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

Publications

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

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

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

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

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

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

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

Auteurs: 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'
Publié dans: The International Journal of High Computing Applications, Numéro 37, 2023, Page(s) 28-44, ISSN 1094-3420
Éditeur: SAGE Publications
DOI: 10.1177/10943420221128233

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

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

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

Auteurs: Deeks, Helen M.; Zinovjev, Kirill; Barnoud, Jonathan; Mulholland, Adrian J.; van der Kamp, Marc W.; Glowacki, David R.
Publié dans: Scientific Reports, Numéro 13, 2023, Page(s) 16665, ISSN 2045-2322
Éditeur: 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

Auteurs: 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
Publié dans: ACS Catalysis, Numéro 14, 2024, Page(s) 4379-4394, ISSN 2155-5435
Éditeur: 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

Auteurs: H. T. Henry Chan; A. Sofia F. Oliveira; Christopher J. Schofield; Adrian J. Mulholland; Fernanda Duarte
Publié dans: JACS Au, Numéro 3, 2023, Page(s) 1767–1774, ISSN 2691-3704
Éditeur: 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

Auteurs: Catherine L. Tooke; Philip Hinchliffe; Michael Beer; Kirill Zinovjev; Charlotte K. Colenso; Christopher J. Schofield; Adrian J. Mulholland; James Spencer
Publié dans: Journal of the American Chemical Society, Numéro 145, 2023, Page(s) 7166-7180, ISSN 0002-7863
Éditeur: 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

Auteurs: 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
Publié dans: Antibody Therapeutics, Numéro 6, 2023, Page(s) 277-297, ISSN 2516-4236
Éditeur: Oxford University Press
DOI: 10.1093/abt/tbad024

Heme binding to the SARS-CoV-2 spike glycoprotein

Auteurs: 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
Publié dans: Journal of Biological Chemistry, Numéro 299, 2023, Page(s) 105014, ISSN 0021-9258
Éditeur: 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

Auteurs: 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
Publié dans: Proceedings of the National Academy of Sciences, Numéro 120, 2023, Page(s) e2306046120, ISSN 1091-6490
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.2306046120

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

Auteurs: Ewa I. Chudyk; Michael Beer; Michael A. L. Limb; Charlotte A. Jones; James Spencer; Marc W. van der Kamp; Adrian J. Mulholland
Publié dans: ACS Infectious Diseases, Numéro 8, 2022, ISSN 2373-8227
Éditeur: American Chemical Society
DOI: 10.1021/acsinfecdis.2c00152

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

Auteurs: 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
Publié dans: Nature Communications, Numéro 14, 2023, Page(s) 6260, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1101/2022.09.01.506225

Fluctuation relations to calculate protein redox potentials from molecular dynamics simulations

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

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