Directed Protein Evolution for Synthetic Biology and Biocatalysis

Información del proyecto

ES-Cat

Identificador del acuerdo de subvención: 722610

DOI

10.3030/722610

Proyecto cerrado

Fecha de la firma de la CE 31 Agosto 2016

Fecha de inicio 1 Marzo 2017

Fecha de finalización 30 Noviembre 2021

Financiado con arreglo a

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Coste total

€ 3 827 031,48

Aportación de la UE

€ 3 827 031,48

Coordinado por

THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
United Kingdom

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

Other (2)

Open Day
School Outreach

Documents, reports (2)

ESR training

540 ESR training months and submission of PhD thesis where applicable

Publication in the high-impact journals

Publication in highimpact journals Open Access Publication compulsory for all participants

Websites, patent fillings, videos etc. (2)

Website, ESR webpages and CamTools operational
Social media presence (Facebook)

Publicaciones

Peer reviewed articles (30)

Fully Automated Ancestral Sequence Reconstruction using FireProtASR

Autores: Rayyan Tariq Khan, Milos Musil, Jan Stourac, Jiri Damborsky, David Bednar
Publicado en: Current Protocols, Edición 1, 2021, Página(s) e30, ISSN 2691-1299
Editor: John Wiley and Sons Inc.
DOI: 10.1002/cpz1.30

Fibroblast Growth Factor 2 Protein Stability Provides Decreased Dependence on Heparin for Induction of FGFR Signaling and Alters ERK Signaling Dynamics

Autores: Zuzana Koledova; Zuzana Koledova; Jakub Sumbal; Jakub Sumbal; Anas Rabata; Gabin de La Bourdonnaye; Gabin de La Bourdonnaye; Radka Chaloupkova; Radka Chaloupkova; Barbara Hrdlickova; Jiri Damborsky; Jiri Damborsky; Jiri Damborsky; Veronika Stepankova
Publicado en: Frontiers in Cell and Developmental Biology, Edición 11, 2019, ISSN 2296-634X
Editor: Frontiers media S.A.
DOI: 10.3389/fcell.2019.00331

Growth amplification in ultrahigh-throughput microdroplet screening increases sensitivity of clonal enzyme assays and minimizes phenotypic variation

Autores: Paul Jannis Zurek, Raphaëlle Hours, Ursula Schell, Ahir Pushpanath, Florian Hollfelder
Publicado en: Lab on a Chip, Edición 21/1, 2021, Página(s) 163-173, ISSN 1473-0197
Editor: Royal Society of Chemistry
DOI: 10.1039/d0lc00830c

Robust ω-Transaminases by Computational Stabilization of the Subunit Interface

Autores: Qinglong Meng, Nikolas Capra, Cyntia M. Palacio, Elisa Lanfranchi, Marleen Otzen, Luc Z. van Schie, Henriëtte J. Rozeboom, Andy-Mark W. H. Thunnissen, Hein J. Wijma, and Dick B. Janssen
Publicado en: ACS Catalysis, Edición 10(5), 2020, Página(s) 2915–2928, ISSN 2155-5435
Editor: American Chemical Society
DOI: 10.1021/acscatal.9b05223

Computational Design of Enantiocomplementary Epoxide Hydrolases for Asymmetric Synthesis of Aliphatic and Aromatic Diols

Autores: Hesam Arabnejad, Elvira Bombino, Dana I. Colpa, Peter A. Jekel, Milos Trajkovic, Hein J. Wijma, Dick B. Janssen
Publicado en: ChemBiochem, Edición 21(13), 2020, Página(s) 1893-1904, ISSN 1439-7633
Editor: Wiley
DOI: 10.1002/cbic.201900726

The impact of tunnel mutations on enzymatic catalysis depends on the tunnel-substrate complementarity and the rate-limiting step

Autores: Piia Kokkonen, Michaela Slanska, Veronika Dockalova, Gaspar P. Pinto, Esther M. Sánchez-Carnerero, Jiri Damborsky, Petr Klán, Zbynek Prokop, David Bednar
Publicado en: Computational and Structural Biotechnology Journal, Edición 18, 2020, Página(s) 805-813, ISSN 2001-0370
Editor: Elsevier
DOI: 10.1016/j.csbj.2020.03.017

A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila

Autores: Brennen Heames, Jonathan Schmitz, Erich Bornberg-Bauer
Publicado en: Journal of Molecular Evolution, Edición 88/4, 2020, Página(s) 382-398, ISSN 0022-2844
Editor: Springer Verlag
DOI: 10.1007/s00239-020-09939-z

Computational Design of Stable and Soluble Biocatalysts

Autores: Milos Musil, Hannes Konegger, Jiri Hon, David Bednar, and Jiri Damborsky*
Publicado en: ACS Catalysis, Edición 9(2), 2018, Página(s) 1033–1054, ISSN 2155-5435
Editor: American Chemical Society
DOI: 10.1021/acscatal.8b03613

Directed Evolution of a Halide Methyltransferase Enables Biocatalytic Synthesis of Diverse SAM Analogs

Autores: Qingyun Tang, Christoph W. Grathwol, Aşkın S. Aslan‐Üzel, Shuke Wu, Andreas Link, Ioannis V. Pavlidis, Christoffel P. S. Badenhorst, Uwe T. Bornscheuer
Publicado en: Angewandte Chemie International Edition, Edición 60/3, 2021, Página(s) 1524-1527, ISSN 1433-7851
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/anie.202013871

Whole‐Cell Photoenzymatic Cascades to Synthesize Long‐Chain Aliphatic Amines and Esters from Renewable Fatty Acids

Autores: Hee‐Jeong Cha, Se‐Yeun Hwang, Da‐Som Lee, Akula Ravi Kumar, Yong‐Uk Kwon, Moritz Voß, Eva Schuiten, Uwe T. Bornscheuer, Frank Hollmann, Deok‐Kun Oh, Jin‐Byung Park
Publicado en: Angewandte Chemie International Edition, Edición 59/18, 2020, Página(s) 7024-7028, ISSN 1433-7851
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201915108

Cac1 WHD and PIP domains have distinct roles in replisome progression and genomic stability.

Autores: Ioannis Tsirkas, Daniel Dovrat, Yang Lei, Angeliki Kalyva, Diana Lotysh, Qing Li & Amir Aharoni
Publicado en: Current Genetics, Edición 67, 2021, Página(s) 129–139, ISSN 0172-8083
Editor: Springer Verlag
DOI: 10.1007/s00294-020-01113-8

High-Throughput, Lysis-Free Screening for Sulfatase Activity Using Escherichia coli Autodisplay in Microdroplets

Autores: Bert van Loo, Magdalena Heberlein, Philip Mair, Anastasia Zinchenko, Jan Schüürmann, Bernard D. G. Eenink, Josephin M. Holstein, Carina Dilkaute, Joachim Jose, Florian Hollfelder, Erich Bornberg-Bauer
Publicado en: ACS Synthetic Biology, Edición 8/12, 2019, Página(s) 2690-2700, ISSN 2161-5063
Editor: American Chemical Society
DOI: 10.1021/acssynbio.9b00274

FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction

Autores: Milos Musil, Rayyan Tariq Khan, Andy Beier, Jan Stourac, Hannes Konegger, Jiri Damborsky, David Bednar
Publicado en: Briefings in Bioinformatics, Edición 22/4, 2021, Página(s) 1-11, ISSN 1467-5463
Editor: Oxford University Press
DOI: 10.1093/bib/bbaa337

A Haloalkane Dehalogenase from Saccharomonospora viridis Strain DSM 43017, a Compost Bacterium with Unusual Catalytic Residues, Unique ( S )-Enantiopreference, and High Thermostability

Autores: Klaudia Chmelova, Eva Sebestova, Veronika Liskova, Andy Beier, David Bednar, Zbynek Prokop, Radka Chaloupkova, Jiri Damborsky
Publicado en: Applied and Environmental Microbiology, Edición 86/17, 2020, Página(s) e02820-19, ISSN 0099-2240
Editor: American Society for Microbiology
DOI: 10.1128/aem.02820-19

Computational Redesign of an ω-Transaminase from Pseudomonas jessenii for Asymmetric Synthesis of Enantiopure Bulky Amines

Autores: Qinglong Meng, Carlos Ramírez-Palacios, Nikolas Capra, Mattijs E. Hooghwinkel, Sebastian Thallmair, Henriëtte J. Rozeboom, Andy-Mark W. H. Thunnissen, Hein J. Wijma, Siewert J. Marrink, and Dick B. Janssen
Publicado en: ACS Catalysis, Edición 11(17), 2021, Página(s) 10733–10747, ISSN 2155-5435
Editor: American Chemical Society
DOI: 10.1021/acscatal.1c02053

Directed evolution of SIRT6 for improved deacylation and glucose homeostasis maintenance

Autores: Or Gertman, Dotan Omer, Adi Hendler, Daniel Stein, Lior Onn, Yana Khukhin, Miguel Portillo, Raz Zarivach, Haim Y. Cohen, Debra Toiber, Amir Aharoni
Publicado en: Scientific Reports, Edición 8/1, 2018, ISSN 2045-2322
Editor: Nature Publishing Group
DOI: 10.1038/s41598-018-21887-9

A bi-specific inhibitor targeting IL-17A and MMP-9 reduces invasion and motility in MDA-MB-231 cells

Autores: Dana Koslawsky, Marianna Zaretsky, Ron Alcalay, Ohad Mazor, Amir Aharoni, Niv Papo
Publicado en: Oncotarget, Edición 9/47, 2018, ISSN 1949-2553
Editor: Impact Journals
DOI: 10.18632/oncotarget.25526

Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization

Autores: Koen Beerens, Stanislav Mazurenko, Antonin Kunka, Sergio M. Marques, Niels Hansen, Milos Musil, Radka Chaloupkova, Jitka Waterman, Jan Brezovsky, David Bednar, Zbynek Prokop, Jiri Damborsky
Publicado en: ACS Catalysis, Edición 8/10, 2018, Página(s) 9420-9428, ISSN 2155-5435
Editor: American Chemical Society
DOI: 10.1021/acscatal.8b01677

Pif1 is essential for efficient replisome progression through lagging strand G-quadruplex DNA secondary structures

Autores: Danielle Dahan, Ioannis Tsirkas, Daniel Dovrat, Melanie A Sparks, Saurabh P Singh, Roberto Galletto, Amir Aharoni
Publicado en: Nucleic Acids Research, Edición 46/22, 2018, Página(s) 11847-11857, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gky1065

A Live-Cell Imaging Approach for Measuring DNA Replication Rates

Autores: Daniel Dovrat, Danielle Dahan, Shachar Sherman, Ioannis Tsirkas, Natalie Elia, Amir Aharoni
Publicado en: Cell Reports, Edición 24/1, 2018, Página(s) 252-258, ISSN 2211-1247
Editor: Cell Press
DOI: 10.1016/j.celrep.2018.06.018

HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information

Autores: Lenka Sumbalova, Jan Stourac, Tomas Martinek, David Bednar, Jiri Damborsky
Publicado en: Nucleic Acids Research, Edición 46/W1, 2018, Página(s) W356-W362, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gky417

CalFitter: a web server for analysis of protein thermal denaturation data

Autores: Stanislav Mazurenko, Jan Stourac, Antonin Kunka, Sava Nedeljković, David Bednar, Zbynek Prokop, Jiri Damborsky
Publicado en: Nucleic Acids Research, Edición 46/W1, 2018, Página(s) W344-W349, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gky358

An Ultrasensitive Fluorescence Assay for the Detection of Halides and Enzymatic Dehalogenation

Autores: Aşkın S. Aslan‐Üzel, Andy Beier, David Kovář, Clemens Cziegler, Santosh K. Padhi, Eva D. Schuiten, Mark Dörr, Dominique Böttcher, Frank Hollmann, Florian Rudroff, Marko D. Mihovilovic, Tomáš Buryška, Jiří Damborský, Zbyněk Prokop, Christoffel P. S. Badenhorst, Uwe T. Bornscheuer
Publicado en: ChemCatChem, Edición 12/7, 2020, Página(s) 2032-2039, ISSN 1867-3880
Editor: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/cctc.201901891

Promiscuous Dehalogenase Activity of the Epoxide Hydrolase CorEH from Corynebacterium sp. C12

Autores: Eva D. Schuiten, Christoffel P. S. Badenhorst, Gottfried J. Palm, Leona Berndt, Michael Lammers, Jan Mican, David Bednar, Jiri Damborsky, Uwe T. Bornscheuer
Publicado en: ACS Catalysis, Edición 11/10, 2021, Página(s) 6113-6120, ISSN 2155-5435
Editor: American Chemical Society
DOI: 10.1021/acscatal.1c00851

Engineering the protein dynamics of an ancestral luciferase

Autores: Andrea Schenkmayerova, Gaspar P. Pinto, Martin Toul, Martin Marek, Lenka Hernychova, Joan Planas-Iglesias, Veronika Daniel Liskova, Daniel Pluskal, Michal Vasina, Stephane Emond, Mark Dörr, Radka Chaloupkova, David Bednar, Zbynek Prokop, Florian Hollfelder, Uwe T. Bornscheuer, Jiri Damborsky
Publicado en: Nature Communications, Edición 12/1, 2021, Página(s) 3616, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-23450-z

Ultrahigh‐Throughput Detection of Enzymatic Alcohol Dehydrogenase Activity in Microfluidic Droplets with a Direct Fluorogenic Assay

Autores: Miriam Klaus, Paul Jannis Zurek, Tomasz S. Kaminski, Ahir Pushpanath, Katharina Neufeld, Florian Hollfelder
Publicado en: ChemBioChem, 2021, Página(s) 1-9, ISSN 1439-4227
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202100322

Biocatalytic Production of Amino Carbohydrates through Oxidoreductase and Transaminase Cascades

Autores: Ville Aumala, Filip Mollerup, Edita Jurak, Fabian Blume, Johanna Karppi, Antti E. Koistinen, Eva Schuiten, Moritz Voß, Uwe Bornscheuer, Jan Deska, Emma R. Master
Publicado en: ChemSusChem, Edición 12/4, 2019, Página(s) 848-857, ISSN 1864-5631
Editor: Wiley - V C H Verlag GmbbH & Co.
DOI: 10.1002/cssc.201802580

Die gerichtete Evolution einer Halogenid‐Methyltransferase erlaubt die biokatalytische Synthese diverser SAM‐Analoga

Autores: Qingyun Tang, Christoph W. Grathwol, Aşkın S. Aslan‐Üzel, Shuke Wu, Andreas Link, Ioannis V. Pavlidis, Christoffel P. S. Badenhorst, Uwe T. Bornscheuer
Publicado en: Angewandte Chemie, Edición 133/3, 2021, Página(s) 1547-1551, ISSN 0044-8249
Editor: John Wiley & Sons Ltd.
DOI: 10.1002/ange.202013871

UMI-linked consensus sequencing enables phylogenetic analysis of directed evolution

Autores: Paul Jannis Zurek, Philipp Knyphausen, Katharina Neufeld, Ahir Pushpanath, Florian Hollfelder
Publicado en: Nature Communications, Edición 11/1, 2020, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-020-19687-9

Structural and functional characterization of a putative de novo gene in Drosophila

Autores: Andreas Lange, Prajal H. Patel, Brennen Heames, Adam M. Damry, Thorsten Saenger, Colin J. Jackson, Geoffrey D. Findlay, Erich Bornberg-Bauer
Publicado en: Nature Communications, Edición 12/1, 2021, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-021-21667-6

Book chapters (1)

Building Scarless Gene Libraries in the Chromosome of Bacteria.

Autores: Gol Mohammad Dorrazehi, Sebastian Worms, Jason Baby Chirakadavil, Johann Mignolet, Pascal Hols, Patrice Soumillion
Publicado en: Peptide and Protein Engineering., Edición Springer Protocols Handbooks, 2020, Página(s) 189-211, ISBN 978-1-0716-0720-6
Editor: Humana, New York, NY.
DOI: 10.1007/978-1-0716-0720-6_11