Biology subjects

Fournet, A.

Publications and source records attributed to Fournet, A..

5 recordsLinked to original sources

bioRxiv2026

Conformational ensembles of flexible multidomain proteins: How close are we to accurate and reliable predictions?

Multidomain proteins connected by flexible linkers populate conformational ensembles that are challenging to characterize using conventional structural biology methods. In domain-linker-domain (DLD) proteins, linker-mediated inter-domain relative positions and orientations are functionally relevant, yet their dynamical behavior in solution normally remain poorly described. Small-angle X-ray scattering (SAXS) provides ensemble-averaged structural information for such systems; however, coupling with computational modeling is required to accurately describe the dynamic behavior of this family of proteins in solution. Here, we present a systematic evaluation of five ensemble-generation strategies applied to a set of eighteen proteins sharing the same two globular domains, connected by naturally occurring linkers of varying length and composition. Modeling methods based on different underlying principles are compared by assessing their agreement to experimental SAXS data, showing a large disparity and systematic structural biases among them. Furthermore, for each approach, we examine the effect of refinement against SAXS restraints and assess its capacity to describe the experimental data, as well as the induced biases in global dimensions and inter-domain distance distributions. This analysis underlines the importance of the initial conformational pool for deriving experimentally compatible ensembles. Overall, this work provides a high-quality benchmark for SAXS-driven ensemble modeling of flexible, multidomain proteins and establishes a framework for the critical interpretation of solution scattering data in systems with pronounced conformational heterogeneity.

biophysics↗

bioRxiv2025

Interplay Between Intrinsically Disordered Proteins and Atomically Precise Gold Nanoclusters Modulates their Optical Properties

Understanding how structural and optical properties of metallic nanoclusters can be tuned by proteins is crucial for the use of these hybrid molecules in biomedical applications. The interaction of proteins with ultrasmall, atomically-precise gold nanoclusters (Au-NCs) has been mainly investigated in the context of structured proteins, while their behavior with intrinsically disordered proteins (IDPs) remains unexplored. This work examines the structural and optical properties of Au-NCs interacting with bioengineered IDPs containing up to three cysteines. We show that, by exploiting the conformational flexibility of cysteine-containing IDPs, we can anchor proteins to Au-NCs in a position-specific manner, leading to new bioconjugates with properties that differ from those of the individual components. We observed an up to 15-fold photoluminescence enhancement depending on the number of cysteines anchored. By combining mass spectrometry, small-angle X-ray scattering (SAXS), and computational modelling, the ensemble structures of nine bioconjugates with different stoichiometries were elucidated, indicating their overall compactness. Our results suggest that the interface between these atomically-precise species and the conformationally fluctuating protein is responsible for the optical properties of these nanobioconjugates. This research improves our understanding of Au-NC- protein interactions, paving the way to novel nano-molecular hybrid conjugates with tunable properties for bioimaging and therapeutic applications.

biochemistry↗

bioRxiv2023

Site-Specific Introduction of Alanines for the NMR Investigation of Low-Complexity Regions and Large Biomolecular Assemblies

NMR studies of large biomolecular machines and highly repetitive proteins remain challenging due to the difficulty of assigning signals to individual nuclei. Here, we present an efficient strategy to address this challenge by engineering a Pyrococcus horikoshii tRNA/alanyl-tRNA synthetase pair that enables the incorporation of up to three isotopically labeled alanine residues in a site-specific manner using in vitro protein expression. We have demonstrated the general applicability of this approach for NMR assignment by introducing isotopically labeled alanines into four proteins, including the 300-kDa molecular chaperone ClpP and the alanine-rich Phox2B transcription factor. For large protein assemblies, our labeling approach enables unambiguous assignments, while avoiding potential artefacts induced by site-specific mutations. When applied to Phox2B, which contains two poly-alanine tracts of nine and twenty alanines, we observe that the helical stability is strongly dependent on the homorepeat length, demonstrating structural cooperativity. The capacity to selectively introduce alanines with distinct labeling patterns is a powerful tool to probe structure and dynamics of biomolecular systems that are out of the reach of traditional structural biology methods.

biochemistry↗

bioRxiv2023

Phosphorylation motif dictates GPCR C-terminal domain conformation and arrestin interaction

Arrestin dependent G protein-coupled receptor (GPCR) signaling pathway is regulated by the phosphorylation state of GPCRs C-terminal domain, but the molecular bases of arrestin:receptor interaction are to be further illuminated. Here we investigated the impact of phosphorylation on the conformational features of the C-terminal region from three Rhodopsin-like GPCRs, the vasopressin V2 Receptor (V2R), the Growth Hormone Secretagogue or ghrelin Receptor type 1a (GHSR) and the {beta}2-Adernergic Receptor ({beta}2AR). Using phosphomimetic variants, we identified pre-formed secondary structure elements, or short linear motif (SLiMs), that undergo specific conformational transitions upon phosphorylation. Of importance, such conformational transition favors arrestin-2 binding. Hence, our results suggest a model in which the cellular signaling specificity of GPCRs is encoded in the phosphorylation-dependent structuration of the C-terminal regions, which will subsequently modulate arrestin conformation and therefore GPCR:arrestin signaling outcomes.

biophysics↗

bioRxiv2022

The structure of pathogenic huntingtin exon-1 defines the bases of its aggregation propensity

Huntingtons Disease is a neurodegenerative disorder caused by a CAG expansion of the first exon of the HTT gene, resulting in an extended poly-glutamine (poly-Q) tract in the N-terminus of the protein huntingtin (httex1). The structural changes occurring to the poly-Q when increasing its length remain poorly understood mainly due to its intrinsic flexibility and the strong compositional bias of the protein. The systematic application of site-specific isotopic labeling has enabled residue-specific NMR investigations of the poly-Q tract of pathogenic httex1 variants with 46 and 66 consecutive glutamines. The integrative analysis of the data reveals that the poly-Q tract adopts long -helical conformations stabilized by glutamine side-chain to backbone hydrogen bonds. 19F-NMR of site-specifically incorporated fluoro-glutamines and molecular dynamics simulations demonstrate that the mechanism propagating -helical conformations towards the poly-Q from the upstream N17 domain is independent of the poly-Q track length. Aggregation and atomic force microscopy experiments show that the presence of long and persistent -helices in the poly-Q tract is a stronger signature in defining the aggregation kinetics and the structure of the resulting fibrils than the number of glutamines. The ensemble of our observations provides a structural perspective of the pathogenicity of expanded httex1 and paves the way to a deeper understanding of poly-Q related diseases.

biophysics↗