is required for determining how frequent synthetic allostery emerges following circular permutation and what types of protein folds are susceptible to it, this study provides motivation and justification for such efforts.

2022-02-10 | PXD031169 | Pride

Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein: HDX-MS analysis of the spike of alpha, beta, delta and omicron variants - in apo state and in complex with the ACE2 receptor

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2023-03-15 | PXD039762 | Pride

Structural dynamics in the evolution of SARS-CoV-2 spike glycoprotein: HDX-MS analysis of the spike of the original Wuhan isolate, G614 spike mutant, and the isolated ancestral RBD - in apo state and in complex with the ACE2 receptor

2023-03-15 | PXD039760 | 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

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

GroEL interaction and folding of MetF studied by hydrogen/deuterium exchange – mass spectrometry

Project description:The cylindrical chaperonin GroEL and its cofactor GroES mediate ATP-dependent protein folding in E. coli by transiently encapsulating non-native substrate in a nano-cage formed by the GroEL ring cavity and the lid-shaped GroES. We analyzed the spontaneous and chaperonin-assisted folding of the essential enzyme 5,10-methylenetetrahydrofolate reductase (MetF) of E. coli, an obligate GroEL/ES substrate. We found that MetF, a homotetramer of 33 kDa subunits with (8) TIM-barrel fold, is unable to fold spontaneously, even in the complete absence of aggregation, and populates a kinetically trapped folding intermediate(s) (MetF-I). GroEL/ES recognized MetF-I and catalyzed its folding with high efficiency, at a half-time of ~4 s and with more than 50% of protein folded in a single round of encapsulation. Analysis by hydrogen/deuterium exchange at peptide resolution showed that the MetF subunit folds to completion in the GroEL/ES nano-cage and binds the co-factor FAD.

2020-03-05 | PXD016666 | Pride

Effects of ATP binding on the conformational flexibility of proNGF

Project description: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.

2023-11-16 | PXD035625 | Pride

Activation loop phosphorylation tunes conformational dynamics underlying Pyk2 tyrosine kinase activation

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