Emmanuelle Bignon

We report a comprehensive study of the photoinduced isomerization–cyclization cascade of o ‐amino(hetero)arylidenethiazolidine‐2,4‐diones (Het)Ar‐TZDs 1 , combining computational, synthetic, and kinetic investigations. Time‐dependent density functional theory (TD‐DFT) calculations were used to predict absorption maxima and to elucidate key structure‐property relationships, highlighting the dominant influence of substitution at position 4 of the aromatic ring of 1 . Guided by these results, a broad library of o ‐amino‐TZDs 1 was designed and synthesized, including heteroaryl analogues. Photochemical investigations demonstrated that the sequence is highly robust, overall, proceeding efficiently across a wide range of substrates and displaying a broad tolerance toward variations in their electronic properties or substitution patterns. A detailed kinetic analysis using ex situ and in situ ¹ H NMR experiments was conducted and enabled a quantitative comparison of reaction efficiencies as a function of substituents on the aromatic ring, the TZD core, and the exocyclic double bond, across series 1(a) to 1(d) . Overall, this work establishes a fine structure‐reactivity framework for this photochemical cascade, identifying the key parameters governing its efficiency.

Nucleopeptide-based hydrogels are attracting growing interest owing to their biocompatibility and wide range of applications, particularly in biotechnology. Their enhanced versatility compared to purely peptide-based systems enables fine-tuning of macroscopic properties to meet specific requirements. However, rational optimization of these materials requires a thorough understanding of their atomic-scale organization, which remains challenging due to the inherent nature of these amorphous, soft, and highly hydrated materials. In this context, nuclear magnetic resonance (NMR) spectroscopy emerges as a powerful technique for gaining valuable insights into both the isotropic and anisotropic phases of the samples. This work focuses on developing a unique combination of NMR methodologies to characterize the structural and dynamical parameters of these hydrogels. Fast-field cycling (FFC) NMR relaxometry is employed to probe the dynamical changes occurring during the gelation process and to elucidate the complex mechanisms driving the liquid-to-gel transition. Furthermore, solid-state NMR (ssNMR) experiments, performed on samples in protonated and deuterated solvents, provide key insights into the intermolecular interactions that structure the three-dimensional gel network. Molecular dynamics (MD) simulations corroborate these experimental findings and assess the stability and prevalence of various noncovalent interactions, while shedding light on the role of Watson–Crick pairing during the initial oligomerization steps.

Eukaryotic genomic DNA is packaged into chromatin as nucleosomes, where it remains susceptible to reactive oxygen species (ROS) that generate the mutagenic lesion 8-oxo-7,8-dihydroguanine (8oxoG). While 8-oxoguanine DNA glycosylase 1 (OGG1) can initiate repair of 8oxoG base paired with C within the nucleosome core particle (NCP) in a position- dependent manner, it is unknown whether MutY homolog (MUTYH), the DNA glycosylase that excises misincorporated A opposite 8oxoG, can initiate repair of 8oxoG:A base pairs within NCPs. To address this, we combined cryo-EM, molecular dynamics (MD) simulations, and biochemical assays. We determined that MUTYH activity on nucleosomal 8oxoG:A is strongly suppressed, with detectable excision limited to the entry/exit region. Cryo-EM structures at four superhelical locations reveal that 8oxoG adopts the syn conformation and Hoogsteen base pairs with A, as in non-nucleosomal DNA, indicating that lesion presentation is not altered by the histone octamer. MD simulations further reveal that 8oxoG:A base pair dynamics and local DNA backbone perturbations are similar in nucleosomal and non-nucleosomal DNA. Together, these data establish that the NCP sterically excludes MUTYH from 8oxoG:A base pairs, making them largely inaccessible to MUTYH processing. This work ultimately provides mechanistic insight for the elevated G to T transversion rate observed in histone-bound DNA following oxidative stress.

Molecular dynamics is a key technique for exploring biomolecular systems at the atomic level. The rapid growth in accessible system sizes and time scales has intensified the need for efficient postprocessing methods that extract meaningful insights from the resulting data. Interaction fingerprint (IFP) analyses are a valuable tool for elucidating key atomic interactions within molecular ensembles; yet current specialized software often struggle with extensive trajectories or complex systems. Here, we introduce InterMap, a Python package designed to accelerate IFP detection on large-scale molecular ensembles. By actively exploiting k-d trees, InterMap efficiently handles the massive amount of distance calculations necessary to detect IFPs, particularly when dealing with intramolecular interactions. The seamless integration with MDAnalysis ensures broad format compatibility and allows using SMARTS patterns for flexible interaction definitions. InterMap adopts a deeply compressed binary encoding to manage IFPs, which makes it very memory-friendly. Furthermore, convenient interactive visualizations are provided to enhance data interpretation through a locally hosted web-browser application. Benchmark results indicate that InterMap significantly outperforms existing tools for processing complex biomolecular systems, achieving up to a 99% reduction in both runtime and peak memory usage. InterMap’s code and issue tracker are available at https://github.com/rglez/intermap, while documentation and tutorials can be found at https://rglez.github.io/intermap/.

Cyanobacteria have produced Earth’s oxygen for 2.4 billion years by adapting to fluctuating irradiance. This adaptation relies on orange carotenoid protein (OCP), which mediates light-intensity– dependent photoprotective energy dissipation using a unique two-photon absorption mechanism. Photon absorption by ground-state OCP (OCP ^O ) generates a metastable intermediate (OCP ^1hν ) that either relaxes thermally or, upon absorption of a second photon within ∼1 s, converts to the active photoprotective state (OCP ^R ). By integrating static and time-resolved crystallography, cryo-EM, computation, spectroscopy and biochemistry, we assign the structure of OCP ^1hν , establish its functional relevance and capture structural snapshots along the OCP ^O →OCP ^1hν and OCP ^1hν →OCP ^R photochemical pathways. We elucidate the molecular mechanism of OCP, which serves as a unique biological circuit breaker protecting the photosynthetic machinery from high light flux.

Eukaryotic genomic DNA is packaged into chromatin through a fundamental repeating unit known as the nucleosome core particle. Within this chromatin context, genomic DNA is constantly exposed to endogenous and exogenous stress that result in the formation of DNA damage, which must be effectively repaired to maintain genome stability. Single-strand breaks (SSBs) are among the most prevalent forms of DNA damage that arise via the oxidation-induced disintegration of the sugar-phosphate backbone or as repair intermediates during base excision repair. DNA ligase IIIα (LigIIIα) is one of the primary enzymes responsible for repairing SSBs containing an intact 5′-phosphate and 3′-OH (nick) during the terminal step of single-strand break repair (SSBR) and base excision repair (BER) pathways. To date, a complete mechanistic description for how LigIIIα processes nicks within chromatin remains elusive. Here, we use a combination of biochemical assays, molecular dynamics simulations, and cryogenic electron microscopy (cryo-EM) to define the molecular basis of nick ligation in the nucleosome by LigIIIα. Quantitative enzyme kinetics reveal that the LigIIIα ligation rate is highly dependent on the translational position of the nick in the nucleosome, where nicks near the nucleosome entry/exit site are ligated with moderate efficiency and nicks near the nucleosome dyad are refractory to ligation. Cryo-EM structures of LigIIIα bound to nicks at four unique translational positions in the nucleosome reveal the structural basis for this position-dependent catalytic activity, identifying that local steric constraints imposed by the histone octamer prevent LigIIIα from readily adopting a ligation-competent conformation. Further biochemical and structural analysis demonstrates that the scaffolding protein XRCC1, which forms a heterodimer with LigIIIα, does not substantially alter the ability of LigIIIα to bind or ligate nicks in the nucleosome. Together, this work provides foundational insight into the processing of nicks in the nucleosome during the terminal step of SSBR/BER.

Étude théorique de lésions complexes de l'ADN : de la formation à la réparation: Ce travail de thèse vise à étudier l'endommagement de l'ADN, de la formation de lésions à leur réparation par des méthodes de modélisation moléculaire. Plusieurs projets ont pris forme dans ce contexte, lesquels peuvent être classés en trois grandes catégories. D'un côté, nous nous sommes intéressés la formation de lésions induites par des agents mutagènes. Nous avons étudié les mécanismes de formation de la 8-oxo-7,8-dihydroguanine (8oxoG), mais aussi le caractère de photosensibilisateur endogène de la pyrimidine 6-4 pyrimidone (6-4PP), et la photosensibilisation de l'ADN par deux anti-inflammatoires : le kétoprofène et l'ibuprofène. D'un autre côté, les propriétés mécaniques de l'ADN endommagé ont été simulées. La structure de lésions complexes est d'une importance capitale pour comprendre la manière dont elles sont réparées. Malheureusement, seulement peu de structures RMN et cristallographiques sont disponibles à ce jour. Pour pallier à ce manque et obtenir des informations sur leur dynamique, nous avons étudié un panel de lésions complexes : les clusters de sites abasiques, les pontages inter-brins, et la photolésion 6-4PP. De même, nous nous sommes penchés sur les modes d'interaction de certaines polyamines avec l'ADN, ces molécules étant connues pour interagir avec la double hélice. Enfin, latroisième partie de cette thèse concerne les interactions ADN-enzyme de réparation. En perspective avec l'étude de clusters d'abasiques, nous avons étudié le comportement dynamique du même système, cette fois-ci en interaction avec l'endonucléase APE1. Nous nous sommes également penchés sur les interactions entre la glycosylase Fpg avec un oligonucléotide contenant un tandem de lésions 8-oxoG d'un côté, etun cluster de lésions 8-oxoG - site abasique de l'autre. Ces multiples projets ont permis l'accumulation de nouvelles connaissances à propos des lésions complexes de l'ADN, et ont également apporté un appuicomputationnel aux expérimentations, qui peuvent se révéler très délicates dans ce domaine. Nos résultats ouvrent de larges perspectives dans le domaine de la pharmacologie, la cosmétique et plus généralementla compréhension du vivant

Motivation: Molecular dynamics is a key technique for exploring biomolecular systems at the atomic level. The rapid growth in accessible system sizes and timescales has intensified the need for efficient post-processing methods that extract meaningful insights from the resulting data. Interaction fingerprint (IFP) analyses are a valuable tool for elucidating key atomic interactions within molecular ensembles, yet current specialized software often struggle with extensive trajectories or complex systems. Here, we introduce InterMap, a Python package designed to accelerate IFP detection on large-scale molecular ensembles. Results: By actively exploiting k-d trees, InterMap efficiently handles the massive amount of distance calculations necessary to detect IFPs, particularly when dealing with intra-molecular interactions. The seamless integration with MDAnalysis ensures broad format compatibility and allows using SMARTS patterns for flexible interaction definitions. InterMap adopts a deeply compressed binary encoding to manage IFPs, which makes it very memory-friendly. Furthermore, convenient interactive visualizations are provided to enhance data interpretation through a locally hosted web-browser application. Benchmark results indicate that InterMap significantly outperforms existing tools for processing complex biomolecular systems, achieving up to a 99% reduction in both runtime and peak memory usage. Availability: InterMap’s code and issue tracker are available at https://github.com/Delta-Research-Team/intermap.git , while documentation and tutorials can be found at https://delta-research-team.github.io/intermap/ . Contact: roy.gonzalez-aleman@inria.fr , yasaman.karami@inria.fr Supplementary information: Supplementary data are available at Nucleic Acid Research online.

Proteins, RNA, and DNA are central to virtually all cellular processes, often assembling into macromolecular complexes to perform their functions. While these molecules are inherently dynamic, most methods for studying their mechanisms focus on static structures. Recent deep learning advances in protein structure prediction highlight the potential of data-driven approaches, yet dynamic behavior that is critical for interactions such as antibody–antigen recognition, intrinsically disordered proteins, and protein–nucleic acid binding, remains underexplored. To address this gap, we present DynaRepo, a repository of macromolecular conformational dynamics comprising $\sim$450 complexes and $\sim$270 single-chain proteins from PDBbind, the Structural Antibody Database (SAbDab), and benchmark sets. Each complex was simulated in triplicate for 500 ns, totaling $>$1100 $\mu$s of molecular dynamics data, with extensive pre-calculated analyses. DynaRepo provides a foundation for dynamics-aware deep learning frameworks and is freely available at: https://dynarepo.inria.fr/.

Sirtuins are a class of NAD-dependent histone deacetylases that regulate important biological pathways in prokaryotes and eukaryotes. This enzyme family comprises seven members, named SIRT1 to SIRT7. Among them, Sirtuin 6 (SIRT6) is a human sirtuin that deacetylates histones and plays a key role in DNA repair, telomere maintenance, carbohydrate and lipid metabolism, and lifespan. SIRT6’s structure consists of a zinc finger domain, a Rossmann fold domain containing the NAD+ binding site, and disordered N-terminal and C-terminal (CTD) extensions. The specific role of the CTD in SIRT6’s interaction with nucleosomes for histone deacetylation remains unclear. Here, we resort to extended molecular dynamics simulations to uncover the dynamical behavior of the full-length SIRT6 bound to a nucleosome core particle. Our simulations reveal that the CTD preferentially interacts with DNA at the entry/exit near the enzyme’s docking site, exhibiting a variety of different binding modes. In specific cases, the CTD contributes to the promotion of DNA unwrapping and enhances H3K27 accessibility to SIRT6’s active site, suggesting a pivotal role of this domain for H3K27 deacetylation. This work provides new structural insights into the binding process of the full-length SIRT6 to a nucleosome core particle, shedding light on the conformational behavior and functional role of its CTD. It constitutes an important step toward understanding of SIRT6 deacetylation mechanisms and specificity.