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

Publicaciones

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

Autores: Abbie Lear; J. L. Ross Anderson; Donald Hilvert; Vickery L. Arcus; Marc W. van der Kamp; H. Adrian Bunzel; Adrian J. Mulholland
Publicado en: ACS Catalysis, Edición 13, 2023, Página(s) 10527–10530, ISSN 2155-5435
Editor: American Chemical Society
DOI: 10.1021/acscatal.3c01906

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

Autores: Hira Jabeen, Michael Beer, James Spencer, Marc W. van der Kamp, H. Adrian Bunzel, Adrian J. Mulholland
Publicado en: ACS Catalysis, Edición 14, 2024, Página(s) 7166-7172, ISSN 2155-5435
Editor: American Chemical Society
DOI: 10.1021/acscatal.3c05302

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

Autores: A Sofia F Oliveira, Deborah K Shoemark, Andrew D Davidson, Imre Berger, Christiane Schaffitzel, Adrian J Mulholland
Publicado en: Journal of Molecular Cell Biology, Edición 15, 2023, Página(s) mjad021, ISSN 1759-4685
Editor: Oxford University Press
DOI: 10.1093/jmcb/mjad021

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

Autores: 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'
Publicado en: The International Journal of High Computing Applications, Edición 37, 2023, Página(s) 28-44, ISSN 1094-3420
Editor: 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

Autores: Matteo Castelli; Filippo Marchetti; Sílvia Osuna; A. Sofia F. Oliveira; Adrian J. Mulholland; Stefano A. Serapian; Giorgio Colombo
Publicado en: Journal of the American Chemical Society, Edición 146, 2024, Página(s) 901-919, ISSN 0002-7863
Editor: American Chemical Society
DOI: 10.1021/jacs.3c11396

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

Autores: Deeks, Helen M.; Zinovjev, Kirill; Barnoud, Jonathan; Mulholland, Adrian J.; van der Kamp, Marc W.; Glowacki, David R.
Publicado en: Scientific Reports, Edición 13, 2023, Página(s) 16665, ISSN 2045-2322
Editor: 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

Autores: 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
Publicado en: ACS Catalysis, Edición 14, 2024, Página(s) 4379-4394, ISSN 2155-5435
Editor: 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

Autores: H. T. Henry Chan; A. Sofia F. Oliveira; Christopher J. Schofield; Adrian J. Mulholland; Fernanda Duarte
Publicado en: JACS Au, Edición 3, 2023, Página(s) 1767–1774, ISSN 2691-3704
Editor: 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

Autores: Catherine L. Tooke; Philip Hinchliffe; Michael Beer; Kirill Zinovjev; Charlotte K. Colenso; Christopher J. Schofield; Adrian J. Mulholland; James Spencer
Publicado en: Journal of the American Chemical Society, Edición 145, 2023, Página(s) 7166-7180, ISSN 0002-7863
Editor: 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

Autores: 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
Publicado en: Antibody Therapeutics, Edición 6, 2023, Página(s) 277-297, ISSN 2516-4236
Editor: Oxford University Press
DOI: 10.1093/abt/tbad024

Heme binding to the SARS-CoV-2 spike glycoprotein

Autores: 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
Publicado en: Journal of Biological Chemistry, Edición 299, 2023, Página(s) 105014, ISSN 0021-9258
Editor: 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

Autores: 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
Publicado en: Proceedings of the National Academy of Sciences, Edición 120, 2023, Página(s) e2306046120, ISSN 1091-6490
Editor: National Academy of Sciences
DOI: 10.1073/pnas.2306046120

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

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

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

Autores: 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
Publicado en: Nature Communications, Edición 14, 2023, Página(s) 6260, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1101/2022.09.01.506225

Fluctuation relations to calculate protein redox potentials from molecular dynamics simulations

Autores: Oliveira, A. S. F.; Rubio, J.; Noble, C. E. M.; Anderson, J. L. R.; Anders, J.; Mulholland, A. J.
Publicado en: J. Chem. Theor. Comput., Edición 20, 2023, Página(s) 385-395, ISSN 1549-9618
Editor: American Chemical Society
DOI: 10.1021/acs.jctc.3c00785

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