SCHOOL OF Chemistry

Dr Elisa Fadda Career Synopsis: Laurea 110/110 cum laude (B.Sc. and M.Sc.) in Physical and Computational Chemistry, Department of Chemistry, Universitá degli Studi di Cagliari, Italy (1999) Ph.D. in Computational Chemistry, Department of Chemistry, Université de Montréal, Canada (2004) Postdoctoral Fellow, Molecular Structure and Function, The Hospital for Sick Children, Toronto, Canada, and Department of Biochemistry, University of Toronto, Canada (2004-08) Research Associate, Computational Glycoscience Laboratory, School of Chemistry, NUI Galway, Ireland (2008-present)

Research Interests

Structure, Dynamics, and Energetics of Carbohydrate-protein Interactions.

Oligo and polysaccharides (glycans) play fundamental roles in the development and function of all living organisms. They are most commonly found covalently bound to proteins or lipids, forming glycoproteins and glycolipids, known collectively as glycoconjugates. These molecular aggregates cover cell surfaces, often providing the first point of contact for host-pathogen, cell-cell, and cell-matrix interactions.  We use computer simulation methods to characterize structure, dynamics, and energetics of carbohydrate-proteins interactions with the aim of designing glycoprotein-based disease diagnostics and therapeutics.

Figure 1: Detail of a complex between antithrombin and heparin (PDBID 1SR5).

DNA Lesions Recognition and Repair Mechanisms

The DNA repair system represents the primary cellular defense for the preservation of genome integrity. DNA-damage is known to be highly mutagenic and specific malfunctions in the DNA-lesion repair processes are directly implicated in aging, cancer, and other serious illnesses. Inhibition of the DNA repair machinery is also used as a chemotherapeutic strategy to treat certain forms of cancer. At present the molecular basis of DNA-lesion recognition and repair remains unclear. My research objective is to elucidate both the molecular determinants of such processes, as well as the molecular mechanism underlying drug-induced inhibition of repair.

Figure 2: Spontaneous opening/closing dynamics of a uracil-adenine (U-A) pair in a DNA dodecamer observed via molecular dynamics simulation.

Recent Publications

1. "On the Role of Water Models in Quantifying the Binding Free Energy of Highly Conserved Water Molecules in Proteins: The Case of Concanavalin A"Elisa Fadda and Robert J. Woods J. Chem. Theory Comput., 2011, 7 (10), pp 3391 DOI: 10.1021/ct200404z

2. R. M. Henry, D. Caplan, E. Fadda and R. Pomes "Molecular Basis of Proton Uptake in Single and Double Mutants of Cytochrome c Oxidase" J. Phys.: Condens. Matter. 2011, 23, 234102.

3. R. Kadirvelraj, O. C. Grant, I. J Goldstein, H. C Winter, H. Tateno, E. Fadda, R. J. Woods "Structure and Binding Analysis of Polyporus squamosus Lectin in Complex with the Neu5Ac{alpha}2-6Gal{beta}1-4GlcNAc Human-type Influenza Receptor", Glycobiology 2011, DOI: 10.1093/glycob/cwr030.
4. E. Fadda and R. Pomes, "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, 2011, 39(2), 767-780.  DOILink
5. E. Fadda and R.J. Woods, “Molecular Simulations of Carbohydrates and Protein-Carbohydrate Interactions: Motivation, Issues, and Prospects”, Drug Discov.Today., 2010, Vol. 15, (issue 15-16), p. 596-609.
6. E. Fadda, C.-H. Yu, N. Chakrabarti and R. Pomès “Electrostatic Control of Proton Pumping in Cytochrome c Oxidase”, Biochim. Biophys. Acta: Bioenergetics, 2008, 1777, 277.
7. E. Fadda, N. Chakrabarti, and R. Pomès “Acidity of a Cu-Bound Histidine in the Binuclear Center of Cytochrome c Oxidase” J. Phys. Chem. B, 109, 22629 (2005); see also, E. Fadda, N. Chakrabarti, and R. Pomès “Reply to the Comment on “Acidity of a Cu-Bound Histidine in the Binuclear Center of Cytochrome c Oxidase”” J. Phys. Chem. B, 2006, 110, 17288.
8. E. Fadda, M.E. Casida, and D.R. Salahub: “NMR Shieldings from Sum-Over-States Density-Functional Perturbation-Theory: Further Testing of the “Loc.3” Approximation”, J. Chem. Phys., 2003, 118, 6758.
9. E. Fadda, M.E. Casida and D.R. Salahub: “14,15N NMR Shielding Constants from Density-Functional Theory”, J. Phys. Chem. A, 2003, 107, 9924.
10. E. Fadda, M.E. Casida, and D.R. Salahub: “Time-Dependent Density-Functional Theory as a Foundation for a Firmer Understanding of Sum-Over-States Density-Functional Perturbation-Theory: “Loc.3” Approximation”, Int. J. Quantum Chem., 2003, 91, 68.

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