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

Pubblicazioni

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

Autori: Abbie Lear; J. L. Ross Anderson; Donald Hilvert; Vickery L. Arcus; Marc W. van der Kamp; H. Adrian Bunzel; Adrian J. Mulholland
Pubblicato in: ACS Catalysis, Numero 13, 2023, Pagina/e 10527–10530, ISSN 2155-5435
Editore: American Chemical Society
DOI: 10.1021/acscatal.3c01906

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

Autori: Hira Jabeen, Michael Beer, James Spencer, Marc W. van der Kamp, H. Adrian Bunzel, Adrian J. Mulholland
Pubblicato in: ACS Catalysis, Numero 14, 2024, Pagina/e 7166-7172, ISSN 2155-5435
Editore: American Chemical Society
DOI: 10.1021/acscatal.3c05302

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

Autori: A Sofia F Oliveira, Deborah K Shoemark, Andrew D Davidson, Imre Berger, Christiane Schaffitzel, Adrian J Mulholland
Pubblicato in: Journal of Molecular Cell Biology, Numero 15, 2023, Pagina/e mjad021, ISSN 1759-4685
Editore: Oxford University Press
DOI: 10.1093/jmcb/mjad021

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

Autori: 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'
Pubblicato in: The International Journal of High Computing Applications, Numero 37, 2023, Pagina/e 28-44, ISSN 1094-3420
Editore: 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

Autori: Matteo Castelli; Filippo Marchetti; Sílvia Osuna; A. Sofia F. Oliveira; Adrian J. Mulholland; Stefano A. Serapian; Giorgio Colombo
Pubblicato in: Journal of the American Chemical Society, Numero 146, 2024, Pagina/e 901-919, ISSN 0002-7863
Editore: American Chemical Society
DOI: 10.1021/jacs.3c11396

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

Autori: Deeks, Helen M.; Zinovjev, Kirill; Barnoud, Jonathan; Mulholland, Adrian J.; van der Kamp, Marc W.; Glowacki, David R.
Pubblicato in: Scientific Reports, Numero 13, 2023, Pagina/e 16665, ISSN 2045-2322
Editore: 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

Autori: 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
Pubblicato in: ACS Catalysis, Numero 14, 2024, Pagina/e 4379-4394, ISSN 2155-5435
Editore: 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

Autori: H. T. Henry Chan; A. Sofia F. Oliveira; Christopher J. Schofield; Adrian J. Mulholland; Fernanda Duarte
Pubblicato in: JACS Au, Numero 3, 2023, Pagina/e 1767–1774, ISSN 2691-3704
Editore: 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

Autori: Catherine L. Tooke; Philip Hinchliffe; Michael Beer; Kirill Zinovjev; Charlotte K. Colenso; Christopher J. Schofield; Adrian J. Mulholland; James Spencer
Pubblicato in: Journal of the American Chemical Society, Numero 145, 2023, Pagina/e 7166-7180, ISSN 0002-7863
Editore: 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

Autori: 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
Pubblicato in: Antibody Therapeutics, Numero 6, 2023, Pagina/e 277-297, ISSN 2516-4236
Editore: Oxford University Press
DOI: 10.1093/abt/tbad024

Heme binding to the SARS-CoV-2 spike glycoprotein

Autori: 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
Pubblicato in: Journal of Biological Chemistry, Numero 299, 2023, Pagina/e 105014, ISSN 0021-9258
Editore: 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

Autori: 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
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 120, 2023, Pagina/e e2306046120, ISSN 1091-6490
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2306046120

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

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

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

Autori: 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
Pubblicato in: Nature Communications, Numero 14, 2023, Pagina/e 6260, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1101/2022.09.01.506225

Fluctuation relations to calculate protein redox potentials from molecular dynamics simulations

Autori: Oliveira, A. S. F.; Rubio, J.; Noble, C. E. M.; Anderson, J. L. R.; Anders, J.; Mulholland, A. J.
Pubblicato in: J. Chem. Theor. Comput., Numero 20, 2023, Pagina/e 385-395, ISSN 1549-9618
Editore: American Chemical Society
DOI: 10.1021/acs.jctc.3c00785

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