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Article ; Online: Refining the Dynamic Network of T2SS Endopilus Tip Heterocomplex Combining cw-EPR and Nitroxide-Gd

Gerbaud, Guillaume / Barbat, Brice / Tribout, Mathilde / Etienne, Emilien / Belle, Valérie / Douzi, Badreddine / Voulhoux, Romé / Bonucci, Alessio

Chembiochem : a European journal of chemical biology

2023 Volume 24, Issue 15, Page(s) e202300099

Abstract: The type 2 secretion system (T2SS) is a bacterial nanomachine composed of an inner membrane assembly platform, an outer membrane pore and a dynamic endopilus. T2SS endopili are organized into a homo-multimeric body formed by the major pilin capped by a ... ...

Abstract	The type 2 secretion system (T2SS) is a bacterial nanomachine composed of an inner membrane assembly platform, an outer membrane pore and a dynamic endopilus. T2SS endopili are organized into a homo-multimeric body formed by the major pilin capped by a heterocomplex of four minor pilins. The first model of the T2SS endopilus was recently released, even if structural dynamics insights are still required to decipher the role of each protein in the full tetrameric complex. Here, we applied continuous-wave and pulse EPR spectroscopy using nitroxide-gadolinium orthogonal labelling strategies to investigate the hetero-oligomeric assembly of the minor pilins. Overall, our data are in line with the endopilus model even if they evidenced conformational flexibility and alternative orientations at local scale of specific regions of minor pilins. The integration of different labelling strategies and EPR experiments demonstrates the pertinence of this approach to investigate protein-protein interactions in such multiprotein heterocomplexes.
MeSH term(s)	Type II Secretion Systems ; Fimbriae Proteins/chemistry ; Fimbriae Proteins/metabolism ; Electron Spin Resonance Spectroscopy/methods ; Proteins ; Spin Labels
Chemical Substances	Type II Secretion Systems ; Fimbriae Proteins (147680-16-8) ; nitroxyl (GFQ4MMS07W) ; Proteins ; Spin Labels
Language	English
Publishing date	2023-06-28
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020469-3
ISSN	1439-7633 ; 1439-4227
ISSN (online)	1439-7633
ISSN	1439-4227
DOI	10.1002/cbic.202300099
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Article ; Online: In-cell

Pierro, Annalisa / Tamburrini, Ketty Concetta / Leguenno, Hugo / Gerbaud, Guillaume / Etienne, Emilien / Guigliarelli, Bruno / Belle, Valérie / Zambelli, Barbara / Mileo, Elisabetta

iScience

2023 Volume 26, Issue 10, Page(s) 107855

Abstract: UreG is a cytosolic GTPase involved in the maturation network of urease, an Ni-containing bacterial enzyme. Previous ... ...

Abstract	UreG is a cytosolic GTPase involved in the maturation network of urease, an Ni-containing bacterial enzyme. Previous investigations
Language	English
Publishing date	2023-09-09
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2023.107855
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Article ; Online: Structural insights into the semiquinone form of human Cytochrome P450 reductase by DEER distance measurements between a native flavin and a spin labelled non-canonical amino acid.

Bizet, Maxime / Byrne, Deborah / Biaso, Frédéric / Gerbaud, Guillaume / Etienne, Emilien / Briola, Giuseppina / Guigliarelli, Bruno / Urban, Philippe / Dorlet, Pierre / Kalai, Tamas / Truan, Gilles / Martinho, Marlène

Chemistry (Weinheim an der Bergstrasse, Germany)

2024 Volume 30, Issue 19, Page(s) e202304307

Abstract: The flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a "locked/closed" to an "unlocked/open" state, is ... ...

Abstract	The flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a "locked/closed" to an "unlocked/open" state, is crucial for electron transfer. To date, however, the factors guiding these changes remain unknown. By Site-Directed Spin Labelling coupled to Electron Paramagnetic Resonance spectroscopy, we have incorporated a non-canonical amino acid onto the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) domains of soluble human CPR, and labelled it with a specific nitroxide spin probe. Taking advantage of the endogenous FMN cofactor, we successfully measured for the first time, the distance distribution by DEER between the semiquinone state FMNH
MeSH term(s)	Humans ; Oxidation-Reduction ; NADPH-Ferrihemoprotein Reductase/metabolism ; Amino Acids/metabolism ; Spin Labels ; Electron Spin Resonance Spectroscopy ; Electron Transport ; NADP/chemistry ; Flavins/chemistry ; Organic Chemicals ; Flavin Mononucleotide/chemistry ; Flavin-Adenine Dinucleotide/chemistry ; Kinetics ; Nitrogen Oxides
Chemical Substances	nitroxyl (GFQ4MMS07W) ; NADPH-Ferrihemoprotein Reductase (EC 1.6.2.4) ; Amino Acids ; Spin Labels ; NADP (53-59-8) ; Flavins ; Organic Chemicals ; Flavin Mononucleotide (7N464URE7E) ; Flavin-Adenine Dinucleotide (146-14-5) ; Nitrogen Oxides
Language	English
Publishing date	2024-02-13
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1478547-X
ISSN	1521-3765 ; 0947-6539
ISSN (online)	1521-3765
ISSN	0947-6539
DOI	10.1002/chem.202304307
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Article ; Online: Investigating the efficiency of silica materials with wall-embedded nitroxide radicals for dynamic nuclear polarisation NMR.

Besson, Eric / Vebr, Aurelien / Ziarelli, Fabio / Bloch, Emily / Gerbaud, Guillaume / Queyroy, Séverine / Thureau, Pierre / Viel, Stéphane / Gastaldi, Stéphane

Physical chemistry chemical physics : PCCP

2022 Volume 24, Issue 41, Page(s) 25279–25286

Abstract: Dynamic nuclear polarisation (DNP) can significantly enhance the sensitivity of solid-state nuclear magnetic resonance (SSNMR) experiments by transferring the electron spin polarisation of paramagnetic species to nuclei through microwave irradiation of ... ...

Abstract	Dynamic nuclear polarisation (DNP) can significantly enhance the sensitivity of solid-state nuclear magnetic resonance (SSNMR) experiments by transferring the electron spin polarisation of paramagnetic species to nuclei through microwave irradiation of the sample at cryogenic temperatures. Paramagnetic species required for DNP can be provided in the form of mesoporous silica materials containing nitroxide radicals either located on the porous surface or embedded in the pore walls. The present study focuses specifically on porous materials with wall-embedded radicals that were synthesised using conventional molecular imprinting protocols. More remarkably, by changing the molecular structure of the TEMPO precursor, the theoretical distance between the oxygen atoms in a pair of wall-embedded face-to-face TEMPO radicals was increased stepwise (0.7, 0.9, 1.1, 1.3 and 1.5 nm). The thermal activation of these five series of materials led to 37 TEMPO-functionalised silica materials with different radical concentrations. Their efficiency as DNP polarising agents was subsequently investigated at 9.4 T and ∼110 K under magic-angle spinning conditions (10 kHz) after impregnating them at room temperature with an aqueous solution of isotopically enriched proline. Our results show that the highest DNP efficiency was obtained for the silica materials that exhibited the shortest theoretical oxygen-oxygen distance between the TEMPO rings, suggesting that the design rules accepted for soluble DNP polarising agents may not be transposed to these materials with wall-embedded pairs of nitroxides.
Language	English
Publishing date	2022-10-27
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d2cp02872g
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Article ; Online: The transport activity of the multidrug ABC transporter BmrA does not require a wide separation of the nucleotide-binding domains.

Di Cesare, Margot / Kaplan, Elise / Rendon, Julia / Gerbaud, Guillaume / Valimehr, Sepideh / Gobet, Alexia / Ngo, Thu-Anh Thi / Chaptal, Vincent / Falson, Pierre / Martinho, Marlène / Dorlet, Pierre / Hanssen, Eric / Jault, Jean-Michel / Orelle, Cédric

The Journal of biological chemistry

2023 Volume 300, Issue 1, Page(s) 105546

Abstract: ATP-binding cassette (ABC) transporters are ubiquitous membrane proteins responsible for the translocation of a wide diversity of substrates across biological membranes. Some of them confer multidrug or antimicrobial resistance to cancer cells and ... ...

Abstract	ATP-binding cassette (ABC) transporters are ubiquitous membrane proteins responsible for the translocation of a wide diversity of substrates across biological membranes. Some of them confer multidrug or antimicrobial resistance to cancer cells and pathogenic microorganisms, respectively. Despite a wealth of structural data gained in the last two decades, the molecular mechanism of these multidrug efflux pumps remains elusive, including the extent of separation between the two nucleotide-binding domains (NBDs) during the transport cycle. Based on recent outward-facing structures of BmrA, a homodimeric multidrug ABC transporter from Bacillus subtilis, we introduced a cysteine mutation near the C-terminal end of the NBDs to analyze the impact of disulfide-bond formation on BmrA function. Interestingly, the presence of the disulfide bond between the NBDs did not prevent the ATPase, nor did it affect the transport of Hoechst 33342 and doxorubicin. Yet, the 7-amino-actinomycin D was less efficiently transported, suggesting that a further opening of the transporter might improve its ability to translocate this larger compound. We solved by cryo-EM the apo structures of the cross-linked mutant and the WT protein. Both structures are highly similar, showing an intermediate opening between their NBDs while their C-terminal extremities remain in close proximity. Distance measurements obtained by electron paramagnetic resonance spectroscopy support the intermediate opening found in these 3D structures. Overall, our data suggest that the NBDs of BmrA function with a tweezers-like mechanism distinct from the related lipid A exporter MsbA.
MeSH term(s)	Adenosine Triphosphate/metabolism ; ATP-Binding Cassette Transporters/metabolism ; Bacillus subtilis/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Disulfides/metabolism ; Nucleotides/metabolism ; Protein Domains ; Carrier Proteins/chemistry ; Carrier Proteins/genetics ; Carrier Proteins/metabolism ; Cysteine/chemistry ; Cysteine/genetics ; Biological Transport
Chemical Substances	Adenosine Triphosphate (8L70Q75FXE) ; ATP-Binding Cassette Transporters ; Bacterial Proteins ; Disulfides ; Nucleotides ; ATP-binding protein, bacteria ; Carrier Proteins ; Cysteine (K848JZ4886)
Language	English
Publishing date	2023-12-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.105546
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Article ; Online: Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme.

Kubiak, Xavier / Polsinelli, Ivan / Chavas, Leonard M G / Fyfe, Cameron D / Guillot, Alain / Fradale, Laura / Brewee, Clémence / Grimaldi, Stéphane / Gerbaud, Guillaume / Thureau, Aurélien / Legrand, Pierre / Berteau, Olivier / Benjdia, Alhosna

Nature chemical biology

2023 Volume 20, Issue 3, Page(s) 382–391

Abstract: D-Amino acid residues, found in countless peptides and natural products including ribosomally synthesized and post-translationally modified peptides (RiPPs), are critical for the bioactivity of several antibiotics and toxins. Recently, radical S-adenosyl- ...

Abstract	D-Amino acid residues, found in countless peptides and natural products including ribosomally synthesized and post-translationally modified peptides (RiPPs), are critical for the bioactivity of several antibiotics and toxins. Recently, radical S-adenosyl-L-methionine (SAM) enzymes have emerged as the only biocatalysts capable of installing direct and irreversible epimerization in RiPPs. However, the mechanism underpinning this biochemical process is ill-understood and the structural basis for this post-translational modification remains unknown. Here we report an atomic-resolution crystal structure of a RiPP-modifying radical SAM enzyme in complex with its substrate properly positioned in the active site. Crystallographic snapshots, size-exclusion chromatography-small-angle x-ray scattering, electron paramagnetic resonance spectroscopy and biochemical analyses reveal how epimerizations are installed in RiPPs and support an unprecedented enzyme mechanism for peptide epimerization. Collectively, our study brings unique perspectives on how radical SAM enzymes interact with RiPPs and catalyze post-translational modifications in natural products.
MeSH term(s)	S-Adenosylmethionine ; Amino Acids ; Anti-Bacterial Agents ; Biological Products ; Peptides
Chemical Substances	S-Adenosylmethionine (7LP2MPO46S) ; Amino Acids ; Anti-Bacterial Agents ; Biological Products ; Peptides
Language	English
Publishing date	2023-12-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2202962-X
ISSN	1552-4469 ; 1552-4450
ISSN (online)	1552-4469
ISSN	1552-4450
DOI	10.1038/s41589-023-01493-1
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Article ; Online: Modulating lifetimes and relaxation times of phenoxyl radicals through their incorporation into different hybrid nanostructures.

Dol, Cyrielle / Gerbaud, Guillaume / Guigliarelli, Bruno / Bloch, Emily / Gastaldi, Stéphane / Besson, Eric

Physical chemistry chemical physics : PCCP

2019 Volume 21, Issue 29, Page(s) 16337–16344

Abstract: The development of new open shell systems is essential for advances in spin science. In this work, we report the synthesis and characterization of three nanostructured materials, namely SBA-15 silicas, periodic mesoporous organosilicas (PMOs) and ... ...

Abstract	The development of new open shell systems is essential for advances in spin science. In this work, we report the synthesis and characterization of three nanostructured materials, namely SBA-15 silicas, periodic mesoporous organosilicas (PMOs) and lamellar polysilsesquioxanes, all functionalized with the same diazene-based phenoxyl radical precursor. The impact of the nature of the material, i.e. loading of radical precursor and structure, on half-lifetimes (t
Language	English
Publishing date	2019-07-16
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/c9cp03052b
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Article ; Online: Probing the Structural Dynamics of a Bacterial Chaperone in Its Native Environment by Nitroxide-Based EPR Spectroscopy.

Pierro, Annalisa / Bonucci, Alessio / Normanno, Davide / Ansaldi, Mireille / Pilet, Eric / Ouari, Olivier / Guigliarelli, Bruno / Etienne, Emilien / Gerbaud, Guillaume / Magalon, Axel / Belle, Valérie / Mileo, Elisabetta

Chemistry (Weinheim an der Bergstrasse, Germany)

2022 Volume 28, Issue 66, Page(s) e202202249

Abstract: One of the greatest current challenges in structural biology is to study protein dynamics over a wide range of timescales in complex environments, such as the cell. Among magnetic resonances suitable for this approach, electron paramagnetic resonance ... ...

Abstract	One of the greatest current challenges in structural biology is to study protein dynamics over a wide range of timescales in complex environments, such as the cell. Among magnetic resonances suitable for this approach, electron paramagnetic resonance spectroscopy coupled to site-directed spin labeling (SDSL-EPR) has emerged as a promising tool to study protein local dynamics and conformational ensembles. In this work, we exploit the sensitivity of nitroxide labels to report protein local dynamics at room temperature. We demonstrate that such studies can be performed while preserving both the integrity of the cells and the activity of the protein under investigation. Using this approach, we studied the structural dynamics of the chaperone NarJ in its natural host, Escherichia coli. We established that spin-labeled NarJ is active inside the cell. We showed that the cellular medium affects NarJ structural dynamics in a site-specific way, while the structural flexibility of the protein is maintained. Finally, we present and discuss data on the time-resolved dynamics of NarJ in cellular context.
MeSH term(s)	Electron Spin Resonance Spectroscopy/methods ; Spin Labels ; Nitrogen Oxides/chemistry ; Molecular Chaperones/chemistry
Chemical Substances	nitroxyl (GFQ4MMS07W) ; Spin Labels ; Nitrogen Oxides ; Molecular Chaperones
Language	English
Publishing date	2022-10-31
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1478547-X
ISSN	1521-3765 ; 0947-6539
ISSN (online)	1521-3765
ISSN	0947-6539
DOI	10.1002/chem.202202249
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Article ; Online: Structural evidence for a reaction intermediate mimic in the active site of a sulfite dehydrogenase.

Djeghader, Ahmed / Rossotti, Melanie / Abdulkarim, Saleh / Biaso, Frédéric / Gerbaud, Guillaume / Nitschke, Wolfgang / Schoepp-Cothenet, Barbara / Soulimane, Tewfik / Grimaldi, Stéphane

Chemical communications (Cambridge, England)

2020 Volume 56, Issue 68, Page(s) 9850–9853

Abstract: By combining X-ray crystallography, electron paramagnetic resonance techniques and density functional theory-based modelling, we provide evidence for a direct coordination of the product analogue, phosphate, to the molybdenum active site of a sulfite ... ...

Abstract	By combining X-ray crystallography, electron paramagnetic resonance techniques and density functional theory-based modelling, we provide evidence for a direct coordination of the product analogue, phosphate, to the molybdenum active site of a sulfite dehydrogenase. This interaction is mimicking the still experimentally uncharacterized reaction intermediate proposed to arise during the catalytic cycle of this class of enzymes. This work opens new perspectives for further deciphering the reaction mechanism of this nearly ubiquitous class of oxidoreductases.
MeSH term(s)	Catalytic Domain ; Crystallography, X-Ray ; Density Functional Theory ; Electron Spin Resonance Spectroscopy ; Hydrogen Bonding ; Molybdenum/chemistry ; Phosphates/chemistry ; Sulfite Dehydrogenase/chemistry ; Sulfite Dehydrogenase/metabolism ; Thermus/enzymology
Chemical Substances	Phosphates ; Molybdenum (81AH48963U) ; Sulfite Dehydrogenase (EC 1.8.2.1)
Language	English
Publishing date	2020-07-27
Publishing country	England
Document type	Journal Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/d0cc03634j
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Article ; Online: Nickel and GTP Modulate

Pierro, Annalisa / Etienne, Emilien / Gerbaud, Guillaume / Guigliarelli, Bruno / Ciurli, Stefano / Belle, Valérie / Zambelli, Barbara / Mileo, Elisabetta

Biomolecules

2020 Volume 10, Issue 7

Abstract: UreG is a P-loop GTP hydrolase involved in the maturation of nickel-containing urease, an essential enzyme found in plants, fungi, bacteria, and archaea. This protein couples the hydrolysis of GTP to the delivery of Ni(II) into the active site of apo- ... ...

Abstract	UreG is a P-loop GTP hydrolase involved in the maturation of nickel-containing urease, an essential enzyme found in plants, fungi, bacteria, and archaea. This protein couples the hydrolysis of GTP to the delivery of Ni(II) into the active site of apo-urease, interacting with other urease chaperones in a multi-protein complex necessary for enzyme activation. Whereas the conformation of
MeSH term(s)	Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Crystallography, X-Ray ; Guanosine Triphosphate/metabolism ; Helicobacter Infections/microbiology ; Helicobacter pylori/chemistry ; Helicobacter pylori/metabolism ; Humans ; Models, Molecular ; Nickel/metabolism ; Phosphate-Binding Proteins/chemistry ; Phosphate-Binding Proteins/metabolism ; Protein Conformation
Chemical Substances	Bacterial Proteins ; Phosphate-Binding Proteins ; ureG protein, Bacteria ; Nickel (7OV03QG267) ; Guanosine Triphosphate (86-01-1)
Keywords	covid19
Language	English
Publishing date	2020-07-16
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom10071062
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