Predictive computational models for Enzyme Dynamics, Antimicrobial resistance, Catalysis and Thermoadaptation for Evolution and Design

Project Information

PREDACTED

Grant agreement ID: 101021207

DOI

10.3030/101021207

EC signature date 11 May 2021

Start date 1 October 2021

End date 30 September 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 482 332,00

EU contribution

€ 2 482 332,00

Coordinated by

UNIVERSITY OF BRISTOL
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 .

Publications

Peer reviewed articles (17)

Signal Propagation in the ATPase Domain of <i>Mycobacterium tuberculosis</i> DNA Gyrase from Dynamical-Nonequilibrium Molecular Dynamics Simulations

Author(s): Bundit Kamsri, Pharit Kamsri, Auradee Punkvang, Aunlika Chimprasit, Patchreenart Saparpakorn, Supa Hannongbua, James Spencer, A. Sofia F. Oliveira, Adrian J. Mulholland, Pornpan Pungpo
Published in: Biochemistry, Issue 63, 2024, Page(s) 1493-1504, ISSN 0006-2960
Publisher: American Chemical Society
DOI: 10.1021/acs.biochem.4c00161

Comment on: “Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme”

Author(s): Abbie Lear; J. L. Ross Anderson; Donald Hilvert; Vickery L. Arcus; Marc W. van der Kamp; H. Adrian Bunzel; Adrian J. Mulholland
Published in: ACS Catalysis, Issue 13, 2023, Page(s) 10527–10530, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.3c01906

Electric Fields Are a Key Determinant of Carbapenemase Activity in Class A β-Lactamases

Author(s): Hira Jabeen, Michael Beer, James Spencer, Marc W. van der Kamp, H. Adrian Bunzel, Adrian J. Mulholland
Published in: ACS Catalysis, Issue 14, 2024, Page(s) 7166-7172, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.3c05302

SARS-CoV-2 spike variants differ in their allosteric responses to linoleic acid

Author(s): A Sofia F Oliveira, Deborah K Shoemark, Andrew D Davidson, Imre Berger, Christiane Schaffitzel, Adrian J Mulholland
Published in: Journal of Molecular Cell Biology, Issue 15, 2023, Page(s) mjad021, ISSN 1759-4685
Publisher: Oxford University Press
DOI: 10.1093/jmcb/mjad021

Epistasis arises from shifting the rate-limiting step during enzyme evolution of a β-lactamase

Author(s): Christopher Frölich, H. Adrian Bunzel, Karol Buda, Adrian J. Mulholland, Marc W. van der Kamp, Pål J. Johnsen, Hanna-Kirsti S. Leiros, Nobuhiko Tokuriki
Published in: Nature Catalysis, 2024, ISSN 2520-1158
Publisher: Spring Nature
DOI: 10.1038/s41929-024-01117-4

"#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol"

Author(s): Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John Russo, Sofia Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel GA Smith, Zhuoran Qiao, Sai K Sirumalla, Michael O'
Published in: The International Journal of High Computing Applications, Issue 37, 2023, Page(s) 28-44, ISSN 1094-3420
Publisher: SAGE Publications
DOI: 10.1177/10943420221128233

Protocols for Metallo- and Serine-β-Lactamase Free Energy Predictions: Insights from Cross-Class Inhibitors

Author(s): J. Jasmin Güven, Marko Hanževački, Papu Kalita, Adrian J. Mulholland, Antonia S. J. S. Mey
Published in: The Journal of Physical Chemistry B, Issue 128, 2024, Page(s) 12416-12424, ISSN 1520-6106
Publisher: American Chemical Society
DOI: 10.1021/acs.jpcb.4c06379

Decrypting Allostery in Membrane-Bound K-Ras4B Using Complementary <i>In Silico</i> Approaches Based on Unbiased Molecular Dynamics Simulations

Author(s): Matteo Castelli; Filippo Marchetti; Sílvia Osuna; A. Sofia F. Oliveira; Adrian J. Mulholland; Stefano A. Serapian; Giorgio Colombo
Published in: Journal of the American Chemical Society, Issue 146, 2024, Page(s) 901-919, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.3c11396

Free energy along drug-protein binding pathways interactively sampled in virtual reality

Author(s): Deeks, Helen M.; Zinovjev, Kirill; Barnoud, Jonathan; Mulholland, Adrian J.; van der Kamp, Marc W.; Glowacki, David R.
Published in: Scientific Reports, Issue 13, 2023, Page(s) 16665, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-43523-x

Cooperative Conformational Transitions Underpin the Activation Heat Capacity in the Temperature Dependence of Enzyme Catalysis

Author(s): Emma J. Walker; Carlin J. Hamill; Rory Crean; Michael S. Connolly; Annmaree K. Warrender; Kirsty L. Kraakman; Erica J. Prentice; Alistair Steyn-Ross; Moira Steyn-Ross; Christopher R. Pudney; Marc W. van der Kamp; Louis A. Schipper; Adrian J. Mulholland; Vickery L. Arcus
Published in: ACS Catalysis, Issue 14, 2024, Page(s) 4379-4394, ISSN 2155-5435
Publisher: American Chemical Society
DOI: 10.1021/acscatal.3c05584

Dynamical Nonequilibrium Molecular Dynamics Simulations Identify Allosteric Sites and Positions Associated with Drug Resistance in the SARS-CoV-2 Main Protease

Author(s): H. T. Henry Chan; A. Sofia F. Oliveira; Christopher J. Schofield; Adrian J. Mulholland; Fernanda Duarte
Published in: JACS Au, Issue 3, 2023, Page(s) 1767–1774, ISSN 2691-3704
Publisher: American Chemical Society
DOI: 10.1021/jacsau.3c00185

Tautomer-Specific Deacylation and Ω-Loop Flexibility Explain the Carbapenem-Hydrolyzing Broad-Spectrum Activity of the KPC-2 β-Lactamase

Author(s): Catherine L. Tooke; Philip Hinchliffe; Michael Beer; Kirill Zinovjev; Charlotte K. Colenso; Christopher J. Schofield; Adrian J. Mulholland; James Spencer
Published in: Journal of the American Chemical Society, Issue 145, 2023, Page(s) 7166-7180, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.2c12123

In vitro generated antibodies guide thermostable ADDomer nanoparticle design for nasal vaccination and passive immunization against SARS-CoV-2

Author(s): Dora Buzas, H Adrian Bunzel, Oskar Staufer, Emily J Milodowski, Grace L Edmunds, Joshua C Bufton, Beatriz V Vidana Mateo, Sathish K N Yadav, Kapil Gupta, Charlotte Fletcher, Maia Kavanagh Williamson, Alexandra Harrison, Ufuk Borucu, Julien Capin, Ore Francis, Georgia Balchin, Sophie Hall, Mirella Vivoli Vega, Fabien Durbesson, Renaud Vincentelli, Joe Roe, Linda Wooldridge, Rachel Burt, J L Ross An
Published in: Antibody Therapeutics, Issue 6, 2023, Page(s) 277-297, ISSN 2516-4236
Publisher: Oxford University Press
DOI: 10.1093/abt/tbad024

Heme binding to the SARS-CoV-2 spike glycoprotein

Author(s): Samuel L Freeman, A Sofia F Oliveira, Andrea E Gallio, Annachiara Rosa, Maria K Simitakou, Christopher J Arthur, Adrian J Mulholland, Peter Cherepanov, Emma L Raven
Published in: Journal of Biological Chemistry, Issue 299, 2023, Page(s) 105014, ISSN 0021-9258
Publisher: American Society for Biochemistry and Molecular Biology Inc.
DOI: 10.1016/j.jbc.2023.105014

An expandable, modular de novo protein platform for precision redox engineering

Author(s): George H Hutchins, Claire EM Noble, H Adrian Bunzel, Christopher Williams, Paulina Dubiel, Sathish KN Yadav, Paul M Molinaro, Rob Barringer, Hector Blackburn, Benjamin J Hardy, Alice E Parnell, Charles Landau, Paul R Race, Thomas AA Oliver, Ronald L Koder, Matthew P Crump, Christiane Schaffitzel, A Sofia F Oliveira, Adrian J Mulholland, JL Ross Anderson
Published in: Proceedings of the National Academy of Sciences, Issue 120, 2023, Page(s) e2306046120, ISSN 1091-6490
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2306046120

QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-Lactamases

Author(s): Ewa I. Chudyk; Michael Beer; Michael A. L. Limb; Charlotte A. Jones; James Spencer; Marc W. van der Kamp; Adrian J. Mulholland
Published in: ACS Infectious Diseases, Issue 8, 2022, ISSN 2373-8227
Publisher: American Chemical Society
DOI: 10.1021/acsinfecdis.2c00152

Human cellular model systems of β-thalassemia enable in-depth analysis of disease phenotype

Author(s): Deborah E Daniels; Ivan Ferrer-Vicens; J Hawksworth; Tatyana N Andrienko; Elizabeth M Finnie; Daniel C J Ferguson; A. Sofia F. Oliveira; Jenn-Yeu A. Szeto; Marieangela C Wilson; Jan Frayne
Published in: Nature Communications, Issue 14, 2023, Page(s) 6260, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2022.09.01.506225

Non-peer reviewed articles (1)

Fluctuation relations to calculate protein redox potentials from molecular dynamics simulations

Author(s): Oliveira, A. S. F.; Rubio, J.; Noble, C. E. M.; Anderson, J. L. R.; Anders, J.; Mulholland, A. J.
Published in: J. Chem. Theor. Comput., Issue 20, 2023, Page(s) 385-395, ISSN 1549-9618
Publisher: American Chemical Society
DOI: 10.1021/acs.jctc.3c00785