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%22NZJVC6YK%22%2C%22library%22%3A%7B%22id%22%3A3888256%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Villa%20et%20al.%22%2C%22parsedDate%22%3A%222026-07-14%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%3BVilla%2C%20J.%20Francisco%2C%20Sumedha%20Kondekar%2C%20Yoann%20Fauconnet%2C%20et%20al.%202026.%20%26%23x201C%3BUnveiling%20a%20Missing%20Component%20of%20the%20Atypical%20Type%20IV%20Secretion%20System%20Required%20for%20Natural%20Transformation%20of%20Helicobacter%20Pylori.%26%23x201D%3B%20%26lt%3Bi%26gt%3BPLoS%20Pathogens%26lt%3B%5C%2Fi%26gt%3B%2022%20%287%29%3A%20e1014140.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1371%5C%2Fjournal.ppat.1014140%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1371%5C%2Fjournal.ppat.1014140%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%20a%20missing%20component%20of%20the%20atypical%20type%20IV%20secretion%20system%20required%20for%20natural%20transformation%20of%20Helicobacter%20pylori%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J.%20Francisco%22%2C%22lastName%22%3A%22Villa%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Sumedha%22%2C%22lastName%22%3A%22Kondekar%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yoann%22%2C%22lastName%22%3A%22Fauconnet%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22M%5Cu00e9rick%22%2C%22lastName%22%3A%22Machouri%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22C%5Cu00e9line%22%2C%22lastName%22%3A%22Lacrouts%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Xavier%22%2C%22lastName%22%3A%22Veaute%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Rapha%5Cu00ebl%22%2C%22lastName%22%3A%22Gu%5Cu00e9rois%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Eduardo%20P.%20C.%22%2C%22lastName%22%3A%22Rocha%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jessica%22%2C%22lastName%22%3A%22Andreani%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22J.%20Pablo%22%2C%22lastName%22%3A%22Radicella%22%7D%5D%2C%22abstractNote%22%3A%22Exchange%20of%20genetic%20information%20by%20natural%20transformation%20shapes%20bacterial%20evolution.%20In%20Helicobacter%20pylori%20it%20is%20thought%20to%20drive%20its%20unusually%20high%20recombination%20rate%2C%20which%20has%20a%20crucial%20role%20in%20the%20evolution%20of%20virulence%20and%20the%20propagation%20of%20antibiotics%20resistance%20genes.%20While%20in%20most%20cases%20uptake%20of%20the%20incoming%20DNA%20into%20the%20periplasm%20is%20mediated%20by%20type%20IV%20pili%2C%20in%20H.%20pylori%20this%20initial%20step%20of%20natural%20transformation%20requires%20ComB%2C%20a%20unique%20competence-specific%20type%20IV%20secretion%20system%20%28T4SS%29.%20The%20mechanisms%20by%20which%20ComB%20mediates%20DNA%20uptake%20are%20still%20poorly%20understood%2C%20since%20T4SS%20are%20usually%20involved%20in%20an%20opposite%20process%20of%20DNA%20export.%20Here%2C%20we%20identify%20a%20gene%20%28hp1421%29%20that%20is%20absolutely%20required%20for%20uptake%20of%20the%20transforming%20DNA%20into%20the%20periplasm%2C%20although%20distant%20from%20the%20comB%20operons.%20We%20show%20that%20hp1421%20codes%20for%20a%20hexameric%20ATPase%20from%20the%20VirB11%20family.%20HP1421%20is%20present%20in%20the%20cytoplasm%20and%20interacts%20with%20ComB4%2C%20another%20ATPase%20of%20the%20T4SS%20inner%20membrane%20subcomplex.%20The%20structural%20modelling%20and%20functional%20analysis%20of%20HP1421%20and%20its%20interaction%20with%20ComB4%20indicate%20that%20HP1421%20is%20a%20missing%20component%20of%20the%20ComB%20inner-membrane%20subcomplex%20that%20we%20propose%20to%20name%20ComB11.%20Phylogenetic%20analyses%20show%20that%20comB11%20is%20a%20H.%20pylori%20core%20gene%20and%20suggest%20that%20the%20competence-dedicated%20ComB%20T4SS%20was%20a%20recent%20acquisition%20within%20Helicobacteraceae.%20Hence%2C%20co-option%20of%20the%20T4SS%20for%20DNA%20transformation%20requires%20nearly%20all%20the%20proteins%20that%20were%20previously%20essential%20for%20DNA%20conjugation.%22%2C%22date%22%3A%222026-07-14%22%2C%22section%22%3A%22%22%2C%22partNumber%22%3A%22%22%2C%22partTitle%22%3A%22%22%2C%22DOI%22%3A%2210.1371%5C%2Fjournal.ppat.1014140%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22%22%2C%22PMID%22%3A%2242447168%22%2C%22PMCID%22%3A%22%22%2C%22ISSN%22%3A%221553-7374%22%2C%22language%22%3A%22eng%22%2C%22collections%22%3A%5B%5D%2C%22dateModified%22%3A%222026-07-15T13%3A30%3A44Z%22%7D%7D%2C%7B%22key%22%3A%22LFD6P4VF%22%2C%22library%22%3A%7B%22id%22%3A3888256%7D%2C%22meta%22%3A%7B%22creatorSummary%22%3A%22Streckaite%20et%20al.%22%2C%22parsedDate%22%3A%222026-07-10%22%2C%22numChildren%22%3A2%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%3BStreckaite%2C%20Simona%2C%20Jevgenij%20Chmeliov%2C%20Vilius%20%26%23x10C%3Birgelis%2C%20et%20al.%202026.%20%26%23x201C%3BPhotoprotection%20in%20a%20Desert%20Moss%3A%20Dynamic%20Excitation%20Quenching%20during%20the%20Hydration%20Cycle%20of%20the%20Syntrichia%20Caninervis.%26%23x201D%3B%20%26lt%3Bi%26gt%3BPhotosynthesis%20Research%26lt%3B%5C%2Fi%26gt%3B%20164%20%284%29%3A%2039.%20%26lt%3Ba%20class%3D%26%23039%3Bzp-DOIURL%26%23039%3B%20href%3D%26%23039%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1007%5C%2Fs11120-026-01230-4%26%23039%3B%26gt%3Bhttps%3A%5C%2F%5C%2Fdoi.org%5C%2F10.1007%5C%2Fs11120-026-01230-4%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%22Photoprotection%20in%20a%20desert%20moss%3A%20dynamic%20excitation%20quenching%20during%20the%20hydration%20cycle%20of%20the%20Syntrichia%20caninervis%22%2C%22creators%22%3A%5B%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Simona%22%2C%22lastName%22%3A%22Streckaite%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Jevgenij%22%2C%22lastName%22%3A%22Chmeliov%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Vilius%22%2C%22lastName%22%3A%22%5Cu010cirgelis%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Marius%22%2C%22lastName%22%3A%22Franckevi%5Cu010dius%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Lena%22%2C%22lastName%22%3A%22Golubewa%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Benfeng%22%2C%22lastName%22%3A%22Yin%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Danielis%22%2C%22lastName%22%3A%22Rutkauskas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Chunhong%22%2C%22lastName%22%3A%22Yang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Leonas%22%2C%22lastName%22%3A%22Valkunas%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Yuanming%22%2C%22lastName%22%3A%22Zhang%22%7D%2C%7B%22creatorType%22%3A%22author%22%2C%22firstName%22%3A%22Bruno%22%2C%22lastName%22%3A%22Robert%22%7D%5D%2C%22abstractNote%22%3A%22Desiccation-tolerant%20mosses%20survive%20extreme%20water%20loss%20by%20activating%20efficient%20photoprotective%20mechanisms%20that%20prevent%20damage%20to%20the%20photosynthetic%20apparatus.%20The%20most%20resistant%20moss%20Syntrichia%20caninervis%20%28S.%20caninervis%29%20represents%20an%20important%20model%20for%20studying%20the%20molecular%20basis%20of%20dehydration%20resilience%3B%20however%2C%20the%20membrane%20and%20protein%20level%20processes%2C%20which%20enable%20rapid%20recovery%20of%20photosynthetic%20activity%20upon%20rehydration%2C%20remain%20insufficiently%20understood.%20In%20this%20work%2C%20we%20investigate%20the%20fluorescence%20%28FL%29%20dynamics%20of%20the%20photosynthetic%20apparatus%20of%20S.%20caninervis%20under%20three%20hydration%20states%20%28hydrated%2C%20dehydrated%20and%20desiccated%29%20in%20whole%20leaves%20using%20time-resolved%20FL%20spectroscopy.%20Time-resolved%20measurements%20with%20~%5Cu200910%20ps%20resolution%20were%20performed%20to%20resolve%20excitation%20dynamics%20in%20both%20photosystems%20I%20%28PSI%29%20and%20II%20%28PSII%29.%20The%20complex%20FL%20datasets%20were%20analysed%20using%20the%20spectral%20decomposition%20approach.%20Dehydrated%20and%20desiccated%20samples%20exhibit%20substantially%20reduced%20FL%20intensity%20compared%20to%20hydrated%20moss%20in%20steady-state%20experiments%2C%20indicating%20efficient%20quenching%20of%20chlorophyll%20excitation%20upon%20drying.%20The%20time-resolved%20FL%20measurements%20revealed%20that%20excitation%20transfer%20rates%20and%20the%20nature%20of%20quenched%20states%20strongly%20depend%20on%20hydration%20level%20in%20S.%20caninervis.%20In%20the%20hydrated%20state%2C%20FL%20dynamics%20are%20consistent%20with%20functional%20photosystems%20in%20plants.%20Upon%20dehydration%2C%20non-photochemical%20quenching%20is%20activated%20in%20both%20PSII%20and%20PSI%2C%20with%20PSII%20quenching%20persisting%20even%20at%20low%20temperatures.%20We%20therefore%20conclude%2C%20that%20S.%20caninervis%20employs%20few%20hydration-dependent%20photoprotective%20regimes%2C%20including%20distinct%20quenching%20mechanisms%20at%20both%20photosystems.%20Our%20results%20suggest%20the%20presence%20of%20ultrafast%20quenching%20processes%20under%20severe%20dehydration%2C%20which%20are%20progressively%20relieved%20during%20rehydration%20and%20replaced%20by%20alternative%20mechanisms%20supporting%20the%20recovery%20of%20photosynthetic%20activity.%22%2C%22date%22%3A%222026-07-10%22%2C%22section%22%3A%22%22%2C%22partNumber%22%3A%22%22%2C%22partTitle%22%3A%22%22%2C%22DOI%22%3A%2210.1007%5C%2Fs11120-026-01230-4%22%2C%22citationKey%22%3A%22%22%2C%22url%22%3A%22%22%2C%22PMID%22%3A%2242429878%22%2C%22PMCID%22%3A%22PMC13354704%22%2C%22ISSN%22%3A%221573-5079%22%2C%22language%22%3A%22eng%22%2C%22collections%22%3A%5B%5D%2C%22dateModified%22%3A%222026-07-15T13%3A35%3A10Z%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%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.
Villa, J. Francisco, Sumedha Kondekar, Yoann Fauconnet, et al. 2026. “Unveiling a Missing Component of the Atypical Type IV Secretion System Required for Natural Transformation of Helicobacter Pylori.” PLoS Pathogens 22 (7): e1014140. https://doi.org/10.1371/journal.ppat.1014140.
Streckaite, Simona, Jevgenij Chmeliov, Vilius Čirgelis, et al. 2026. “Photoprotection in a Desert Moss: Dynamic Excitation Quenching during the Hydration Cycle of the Syntrichia Caninervis.” Photosynthesis Research 164 (4): 39. https://doi.org/10.1007/s11120-026-01230-4.
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.

Education

Scroll to Top