Dr Elisa Fadda

    Chemistry, Hamilton Institute, Human Health Institute

    Senior Lecturer
    Associate Professor

    (01) 708 4616

    Biography

    2014-present Lecturer, Department of Chemistry, Maynooth University, 2013 Assistant Lecturer, Department of Chemistry, Maynooth University,  2012-2013: Honorary Research Lecturer, School of Chemistry, National University of Ireland, Galway 2008-2013: Research Fellow (Prof. R.J. Woods lab), School of Chemistry, National University of Ireland, Galway 2004-2008: Postdoctoral Fellow (Dr. R. Pomès lab), Molecular Structure and Function, The Hospital for Sick Children and Department of Biochemistry, University of Toronto 2004: Ph.D. in Computational Chemistry (Prof. D.R. Salahub lab), Department of Chemistry, Université de Montréal 1999: BSc and MSc in Chemistry, Universitá degli Studi di Cagliari

    Research Interests

    Current research in my lab focuses on the study of the diverse functional roles of structural disorder and its modulation in carbohydrates (glycans), proteins and glycoproteins with implications on molecular recognition. Our main investigative tools are based on molecular simulations based on classical mechanics with particular emphasis on deterministic and enhanced conformational sampling methods and free energy calculations (equilibrium, non-equilibrium and end-point). We have also expert knowledge of ab-initio approaches, in particular of DFT and TD-DFT, and we have been recently broadening our field of expertise to include machine learning.   

    Our current interests and work is on the following topics: 1) Understanding the sequence-to-structure relationships in complex carbohydrates (glycans) and its roles in molecular recognition 2) Design and development of new computational tools for the rapid advancement of glycoanalytics 3) Understanding the sequence-to-function relationships in glycosylated proteins of biopharmaceutical interest 4) molecular recognition of disordered motifs   

    Post Doctoral Fellows/Research Team

      Researcher Name Project Role Funding Body
    Aoife Martha Harbison Sequence-to-structure relationships in glycans and glycosylated proteins Postgraduate student
    Matthew Gordon Nixon Molecular Recognition of Intrinsically Disordered Motifs Postgraduate student

    Peer Reviewed Journals

      Year Publication
    2020 'An atomistic perspective on ADCC quenching by core-fucosylation of IgG1 Fc N-glycans from enhanced sampling molecular dynamics'
    Harbison A;Fadda E; (2020) 'An atomistic perspective on ADCC quenching by core-fucosylation of IgG1 Fc N-glycans from enhanced sampling molecular dynamics'. Glycobiology, 30 [DOI] [Details]
    2019 'Sequence-to-structure dependence of isolated IgG Fc complex biantennary N-glycans: a molecular dynamics study'
    Harbison AM;Brosnan LP;Fenlon K;Fadda E; (2019) 'Sequence-to-structure dependence of isolated IgG Fc complex biantennary N-glycans: a molecular dynamics study'. Glycobiology, 29 (1) [DOI] [full-text] [Details]
    2017 'The transient manifold structure of the p53 extreme C-terminal domain: Insight into disorder, recognition, and binding promiscuity by molecular dynamics simulations'
    Fadda E.;Nixon M. (2017) 'The transient manifold structure of the p53 extreme C-terminal domain: Insight into disorder, recognition, and binding promiscuity by molecular dynamics simulations'. Physical Chemistry Chemical Physics, 19 (32):21287-21296 [DOI] [full-text] [Details]
    2017 'Aminoquinoline Fluorescent Labels Obstruct Efficient Removal of N-Glycan Core α(1-6) Fucose by Bovine Kidney α- L -Fucosidase (BKF)'
    O'Flaherty R.;Harbison A.;Hanley P.;Taron C.;Fadda E.;Rudd P. (2017) 'Aminoquinoline Fluorescent Labels Obstruct Efficient Removal of N-Glycan Core α(1-6) Fucose by Bovine Kidney α- L -Fucosidase (BKF)'. Journal of Proteome Research, 16 (11):4237-4243 [DOI] [full-text] [Details]
    2016 'Synthesis and characterisation of new copper(II) coordination polymers constructed from pyrazine–tetrazole ligands with the formation of a water cluster'
    Sheridan U.;Gallagher J.;Fadda E.;Bjerrum M.;McGinley J. (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):707-719 [DOI] [full-text] [Details]
    2016 'Role of the XPA protein in the NER pathway: A perspective on the function of structural disorder in macromolecular assembly'
    Fadda E. (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 :78-85 [DOI] [full-text] [Details]
    2015 'A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence'
    Brien, GL;Healy, E;Jerman, E;Conway, E;Fadda, E;O'Donovan, D;Krivtsov, AV;Rice, AM;Kearney, CJ;Flaus, A;McDade, SS;Martin, SJ;McLysaght, A;O'Connell, DJ;Armstrong, SA;Bracken, AP (2015) 'A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence'. Genes and Development, 29 :2231-2243 [DOI] [full-text] [Details]
    2015 'The role of conformational selection in the molecular recognition of the wild type and mutants XPA(67-80) peptides by ERCC1'
    Fadda, E (2015) 'The role of conformational selection in the molecular recognition of the wild type and mutants XPA(67-80) peptides by ERCC1'. Proteins: Structure, Function and Genetics, 83 :1341-1351 [DOI] [full-text] [Details]
    2015 'Lower rim isoxazole-calix[4]arene derivatives as fluorescence sensors for copper(II) ions'
    Maher, NJ;Diao, HW;O'Sullivan, J;Fadda, E;Heaney, F;McGinley, J (2015) 'Lower rim isoxazole-calix[4]arene derivatives as fluorescence sensors for copper(II) ions'. Tetrahedron, 71 :9223-9233 [DOI] [full-text] [Details]
    2013 'Contribution of the empirical dispersion correction on the conformation of short alanine peptides obtained by gas-phase QM calculations'
    Fadda E;Woods RJ; (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) [DOI] [full-text] [Details]
    2013 'The Influence of N-Linked Glycans on the Molecular Dynamics of the HIV-1 gp120 V3 Loop'
    Wood, NT;Fadda, E;Davis, R;Grant, OC;Martin, JC;Woods, RJ;Travers, SA (2013) 'The Influence of N-Linked Glycans on the Molecular Dynamics of the HIV-1 gp120 V3 Loop'. PLoS ONE, 8 [DOI] [full-text] [Details]
    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'
    Fadda E;Woods RJ; (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) [DOI] [full-text] [Details]
    2014 'Defining the Structural Origin of the Substrate Sequence Independence of O-GlcNAcase Using a Combination of Molecular Docking and Dynamics Simulation'
    Joanne C Martin, Elisa Fadda, Keigo Ito, Robert J Woods (2014) 'Defining the Structural Origin of the Substrate Sequence Independence of O-GlcNAcase Using a Combination of Molecular Docking and Dynamics Simulation'. Glycobiology, 24 :85-96 [DOI] [full-text] [Details]
    2014 'Presentation, Presentation, Presentation! Molecular Level Insight into Linker Effects on Glycan Array Screening Data'
    O.C. Grant, H.M. Smith, D. Firsova, E. Fadda, and R.J. Woods (2014) 'Presentation, Presentation, Presentation! Molecular Level Insight into Linker Effects on Glycan Array Screening Data'. Glycobiology, 24 :17-25 [DOI] [full-text] [Details]
    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'
    Elisa Fadda (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 :2503-2511 [DOI] [full-text] [Details]
    2011 'Molecular basis of proton uptake in single and double mutants of cytochrome c oxidase'
    R. Henry, D. Caplan, E. Fadda and R. Pomes (2011) 'Molecular basis of proton uptake in single and double mutants of cytochrome c oxidase'. Journal of Physics Condensed Matter, 21 [DOI] [full-text] [Details]
    2011 'Structure and binding of polyporus squamosus lectin in complex with Neu5Ac(alpha)2-6Gal(beta)1-4GlcNAc human-type influenza receptor'
    R. Kadirvelraj, O.C. Grant, I.J. Goldstein, H.C. Winter, H. Tateno, E. Fadda, R.J. Woods (2011) 'Structure and binding of polyporus squamosus lectin in complex with Neu5Ac(alpha)2-6Gal(beta)1-4GlcNAc human-type influenza receptor'. Glycobiology, 21 [DOI] [full-text] [Details]
    2010 'Molecular simulations of carbohydrates and protein-carbohydrates interactions: motivations, issues and prospects'
    E. Fadda and R.J. Woods (2010) 'Molecular simulations of carbohydrates and protein-carbohydrates interactions: motivations, issues and prospects'. Drug Discovery Today, 15 [DOI] [full-text] [Details]
    2010 'On the Molecular Basis of Uracil Recognition in DNA: Comparative study of T:A vs. U:A Structure, Dynamics and Open Base Pair Kinetics'
    E. Fadda and R. Pomes (2010) 'On the Molecular Basis of Uracil Recognition in DNA: Comparative study of T:A vs. U:A Structure, Dynamics and Open Base Pair Kinetics'. Nucleic Acids Research, 39 :767-780 [DOI] [full-text] [Details]
    2008 'Electrostatic control of proton pumping in cytochrome c oxidase'
    E. Fadda, C-H. Yu, R. Pomes (2008) 'Electrostatic control of proton pumping in cytochrome c oxidase'. Biochimica et Biophysica Acta - Bioenergetics, 1777 [DOI] [full-text] [Details]
    2006 'Acidity of a Cu-bound histidine in the binuclear centre of cytochrome c oxidase'
    E. Fadda, N. Chakrabarti, R. Pomes (2006) 'Acidity of a Cu-bound histidine in the binuclear centre of cytochrome c oxidase'. Journal of Physical Chemistry B, 109 [DOI] [full-text] [Details]
    2003 'NMR shieldings from Sum-Over-States Density-Functional Theory: Further testing of the Loc.3 approximation'
    E. Fadda, M.E. Casida, D.R. Salahub (2003) 'NMR shieldings from Sum-Over-States Density-Functional Theory: Further testing of the Loc.3 approximation'. Journal of Chemical Physics, 118 [DOI] [full-text] [Details]
    2003 '14,15N NMR shielding constants from Density-Functional Theory'
    E. Fadda, M.E. Casida, D.R. Salahub (2003) '14,15N NMR shielding constants from Density-Functional Theory'. Journal of Physical Chemistry A, 107 [DOI] [full-text] [Details]

    Book Chapters

      Year Publication
    2019 'Binding Free Energies of Conformationally Disordered Peptides Through Extensive Sampling and End-Point Methods'
    Nixon M.;Fadda E. (2019) 'Binding Free Energies of Conformationally Disordered Peptides Through Extensive Sampling and End-Point Methods' In: Methods in molecular biology. New Jersey: Clifton, N.J. [DOI] [Details]
    2015 'Calculating binding free energies for protein-carbohydrate complexes'
    Hadden JA;Tessier MB;Fadda E;Woods RJ; (2015) 'Calculating binding free energies for protein-carbohydrate complexes' In: Methods in molecular biology. New Jersey: Clifton, N.J. [DOI] [Details]

    Conference Publications

      Year Publication
    2003 Time-dependent density functional theory as a foundation for a firmer understanding of sum-over-states density functional perturbation theory: Loc.3 approximation
    Fadda E.;Casida M.;Salahub D. (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 , pp.67-83 [DOI] [Details]

    Reviews

      Year Publication
    2010 Molecular simulations of carbohydrates and protein-carbohydrate interactions: Motivation, issues and prospects.
    Fadda E.;Woods R. (2010) Molecular simulations of carbohydrates and protein-carbohydrate interactions: Motivation, issues and prospects. Reviews [DOI] [Details]

    Honours and Awards

      Year Title Awarding Body
    2013 International Relations Committee Travel Award Biophysical Society
    2016 Young Innovator Award Canadian Society for Chemistry

    Professional Associations

      Association Function From / To
    Society for Glycobiology Responsible for the SFG Social Media Presence in Europe 25-NOV-19 /

    Employment

      Employer Position From / To
    Maynooth University Assistant Lecturer 01-AUG-13 / 31-MAY-14
    National University of Ireland, Galway Research Fellow 15-MAY-08 / 31-MAY-13
    The Hospital for Sick Children Postdoctoral Fellow 01-APR-04 / 30-APR-08
    Maynooth University Lecturer (Assistant Professor) 01-SEP-14 /

    Education

      Year Institution Qualification Subject
    2013 Centre for Learning and Teaching (CELT) Postgraduate Certificate
    2004 Department of Chemistry PhD

    Languages

      Language Reading Writing Speaking
    Italian Fluent Fluent Fluent
    English Fluent Fluent Fluent
    French Fluent Fluent Fluent

    Outreach Activities

      Description

    Cell EXPLORERS is a science education and outreach programme based in the School of Natural Sciences in the National University of Ireland, Galway, with the aim to promote hands-on discovery of molecular and cellular biology in primary schools. Link

    Based in NUI Galway and supported by the Science Foundation Ireland Discover programme, the Community Knowledge Initiative, the CÚRAM Centre for Research in Medical Devices and the Cell EXPLORERS programme, ReelLIFE SCIENCE challenges Irish schools and community groups to communicate science and technology via engaging and educational short videos. I contribute to the project as a judge for the yearly ReelLife Science competition Link