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

Publikacje

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

Autorzy: Abbie Lear; J. L. Ross Anderson; Donald Hilvert; Vickery L. Arcus; Marc W. van der Kamp; H. Adrian Bunzel; Adrian J. Mulholland
Opublikowane w: ACS Catalysis, Numer 13, 2023, Strona(/y) 10527–10530, ISSN 2155-5435
Wydawca: American Chemical Society
DOI: 10.1021/acscatal.3c01906

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

Autorzy: Hira Jabeen, Michael Beer, James Spencer, Marc W. van der Kamp, H. Adrian Bunzel, Adrian J. Mulholland
Opublikowane w: ACS Catalysis, Numer 14, 2024, Strona(/y) 7166-7172, ISSN 2155-5435
Wydawca: American Chemical Society
DOI: 10.1021/acscatal.3c05302

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

Autorzy: A Sofia F Oliveira, Deborah K Shoemark, Andrew D Davidson, Imre Berger, Christiane Schaffitzel, Adrian J Mulholland
Opublikowane w: Journal of Molecular Cell Biology, Numer 15, 2023, Strona(/y) mjad021, ISSN 1759-4685
Wydawca: Oxford University Press
DOI: 10.1093/jmcb/mjad021

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

Autorzy: 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'
Opublikowane w: The International Journal of High Computing Applications, Numer 37, 2023, Strona(/y) 28-44, ISSN 1094-3420
Wydawca: 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

Autorzy: Matteo Castelli; Filippo Marchetti; Sílvia Osuna; A. Sofia F. Oliveira; Adrian J. Mulholland; Stefano A. Serapian; Giorgio Colombo
Opublikowane w: Journal of the American Chemical Society, Numer 146, 2024, Strona(/y) 901-919, ISSN 0002-7863
Wydawca: American Chemical Society
DOI: 10.1021/jacs.3c11396

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

Autorzy: Deeks, Helen M.; Zinovjev, Kirill; Barnoud, Jonathan; Mulholland, Adrian J.; van der Kamp, Marc W.; Glowacki, David R.
Opublikowane w: Scientific Reports, Numer 13, 2023, Strona(/y) 16665, ISSN 2045-2322
Wydawca: 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

Autorzy: 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
Opublikowane w: ACS Catalysis, Numer 14, 2024, Strona(/y) 4379-4394, ISSN 2155-5435
Wydawca: 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

Autorzy: H. T. Henry Chan; A. Sofia F. Oliveira; Christopher J. Schofield; Adrian J. Mulholland; Fernanda Duarte
Opublikowane w: JACS Au, Numer 3, 2023, Strona(/y) 1767–1774, ISSN 2691-3704
Wydawca: 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

Autorzy: Catherine L. Tooke; Philip Hinchliffe; Michael Beer; Kirill Zinovjev; Charlotte K. Colenso; Christopher J. Schofield; Adrian J. Mulholland; James Spencer
Opublikowane w: Journal of the American Chemical Society, Numer 145, 2023, Strona(/y) 7166-7180, ISSN 0002-7863
Wydawca: 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

Autorzy: 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
Opublikowane w: Antibody Therapeutics, Numer 6, 2023, Strona(/y) 277-297, ISSN 2516-4236
Wydawca: Oxford University Press
DOI: 10.1093/abt/tbad024

Heme binding to the SARS-CoV-2 spike glycoprotein

Autorzy: 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
Opublikowane w: Journal of Biological Chemistry, Numer 299, 2023, Strona(/y) 105014, ISSN 0021-9258
Wydawca: 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

Autorzy: 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
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 120, 2023, Strona(/y) e2306046120, ISSN 1091-6490
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.2306046120

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

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

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

Autorzy: 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
Opublikowane w: Nature Communications, Numer 14, 2023, Strona(/y) 6260, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1101/2022.09.01.506225

Fluctuation relations to calculate protein redox potentials from molecular dynamics simulations

Autorzy: Oliveira, A. S. F.; Rubio, J.; Noble, C. E. M.; Anderson, J. L. R.; Anders, J.; Mulholland, A. J.
Opublikowane w: J. Chem. Theor. Comput., Numer 20, 2023, Strona(/y) 385-395, ISSN 1549-9618
Wydawca: American Chemical Society
DOI: 10.1021/acs.jctc.3c00785

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