Biology subjects

Riviere, G.

Publications and source records attributed to Riviere, G..

5 recordsLinked to original sources

bioRxiv2026

A Heart Disease-Associated TSPO Variant Alters Transmembrane Helix Dynamics

The 18-kDa translocator protein TSPO is an outer mitochondrial membrane protein involved in cholesterol transport, stress response, and cellular metabolism. Although its five-helix architecture is conserved across species, the structural and dynamic features of human TSPO remain unresolved. Using solution NMR spectroscopy, we characterize the conformational dynamics of human TSPO in complex with a third-generation diagnostic ligand. We identify a dynamic N-terminal segment of the first transmembrane helix that does not form a stably populated helix but instead defines a flexible boundary between the cytosolic region and the transmembrane core. The common disease-associated A14V variant reduces this conformational heterogeneity by introducing short-range contacts and redistributing backbone dynamics across the protein. These changes preserve the overall fold while locally stabilizing the N-terminal transmembrane helix toward the VDAC interaction interface. Our findings reveal a human-specific dynamic architecture of TSPO and link variant-induced stabilization to modulation of transmembrane helix dynamics.

biophysics↗

bioRxiv2026

Allosteric Inhibition of NDM-1 by Thanatin Preserves the Di-Zinc Center While Restricting Dynamics

The New Delhi metallo-{beta}-lactamase 1 (NDM-1) is a major driver of carbapenem resistance in Gram-negative pathogens, yet the molecular basis by which antimicrobial peptides inhibit this enzyme has remained unresolved. Thanatin, a disulfide-stabilized {beta}-hairpin peptide, was previously proposed to inactivate NDM-1 by displacing catalytic Zn{superscript 2} ions, but this model lacked direct structural support. Here, we combine high-resolution NMR spectroscopy, intermolecular NOE mapping, HADDOCK-guided docking, and molecular dynamics simulations to reveal a distinct zinc-retaining dynamic allosteric mechanism. Thanatin binds adjacent to the catalytic groove, preserving the native di-zinc coordination environment while simultaneously rigidifying the L3 catalytic loop, as confirmed by Zn-bound spectral fingerprints and EDTA titration experiments. This conformational restriction explains how the peptide inhibits the enzyme while maintaining a zinc-bound but catalytically compromised state, a finding that contrasts with zinc-displacement hypotheses and reconciles prior biochemical observations with structural data. In bacterial assays, this allosteric inhibition translates to a moderate restoration of carbapenem sensitivity, resulting in a 50% reduction in viable cell output even under high-level enzyme expression. Our findings establish a mechanistic framework for designing next-generation peptide inhibitors that target the dynamic vulnerabilities of metallo-{beta}-lactamases.

biophysics↗

bioRxiv2021

A novel mutation (E83Q) unlocks the pathogenicity of human alpha-synuclein fibrils and recapitulates its pathological diversity

A novel mutation (E83Q), the first in the NAC domain of alpha-synuclein (aSyn), was recently identified in a patient with dementia with Lewy bodies. We investigated the effects of this mutation on the aggregation of aSyn monomers and the structure, morphology, dynamic, and seeding activity of the aSyn fibrils in neurons. We found that it dramatically accelerates aSyn fibrillization and results in the formation of fibrils with distinct structural and dynamic properties. In cells, this mutation is associated with higher levels of aSyn, accumulation of pS129, and increased toxicity. In a neuronal seeding model of Lewy bodies (LB) formation, the E83Q mutation significantly enhances the internalization of fibrils into neurons, induce higher seeding activity and results in the formation of diverse aSyn pathologies, including the formation of LB-like inclusions that recapitulate the immunohistochemical and morphological features of brainstem LBs observed in PD patient brains. TeaserA novel mutation (E83Q) exacerbates alpha-synuclein aggregation and toxicity and reproduces PD pathological diversity.

neuroscience↗

bioRxiv2021

Profiling of N6-methyladenosine dynamics indicates regulation of oyster development by m6A-RNA epitranscriptomes

The N6-methylation of RNA adenosines (m6A) is an important regulator of gene expression with critical implications in vertebrate and insect development. However, the developmental significance of epitranscriptomes in lophotrochozoan organisms remains unknown. Using MeRIP-seq, we generated transcriptome-wide m6A-RNA methylomes covering the whole development of the oyster from oocytes to juveniles. Oyster RNA classes display specific m6A signatures, with mRNAs and lncRNAs exhibiting distinct profiles and being highly methylated compared to transposon transcripts. Epitranscriptomes are dynamic and correspond to chronological steps of development (cleavage, gastrulation, organogenesis and metamorphosis), with a minimal mRNA and lncRNA methylation at the morula stage followed by a global increase. mRNA m6A levels are correlated to transcript levels and shifts in methyladenine profiles correspond to expression kinetics. Differentially methylated transcripts cluster according to embryo-larval stages and bear the corresponding developmental functions (cell division, signal transduction, morphogenesis and cell differentiation). The m6A level of transposon transcripts is also regulated and peaks during the gastrulation. We demonstrate that m6A-RNA methylomes are dynamic and associated to gene expression regulation during oyster development. The putative epitranscriptome implication in the cleavage, maternal-to-zygotic transition and cell differentiation in a lophotrochozoan model brings new insights into the control and evolution of developmental processes

genomics↗

bioRxiv2021

Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate

NMR-assisted crystallography - the synergistic combination of solid-state NMR, X-ray crystallography, and first-principles computational chemistry - holds remarkable promise for mechanistic enzymology: by providing atomic-resolution characterization of stable intermediates in the enzyme active site - including hydrogen atom locations and tautomeric equilibria - it offers insight into structure, dynamics, and function. Here, we make use of this combined approach to characterize the -aminoacrylate intermediate in tryptophan synthase, a defining species for pyridoxal-5'-phosphate-dependent enzymes on the {beta}-elimination and replacement pathway. By uniquely identifying the protonation states of ionizable sites on the cofactor, substrates, and catalytic side chains, as well as the location and orientation of structural waters in the active site, a remarkably clear picture of structure and reactivity emerges. Most incredibly, this intermediate appears to be mere tenths of angstroms away from the preceding transition state in which the {beta}-hydroxyl of the serine substrate is lost. The position and orientation of the structural water immediately adjacent to the substrate {beta}-carbon suggests not only the fate of the hydroxyl group, but also the pathway back to the transition state and the identity of the active site acid-base catalytic residue. Reaction of this intermediate with benzimidazole (BZI), an isostere of the natural substrate, indole, shows BZI bound in the active site and poised for, but unable to initiate, the subsequent bond formation step. When modeled into the BZI position, indole is positioned with C3 in contact with the -aminoacrylate C{beta} and aligned for nucleophilic attack. Significance StatementThe determination of active site protonation states is critical to gaining a full mechanistic understanding of enzymatic transformations; yet hydrogen positions are challenging to extract using the standard tools of structural biology. Here we make use of a joint solid-state NMR, X-ray crystallography, and first-principles computational approach that unlocks the investigation of enzyme catalytic mechanism at this fine level of chemical detail. For tryptophan synthase, this allows us to peer along the reaction coordinates into and out of the -aminoacrylate intermediate. Through this process, we are developing a high-resolution probe for structural biology that is keenly sensitive to proton positions - rivaling that of neutron diffraction, yet able to be applied under conditions of active catalysis to microcrystalline and non-crystalline materials.

biophysics↗