Biochemistry, Biophysics & Structural Biology Department

Biochemistry, Biophysics and Structural Biology Department

Head: 

Julie Ménétrey

Deputy  heads:

    Benoit D’Autréaux 

Virginie Gervais 

From Atoms to Function : Decoding How Macromolecular Structures and Dynamics Orchestrate Life

Focus

The B3S teams study soluble and membrane protein assemblies involved in major biological processes of eukaryotic and bacterial cells. 

Our aim is to  understand the molecular mechanisms of biological structures and biochemical reactions at different scales, from electrons and protons via atoms and molecules to multicellular organisms. Successfully introduced new technologies to promote product innovation and upgrades.

Approaches

Biochemical reactions, interactions and enzymatic processes, including large conformational changes and rearrangements within proteins and their complexes, are often initiated by a transfer of subatomic particles – electrons and protons. Studying the atomic structures of proteins with and without ligands can for example help determine how the structure of the active site enables an enzyme to perform its activity.

At molecular scales, biochemical and biophysical analyses as well as structure determination of protein-protein, or protein-nucleic acid complexes, helps in describing the interaction of biological assemblies and understanding biochemical reactions.  In vitro reconstitution of cellular functions leads to an understanding of the regulation of complex processes in vivo.

Research groups

Publications

3888256 B3S 1 chicago-author-date 5 date desc year 36406 https://www.i2bc.paris-saclay.fr/wp-content/plugins/zotpress/
%7B%22status%22%3A%22success%22%2C%22updateneeded%22%3Afalse%2C%22instance%22%3Afalse%2C%22meta%22%3A%7B%22request_last%22%3A0%2C%22request_next%22%3A0%2C%22used_cache%22%3Atrue%7D%2C%22data%22%3A%5B%7B%22key%22%3A%22G9BYRPDS%22%2C%22library%22%3A%7B%22id%22%3A3888256%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Bo%5Cu00ebffard-Dosierre%20et%20al.%22%2C%22parsedDate%22%3A%222026-12-31%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BBo%26%23xEB%3Bffard-Dosierre%2C%20Liza%2C%20Camille%20Dagallier%2C%20G%26%23xE9%3Braldine%20Eudier%2C%20et%20al.%202026.%20%26%23x201C%3BNMR%20Detects%20Clustering%20and%20Ultra-Weak%20Excipient%20Interactions%20Governing%20Monoclonal%20Antibody%20Viscosity%20in%20Formulation-Relevant%20Conditions.%26%23x201D%3B%20%26lt%3Bi%26gt%3BmAbs%26lt%3B%5C%2Fi%26gt%3B%2018%20%281%29%3A%202685366.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1080%5C%2F19420862.2026.2685366%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1080%5C%2F19420862.2026.2685366%26lt%3B%5C%2Fa%26gt%3B.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22NMR%20detects%20clustering%20and%20ultra-weak%20excipient%20interactions%20governing%20monoclonal%20antibody%20viscosity%20in%20formulation-relevant%20conditions%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Liza%22%2C%22lastName%22%3A%22Bo%5Cu00ebffard-Dosierre%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Camille%22%2C%22lastName%22%3A%22Dagallier%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22G%5Cu00e9raldine%22%2C%22lastName%22%3A%22Eudier%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Vasco%22%2C%22lastName%22%3A%22Filipe%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Atifa%22%2C%22lastName%22%3A%22Badar-Majeed%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sol%5Cu00e8ne%22%2C%22lastName%22%3A%22Fraumont%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sophie%22%2C%22lastName%22%3A%22Zinn-Justin%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Francois-Xavier%22%2C%22lastName%22%3A%22Theillet%22%7D%5D%2C%22abstractNote%22%3A%22High-concentration%20formulations%20of%20monoclonal%20antibodies%20%28mAbs%29%20are%20required%20for%20subcutaneous%20administration%20but%20are%20frequently%20challenging%20to%20develop%20due%20to%20elevated%20viscosity%20and%20colloidal%20instability.%20These%20properties%20are%20governed%20by%20mAb-mAb%20interactions%20that%20are%20regulated%20by%20additional%20mAb-excipient%20interactions.%20These%20ultra-weak%20interactions%20remain%20difficult%20to%20characterize%20using%20conventional%20techniques.%20Here%2C%20we%20combined%20nuclear%20magnetic%20resonance%20%28NMR%29%20spectroscopy%20with%20rheometry%20and%20dynamic%20light%20scattering%20to%20investigate%20mAb%20interactions%20under%20formulation-relevant%20conditions.%20Rheological%20measurements%20showed%20that%2C%20in%20the%20case%20of%20the%20chosen%20mAb%2C%20the%20excipients%20arginine%20and%20lysine%20strongly%20reduce%20the%20macroscopic%20viscosity%2C%20whereas%20other%20excipients%20display%20a%20moderate%20effect%20by%20themselves.%20Characterization%20of%20the%20mAb%20oligomeric%20state%20by%201H%20NMR%20confirmed%20that%20arginine%20and%20lysine%20are%20the%20most%20efficient%20at%20reducing%20mAb%20self-assembly%2C%20while%20proline%20and%20glycine%20promote%20clustering.%20Interactions%20between%20mAb%20and%20excipients%20were%20first%20analyzed%20by%20measuring%20excipient%20diffusion%20coefficients%2C%20but%20these%20are%20only%20weakly%20affected%20by%20the%20addition%20of%20concentrated%20mAb.%20The%20mAb-excipient%20interactions%20were%20further%20detected%20by%20measuring%20excipient%201H%20and%2013C%20chemical%20shifts%2C%20mAb-excipient%20saturation%20transfers%2C%20and%20excipient%201H%20transverse%20relaxation%20rates.%20These%20experiments%20provided%20complementary%20information%20on%20excipient%20interactions%20with%20the%20different%20mAb%20oligomers.%20Lysine%20was%20identified%20as%20the%20best%20mAb%20binder.%20However%2C%20several%20excipients%20such%20as%20sucrose%20that%20do%20not%20reduce%20the%20macroscopic%20viscosity%20also%20bind%20to%20concentrated%20mAb%2C%20highlighting%20that%20excipient%20binding%20can%20have%20various%20consequences%20on%20the%20transient%20interactions%20between%20mAb%20species.%20Altogether%2C%20this%20work%20proposes%20a%20powerful%20NMR%20pipeline%20to%20dissect%20ultra-weak%20molecular%20interactions%20that%20govern%20viscosity%20and%20developability%20in%20therapeutic%20antibody%20formulations.%22%2C%22date%22%3A%222026-12-31%22%2C%22section%22%3A%22%22%2C%22partNumber%22%3A%22%22%2C%22partTitle%22%3A%22%22%2C%22DOI%22%3A%2210.1080%5C%2F19420862.2026.2685366%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22%22%2C%22PMID%22%3A%2242272436%22%2C%22PMCID%22%3A%22%22%2C%22ISSN%22%3A%221942-0870%22%2C%22language%22%3A%22eng%22%2C%22collections%22%3A%5B%5D%2C%22dateModified%22%3A%222026-06-12T07%3A26%3A39Z%22%7D%7D%2C%7B%22key%22%3A%22V26C5J8Q%22%2C%22library%22%3A%7B%22id%22%3A3888256%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Ba%5Cu00f1os-Guti%5Cu00e9rrez%20et%20al.%22%2C%22parsedDate%22%3A%222026-07-07%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BBa%26%23xF1%3Bos-Guti%26%23xE9%3Brrez%2C%20J.%2C%20R.%20Bercy%2C%20Y.%20Garc%26%23xED%3Ba%20Jomaso%2C%20et%20al.%202026.%20%26%23x201C%3BMolecular%20Structure%2C%20Binding%2C%20and%20Disorder%20in%20TDBC-Ag%20Plexcitonic%20Assemblies.%26%23x201D%3B%20%26lt%3Bi%26gt%3BThe%20Journal%20of%20Chemical%20Physics%26lt%3B%5C%2Fi%26gt%3B%20165%20%281%29%3A%20014702.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1063%5C%2F5.0325564%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1063%5C%2F5.0325564%26lt%3B%5C%2Fa%26gt%3B.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Molecular%20structure%2C%20binding%2C%20and%20disorder%20in%20TDBC-Ag%20plexcitonic%20assemblies%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J.%22%2C%22lastName%22%3A%22Ba%5Cu00f1os-Guti%5Cu00e9rrez%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22R.%22%2C%22lastName%22%3A%22Bercy%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Y.%20Garc%5Cu00eda%22%2C%22lastName%22%3A%22Jomaso%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22S.%22%2C%22lastName%22%3A%22Balci%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22G.%22%2C%22lastName%22%3A%22Pirruccio%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J.%20Halldin%22%2C%22lastName%22%3A%22Stenlid%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22M.%20J.%22%2C%22lastName%22%3A%22Llansola-Portoles%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22D.%22%2C%22lastName%22%3A%22Finkelstein-Shapiro%22%7D%5D%2C%22abstractNote%22%3A%22Plexcitonic%20assemblies%20are%20hybrid%20materials%20composed%20of%20a%20plasmonic%20nanoparticle%20and%20molecular%20or%20semiconducting%20emitters%20whose%20electronic%20transitions%20are%20strongly%20coupled%20to%20the%20plasmonic%20mode.%20This%20coupling%20hybridizes%20the%20system%20modes%20into%20upper%20and%20lower%20polariton%20branches.%20The%20interaction%20strength%20depends%20on%20the%20number%20of%20emitters%20and%20on%20their%20orientation%20and%20spatial%20arrangement%20relative%20to%20the%20metallic%20surface.%20These%20structural%20factors%20have%20profound%20consequences%20for%20the%20ensuing%20photoexcited%20dynamics.%20Despite%20the%20extensive%20spectroscopic%20work%20on%20plexcitonic%20systems%2C%20direct%20understanding%20of%20the%20molecular%20geometry%20at%20the%20metal%20interface%20remains%20limited.%20We%20present%20a%20comprehensive%20structural%20characterization%20of%20a%20model%20plexciton%20formed%20by%20the%20cyanine%20dye%205%2C5%26%23039%3B%2C6%2C6%26%23039%3B-tetrachloro-1%2C1%26%23039%3B-diethyl-3%2C3%26%23039%3B-di%284-sulfobutyl%29-benzimidazolocarbocyanine%20%28TDBC%29%20and%20silver%20nanodisks%20using%20NMR%2C%20THz-Raman%20spectroscopy%2C%20and%20density%20functional%20theory%20calculations.%20By%20comparing%20the%20signals%20from%20the%20monomeric%20and%20aggregated%20forms%20of%20TDBC%20with%20those%20of%20the%20plexciton%2C%20we%20identify%20shared%20spectral%20fingerprints%20that%20reveal%20how%20molecular%20packing%20is%20modified%20when%20the%20aggregate%20adsorbs%20on%20the%20silver%20surface.%20We%20observe%20Raman%20modes%20specific%20to%20plexciton%20systems%20and%20identify%20NOESY%20cross-peaks%20in%20the%20aliphatic%20region%20that%2C%20along%20with%20several%20Raman%20modes%2C%20are%20sensitive%20indicators%20of%20aggregation%20geometry%20and%20adsorption.%20We%20find%20that%20TDBC%20monomers%20adopt%20an%20asymmetric%20conformation%20in%20which%20both%20sulfobutyl%20chains%20lie%20on%20the%20same%20side%20of%20the%20chromophore%2C%20while%20J-aggregates%20adopt%20a%20symmetric%20up-down%20alternation%20of%20the%20chains%20from%20molecule%20to%20molecule%2C%20which%20becomes%20distorted%20and%20loses%20long%20range%20periodicity%20when%20adsorbed%20on%20Ag%20nanodisks.%20This%20work%20constrains%20the%20molecular%20geometry%20and%20interfacial%20arrangement%20of%20a%20prototypical%20TDBC-silver%20plexciton%2C%20providing%20a%20structural%20benchmark%20for%20understanding%20geometry-dependent%20photophysics%20in%20exciton-plasmon%20systems.%22%2C%22date%22%3A%222026-07-07%22%2C%22section%22%3A%22%22%2C%22partNumber%22%3A%22%22%2C%22partTitle%22%3A%22%22%2C%22DOI%22%3A%2210.1063%5C%2F5.0325564%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22%22%2C%22PMID%22%3A%2242383615%22%2C%22PMCID%22%3A%22%22%2C%22ISSN%22%3A%221089-7690%22%2C%22language%22%3A%22eng%22%2C%22collections%22%3A%5B%5D%2C%22dateModified%22%3A%222026-07-02T06%3A49%3A54Z%22%7D%7D%2C%7B%22key%22%3A%224LUILZSI%22%2C%22library%22%3A%7B%22id%22%3A3888256%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22He%20et%20al.%22%2C%22parsedDate%22%3A%222026-06-26%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BHe%2C%20Wei%2C%20Jen-Wei%20Huang%2C%20Yalong%20Wang%2C%20et%20al.%202026.%20%26%23x201C%3BDeciphering%20Protein%20Mutation-Phenotype%20Linkages%20from%20CRISPR-Based%20Tiling%20Mutagenesis%20Screens.%26%23x201D%3B%20%26lt%3Bi%26gt%3BCell%20Systems%26lt%3B%5C%2Fi%26gt%3B%2C%20June%2026%2C%20101651.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.cels.2026.101651%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.cels.2026.101651%26lt%3B%5C%2Fa%26gt%3B.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Deciphering%20protein%20mutation-phenotype%20linkages%20from%20CRISPR-based%20tiling%20mutagenesis%20screens%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Wei%22%2C%22lastName%22%3A%22He%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jen-Wei%22%2C%22lastName%22%3A%22Huang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yalong%22%2C%22lastName%22%3A%22Wang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Samuel%20B.%22%2C%22lastName%22%3A%22Hayward%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Giuseppe%22%2C%22lastName%22%3A%22Leuzzi%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Rongjie%22%2C%22lastName%22%3A%22Fu%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Shuyue%22%2C%22lastName%22%3A%22Wang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alina%22%2C%22lastName%22%3A%22Vaitsiankova%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yiwen%22%2C%22lastName%22%3A%22Chen%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mark%20T.%22%2C%22lastName%22%3A%22Bedford%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Raphael%22%2C%22lastName%22%3A%22Guerois%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alberto%22%2C%22lastName%22%3A%22Ciccia%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Han%22%2C%22lastName%22%3A%22Xu%22%7D%5D%2C%22abstractNote%22%3A%22CRISPR-based%20high-throughput%20mutagenesis%20screens%20enable%20systematic%20mapping%20of%20mutations%20to%20phenotypes%2C%20yet%20deciphering%20mutation-phenotype%20links%20remains%20challenging.%20Here%2C%20we%20present%20ProTiler-Mut%2C%20a%20versatile%20computational%20framework%20that%20leverages%20tiling%20mutagenesis%20screens%2C%20which%20introduce%20variants%20across%20entire%20protein%20sequences%2C%20to%20analyze%20mutation%20effects%20at%20the%20levels%20of%20residues%2C%20substructures%2C%20and%20protein-protein%20interactions%20%28PPIs%29.%20Applying%20ProTiler-Mut%20to%20multi-condition%20base-editing%20%28BE%29%20screens%20targeting%20DNA%20damage%20response%20proteins%20and%20T%20cell%20regulators%2C%20we%20define%20a%20separation-of-function%20%28SoF%29%20category%20beyond%20the%20conventional%20loss-of-function%20%28LoF%29%20and%20gain-of-function%20%28GoF%29%20classes%2C%20where%20SoF%20mutations%20show%20the%20strongest%20enrichment%20for%20ClinVar-annotated%20pathogenic%20variants.%20ProTiler-Mut%20also%20identifies%20candidate%20substructures%20that%20enable%20functional%20inference%20of%20unscreened%20pathogenic%20mutations%20and%20prioritizes%20candidate%20phenotype-associated%20PPIs%20potentially%20disrupted%20by%20functional%20variants.%20Using%20ProTiler-Mut%2C%20in%20cells%20with%20elevated%20programmed%20cell%20death%201%20%28PD-1%29%20expression%2C%20we%20identify%20pathogenic%20GoF%20mutations%20that%20constitute%20a%20substructure%20that%20may%20disrupt%20mitogen-activated%20protein%20kinase%20%28MAPK%291-RSK1%20interactions%20and%20lead%20to%20MAPK%20activation.%20Finally%2C%20we%20show%20that%20ProTiler-Mut%20is%20applicable%20across%20different%20mutagenesis%20screening%20platforms.%20A%20record%20of%20this%20paper%26%23039%3Bs%20transparent%20peer%20review%20process%20is%20included%20in%20the%20supplemental%20information.%22%2C%22date%22%3A%222026-06-26%22%2C%22section%22%3A%22%22%2C%22partNumber%22%3A%22%22%2C%22partTitle%22%3A%22%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.cels.2026.101651%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22%22%2C%22PMID%22%3A%2242361799%22%2C%22PMCID%22%3A%22%22%2C%22ISSN%22%3A%222405-4720%22%2C%22language%22%3A%22eng%22%2C%22collections%22%3A%5B%5D%2C%22dateModified%22%3A%222026-06-29T07%3A27%3A11Z%22%7D%7D%2C%7B%22key%22%3A%22B39WE9KU%22%2C%22library%22%3A%7B%22id%22%3A3888256%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Barbe%20et%20al.%22%2C%22parsedDate%22%3A%222026-06-19%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BBarbe%2C%20Val%26%23xE9%3Brie%2C%20Camille%20Saint-Picq%2C%20Charl%26%23xE8%3Bne%20Odobel%2C%20et%20al.%202026.%20%26%23x201C%3BUnveiling%20Plastic%20Biodegradation%20Pathways%20through%2013C-DNA%20Stable%20Isotope%20Probing%20and%20Metagenomics.%26%23x201D%3B%20%26lt%3Bi%26gt%3BJournal%20of%20Hazardous%20Materials%26lt%3B%5C%2Fi%26gt%3B%20514%20%28June%29%3A%20142755.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.jhazmat.2026.142755%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1016%5C%2Fj.jhazmat.2026.142755%26lt%3B%5C%2Fa%26gt%3B.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Unveiling%20plastic%20biodegradation%20pathways%20through%2013C-DNA%20stable%20isotope%20probing%20and%20metagenomics%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Val%5Cu00e9rie%22%2C%22lastName%22%3A%22Barbe%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Camille%22%2C%22lastName%22%3A%22Saint-Picq%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Charl%5Cu00e8ne%22%2C%22lastName%22%3A%22Odobel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marion%22%2C%22lastName%22%3A%22Hingant%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Mireille%22%2C%22lastName%22%3A%22Pujo-Pay%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Corinne%22%2C%22lastName%22%3A%22Cruaud%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jean-Louis%22%2C%22lastName%22%3A%22Petit%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22C%5Cu00e9cile%22%2C%22lastName%22%3A%22Fischer%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yves%22%2C%22lastName%22%3A%22Boulard%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Aur%5Cu00e9lie%22%2C%22lastName%22%3A%22C%5Cu00e9bron%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Alexandra%22%2C%22lastName%22%3A%22Ter%20Halle%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Boris%22%2C%22lastName%22%3A%22Eyheraguibel%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Pierre%22%2C%22lastName%22%3A%22Lemechko%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22St%5Cu00e9phane%22%2C%22lastName%22%3A%22Bruzaud%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jean-Fran%5Cu00e7ois%22%2C%22lastName%22%3A%22Ghiglione%22%7D%5D%2C%22abstractNote%22%3A%22Polyhydroxyalkanoates%20%28PHAs%29%20are%20promising%20biobased%20and%20biodegradable%20alternatives%20to%20conventional%20plastics%2C%20yet%20their%20degradation%20mechanisms%20and%20the%20diversity%20of%20microorganisms%20involved%20remain%20poorly%20characterized%20in%20marine%20ecosystems.%20Here%2C%20we%20used%2013C-labeled%20poly%283-hydroxybutyrate%29%20%28PHB%29%20and%20combined%20DNA-stable%20isotope%20probing%20%28DNA-SIP%29%20with%20metagenomic%20to%20identify%20and%20functionally%20characterize%20active%20PHB-degrading%20bacteria%20in%20seawater.%20We%20identified%20three%20metagenome-assembled%20genomes%20%28MAGs%29%20affiliated%20with%20the%20genus%20Agarilytica%20that%20exhibited%20an%20exceptional%20expansion%20of%20preficted%20extracellular%20short-chain-length%20PHA%20depolymerase%20genes%20%28ephaZscl%29%20with%20up%20to%2014%20copies%20per%20genome%2C%20far%20exceeding%20the%20one-to-two%20copies%20typically%20reported.%20Comparative%20genomic%20and%20structural%20analyses%20revealed%20gene%20duplication%20and%20fusion%20events%2C%20given%20rise%20to%20tandem%20or%20chimeric%20depolymerases%20that%20may%20enhance%20catalytic%20diversity%20and%20substrate%20accessibility.%20Three-dimensional%20structural%20modeling%20confirmed%20that%20these%20fusion%20proteins%20retained%20functional%20catalytic%20domains%20with%20potential%20cooperative%20or%20independent%20activity.%20Such%20genomic%20redundancy%20and%20structural%20diversification%20likely%20confer%20an%20adaptive%20advantage%20for%20PHB%20biodegradation%20in%20marine%20environment.%20Collectively%2C%20our%20findings%20provide%20new%20insights%20into%20the%20ecological%20and%20evolutionary%20strategies%20of%20marine%20PHB%20degraders%20and%20highlight%20the%20power%20of%20DNA-SIP%20metagenomic%20for%20elucidating%20active%20plastic%20biodegradation%20pathways%20under%20natural%20conditions.%22%2C%22date%22%3A%222026-06-19%22%2C%22section%22%3A%22%22%2C%22partNumber%22%3A%22%22%2C%22partTitle%22%3A%22%22%2C%22DOI%22%3A%2210.1016%5C%2Fj.jhazmat.2026.142755%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22%22%2C%22PMID%22%3A%2242330901%22%2C%22PMCID%22%3A%22%22%2C%22ISSN%22%3A%221873-3336%22%2C%22language%22%3A%22eng%22%2C%22collections%22%3A%5B%5D%2C%22dateModified%22%3A%222026-06-23T07%3A38%3A32Z%22%7D%7D%2C%7B%22key%22%3A%22SSDR4QCE%22%2C%22library%22%3A%7B%22id%22%3A3888256%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Un%20et%20al.%22%2C%22parsedDate%22%3A%222026-06-08%22%2C%22numChildren%22%3A1%7D%2C%22bib%22%3A%22%26lt%3Bdiv%20class%3D%26quot%3Bcsl-bib-body%26quot%3B%20style%3D%26quot%3Bline-height%3A%201.35%3B%20padding-left%3A%201em%3B%20text-indent%3A-1em%3B%26quot%3B%26gt%3B%5Cn%20%20%26lt%3Bdiv%20class%3D%26quot%3Bcsl-entry%26quot%3B%26gt%3BUn%2C%20Sun%2C%20Zolt%26%23xE1%3Bn%20Garda%2C%20Damila%20Mihovilcevic%2C%20Tania%20Tibiletti%2C%20and%20%26%23xC9%3Bva%20T%26%23xF3%3Bth.%202026.%20%26%23x201C%3BMn%28II%29%2019F%20Electron-Nuclear%20Double%20Resonance%20Spectroscopy%20as%20a%20Structural%20Tool%3A%20Resolution%20of%20the%20Structural%20Diversity%20of%20a%20Mn%28II%29%20Dual%2019F%5C%2F1H%20MRI%20Probe.%26%23x201D%3B%20%26lt%3Bi%26gt%3BJournal%20of%20the%20American%20Chemical%20Society%26lt%3B%5C%2Fi%26gt%3B%2C%20ahead%20of%20print%2C%20June%208.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1021%5C%2Fjacs.6c00899%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1021%5C%2Fjacs.6c00899%26lt%3B%5C%2Fa%26gt%3B.%26lt%3B%5C%2Fdiv%26gt%3B%5Cn%26lt%3B%5C%2Fdiv%26gt%3B%22%2C%22data%22%3A%7B%22itemType%22%3A%22journalArticle%22%2C%22title%22%3A%22Mn%28II%29%2019F%20Electron-Nuclear%20Double%20Resonance%20Spectroscopy%20as%20a%20Structural%20Tool%3A%20Resolution%20of%20the%20Structural%20Diversity%20of%20a%20Mn%28II%29%20Dual%2019F%5C%2F1H%20MRI%20Probe%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sun%22%2C%22lastName%22%3A%22Un%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Zolt%5Cu00e1n%22%2C%22lastName%22%3A%22Garda%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Damila%22%2C%22lastName%22%3A%22Mihovilcevic%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Tania%22%2C%22lastName%22%3A%22Tibiletti%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22%5Cu00c9va%22%2C%22lastName%22%3A%22T%5Cu00f3th%22%7D%5D%2C%22abstractNote%22%3A%22The%20use%20of%20bio-orthogonal%2019F%20nuclei%20has%20an%20important%20impact%20on%20magnetic%20resonance.%2019F%20MRI%20and%2019F%20electron-nuclear%20double-resonance%20%28ENDOR%29-based%20structural%20measurements%20are%20two%20prominent%20examples.%20We%20demonstrate%20here%20the%20first%20application%20of%20Mn%28II%29%20for%2019F%20ENDOR%20distance%20measurements%20and%20its%20potential%20to%20reveal%20otherwise%20inaccessible%20structural%20details%20in%20an%20emerging%20class%20of%20fluorinated%20Mn%28II%29%20MRI%20agents.%20We%20show%20that%20Mn%28II%29%2019F%20ENDOR%20spectroscopy%20can%20not%20only%20provide%20accurate%20nominal%20Mn-19F%20distances%20but%20also%20their%20distributions%20using%20well-established%20Tikhonov%20regularization%20techniques.%20Even%20the%20individual%20fluorines%20of%20an%20F3C%20group%20could%20be%20resolved.%20DFT%20calculations%20allow%20the%20translation%20of%20the%20ENDOR%20data%20to%20molecular%20structures.%20The%20potential%20of%20using%20ab%20initio%20molecular%20dynamics%20%28AIMD%29%20to%20connect%20these%20frozen%20solution%20structures%20to%20the%20room-temperature%20ones%20relevant%20to%20MRI%20applications%20is%20demonstrated.%20Distance%20measurements%20using%20Mn%28II%29%2019F%20ENDOR%20and%20Tikhonov%20analysis%20represent%20a%20promising%20approach%2C%20relevant%20also%20to%20structural%20biological%20applications%20where%20the%20use%20of%20the%20redox-stable%2C%20nontoxic%20Mn%28II%29%20has%20an%20obvious%20advantage.%22%2C%22date%22%3A%222026-06-08%22%2C%22section%22%3A%22%22%2C%22partNumber%22%3A%22%22%2C%22partTitle%22%3A%22%22%2C%22DOI%22%3A%2210.1021%5C%2Fjacs.6c00899%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22%22%2C%22PMID%22%3A%2242253145%22%2C%22PMCID%22%3A%22%22%2C%22ISSN%22%3A%221520-5126%22%2C%22language%22%3A%22eng%22%2C%22collections%22%3A%5B%5D%2C%22dateModified%22%3A%222026-06-09T14%3A09%3A51Z%22%7D%7D%5D%7D
Boëffard-Dosierre, Liza, Camille Dagallier, Géraldine Eudier, et al. 2026. “NMR Detects Clustering and Ultra-Weak Excipient Interactions Governing Monoclonal Antibody Viscosity in Formulation-Relevant Conditions.” mAbs 18 (1): 2685366. https://doi.org/10.1080/19420862.2026.2685366.
Baños-Gutiérrez, J., R. Bercy, Y. García Jomaso, et al. 2026. “Molecular Structure, Binding, and Disorder in TDBC-Ag Plexcitonic Assemblies.” The Journal of Chemical Physics 165 (1): 014702. https://doi.org/10.1063/5.0325564.
He, Wei, Jen-Wei Huang, Yalong Wang, et al. 2026. “Deciphering Protein Mutation-Phenotype Linkages from CRISPR-Based Tiling Mutagenesis Screens.” Cell Systems, June 26, 101651. https://doi.org/10.1016/j.cels.2026.101651.
Barbe, Valérie, Camille Saint-Picq, Charlène Odobel, et al. 2026. “Unveiling Plastic Biodegradation Pathways through 13C-DNA Stable Isotope Probing and Metagenomics.” Journal of Hazardous Materials 514 (June): 142755. https://doi.org/10.1016/j.jhazmat.2026.142755.
Un, Sun, Zoltán Garda, Damila Mihovilcevic, Tania Tibiletti, and Éva Tóth. 2026. “Mn(II) 19F Electron-Nuclear Double Resonance Spectroscopy as a Structural Tool: Resolution of the Structural Diversity of a Mn(II) Dual 19F/1H MRI Probe.” Journal of the American Chemical Society, ahead of print, June 8. https://doi.org/10.1021/jacs.6c00899.

Education

Scroll to Top