M. Alfonso-Prieto

发表

Multi-scale simulations of membrane proteins: The case of bitter taste receptors

P. Carloni, A. Giorgetti, Eda Suku, 2017 .

Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis

S. Cichon, P. Carloni, A. Giorgetti, 2017, Front. Mol. Biosci..

The molecular mechanism of the catalase reaction.

Pietro Vidossich, M. Alfonso-Prieto, X. Biarnés, 2009, Journal of the American Chemical Society.

Photocontrol of Endogenous Glycine Receptors In Vivo.

P. Bregestovski, P. Gorostiza, M. Alfonso-Prieto, 2020, Cell Chemical Biology.

Photocontrol of endogenous glycine receptors in vivo

P. Bregestovski, P. Gorostiza, M. Alfonso-Prieto, 2019, bioRxiv.

Structure-function relationships of the disease-linked A218T oxytocin receptor variant

P. Carloni, A. Giorgetti, M. Alfonso-Prieto, 2022, Molecular Psychiatry.

The effect of a water molecule on the mechanism of formation of compound 0 in horseradish peroxidase.

S. Shaik, M. Alfonso-Prieto, Pietro Vidossich, 2007, Journal of the American Chemical Society.

On the role of water in peroxidase catalysis: a theoretical investigation of HRP compound I formation.

S. Shaik, M. Alfonso-Prieto, Pietro Vidossich, 2010, The journal of physical chemistry. B.

Dual binding mode of “bitter sugars” to their human bitter taste receptor target

P. Carloni, A. Giorgetti, W. Meyerhof, 2019, Scientific Reports.

Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations

P. Carloni, M. Alfonso-Prieto, L. Navarini, 2019, Front. Mol. Biosci..

Multiscale simulations on human Frizzled and Taste2 GPCRs.

P. Carloni, A. Giorgetti, M. Alfonso-Prieto, 2019, Current opinion in structural biology.

Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site

J. Varghese, Jean‐Didier Maréchal, J. M. Lluch, 2019, Nature Communications.

Hybrid MM/CG Webserver: Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes

P. Carloni, A. Giorgetti, M. Alfonso-Prieto, 2020, Frontiers in Molecular Biosciences.

Characterization of cancer-associated IDH2 mutations that differ in tumorigenicity, chemosensitivity and 2-hydroxyglutarate production

M. Alfonso-Prieto, A. Gamero, S. Ramirez, 2019, Oncotarget.

Hydrogen-bond networks for proton couplings in G-Protein coupled receptors

M. Alfonso-Prieto, A. Bondar, 2022, Frontiers in Physics.

Modulation of A (cid:1) 42 ﬁbrillogenesis by glycosaminoglycan structure

S. Ventura, M. Alfonso-Prieto, J. J. Valle-Delgado, 2010 .

A photoswitchable GABA receptor channel blocker

P. Bregestovski, P. Gorostiza, M. Alfonso-Prieto, 2019, British journal of pharmacology.

The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations.

G. Murshudov, M. Alfonso-Prieto, C. Rovira, 2007, Journal of the American Chemical Society.

Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB

M. Klein, V. Carnevale, M. Alfonso-Prieto, 2015, Proteins.

Substrate recognition in the Escherichia coli ammonia channel AmtB: a QM/MM investigation.

M. Jensen, G. Peters, M. Alfonso-Prieto, 2010, The journal of physical chemistry. B.

Catalytic metal ions and enzymatic processing of DNA and RNA.

A. Cavalli, M. Klein, G. Palermo, 2015, Accounts of chemical research.

Magnesium-dependent RNA binding to the PA endonuclease domain of the avian influenza polymerase.

David N. LeBard, Benjamin G. Levine, M. Klein, 2014, The journal of physical chemistry. B.

Bitter Taste and Olfactory Receptors: Beyond Chemical Sensing in the Tongue and the Nose

M. Alfonso-Prieto, 2021, The Journal of Membrane Biology.

Photopharmacology of Ion Channels through the Light of the Computational Microscope

M. Alfonso-Prieto, C. Rovira, C. Molteni, 2021, International journal of molecular sciences.

The dynamic role of distal side residues in heme hydroperoxidase catalysis. Interplay between X-ray crystallography and ab initio MD simulations.

M. Alfonso-Prieto, Pietro Vidossich, C. Rovira, 2010, Archives of biochemistry and biophysics.

Role of the Axial Base in the Modulation of the Cob(I)alamin Electronic Properties: Insight from QM/MM, DFT, and CASSCF Calculations.

Piotr Lodowski, Maria Jaworska, M. Alfonso-Prieto, 2011, Journal of chemical theory and computation.

Reductive cleavage mechanism of Co-C bond in cobalamin-dependent methionine synthase.

Manoj Kumar, M. Alfonso-Prieto, X. Biarnés, 2010, The journal of physical chemistry. B.

Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations.

Ksenia Korshunova, Paolo Carloni, Alejandro Giorgetti, 2018, Biochemical and biophysical research communications.

Machine Learning-based Modeling of Olfactory Receptors: Human OR51E2 as a Case Study

M. Alfonso-Prieto, Riccardo Capelli, 2023, bioRxiv.

A first principles study of the binding of formic acid in catalase complementing high resolution X-ray structures

M. Alfonso-Prieto, X. Biarnés, C. Rovira, 2006 .

Mechanisms Underlying Proton Release in CLC-type F-/H+ Antiporters.

P. Carloni, M. Alfonso-Prieto, E. Ippoliti, 2021, The journal of physical chemistry letters.

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

U. Rothlisberger, M. Alfonso-Prieto, C. Rovira, 2015, Journal of the American Chemical Society.

The reaction mechanisms of heme catalases: an atomistic view by ab initio molecular dynamics.

M. Alfonso-Prieto, Pietro Vidossich, C. Rovira, 2012, Archives of biochemistry and biophysics.

Molecular determinants of acrylamide neurotoxicity through covalent docking

P. Carloni, M. Alfonso-Prieto, Nicolas Pierre Friedrich Mueller, 2023, Frontiers in Pharmacology.

Machine Learning-based Modeling of Olfactory Receptors: Human OR51E2 as a Case Study

M. Alfonso-Prieto, Riccardo Capelli, 2023, bioRxiv.

Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site

J. Varghese, Jean‐Didier Maréchal, J. M. Lluch, 2019, Nature Communications.

An Integrated Biological Approach to Guide the Development of Metal-Chelating Inhibitors of Influenza Virus PA Endonuclease

Robert A. Domaoal, L. Naesens, Baek Kim, 2015, Molecular Pharmacology.

Density Functional Theory-Based Treatments of Metal-Binding Sites in Metalloenzymes: Challenges and Opportunities

M. Klein, M. Alfonso-Prieto, 2015 .

Oxazoline or Oxazolinium Ion? The Protonation State and Conformation of the Reaction Intermediate of Chitinase Enzymes Revisited.

M. Alfonso-Prieto, X. Biarnés, C. Rovira, 2018, Chemistry.

Catalases versus peroxidases: DFT investigation of H₂O₂ oxidation in models systems and implications for heme protein engineering.

M. Alfonso-Prieto, Pietro Vidossich, C. Rovira, 2012, Journal of inorganic biochemistry.

Robust principal component analysis‐based prediction of protein‐protein interaction hot spots

P. Carloni, A. Giorgetti, M. Alfonso-Prieto, 2021, Proteins.

Mechanism of Ribonuclease III Catalytic Regulation by Serine Phosphorylation

M. Alfonso-Prieto, A. Nicholson, Samridhdi Paudyal, 2016, Scientific Reports.

High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction

M. Klein, W. DeGrado, J. Fraser, 2015, Proceedings of the National Academy of Sciences.

Substrate-Assisted Mechanism for the Degradation of N-Glycans by a Gut Bacterial Mannoside Phosphorylase

I. André, G. Potocki-Veronese, M. Alfonso-Prieto, 2023, ACS Catalysis.

Proton transfer drives protein radical formation in Helicobacter pylori catalase but not in Penicillium vitale catalase.

M. Klein, H. Oberhofer, M. Alfonso-Prieto, 2011, Journal of the American Chemical Society.

Modulation of Aβ42 fìbrillogenesis by glycosaminoglycan structure

J. Samitier, S. Ventura, M. Alfonso-Prieto, 2010, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-Based Hybrid Molecular Mechanics/Coarse-Grained Approach

Ksenia Korshunova, Paolo Carloni, Alejandro Giorgetti, 2020, J. Chem. Inf. Model..

Subunit-Specific Photocontrol of Glycine Receptors by Azobenzene-Nitrazepam Photoswitcher

P. Bregestovski, P. Gorostiza, M. Alfonso-Prieto, 2020, eNeuro.

Electronic state of the molecular oxygen released by catalase.

M. Alfonso-Prieto, Pietro Vidossich, C. Rovira, 2008, The journal of physical chemistry. A.

Versatility of the electronic structure of compound I in catalase-peroxidases.

M. Alfonso-Prieto, Pietro Vidossich, C. Rovira, 2007, Journal of the American Chemical Society.

Neprilysin-dependent neuropeptide Y cleavage in the liver promotes fibrosis by blocking NPY-receptor 1

C. Hellerbrand, J. Trebicka, S. Zeuzem, 2021, Cell reports.

Low Molecular Weight Inhibitors Targeting the RNA-Binding Protein HuR

P. Carloni, A. Giorgetti, M. Alfonso-Prieto, 2023, International journal of molecular sciences.

Characterization of cancer-associated IDH2 mutations that differ in tumorigenicity, chemosensitivity and 2-hydroxyglutarate production

M. Alfonso-Prieto, A. Gamero, S. Ramirez, 2019, Oncotarget.

Versatility of the electronic structure of compound I in catalase-peroxidases.

M. Alfonso-Prieto, Pietro Vidossich, C. Rovira, 2007, Journal of the American Chemical Society.

Fluoride Transport and Inhibition Across CLC Transporters.

P. Carloni, M. Spehr, M. Alfonso-Prieto, 2022, Handbook of experimental pharmacology.

The dynamic role of distal side residues in heme hydroperoxidase catalysis. Interplay between X-ray crystallography and ab initio MD simulations.

M. Alfonso-Prieto, Pietro Vidossich, C. Rovira, 2010, Archives of biochemistry and biophysics.

Machine Learning-Based Modeling of Olfactory Receptors in Their Inactive State: Human OR51E2 as a Case Study

M. Alfonso-Prieto, Riccardo Capelli, 2023, bioRxiv.