Article

Nguyen, Linh and Ives, Callum M and Fogarty, Carl A. and Harbison, Aoife M and Durocher, Yves and Klassen, John and Fadda, Elisa (2024) Role of N343 glycosylation on the SARS-CoV-2 S RBD structure and co-receptor binding across variants of concern. eLife, 13. ISSN 2050-084X

Newby, Maddy L. and Fogarty, Carl A. and Allen, Joel D. and Butler, John and Fadda, Elisa and Crispin, Max (2023) Variations within the Glycan Shield of SARS-CoV-2 Impact Viral Spike Dynamics. Journal of Molecular Biology, 435 (4). p. 167928. ISSN 0022-2836

Harbison, Aoife M. and Fogarty, Carl A. and Phung, Toan K. and Satheesan, Akash and Schulz, Benjamin L. and Fadda, Elisa (2022) Fine-tuning the spike: role of the nature and topology of the glycan shield in the structure and dynamics of the SARS-CoV-2 S. Chemical Science, 13 (2). pp. 386-395. ISSN 2041-6520

Fadda, Elisa (2022) Molecular simulations of complex carbohydrates and glycoconjugates. Current Opinion in Chemical Biology, 69 (102175). pp. 1-10. ISSN 1367-5931

Chawla, Himanshi and Fadda, Elisa and Crispin, Max (2022) Principles of SARS-CoV-2 glycosylation. Current Opinion in Structural Biology, 75 (102402). pp. 1-9. ISSN 0959-440X

Perez, Serge and Fadda, Elisa and Makshakova, Olga (2021) Computational Modeling in Glycoscience. Comprehensive Glycoscience: Second Edition. pp. 374-404. ISSN 9780128222447

Fogarty, Carl A and Fadda, Elisa (2021) Oligomannose N-Glycans 3D Architecture and Its Response to the FcγRIIIa Structural Landscape. The Journal of Physical Chemistry B, 125 (10). pp. 2607-2616. ISSN 1520-6106

Fadda, Elisa (2021) Understanding the Structure and Function of Viral Glycosylation by Molecular Simulations: State-of-the-Art and Recent Case Studies. National Library of Medicine. pp. 405-415.

Bagdonas, Haroldas and Fogarty, Carl A. and Fadda, Elisa and Agirre, Jon (2021) The case for post-predictional modifications in the AlphaFold Protein Structure Database. Nature Structural & Molecular Biology, 28 (11). pp. 869-870. ISSN 1545-9993

Cassalino, Lorenzo and Gaieb, Zied and Goldsmith, Jory A. and Hjorth, Christy K. and Dommer, Abigail C. and Harbison, Aoife M. and Fogarty, Carl A. and Barros, Emilia P. and Taylor, Bryn C. and McLellan, Jason S. and Fadda, Elisa and Amaro, Rommie E. (2020) Beyond Shielding: The Roles of Glycans in the SARS-CoV‑2 Spike Protein. ACS Central Science, 6. pp. 1722-1734. ISSN 2374-7951

Fogarty, C.A. and Harbison, Aoife M. and Dugdale, A.R. and Fadda, Elisa (2020) How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates. Beilstein Journal of Organic Chemistry. ISSN 1860-5397

Zimmerman, Maxwell I. and Porter, Justin R. and Ward, Michael D. and Singh, Sukrit and Vithani, Neha and Meller, Artur and Mallimadugula, Upasana L. and Kuhn, Catherine E. and Borowsky, Jonathan H. and Wiewiora, Rafal P. and Hurley, Matthew F. D. and Harbison, Aoife M and Fogarty, Carl A and Coffland, Joseph E. and Fadda, Elisa and Voelz, Vincent A. and Chodera, John D. and Bowman, Gregory R. (2020) SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome. bioRxiv.

Thomson, Emma C. and Rosen, Laura E. and Shepherd, James G. and Spreafico, Roberto and da Silva Filipe, Ana and Wojcechowskyj, Jason A. and Davis, Chris and Piccoli, Luca and Pascall, David J. and Dillen, Josh and Lytras, Spyros and Czudnochowski, Nadine and Shah, Rajiv and Meury, Marcel and Jesudason, Natasha and De Marco, Anna and Li, Kathy and Bassi, Jessica and O’Toole, Aine and Pinto, Dora and Colquhoun, Rachel M. and Culap, Katja and Jackson, Ben and Zatta, Fabrizia and Rambaut, Andrew and Jaconi, Stefano and Sreenu, Vattipally B. and Nix, Jay and Jarrett, Ruth F. and Beltramello, Martina and Nomikou, Kyriaki and Pizzuto, Matteo and Tong, Lily and Cameroni, Elisabetta and Johnson, Natasha and Wickenhagen, Arthur and Ceschi, Alessandro and Mair, Daniel and Ferrari, Paolo and Smollett, Katherine and Sallusto, Federica and Carmichael, Stephen and Garzoni, Christian and Nichols, Jenna and Galli, Massimo and Hughes, Joseph and Riva, Agostino and Ho, Antonia and Semple, Malcolm G. and Openshaw, Peter J.M. and Baillie, J. Kenneth and Rihn, Suzannah J. and Lycett, Samantha J. and Virgin, Herbert W. and Telenti, Amalio and Corti, Davide and Robertson, David L. and Snell, Gyorgy and Fadda, Elisa (2020) The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity. bioRxiv.

Harbison, Aoife M. and Fadda, Elisa (2019) An atomistic perspective on ADCC quenching by core-fucosylation of IgG1 Fc Nglycans from enhanced sampling molecular dynamics. Glycobiology, 30 (6). pp. 407-414. ISSN 0959-6658

Harbison, Aoife M. and Brosnan, Lorna P. and Fenlon, Keith and Fadda, Elisa (2018) Sequence-to-structure dependence of isolated IgG Fc complex biantennary N-glycans: a molecular dynamics study. Glycobiology, 29 (1). pp. 94-103. ISSN 0959-6658

Fadda, Elisa and Nixon, Matthew G. (2017) The transient manifold structure of the p53extreme C-terminal domain: insight into disorder,recognition, and binding promiscuity bymolecular dynamics simulations†. Physical Chemistry Chemical Physics, 19 (32). pp. 21287-21296. ISSN 1463-9076

O'Flaherty, Roisin and Harbison, Aoife M. and Hanley, Philip J. and Taron, Christopher H. and Fadda, Elisa and Rudd, Pauline M. (2017) Aminoquinoline Fluorescent Labels Obstruct Efficient Removal ofN‑Glycan Core α(1−6) Fucose by Bovine Kidney α‑L‑Fucosidase (BKF). Journal of Proteome Research, 16. pp. 4237-4243. ISSN 1535-3893

Sheridan, Ursula and Gallagher, John F. and Fadda, Elisa and Bjerrum, Morten J. and McGinley, John (2016) Synthesis and characterisation of new copper(II) coordination polymers constructed from pyrazine–tetrazole ligands with the formation of a water cluster. Supramolecular Chemistry, 28 (7-8). pp. 707-719. ISSN 1061-0278

Fadda, Elisa (2016) Role of the XPA protein in the NER pathway: A perspective on the function of structural disorder in macromolecular assembly. Computational and Structural Biotechnology Journal, 14. pp. 78-85. ISSN 2001-0370

Maher, Niall and Diao, Haowen and O'Sullivan, Justine and Fadda, Elisa and Heaney, Frances and McGinley, John (2015) Lower rim isoxazole-calix[4]arene derivatives as fluorescence sensors for copper(II) ions. Tetrahedron, 71 (49). pp. 9223-9233. ISSN 0040-4020

Brien, Gerard L. and Healy, Evan and Jerman, Emilia and Conway, Eric and Fadda, Elisa and O'Donovan, Darragh and Krivtsov, Andrei V. and Rice, Alan M. and Kearney, Conor J. and Flaus, Andrew and McDade, Simon S. and Martin, Seamus and McLysaght, Aiofe and O'Connell, David J. and Armstrong, Scott and Bracken, Adrian P. (2015) A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence. Genes and Development, 29. pp. 2231-2243. ISSN 1549-5477

Fadda, Elisa (2015) The role of conformational selection in the molecular recognition of the wild type and mutants XPA67‐80 peptides by ERCC1. Proteins, 83. pp. 1341-1351. ISSN 1097-0134

Martin, Joanne C. and Fadda, Elisa and Keigo, Ito and Woods, Robert J. (2014) Defining the structural origin of the substrate sequence independence of O-GlcNAcase using a combination of molecular docking and dynamics simulation. Glycobiology, 24 (1). pp. 85-96. ISSN 0959-6658

Grant, Oliver C. and Smith, Hannah M.K. and Firsova, Daria and Fadda, Elisa and Woods, Robert J. (2014) Presentation, presentation, presentation! Molecular-level insight into linker effects on glycan array screening data. Glycobiology, 24 (1). pp. 17-25. ISSN 0959-6658

Fadda, Elisa and Woods, Robert J. (2013) Contribution of the empirical dispersion correction on the conformation of short alanine peptides obtained by gas-phase QM calculations. Canadian Journal of Chemistry, 91 (9). pp. 859-865. ISSN 0008-4042

Fadda, Elisa (2013) Conformational Determinants for the Recruitment of ERCC1 by XPA in the Nucleotide Excision Repair (NER) Pathway: Structure and Dynamics of the XPA Binding Motif. Biophysical Journal, 104 (11). pp. 2503-2511. ISSN 0006-3495

Fadda, Elisa and Woods, Robert J. (2013) Contribution of the empirical dispersion correction on the conformation of short alanine peptides obtained by gas-phase QM calculations. Canadian Journal of Chemistry, 91 (9). pp. 859-865. ISSN 0008-4042

Wood, Natasha T. and Fadda, Elisa and Davis, Robert and Grant, Oliver C. and Martin, Joanne C. and Woods, Robert J. and Travers, Simon A. (2013) The Influence of N-Linked Glycans on the Molecular Dynamics of the HIV-1 gp120 V3 Loop. PLoS ONE, 8 (11). e80301. ISSN 1932-6203

Wu, Yuntao and Wood, Natasha T. and Fadda, Elisa and Davis, Robert and Grant, Oliver C. and Martin, Joanne C. and Woods, Robert J. and Travers, Simon A. (2013) The Influence of N-Linked Glycans on the Molecular Dynamics of the HIV-1 gp120 V3 Loop. PLoS ONE, 8 (11). e80301. ISSN 1932-6203

Henry, Rowan M. and Caplan, David and Fadda, Elisa and Pomès, Régis (2011) Molecular basis of proton uptake in single and double mutants of cytochrome c oxidase. Journal of Physics: Condensed Matter, 23 (22). p. 234102. ISSN 0953-8984

Fadda, Elisa and Woods, Robert J. (2011) On the Role of Water Models in Quantifying the Binding Free Energy of Highly Conserved Water Molecules in Proteins: The Case of Concanavalin A. Journal of Chemical Theory and Computation, 7 (10). pp. 3391-3398. ISSN 1549-9618

Fadda, Elisa and Pomès, Régis (2011) On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics. Nucleic Acids Research, 39 (2). pp. 767-780. ISSN 0305-1048

Kadirvelraj, Renuka and Grant, Oliver C. and Goldstein, Irwin J. and Winter, Harry C. and Tateno, Hiroaki and Fadda, Elisa and Woods, Robert J. (2011) Structure and binding analysis of Polyporus squamosus lectin in complex with the Neu5Acα2-6Galβ1-4GlcNAc human-type influenza receptor. Glycobiology, 21 (7). pp. 973-984. ISSN 0959-6658

Fadda, Elisa and Woods, Robert J. (2010) Molecular simulations of carbohydrates and protein–carbohydrate interactions: motivation, issues and prospects. Drug Discovery Today, 15 (15-16). pp. 596-609. ISSN 1359-6446

Fadda, Elisa and Yu, hing-Hsing and Pomès, Régis (2008) Electrostatic control of proton pumping in cytochrome c oxidase. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1777 (3). pp. 277-284. ISSN 0005-2728

Fadda, Elisa and Chakrabarti, Nilmadhab and Pomès, Régis (2005) Acidity of a Cu-Bound Histidine in the Binuclear Center of Cytochrome c Oxidase. Journal of Physical Chemistry B, 109 (47). pp. 22629-22640. ISSN 1520-6106

Fadda, Elisa and Casida, Mark E. and Salahub, Dennis R. (2003) 14,15N NMR Shielding Constants from Density Functional Theory. Journal of Physical Chemistry A, 107 (46). pp. 9924-9930. ISSN 1089-5639

Fadda, Elisa and Casida, Mark E. and Salahub, Dennis R. (2003) NMR shieldings from sum-over-states density-functional-perturbation theory: Further testing of the ‘‘Loc.3’’ approximation. Journal of Chemical Physics, 118 (15). pp. 6758-6768. ISSN 0021-9606

Fadda, Elisa and Casida, Mark E. and Salahub, Dennis R. (2003) Time-Dependent Density Functional Theory as a Foundation for a Firmer Understanding of Sum-Over-States Density Functional Perturbation Theory: “Loc.3” Approximation. International Journal of Quantum Chemistry, 91 (2). pp. 67-83. ISSN 0020-7608