A Quantum of Matter
From protein-ligand interactions to protein regulation: insights from molecular dynamics simulations
Alessio Bartocci
Department of Physics, University of Trento
Friday October 13, 2023 – 15.30
Aula B107 – Polo Ferrari, Povo 2
Bindings of small ligands to proteins are ruled by interactions between the ligand and residues in the protein binding site, which can be located in a small binding pocket or on the protein surface. Such interactions can directly modulate protein functions and conformations, which find considerable application in biochemical and pharmaceutical fields for selective drug design and surface recognition binding. Computational ways to investigate such systems are molecular dynamics simulations (MDs) which, spanning from atomistic to coarse-grained resolution, can give insights into the mechanisms, kinetics, and thermodynamics underpinning the protein-ligand complex formation. Here, it will be discussed how supramolecular complexes, formed by small proteins (as ubiquitine, cytochrome-C, penicillum antifungal) interacting with “molecular glue” and “binding tag” ligands as calixarenes and lanthanide-based coordination complexes, or trans-membrane protein as the glycine receptor interacting with allosteric modulators, can be described by MDs approaches.
Who is Alessio Bartocci?
Alessio Bartocci achieved his Ph.D. in Chemical Sciences (Theoretical and Computational Chemistry) at the Department of Chemistry of the University of Perugia in 2015, focusing on the characterization of weak hydrogen and halogen bonds in gas phase through collisional scattering experiments and ab-initio calculations. He spent 6 years as a post-doc, initially at the Department of Physics of the University of Genoa (2017), studying the interactions between phospholipid bilayers and charged nanoparticles, and subsequently in France at the Department of Chemistry firstly of the École Normale Supérieure (ENS) de Lyon (2019) and subsequently of the University of Strasbourg (2021), studying the interactions of small ligands and proteins, by molecular dynamics simulations. Since June 2023 is post-doc in the Statistical and Biological Physics (SBP) Group of the University of Trento. His current projects and research focus on conformational changes of pore-forming toxins (PFT), their aggregation mechanisms, and on protein-ligand interactions via classical and ab-initio molecular dynamics simulations.
