Network models for the computational design of proficient enzymes

Project Information

NetMoDEzyme

Grant agreement ID: 679001

DOI 10.3030/679001

Project closed

EC signature date 9 February 2016

Start date 1 May 2016

End date 31 December 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 445 587,50

EU contribution € 1 445 587,50

Coordinated by

UNIVERSITAT DE GIRONA
Spain

Publications

Peer reviewed articles (30)

Enzyme Conformation Influences the Performance of Lipase-powered Nanomotors

Author(s): Lei Wang; Marzia Marciello; Miquel Estévez-Gay; Paul Eduardo David Soto Rodriguez; Yurena Luengo Morato; Javier Iglesias-Fernández; Xin Huang; Sílvia Osuna; Sílvia Osuna; Marco Filice; Marco Filice; Samuel Sanchez
Published in: Angew. Chem. Int. Ed., Issue 1, 2020, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202008339

Exploring the Conversion of a d -Sialic Acid Aldolase into a l -KDO Aldolase

Author(s): Adrian Romero-Rivera, Javier Iglesias-Fernández, Sílvia Osuna
Published in: European Journal of Organic Chemistry, Issue 2018/20-21, 2018, Page(s) 2603-2608, ISSN 1434-193X
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/ejoc.201800103

Intrinsic enzymatic properties modulate the self-propulsion of micromotors

Author(s): Xavier Arqué, Adrian Romero-Rivera, Ferran Feixas, Tania Patiño, Sílvia Osuna, Samuel Sánchez
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-10726-8

Regio‐ and Stereoselective Steroid Hydroxylation at C7 by Cytochrome P450 Monooxygenase Mutants

Author(s): Aitao Li, Carlos G. Acevedo-Rocha, Lorenzo D'Amore, Jinfeng Chen, Yaqin Peng, Marc Garcia-Borràs, Chenghua Gao, Jinmei Zhu, Harry Rickerby, Sílvia Osuna, Jiahai Zhou, Manfred T. Reetz
Published in: Angew. Chem. Int. Ed, 2020, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202003139

Insights into the molecular determinants of thermal stability in halohydrin dehalogenase HheD2.

Author(s): Julia Wessel; Giovanna Petrillo; Miquel Estévez-Gay; Sandra Bosch; Margarita Seeger; Willem P. Dijkman; Javier Iglesias-Fernández; Aurelio Hidalgo; Isabel Usón; Sílvia Osuna; Anett Schallmey
Published in: FEBS Journal, Issue 19, 2021, ISSN 1742-464X
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/febs.15777

Molecular Dynamics Simulations on Aspergillus niger Monoamine Oxidase: Conformational Dynamics and Inter‐monomer Communication Essential for Its Efficient Catalysis

Author(s): Christian Curado-Carballada,FerranFeixas, and Sílvia Osuna
Published in: Adv. Synth. Catal, 2019, ISSN 1615-4150
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/adsc.201900158

Conformational Landscapes of Halohydrin Dehalogenases and Their Accessible Active Site Tunnels

Author(s): Miquel Estévez-Gay; Javier Iglesias-Fernández; Sílvia Osuna
Published in: Catalysts, Issue 13, 2020, ISSN 2073-4344
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/catal10121403

In Vivo Selection for Formate Dehydrogenases with High Efficiency and Specificity toward NADP +

Author(s): Liliana Calzadiaz-Ramirez, Carla Calvó-Tusell, Gabriele M. M. Stoffel, Steffen N. Lindner, Sílvia Osuna, Tobias J. Erb, Marc Garcia-Borràs, Arren Bar-Even, Carlos G. Acevedo-Rocha
Published in: ACS Catalysis, Issue 10/14, 2020, Page(s) 7512-7525, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.0c01487

From the Design to the In Vivo Evaluation of Benzohomoadamantane-Derived Soluble Epoxide Hydrolase Inhibitors for the Treatment of Acute Pancreatitis.

Author(s): Sandra Codony; Carla Calvó-Tusell; Elena Valverde; Sílvia Osuna; Christophe Morisseau; M. Isabel Loza; José Brea; Concepción Pérez; María Isabel Rodríguez-Franco; Javier Pizarro-Delgado; Javier Pizarro-Delgado; Rubén Corpas; Rubén Corpas; Christian Griñán-Ferré; Mercè Pallàs; Coral Sanfeliu; Coral Sanfeliu; Manuel Vázquez-Carrera; Manuel Vázquez-Carrera; Bruce D. Hammock; Ferran Fe
Published in: J. Med. Chem, Issue 10, 2021, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.0c01601

Discovery and in Vivo Proof of Concept of a Highly Potent Dual Inhibitor of Soluble Epoxide Hydrolase and Acetylcholinesterase for the Treatment of Alzheimer's Disease

Author(s): Codony Gisbert, Sandra; Pont Masanet, Caterina; Griñán Ferré, Christian; Di Pede-Mattatelli, Ania; Calvó-Tusell, Carla; Feixas, Ferran; Osuna, Sílvia; Jarné-Ferrer, Júlia; Naldi, Marina; Bartolini, Manuela; Loza, María Isabel; Brea, José; Bartolini; Pérez, Belén; Bartra, Clara; Sanfeliu i Pujol, Coral; Juárez Jiménez, Jordi; Morisseau, Christophe; Hammock, Bruce D.; Pallàs i Lliberí
Published in: J. Med. Chem., Issue 3, 2022, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.1c02150

In Silico Identification and Experimental Validation of Distal Activity-Enhancing Mutations in Tryptophan Synthase.

Author(s): Miguel A. Maria-Solano; Miguel A. Maria-Solano; Thomas Kinateder; Javier Iglesias-Fernández; Reinhard Sterner; Sílvia Osuna
Published in: ACS Catalysis, Issue 19, 2021, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.1c03950

Biocatalysis

Author(s): Elizabeth L. Bell, William Finnigan, Scott P. France, Anthony P. Green, Martin A. Hayes, Lorna J. Hepworth, Sarah L. Lovelock, Haruka Niikura, Sílvia Osuna, Elvira Romero, Katherine S. Ryan, Nicholas J. Turner, Sabine L. Flitsch
Published in: Nature Reviews Methods Primers, 2021, ISSN 2662-8449
Publisher: Nature Publishing Group
DOI: 10.1038/s43586-021-00044-z

Synthesis, In Vitro Profiling, and In Vivo Evaluation of Benzohomoadamantane-Based Ureas for Visceral Pain: A New Indication for Soluble Epoxide Hydrolase Inhibitors

Author(s): Sandra Codony; José M. Entrena; Carla Calvó-Tusell; Beatrice Jora; Rafael González-Cano; Sílvia Osuna; Rubén Corpas; Christophe Morisseau; Belén Pérez; Marta Barniol-Xicota; Christian Griñán-Ferré; Concepción Pérez; María Isabel Rodríguez-Franco; Antón L. Martínez; M. Isabel Loza; Mercè Pallàs; Steven H. L. Verhelst; Coral Sanfeliu; Ferran Feixas; Bruce D. Hammock; José Brea; En
Published in: J. Med. Chem, Issue 8, 2022, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.2c00515

Deciphering the Allosterically Driven Conformational Ensemble in Tryptophan Synthase Evolution

Author(s): Miguel A. Maria-Solano, Javier Iglesias-Fernández, Sílvia Osuna
Published in: Journal of the American Chemical Society, Issue 141/33, 2019, Page(s) 13049-13056, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.9b03646

Inducing high activity of a thermophilic enzyme at ambient temperatures by directed evolution

Author(s): Guangyue Li, Miguel A. Maria-Solano, Adrian Romero-Rivera, Sílvia Osuna, Manfred T. Reetz
Published in: Chemical Communications, Issue 53/68, 2017, Page(s) 9454-9457, ISSN 1359-7345
Publisher: Royal Society of Chemistry
DOI: 10.1039/C7CC05377K

Role of Conformational Dynamics in the Evolution of Retro-Aldolase Activity

Author(s): Adrian Romero-Rivera, Marc Garcia-Borràs, Sílvia Osuna
Published in: ACS Catalysis, Issue 7/12, 2017, Page(s) 8524-8532, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.7b02954

Exploring the origins of selectivity in soluble epoxide hydrolase from Bacillus megaterium

Author(s): Eila Serrano-Hervás, Marc Garcia-Borràs, Sílvia Osuna
Published in: Organic & Biomolecular Chemistry, Issue 15/41, 2017, Page(s) 8827-8835, ISSN 1477-0520
Publisher: Royal Society of Chemistry
DOI: 10.1039/C7OB01847A

Computational tools for the evaluation of laboratory-engineered biocatalysts

Author(s): Adrian Romero-Rivera, Marc Garcia-Borràs, Sílvia Osuna
Published in: Chem. Commun., Issue 53/2, 2017, Page(s) 284-297, ISSN 1359-7345
Publisher: Royal Society of Chemistry
DOI: 10.1039/C6CC06055B

Exploring the reversal of enantioselectivity on a zinc-dependent alcohol dehydrogenase

Author(s): Miguel A. Maria-Solano, Adrian Romero-Rivera, Sílvia Osuna
Published in: Organic & Biomolecular Chemistry, Issue 15/19, 2017, Page(s) 4122-4129, ISSN 1477-0520
Publisher: Royal Society of Chemistry
DOI: 10.1039/c7ob00482f

Epoxide Hydrolase Conformational Heterogeneity for the Resolution of Bulky Pharmacologically Relevant Epoxide Substrates

Author(s): Eila Serrano-Hervás, Guillem Casadevall, Marc Garcia-Borràs, Ferran Feixas, Sílvia Osuna
Published in: Chemistry - A European Journal, Issue 24/47, 2018, Page(s) 12254-12258, ISSN 0947-6539
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/chem.201801068

Role of conformational dynamics in the evolution of novel enzyme function

Author(s): Miguel A. Maria-Solano, Eila Serrano-Hervás, Adrian Romero-Rivera, Javier Iglesias-Fernández, Sílvia Osuna
Published in: Chemical Communications, Issue 54/50, 2018, Page(s) 6622-6634, ISSN 1359-7345
Publisher: Royal Society of Chemistry
DOI: 10.1039/c8cc02426j

Hidden Conformations in Aspergillus niger Monoamine Oxidase are Key for Catalytic Efficiency

Author(s): Christian Curado-Carballada, Ferran Feixas, Javier Iglesias-Fernández, Sílvia Osuna
Published in: Angewandte Chemie International Edition, Issue 58/10, 2019, Page(s) 3097-3101, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201812532

2-Oxaadamant-1-yl Ureas as Soluble Epoxide Hydrolase Inhibitors: In Vivo Evaluation in a Murine Model of Acute Pancreatitis.

Author(s): Sandra Codony; Eugènia Pujol; Javier G. Pizarro; Javier G. Pizarro; Ferran Feixas; Elena Valverde; M. Isabel Loza; José Brea; Elena Sáez; Julen Oyarzabal; Antonio Pineda-Lucena; Belén Pérez; Concepción Pérez; María Isabel Rodríguez-Franco; Rosana Leiva; Sílvia Osuna; Christophe Morisseau; Bruce D. Hammock; Manuel Vázquez-Carrera; Manuel Vázquez-Carrera; Santiago Vázquez
Published in: J. Med. Chem., Issue 11, 2020, ISSN 0022-2623
Publisher: American Chemical Society
DOI: 10.1021/acs.jmedchem.0c00310

Mutational Analysis of Linalool Dehydratase Isomerase Suggests That Alcohol and Alkene Transformations Are Catalyzed Using Noncovalent Mechanisms

Author(s): Anibal Cuetos, Javier Iglesias-Fernández, Hamid-Reza Danesh-Azari, Erna Zukic, Adam Dowle, Sílvia Osuna, Gideon Grogan
Published in: ACS Catalysis, Issue 10/19, 2020, Page(s) 11136-11146, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.0c02958

Pervasive cooperative mutational effects on multiple catalytic enzyme traits emerge via long-range conformational dynamics

Author(s): Carlos G. Acevedo-Rocha; Aitao Li; Aitao Li; Lorenzo D’Amore; Sabrina Hoebenreich; Joaquin Sanchis; Paul Lubrano; Paul Lubrano; Matteo P. Ferla; Marc Garcia-Borràs; Sílvia Osuna; Manfred T. Reetz; Manfred T. Reetz; Manfred T. Reetz
Published in: Nature Communications, Issue 5, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2020.04.14.041590

Estimating conformational heterogeneity of tryptophan synthase with a template-based Alphafold2 approach

Author(s): Guillem Casadevall; Cristina Duran; Miquel Estévez‐Gay; Sílvia Osuna
Published in: Prot. Sci., Issue 5, 2022, ISSN 1359-5040
Publisher: Wiley-Blackwell
DOI: 10.1002/pro.4426

SBMOpenMM: A Builder of Structure-Based Models for OpenMM.

Author(s): Martin Floor; Kengjie Li; Miquel Estévez-Gay; Luis Agulló; Pau Marc Muñoz-Torres; Jenn K. Hwang; Sílvia Osuna; Jordi Villà-Freixa; Jordi Villà-Freixa
Published in: J. Chem. Inf. Model., Issue 1, 2021, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.1c00122

Time Evolution of the Millisecond Allosteric Activation of Imidazole Glycerol Phosphate Synthase

Author(s): Carla Calvó-Tusell; Miguel A. Maria-Solano; Sílvia Osuna; Ferran Feixas
Published in: J. Am. Chem. Soc., Issue 10, 2022, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.1c12629

p38γ is essential for cell cycle progression and liver tumorigenesis

Author(s): Antonia Tomás-Loba; Elisa Manieri; Elisa Manieri; Bárbara González-Terán; Alfonso Mora; Luis Leiva-Vega; Ayelén M Santamans; Rafael Romero-Becerra; Elena Rodríguez; Aránzazu Pintor-Chocano; Ferran Feixas; Juan Antonio López; Beatriz Caballero; Marianna Trakala; Oscar Blanco; Jorge L Torres; Lourdes Hernández-Cosido; Valle Montalvo-Romeral; Nuria Matesanz; Marta Roche-Molina; Juan A. Berna
Published in: Nature, Issue 15, 2019, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-019-1112-8

The challenge of predicting distal active site mutations in computational enzyme design

Author(s): Sílvia Osuna
Published in: WIREs Computational Molecular Science, 2020, ISSN 1759-0876
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/wcms.1502