Publications by Stefano Vanni | EPFL Graph Search

An Atomistic Look into Bio-inspired Nanoparticles and their Molecular Interactions with Cells

Alke Fink, Pablo Campomanes Ramos, Stefano Vanni, Francesco Stellacci

Nanoparticles (NPs) have sizes that approach those of pathogens and they can interact with the membranes of eukaryotic cells in an analogous fashion. Typically, NPs are taken up by the cell via the plasma membrane by receptor-mediated processes and subsequ ...

SWISS CHEMICAL SOC2019

Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Pablo Campomanes Ramos, Stefano Vanni, Bruno Araujo Cautiero Horta

A combined strategy based on the computation of absorption energies, using the ZINDO/S semiempirical method, for a statistically relevant number of thermally sampled configurations extracted from QM/MM trajectories is used to establish a one-to-one corresp ...

2014

A Closer Look into G Protein Coupled Receptor Activation: X-Ray Crystallography and Long-Scale Molecular Dynamics Simulations

Ursula Röthlisberger, Stefano Vanni

G protein coupled receptors (GPCRs) are a large eukaryotic protein family of transmembrane receptors that react to a signal coming from the extracellular environment to generate an intracellular response through the activation of a signal transduction path ...

2012

Ion Binding and Internal Hydration in the Multidrug Resistance Secondary Active Transporter NorM Investigated by Molecular Dynamics Simulations

Ursula Röthlisberger, Pablo Campomanes Ramos, Stefano Vanni

Recently, a 3.65 angstrom resolution structure of the transporter, NorM from the multidrug and toxic compound extrusion family has been determined in the outward-facing conformation. This antiporter uses electrochemical gradients to drive substrate export ...

2012

Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) simulations of Adiabatic and Nonadiabatic Ultrafast Phenomena

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Marilisa Neri, Pablo Campomanes Ramos, Stefano Vanni, Andrey Laktionov, Thomas James Penfold

A thorough theoretical description of ultrafast phenomena that occur in complex systems constitutes a formidable challenge. It not only necessitates the use of quantum mechanical methods that can describe ground and possibly even electronically excited sta ...

Schweizerische Chemische Gesellschaft2011

Exploring G-Protein Coupled Receptor Activation with Multiscale Molecular Simulations

Stefano Vanni

This thesis is devoted to the study of the activation mechanism of G-protein coupled receptors (GPCRs), one of the largest and most diverse protein families in mammalian genomes, by means of different computer-based simulation techniques. Using force field ...

EPFL2011

Identification of clustering artifacts in photoactivated localization microscopy

Ursula Röthlisberger, Aleksandra Radenovic, Stefano Vanni, Paolo Annibale, Marco Scarselli

Nature Publishing Group2011

Predicting Novel Binding Modes of Agonists to β Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Stefano Vanni

Understanding the binding mode of agonists to adrenergic receptors is crucial to enabling improved rational design of new therapeutic agents. However, so far the high conformational flexibility of G protein-coupled receptors has been an obstacle to obtaini ...

Public Library of Science2011

Pushing the Frontiers of First-Principles Based Computer Simulations of Chemical and Biological Systems

Ursula Röthlisberger, Ivano Tavernelli, Basile Curchod, Marilisa Neri, Pablo Campomanes Ramos, Stefano Vanni, Elizabeth Claire Brunk, Manuel Dömer, Andrey Laktionov, Negar Ashari Astani, Polydefkis Diamantis, Thomas James Penfold, Giulia Palermo

The Laboratory of Computational Chemistry and Biochemistry is active in the development and application of first-principles based simulations of complex chemical and biochemical phenomena. Here, we review some of our recent efforts in extending these metho ...

2011

Role of Aggregation in Rhodopsin Signal Transduction

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Stefano Vanni

Many G protein-coupled receptors (GPCRs) are known to form dimers or even oligomers, and these aggregated states have been proposed as functional units responsible for signal transduction and G protein activation. However, the nature of their involvement h ...

2010

A conserved protonation-induced switch can trigger "ionic lock" formation in adrenergic receptors

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Stefano Vanni

The mechanism of signal transduction in G-protein-coupled receptors (GPCRs) is a crucial step in cell signaling. However, the molecular details of this process are still largely undetermined. Carrying out submicrosecond molecular dynamics simulations of be ...

Elsevier2010

Observation of Ionic Lock Formation in Molecular Dynamics Simulations of Wild-Type Beta1 and Beta2 Adrenergic Receptors

Ursula Röthlisberger, Ivano Tavernelli, Marilisa Neri, Stefano Vanni

2009