Publications by Giulia Palermo

Editorial: Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations

FRONTIERS MEDIA SA2020

Pre-mRNA Splicing: The Gene Maturation Symphony of the Intron Lariat Spliceosome Revealed by Molecular Dynamics Simulations

Ursula Röthlisberger, Giulia Palermo, Lorenzo Casalino

CELL PRESS2019

Allostery in Its Many Disguises: From Theory to Applications

Jingshi Li, Giulia Palermo, Matthieu Wyart, Riccardo Ravasio, Carolina Brito Carvalho dos Santos, Jing Li

Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, andmetabolism. Allostery is rooted in the fundamental physical properties of macromolecular systems, but its underlying mec ...

CELL PRESS2019

All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome

Ursula Röthlisberger, Giulia Palermo, Lorenzo Casalino

National Academy of Sciences2018

Development of Site-Specific Mg2+-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations

Ursula Röthlisberger, Giulia Palermo, Lorenzo Casalino

The vital contribution of Mg2+ ions to RNA biology is challenging to dissect at the experimental level. This calls for the integrative support of atomistic simulations, which at the classical level are plagued by limited accuracy. Indeed, force fields intr ...

2017

Allosteric cross-talk in chromatin can mediate drug-drug synergy

Paul Joseph Dyson, Ursula Röthlisberger, Giulia Palermo, Tina Riedel

Exploitation of drug-drug synergism and allostery could yield superior therapies by capitalizing on the immensely diverse, but highly specific, potential associated with the biological macromolecular landscape. Here we describe a drug-drug synergy mediated ...

Nature Research2017

Computational Characterization of the Dependence of Halide Perovskite Effective Masses on Chemical Composition and Structure

Michael Graetzel, Ursula Röthlisberger, Amir Hesam Salavati, Negar Ashari Astani, Giulia Palermo, Simone Meloni

Effective masses are calculated for a large variety of perovskites of the form ABX(3) differing in chemical composition (A= Na, Li, Cs; B = Pb, Sn; X= Cl, Br, I) and crystal structure. In addition, the effects of some defects and dopants are assessed. We s ...

2017

Computational Chemistry for Drug Discovery

Giulia Palermo

Springer Netherlands2016

The Molecular Basis for Dual Fatty Acid Amide Hydrolase (FAAH)/Cyclooxygenase (COX) Inhibition

Giulia Palermo

The design of multitarget-directed ligands is a promising strategy for discovering innovative drugs. Here, we report a mechanistic study that clarifies key aspects of the dual inhibition of the fatty acid amide hydrolase (FAAH) and the cyclooxygenase (COX) ...

Wiley-V C H Verlag Gmbh2016

Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns

Ursula Röthlisberger, Giulia Palermo, Lorenzo Casalino

Group II introns are Mg2+-dependent ribozymes that are considered to be the evolutionary ancestors of the eukaryotic spliceosome, thus representing an ideal model system to understand the mechanism of conversion of premature messenger RNA (mRNA) into matur ...

2016

Valence and conduction band tuning in halide perovskites for solar cell applications

Ursula Röthlisberger, Negar Ashari Astani, Giulia Palermo, Simone Meloni

We performed density functional calculations aimed at identifying the atomistic and electronic structure origin of the valence and conduction band, and band gap tunability of halide perovskites ABX(3) upon variations of the monovalent and bivalent cations ...

Royal Society of Chemistry2016

Molecular Mechanism of Chromatin Targeting by a Potent Anticancer Agent Acting at the Nucleosome Core Particle

Paul Joseph Dyson, Ursula Röthlisberger, Giulia Palermo

Cell Press2016

Fighting Cancer with Transition Metal Complexes: From Naked DNA to Protein and Chromatin Targeting Strategies

Paul Joseph Dyson, Ursula Röthlisberger, Thibaud Edouard Alistair von Erlach, Giulia Palermo, Tina Riedel

Many transition metal complexes have unique physicochemical properties that can be efficiently exploited in medicinal chemistry for cancer treatment. Traditionally, double-stranded DNA has been assumed to be the main binding target; however, recent studies ...

2016

An Organometallic Compound which Exhibits a DNA Topology-Dependent One-Stranded Intercalation Mode

Paul Joseph Dyson, Ursula Röthlisberger, Thibaud Edouard Alistair von Erlach, Giulia Palermo, Benjamin Samuel Murray

Understanding how small molecules interact with DNA is essential since it underlies a multitude of pathological conditions and therapeutic interventions. Many different intercalator compounds have been studied because of their activity as mutagens or drugs ...

Wiley-VCH Verlag GmbH2016

Molecular Simulations Integrated with Experiments Unravel the Key Factors of Lipid Selection in Fatty Acid Amide Hydrolase and Suggest A General Mechanism of Lipid-Processing in the Parent Enzymes

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

Cell Press2016

Catalytic Metal Ions and Enzymatic Processing of DNA and RNA

Matteo Dal Peraro, Giulia Palermo, Andrea Cavalli

Two-metal-ion-dependent nucleases cleave the phosphodiester bonds of nucleic acids via the two-metal-ion (2M) mechanism. Several high-resolution X-ray structures portraying the two-metal-aided catalytic site, together with mutagenesis and kinetics studies, ...

Amer Chemical Soc2015

Molecular Mechanism of Ruthenium and Gold Anticancer Agents in the Allosteric Regulation of the Histone Proteins of Chromatin

Paul Joseph Dyson, Ursula Röthlisberger, Giulia Palermo, Tina Riedel

Cell Press2015

Anandamide Hydrolysis in FAAH Reveals a Dual Strategy for Efficient Enzyme-Assisted Amide Bond Cleavage via Nitrogen Inversion

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

Herein, we combined classical molecular dynamics (MD) and quantum mechanical/molecular mechanics (QM/MM) simulations to unravel the whole catalytic cycle of fatty acid amide hydrolase (FAAH) in complex with anandamide, the main neurotransmitters involved i ...

2015

Computational insights into function and inhibition of fatty acid amide hydrolase

Ursula Röthlisberger, Giulia Palermo, Andrea Cavalli

The Fatty Acid Amide Hydrolase (FAAH) enzyme is a membrane-bound serine hydrolase responsible for the deactivating hydrolysis of a family of naturally occurring fatty acid amides. FAAH is a critical enzyme of the endocannabinoid system, being mainly respon ...

Elsevier2015

Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets

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

The fatty acid amide hydrolase (FAAH) regulates the endocannabinoid system cleaving primarily the lipid messenger anandamide. FAAH has been well characterized over the years and, importantly, it represents a promising drug target to treat several diseases, ...

2015