P. Carloni

Transport mechanism of DgoT, a bacterial homolog of SLC17 organic anion transporters

This study elucidates the transport mechanism of DgoT, a bacterial homolog of SLC17 transporters, revealing key proton and substrate interactions that drive conformational changes and transport.

Physical Chemistry of Drug Permeation through the Cell Membrane with Atomistic Detail

The paper uses molecular dynamics simulations to study drug permeation through cell membranes, finding that the neutral form of chloroquine is the only permeating species.

Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution

This study uses molecular simulations to investigate how phosphorylation at serine 129 affects the structure of human alpha-synuclein in aqueous solution, finding no significant impact on its conformational ensemble.

Proton Transfers to DNA in Native Electrospray Ionization Mass Spectrometry: A QM/MM Study.

This paper uses QM/MM simulations to study proton transfer mechanisms in DNA during native electrospray ionization mass spectrometry, revealing complex hydration and droplet size-dependent behavior.

Water-triggered, irreversible conformational change of SARS-CoV-2 main protease on passing from the solid state to aqueous solution

The paper shows that water molecules trigger an irreversible conformational change in SARS-CoV-2 main protease when transitioning from solid to aqueous state, leading to asymmetric subunit conformations.

An Enhanced Sampling Approach to the Induced Fit Docking Problem in Protein-Ligand Binding: the case of mono-ADP-ribosylation hydrolases inhibitors

The paper introduces an enhanced sampling method for protein-ligand binding with induced fit, validated on ADPr and MacroD1/MacroD2 complexes, showing accurate free energy predictions and structural changes.

A blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics

The paper identifies a blueprint for high affinity SARS-CoV-2 Mpro inhibitors by analyzing protein dynamics and redefining druggability through virtual screening and pharmacophore modeling.

On the accuracy of molecular simulation-based predictions of koff values: a Metadynamics study

This paper evaluates the accuracy of molecular simulations in predicting koff values for drug unbinding using metadynamics and QM/MM methods, finding discrepancies due to force field limitations.

Chasing the full free energy landscape of neuroreceptor/ligand unbinding by metadynamics simulations

The paper uses metadynamics simulations to reconstruct the full free energy landscape of neuroreceptor/ligand unbinding and identifies two escape routes for the ligand.