Marilisa Neri

Cette personne n’est plus à l’EPFL

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Publications associées (51)

Fatty acid amide hydrolase (FAAH) substrate specificity understood via molecular dynamics

Ursula Röthlisberger, Marilisa Neri, Pablo Campomanes Ramos, Giulia Palermo, Andrea Cavalli

Amer Chemical Soc2013

Integrating computational methods to retrofit enzymes to synthetic pathways

Ursula Röthlisberger, Ivano Tavernelli, Vassily Hatzimanikatis, Marilisa Neri, Elizabeth Claire Brunk

Microbial production of desired compounds provides an efficient framework for the development of renewable energy resources. To be competitive to traditional chemistry, one requirement is to utilize the full capacity of the microorganism to produce target ...

Wiley-Blackwell2012

Characterization of Molecular Determinants of the Conformational Stability of Macrophage Migration Inhibitory Factor: Leucine 46 Hydrophobic Pocket

Ursula Röthlisberger, Bruno Claude Daniel Fauvet, Hilal Lashuel, Hajer Ouertatani-Sakouhi, Michele Cascella, Farah El Turk, Marilisa Neri, Florence Pojer, Amer Ashrafi, Min Kyu Cho, Magdalena Zweckstetter

Macrophage Migration Inhibitory Factor (MIF) is a key mediator of inflammatory responses and innate immunity and has been implicated in the pathogenesis of several inflammatory and autoimmune diseases. The oligomerization of MIF, more specifically trimer f ...

Public Library of Science2012

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

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

Multi-scale modeling of HIV-1 proteins

Marilisa Neri, Paolo Carloni

The efficiency of protease inhibiting drugs is hampered by the rapid emergence of protease variants. Understanding this phenomenon requires the characterization of the salient steps of HIV-1 protease's catalytic cycle. We summarize Our investigations on th ...

2009

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

Topologically-based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins

Michele Cascella, Marilisa Neri, Matteo Dal Peraro

2008

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