A5025198449- Protein Structure and Dynamics
- Advanced Chemical Physics Studies
- Enzyme Structure and Function
- Mass Spectrometry Techniques and Applications
- DNA and Nucleic Acid Chemistry
- Molecular Spectroscopy and Structure
- Monoclonal and Polyclonal Antibodies Research
- Quantum, superfluid, helium dynamics
- Protein purification and stability
- X-ray Diffraction in Crystallography
- Crystallization and Solubility Studies
- RNA Interference and Gene Delivery
- DNA Repair Mechanisms
- Inorganic Fluorides and Related Compounds
- Amino Acid Enzymes and Metabolism
- Crystallography and molecular interactions
- Mitochondrial Function and Pathology
- Lanthanide and Transition Metal Complexes
- Supramolecular Chemistry and Complexes
- Receptor Mechanisms and Signaling
- RNA modifications and cancer
- Lipid Membrane Structure and Behavior
- RNA and protein synthesis mechanisms
- ATP Synthase and ATPases Research
- Synthesis and Reactivity of Heterocycles
University of Trento
2023-2025
Istituto Nazionale di Fisica Nucleare, Trento Institute for Fundamental Physics And Applications
2023-2025
Université de Strasbourg
2022-2024
Institut de Chimie de Strasbourg
2022-2024
Centre National de la Recherche Scientifique
2020-2024
Istituto Nazionale di Fisica Nucleare
2024
Laboratoire de Chimie
2020-2022
École Normale Supérieure de Lyon
2020-2022
Université Claude Bernard Lyon 1
2020-2021
Canadian Nautical Research Society
2021
The complexes of helium and neon with gaseous neutral molecules are generally perceived to be van der Waals adducts held together by physical (non-covalent) forces, owing the combination size (exchange) repulsion dispersion/induction attraction. Molecular beam experiments confirm that this is case for He-CF4 , Ne-CF4 adducts, but revealed interaction He Ne CCl4 features an appreciable contribution chemical components arise from anisotropy electron density enhances a charge transfer Ng...
Abstract Recent experiments on the title subject, performed with a high‐resolution crossed‐beam apparatus, have provided total ionization cross sections as function of collision energy between noble gas atoms, electronically excited in their metastable states (Ng*), and H 2 O, S, NH 3 reagents, well emitted electron spectra. This paper presents rationalization all experimental findings unifying picture to cast light basic chemical properties Ng* under conditions great relevance both from...
The systems studied in this work are gas-phase weakly bound adducts of the noble-gas (Ng) atoms with CCl4 and CF4. Their investigation was motivated by widespread current interest for intermolecular halogen bonding (XB), a structural motif recognized to play role fields ranging from elementary processes biochemistry. simulation static dynamic behaviors complex featuring XB requires formulation reliable accurate model potentials, whose development relies on detailed characterization strength...
Variants found in the respiratory complex I (CI) subunit genes encoded by mitochondrial DNA can cause severe genetic diseases. However, it is difficult to establish a priori whether single or combination of CI variants may impact oxidative phosphorylation. Here we propose computational approach based on coarse-grained molecular dynamics simulations aimed at investigating new variants. One primary associated with Leber hereditary optic neuropathy (m.14484T>C/MT-ND6) was used as test case and...
Understanding the impact of common germline variants on protein structure, function, and disease progression is crucial in cancer research. This study presents a comprehensive analysis EXO5 gene, which encodes DNA exonuclease involved repair that was previously associated with susceptibility. We employed an integrated approach combining genomic clinical data analysis, deep learning variant effect prediction, molecular dynamics (MD) simulations to investigate effects haplotypes dynamics,...
This study investigates, for the first time, ability of calixarene ligands to interact with G-quadruplex (GQ) DNA assemblies, which play a critical role in many biological processes, including gene expression regulation, telomere maintenance, and surveillance genome stability repair mechanisms. Specifically, interaction between two calix[4]arene compounds, featuring cationic or zwitterionic functional groups on their upper rim, parallel tetramolecular (TG4T)4 used as model, was analyzed...
Electron density redistribution upon the formation of water–methane complex arises from polarisation and charge transfer effects.
A combined analysis of both new (energy spectra emitted electrons) and previously published (ionization cross sections) experimental data, measured under the same conditions concerning electronically excited lighter noble gas -NH3 collisional autoionization processes, is carried out. Such an analysis, performed by exploiting a formulation full potential energy surface in real imaginary parts, provides direct information on energetics, structure, lifetime intermediate collision complex over...
Gas phase collisions of O2 by CH4, CF4, and CCl4 have been investigated with the molecular beam technique measuring both integral cross section value, Q, its dependence on collision velocity, v. The adopted experimental conditions appropriate to resolve oscillating "glory" pattern, a quantum interference effect controlled features intermolecular interaction, for all three case studies. analysis Q(v) data, performed adopting suitable representation potential function, provided basic...
Protein–calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as dynamics simulations. In this paper, we rely on all-atom, explicit-solvent simulations capture the electrostatically driven association of phosphonated calix-[4]-arene with cytochome-C, critically relies...
Glycine receptors (GlyR) are regulated by small-molecule binding at several allosteric sites. Cannabinoids like tetrahydrocannabinol (THC) and N-arachidonyl-ethanol-amide (AEA) potentiate the GlyR response but their mechanism of action is not fully established. By combining millisecond coarse-grained (CG) MD simulations powered Martini 3 with backmapping to all-atom representations, we have characterized cannabinoid-binding site(s) zebrafish GlyR-α1 active state atomic resolution. Based on...
New molecular beam scattering experiments are reported for the H2S-H2 system recording, under high angular and velocity resolution conditions, "glory" quantum interference in dependence of total cross section. The analysis experimental data permits determination, first time, a spherically averaged intermolecular potential this system. An evaluation significant cuts energy surface, obtained by accurate ab initio CCSD(T) calculations using large basis sets, combined with electronic charge...
Functionalized supramolecular cages are of growing importance in biology and biochemistry. They have recently been proposed as efficient auxiliaries to obtain high-resolution cocrystallized proteins. Here, we propose a molecular dynamics investigation the association sulfonated calix-[8]-arenes cytochrome c starting from initially distant proteins ligands. We characterize two main binding sites for calixarene on surface which perfect agreement with previous experiments regard structure...
Sequence dependence of the (6–4) photoproduct conformational landscape when embedded in six 25-bp duplexes is evaluated along extensive unbiased and enhanced (replica exchange with solute tempering, REST2) molecular dynamics simulations. The structural reorganization as central pyrimidines become covalently tethered traced back terms non-covalent interactions, DNA bending, extrusion adenines opposite strands. close sequence pattern impacts around lesion, inducing different upstream...
Calix[n]arenes' selective recognition of protein surfaces covers a broad range timely applications, from controlling assembly and crystallization to trapping partially disordered proteins. Here, the interaction para-sulfonated calix-[4]-arenes with cytochrome c is investigated through all-atom, explicit water molecular dynamics simulations which allow characterization two binding sites in quantitative agreement experimental evidence. Free energy calculations based on MM-PBSA...
Calcein leakage assays are a standard experimental set-up for probing the extent of damage induced by external agents on synthetic lipid vesicles. The fluorescence signal associated with calcein release from liposomes is signature vesicle disruption, transient pore formation or fusion. This type assay widely used to test membrane disruptive effect biological macromolecules, such as proteins, antimicrobial peptides and RNA also nanoparticles polymer, metal oxide core. Little known about that...
The interaction of para -sulfonato-calix[4]arene with a small antifungal protein is analyzed by molecular dynamics simulations, corroborating the presence two main binding sites at surface.
The main point of this paper concerns the theoretical characterisation effects induced by intermolecular interaction on electron density upon formation CH4-H2X (X=O,S) and CH4–Ng (Ng=Ar,Xe) complexes. work has been stimulated recent molecular scattering beams experiments, which out differences in both strength anisotropy potential between CH4–H2X respect to reference systems. Herein, attention is focused electronic charge polarisation particularly transfer (CT) involved partners, directly...
The supramolecular interaction between lanthanide complexes and proteins is at the heart of numerous chemical biological studies. Some these have demonstrated remarkable properties with or peptides in solution crystalline state. Here we used paramagnetism ions to characterize affinity two for ubiquitin. As process dynamic, acquired NMR data only reflect time average different steps. We molecular dynamics (MD) simulations get a deeper insight into detailed scenario microsecond scale. This...
We study the supramolecular interaction between ubiquitin and lanthanide complexes by paramagnetic NMR molecular dynamics. Our observations shed new light on dynamic processes these surface of protein.
We combine NMR and molecular dynamics to decipher the dynamic supramolecular association process between a peptide lanthanide complex.