Publications de Pablo Campomanes Ramos

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

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

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

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

The Molecular Mechanism of the Catalase-like Activity in Horseradish Peroxidase

Ursula Röthlisberger, Pablo Campomanes Ramos

Horseradish peroxidase (HRP) is one of the most relevant peroxidase enzymes, used extensively in immunochemistry and biocatalysis applications. Unlike the closely related catalase enzymes, it exhibits a low activity to disproportionate hydrogen peroxide (H ...

2015

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

Generalized QM/MM Force Matching Approach Applied to the 11-cis Protonated Schiff Base Chromophore of Rhodopsin

Ursula Röthlisberger, Ivano Tavernelli, Pablo Campomanes Ramos, Manuel Dömer

We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the reti ...

2014

Molecular dynamics and mutagenesis studies indicate structural flexibility as a key factor for substrate specificity in FAAH catalysis

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

Amer Chemical Soc2014

Ligand substitutions between ruthenium-cymene compounds can control protein versus DNA targeting and anticancer activity

Paul Joseph Dyson, Ursula Röthlisberger, Wee Han Ang, Pablo Campomanes Ramos, Alexey Nazarov, Michael Groessl, Catherine Marie Amélie Clavel

Ruthenium compounds have become promising alternatives to platinum drugs by displaying specific activities against different cancers and favourable toxicity and clearance properties. Nonetheless, their molecular targeting and mechanism of action are poorly ...

Nature Research2014

Lessons from Nature: Computational Design of Biomimetic Compounds and Processes

Ursula Röthlisberger, Pablo Campomanes Ramos, Elizabeth Claire Brunk, Negar Ashari Astani, Esra Bozkurt, Marta Andreia Da Silva Perez, Nicholas John Browning

Through millions of years of evolution, Nature has accomplished the development of highly efficient and sustainable processes and the idea to understand and copy natural strategies is therefore very appealing. However, in spite of intense experimental and ...

2014

Hydrolysis of anandamide in FAAH shows that nitrogen inversion is key to efficient enzyme-assisted amide bond cleavage

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

Amer Chemical Soc2014

Assigning the EPR Fine Structure Parameters of the Mn(II) Centers in Bacillus subtilis Oxalate Decarboxylase by Site-Directed Mutagenesis and DFT/MM Calculations

Ursula Röthlisberger, Pablo Campomanes Ramos

Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. EPR-based strategies for investigating the catalytic mechanism of decarboxylation are complicated by the difficulty of assigning the signals a ...

2014

Wagging the Tail: Essential Role of Substrate Flexibility in FAAH Catalysis

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

The serine hydrolase, fatty acid amide hydrolase (FAAH), is responsible for the intracellular degradation of anandamide and other bioactive fatty acid ethanolamides involved in the regulation of pain, inflammation, and other pathophysiological processes. T ...

Amer Chemical Soc2013

Structural element that controls the redox preferences of the active site manganese in oxalate decarboxylase

Ursula Röthlisberger, Pablo Campomanes Ramos

Amer Chemical Soc2013

Computational assignment of EPR fine structure parameters for the Mn(II) centers in Bacillus subtilis oxalate decarboxylase

Ursula Röthlisberger, Pablo Campomanes Ramos

Amer Chemical Soc2013

Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls

Ursula Röthlisberger, Ivano Tavernelli, Pablo Campomanes Ramos

Bovine rhodopsin is the most extensively studied retinal protein and is considered the prototype of this important class of photosensitive biosystems involved in the process of vision. Many theoretical investigations have attempted to elucidate the role of ...

Amer Chemical Soc2013

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

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

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