Directed Protein Evolution for Synthetic Biology and Biocatalysis

Project Information

ES-Cat

Grant agreement ID: 722610

DOI

10.3030/722610

Project closed

EC signature date 31 August 2016

Start date 1 March 2017

End date 30 November 2021

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 3 827 031,48

EU contribution

€ 3 827 031,48

Coordinated by

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

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

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)

Publications

Peer reviewed articles (30)

Fully Automated Ancestral Sequence Reconstruction using FireProtASR

Author(s): Rayyan Tariq Khan, Milos Musil, Jan Stourac, Jiri Damborsky, David Bednar
Published in: Current Protocols, Issue 1, 2021, Page(s) e30, ISSN 2691-1299
Publisher: 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

Author(s): 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
Published in: Frontiers in Cell and Developmental Biology, Issue 11, 2019, ISSN 2296-634X
Publisher: 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

Author(s): Paul Jannis Zurek, Raphaëlle Hours, Ursula Schell, Ahir Pushpanath, Florian Hollfelder
Published in: Lab on a Chip, Issue 21/1, 2021, Page(s) 163-173, ISSN 1473-0197
Publisher: Royal Society of Chemistry
DOI: 10.1039/d0lc00830c

Robust ω-Transaminases by Computational Stabilization of the Subunit Interface

Author(s): 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
Published in: ACS Catalysis, Issue 10(5), 2020, Page(s) 2915–2928, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.9b05223

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

Author(s): Hesam Arabnejad, Elvira Bombino, Dana I. Colpa, Peter A. Jekel, Milos Trajkovic, Hein J. Wijma, Dick B. Janssen
Published in: ChemBiochem, Issue 21(13), 2020, Page(s) 1893-1904, ISSN 1439-7633
Publisher: 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

Author(s): Piia Kokkonen, Michaela Slanska, Veronika Dockalova, Gaspar P. Pinto, Esther M. Sánchez-Carnerero, Jiri Damborsky, Petr Klán, Zbynek Prokop, David Bednar
Published in: Computational and Structural Biotechnology Journal, Issue 18, 2020, Page(s) 805-813, ISSN 2001-0370
Publisher: Elsevier
DOI: 10.1016/j.csbj.2020.03.017

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

Author(s): Brennen Heames, Jonathan Schmitz, Erich Bornberg-Bauer
Published in: Journal of Molecular Evolution, Issue 88/4, 2020, Page(s) 382-398, ISSN 0022-2844
Publisher: Springer Verlag
DOI: 10.1007/s00239-020-09939-z

Computational Design of Stable and Soluble Biocatalysts

Author(s): Milos Musil, Hannes Konegger, Jiri Hon, David Bednar, and Jiri Damborsky*
Published in: ACS Catalysis, Issue 9(2), 2018, Page(s) 1033–1054, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.8b03613

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

Author(s): Qingyun Tang, Christoph W. Grathwol, Aşkın S. Aslan‐Üzel, Shuke Wu, Andreas Link, Ioannis V. Pavlidis, Christoffel P. S. Badenhorst, Uwe T. Bornscheuer
Published in: Angewandte Chemie International Edition, Issue 60/3, 2021, Page(s) 1524-1527, ISSN 1433-7851
Publisher: 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

Author(s): 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
Published in: Angewandte Chemie International Edition, Issue 59/18, 2020, Page(s) 7024-7028, ISSN 1433-7851
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/anie.201915108

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

Author(s): Ioannis Tsirkas, Daniel Dovrat, Yang Lei, Angeliki Kalyva, Diana Lotysh, Qing Li & Amir Aharoni
Published in: Current Genetics, Issue 67, 2021, Page(s) 129–139, ISSN 0172-8083
Publisher: Springer Verlag
DOI: 10.1007/s00294-020-01113-8

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

Author(s): 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
Published in: ACS Synthetic Biology, Issue 8/12, 2019, Page(s) 2690-2700, ISSN 2161-5063
Publisher: American Chemical Society
DOI: 10.1021/acssynbio.9b00274

FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction

Author(s): Milos Musil, Rayyan Tariq Khan, Andy Beier, Jan Stourac, Hannes Konegger, Jiri Damborsky, David Bednar
Published in: Briefings in Bioinformatics, Issue 22/4, 2021, Page(s) 1-11, ISSN 1467-5463
Publisher: 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

Author(s): Klaudia Chmelova, Eva Sebestova, Veronika Liskova, Andy Beier, David Bednar, Zbynek Prokop, Radka Chaloupkova, Jiri Damborsky
Published in: Applied and Environmental Microbiology, Issue 86/17, 2020, Page(s) e02820-19, ISSN 0099-2240
Publisher: 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

Author(s): 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
Published in: ACS Catalysis, Issue 11(17), 2021, Page(s) 10733–10747, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.1c02053

Directed evolution of SIRT6 for improved deacylation and glucose homeostasis maintenance

Author(s): Or Gertman, Dotan Omer, Adi Hendler, Daniel Stein, Lior Onn, Yana Khukhin, Miguel Portillo, Raz Zarivach, Haim Y. Cohen, Debra Toiber, Amir Aharoni
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
Publisher: 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

Author(s): Dana Koslawsky, Marianna Zaretsky, Ron Alcalay, Ohad Mazor, Amir Aharoni, Niv Papo
Published in: Oncotarget, Issue 9/47, 2018, ISSN 1949-2553
Publisher: Impact Journals
DOI: 10.18632/oncotarget.25526

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

Author(s): 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
Published in: ACS Catalysis, Issue 8/10, 2018, Page(s) 9420-9428, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.8b01677

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

Author(s): Danielle Dahan, Ioannis Tsirkas, Daniel Dovrat, Melanie A Sparks, Saurabh P Singh, Roberto Galletto, Amir Aharoni
Published in: Nucleic Acids Research, Issue 46/22, 2018, Page(s) 11847-11857, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky1065

A Live-Cell Imaging Approach for Measuring DNA Replication Rates

Author(s): Daniel Dovrat, Danielle Dahan, Shachar Sherman, Ioannis Tsirkas, Natalie Elia, Amir Aharoni
Published in: Cell Reports, Issue 24/1, 2018, Page(s) 252-258, ISSN 2211-1247
Publisher: 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

Author(s): Lenka Sumbalova, Jan Stourac, Tomas Martinek, David Bednar, Jiri Damborsky
Published in: Nucleic Acids Research, Issue 46/W1, 2018, Page(s) W356-W362, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky417

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

Author(s): Stanislav Mazurenko, Jan Stourac, Antonin Kunka, Sava Nedeljković, David Bednar, Zbynek Prokop, Jiri Damborsky
Published in: Nucleic Acids Research, Issue 46/W1, 2018, Page(s) W344-W349, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky358

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

Author(s): 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
Published in: ChemCatChem, Issue 12/7, 2020, Page(s) 2032-2039, ISSN 1867-3880
Publisher: Wiley - VCH Verlag GmbH & CO. KGaA
DOI: 10.1002/cctc.201901891

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

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

Engineering the protein dynamics of an ancestral luciferase

Author(s): 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
Published in: Nature Communications, Issue 12/1, 2021, Page(s) 3616, ISSN 2041-1723
Publisher: 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

Author(s): Miriam Klaus, Paul Jannis Zurek, Tomasz S. Kaminski, Ahir Pushpanath, Katharina Neufeld, Florian Hollfelder
Published in: ChemBioChem, 2021, Page(s) 1-9, ISSN 1439-4227
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/cbic.202100322

Biocatalytic Production of Amino Carbohydrates through Oxidoreductase and Transaminase Cascades

Author(s): Ville Aumala, Filip Mollerup, Edita Jurak, Fabian Blume, Johanna Karppi, Antti E. Koistinen, Eva Schuiten, Moritz Voß, Uwe Bornscheuer, Jan Deska, Emma R. Master
Published in: ChemSusChem, Issue 12/4, 2019, Page(s) 848-857, ISSN 1864-5631
Publisher: 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

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

UMI-linked consensus sequencing enables phylogenetic analysis of directed evolution

Author(s): Paul Jannis Zurek, Philipp Knyphausen, Katharina Neufeld, Ahir Pushpanath, Florian Hollfelder
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-19687-9

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

Author(s): Andreas Lange, Prajal H. Patel, Brennen Heames, Adam M. Damry, Thorsten Saenger, Colin J. Jackson, Geoffrey D. Findlay, Erich Bornberg-Bauer
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-21667-6

Book chapters (1)

Building Scarless Gene Libraries in the Chromosome of Bacteria.

Author(s): Gol Mohammad Dorrazehi, Sebastian Worms, Jason Baby Chirakadavil, Johann Mignolet, Pascal Hols, Patrice Soumillion
Published in: Peptide and Protein Engineering., Issue Springer Protocols Handbooks, 2020, Page(s) 189-211, ISBN 978-1-0716-0720-6
Publisher: Humana, New York, NY.
DOI: 10.1007/978-1-0716-0720-6_11