Dr Fiona Whelan
Grant-Funded Researcher (B)
School of Biological Sciences
Faculty of Sciences, Engineering and Technology
Eligible to supervise Masters and PhD (as Co-Supervisor), but is currently at capacity - email supervisor to discuss availability.
- My Research
- Career
- Publications
- Grants and Funding
- Teaching
- Supervision
- Professional Activities
- Contact
Previously based at the University of York, UK, my research is focused on the structural biology of viral and bacterial nucleic acid binding proteins; Staphylococcal cell surface adhesins and two-component sensors. I use methods including bioinformatics, structure prediction, molecular biology, bacterial recombinant protein expression and purification, X-ray crystallography and small angle X-ray scattering to determine the relationship between the structure and the function of target proteins. Having relocated to the University of Adelaide, I have been developing the use of cryo electron microscopy in analysis of bacteriophage transcriptional regulators.
I am now engaged in protein engineering to develop a pipeline for directed evolution of novel small molecule binding proteins based on natural bacterial two-component sensor systems, transcription factors and enzymes. We aim to select for new sensor/small molecule binding by building bacterial circuitry to diversify and modulate sensor activation. This synthetic biology approach is anticipated to provide the foundation for development of a small molecule binding protein library able to specifically detect the presence of target molecules for deployment in diverse industries including medical diagnostics, food security, biomonitoring and bioremediation. This work is supported by the Ramsay Fellowship in Applied Science and an ARC discovery project, commencing 2023.
-
Appointments
Date Position Institution name 2019 - ongoing Ramsay Fellow in Applied Science University of Adelaide 2018 - 2019 Postdoctoral Research Associate University of Adelaide 2012 - 2018 Postdoctoral Research Associate University of York 2009 - 2012 Postdoctoral Research Associate University of York -
Education
Date Institution name Country Title 2003 - 2009 University of Adelaide Australia PhD 2002 - 2002 University of Adelaide Australia B.Sc. Hons. (Biochemistry) 1998 - 2001 University of Adelaide Australia B.Sc. (Mol. Biol.) -
Certifications
Date Title Institution name Country 2020 ADEPT Introduction to University Teaching University of Adelaide - 2019 Epigeum: Supervising Doctoral Studies University of Adelaide -
-
Journals
Year Citation 2023 Clark, L. C., Atkin, K. E., Whelan, F., Brentnall, A. S., Harris, G., Towell, A. M., . . . Potts, J. R. (2023). Staphylococcal Periscope proteins Aap, SasG, and Pls project noncanonical legume-like lectin adhesin domains from the bacterial surface. Journal of Biological Chemistry, 299(3), 102936.
2022 Whelan, F. (2022). The long and the short of Periscope Proteins. Biochemical Society Transactions, 50(5), 1293-1302.
Scopus12022 Harlington, A. C., Shearwin, K. E., Bell, S. G., & Whelan, F. (2022). Efficient O-demethylation of lignin monoaromatics using the peroxygenase activity of cytochrome P450 enzymes. Chemical Communications, 58(96), 13321-13324.
2021 Hutvagner, A., Scopelliti, D., Whelan, F., & Jaschke, P. (2021). Orthogonal translation initiation using the non-canonical initiator tRNA(AAC) alters protein sequence and stability in vivo.
2021 Whelan, F., Lafita, A., Gilburt, J., Dégut, C., Griffiths, S. C., Jenkins, H. T., . . . Potts, J. R. (2021). Periscope Proteins are variable-length regulators of bacterial cell surface interactions. Proceedings of the National Academy of Sciences, 118(23), e2101349118-1-e2101349118-10.
Scopus8 WoS8 Europe PMC82020 Jasaitis, L., Silver, C. D., Rawlings, A. E., Peters, D. T., Whelan, F., Regan, L., . . . Staniland, S. S. (2020). Rational Design and Self-Assembly of Coiled-Coil Linked SasG Protein Fibrils. ACS synthetic biology, 9(7), 1599-1607.
Scopus2 WoS12019 Whelan, F., Lafita, A., Griffiths, S. C., Cooper, R. E. M., Whittingham, J. L., Turkenburg, J. P., . . . Potts, J. R. (2019). Defining the remarkable structural malleability of a bacterial surface protein Rib domain implicated in infection.. Proc Natl Acad Sci U S A, 116(52), 26540-26548.
Scopus10 WoS9 Europe PMC82017 Devine, P., Fisher, H., Calabrese, A., Whelan, F., Higazi, D., Potts, J., . . . Ashcroft, A. (2017). Investigating the Structural Compaction of Biomolecules Upon Transition to the Gas-Phase Using ESI-TWIMS-MS. Journal of the American Society for Mass Spectrometry, 28(9), 1855-1862.
Scopus37 WoS37 Europe PMC152016 Gruszka, D., Mendonça, C., Paci, E., Whelan, F., Hawkhead, J., Potts, J., & Clarke, J. (2016). Disorder drives cooperative folding in a multidomain protein. Proceedings of the National Academy of Sciences of the United States of America, 113(42), 11841-11846.
Scopus20 WoS15 Europe PMC142015 Whelan, F., & Potts, J. (2015). Two repetitive, biofilm-forming proteins from Staphylococci: From disorder to extension. Biochemical Society Transactions, 43(5), 861-866.
Scopus5 WoS4 Europe PMC42015 Byrne, R. T., Jenkins, H. T., Peters, D. T., Whelan, F., Stowell, J., Aziz, N., . . . Antson, A. A. (2015). Major reorientation of tRNA substrates defines specificity of dihydrouridine synthases.. Proceedings of the National Academy of Sciences of the United States of America, 112(19), 6033-6037.
Scopus31 WoS28 Europe PMC222015 Gruszka, D. T., Whelan, F., Farrance, O. E., Fung, H. K. H., Paci, E., Jeffries, C. M., . . . Clarke, J. (2015). Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein. Nature Communications, 6(1), 7271.
Scopus43 WoS38 Europe PMC242015 Whelan, F., Jenkins, H. T., Griffiths, S. C., Byrne, R. T., Dodson, E. J., & Antson, A. A. (2015). From bacterial to human dihydrouridine synthase: automated structure determination.. Acta crystallographica. Section D, Biological crystallography, 71(Pt 7), 1564-1571.
Scopus12 WoS11 Europe PMC82015 Chaban, Y., Stead, J. A., Ryzhenkova, K., Whelan, F., Lamber, E. P., Antson, A., . . . Orlova, E. V. (2015). Structural basis for DNA strand separation by a hexameric replicative helicase.. Nucleic acids research, 43(17), 8551-8563.
Scopus8 WoS7 Europe PMC82013 Byrne, R. T., Whelan, F., Aller, P., Bird, L. E., Dowle, A., Lobley, C. M. C., . . . Waterman, D. G. (2013). S-Adenosyl-S-carboxymethyl-l-homocysteine: A novel cofactor found in the putative tRNA-modifying enzyme CmoA. Acta Crystallographica Section D: Biological Crystallography, 69(6), 1090-1098.
Scopus17 WoS16 Europe PMC142012 Whelan, F., Stead, J. A., Shkumatov, A. V., Svergun, D. I., Sanders, C. M., & Antson, A. A. (2012). A flexible brace maintains the assembly of a hexameric replicative helicase during DNA unwinding. Nucleic Acids Research, 40(5), 2271-2283.
Scopus11 WoS11 Europe PMC112012 Griffiths, S., Byrne, R. T., Antson, A. A., & Whelan, F. (2012). Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of human dihydrouridine synthase. Acta Crystallographica Section F: Structural Biology and Crystallization Communications, 68(3), 333-336.
Scopus4 WoS4 Europe PMC22010 Whelan, F., Hao, N., Furness, S., Whitelaw, M., & Chapman-Smith, A. (2010). Amino acid substitutions in the aryl hydrocarbon receptor ligand binding domain reveal YH439 as an atypical AhR activator. Molecular Pharmacology, 77(6), 1037-1046.
Scopus19 WoS16 Europe PMC152009 Dave, K., Whelan, F., Bindloss, C., Furness, S., Chapman-Smith, A., Whitelaw, M., & Gorman, J. (2009). Sulfonation and Phosphorylation of Regions of the Dioxin Receptor Susceptible to Methionine Modifications. Molecular and Cellular Proteomics, 8(4), 706-719.
Scopus12 WoS10 Europe PMC52009 Furness, S. G. B., & Whelan, F. (2009). The pleiotropy of dioxin toxicity - Xenobiotic misappropriation of the aryl hydrocarbon receptor's alternative physiological roles. Pharmacology and Therapeutics, 124(3), 336-353.
Scopus52 WoS46 Europe PMC362001 Chapman-Smith, A., Mulhern, T., Whelan, F., Cronan Jr., J., & Wallace, J. (2001). The C-terminal domain of biotin protein ligase from E-coli is required for catalytic activity. Protein Science, 10(12), 2608-2617.
2001 Chapman-Smith, A., Mulhern, T. D., Whelan, F., Cronan, J. E., & Wallace, J. C. (2001). The C-terminal domain of biotin protein ligase from E. coli is required for catalytic activity. Protein Science, 10(12), 2608-2617.
Scopus61 WoS57 Europe PMC45 -
Conference Papers
Year Citation 2015 Gruszka, D., Whelan, F., Paci, E., Brockwell, D., Potts, J., & Clarke, J. (2015). The Folding of SasG: A Long and Remarkably Strong Monomeric Protein Responsible for Biofilm Formation is a Highly Cooperative System. In Biophysical Journal Vol. 108 (pp. 346a). Baltimore: Biophysical Society. 2014 Whelan, F., Gruszka, D., Clarke, J., & Potts, J. (2014). The SasG E-G5 Protein Fold Forms A Stable Contiguous Rigid Nanorod Of Tunable Length. In Protein Science Vol. 23. San Diego. 2008 Gorman, J. J., Dave, K. A., Whelan, F., Hamilton, B. R., Wallis, T. P., Headlam, M. J., . . . Whitelaw, M. L. (2008). Comparison of Stable-Isotope Labelling Strategies for Quantification of Phosphosite Occupancy and Differentiation Between Phosphorylation and Sulfonation of the Murine Dioxin Receptor. In Journal of Proteomics & Bioinformatics Vol. S2 (pp. 067-068). OMICS Publishing Group.
2008 Gorman, J. J., Dave, K. A., Whelan, F., Hamilton, B. R., Wallis, T. P., Headlam, M. J., . . . Whitelaw, M. L. (2008). Comparison of Stable-Isotope Labelling Strategies for Quantification of Phosphosite Occupancy and Differentiation Between Phosphorylation and Sulfonation of the Murine Dioxin Receptor. In Journal of Proteomics & Bioinformatics Vol. S2 (pp. 067-068). OMICS Publishing Group.
-
Conference Items
Year Citation 2018 Gilburt, J. A. H., Baumann, C. G., Potts, J. R., & Whelan, F. (2018). Probing the Elongated Structure of a Streptococcal Surface Protein using Structural and Single-Molecule Biophysical Approaches. Poster session presented at the meeting of Biophysical Journal. Elsevier BV.
2018 Gilburt, J. A. H., Baumann, C. G., Potts, J. R., & Whelan, F. (2018). Probing the Elongated Structure of a Streptococcal Surface Protein using Structural and Single-Molecule Biophysical Approaches. Poster session presented at the meeting of Biophysical Journal. Elsevier BV.
2017 Whelan, F., Baumann, C., & Potts, J. (2017). Structure and function of highly repetitive bacterial surface proteins involved in infection. Poster session presented at the meeting of EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS. Edinburgh, Scotland. 2017 Whelan, F., Baumann, C., & Potts, J. (2017). Structure and function of highly repetitive bacterial surface proteins involved in infection. Poster session presented at the meeting of EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS. Edinburgh, Scotland. 2017 Abstracts (2017). Poster session presented at the meeting of European Biophysics Journal. Springer Science and Business Media LLC.
2016 Jenkins, H., Whelan, F., Peters, D., Byrne, R., Konevega, A., Koonin, E., & Antson, F. (2016). Recognition of Specific Uridines in tRNA Substrates by Dihydrouridine Synthases. Poster session presented at the meeting of Biophysical Journal. Elsevier BV.
ARC Discovery Project
Whelan, Shearwin and Potts
Title: Discovery and directed evolution of small molecule biosensors
2023–2026
Total Awarded: $522,724
AWRI/University of Adelaide Collaborative Research Fund
Title: Predicting wine haze potential
2023
Total Awarded: $30,000
Research Roadmap grant scheme
Title: Biodegradation of Plastics via Bioengineered Enzyme Systems
September 2021 – December 2022
Total Awarded: $50,000
Agrifood and Wine FAME Strategy internal grant
Title: Pesticide biosensors for viticulture and winemaking industries
August 2021 – December 2022
Total Awarded: $20,000
Sandland Bequest
Title: Pesticide biosensor development and hybrid device integration for agricultural and environmental analytics
May 2021 — Dec 2022
Total Awarded: $25,000
Wine Australia top-up scholarship
Title: Engineering biosensors for smoke taint
February 2021—2024
Total awarded: $49,509
Wine Australia top-up scholarship
Title: Engineering biosensors for wine spoilage
February 2021—2024
Total awarded $49,509
Biochemistry Trust Fund
Title: Evolution of bespoke small molecule in-cell sensors
Oct 2020 — Dec 2021
Total awarded: $27,000
Ramsay Fellowship in Applied Science
Title: Making bacteria sense what they've never seen
Nov 2019 — Nov 2023
Total awarded: $459,282
Travel Award
Australian Microscopy and Microanalysis Society – June 2019
CRYOZ 2019 2nd AMMS Cryo EM symposium (June 5—7, 2019)
Total awarded $800
Lecturer – Microbiology II – B.Sc. 2nd Year cohort – 1 lecture, Semester 1 2022.
Molecular and Biomedical Science, University of Adelaide
Lecturer – Cancer, Stem cells and Development/Biochemistry III – B.Sc. 3rd Year cohort – 3 lectures, 4 tutorials, Semester 1/2, 2020-2022
Molecular and Biomedical Science, University of Adelaide
Lecturer – Advanced Research Platforms – M.Sc (Biotechnology) – 1 lecture, Semester 1, 2020-2022
Molecular and Biomedical Science, University of Adelaide
Journal Club Organiser/Assessor, B.Sc. (Honours) – 2019, 2020
Molecular and Biomedical Science, University of Adelaide
Thesis examiner, M.Sc (Biotechnology) – 2019, 2020
Molecular and Biomedical Science, University of Adelaide
Examiner - B.Sc.(Hons.) Research Proposal - 2020
Molecular and Biomedical Science, University of Adelaide
Laboratory supervisor – PhD (2), Undergraduate (7), 2010—2018
Dept. of Chemistry and Biology Department, University of York
Student mentoring – PhD (4), Undergraduate (2), 2008—2019
Molecular and Biomedical Science, University of Adelaide; Dept. of Chemistry and Biology Department, University of York
-
Current Higher Degree by Research Supervision (University of Adelaide)
Date Role Research Topic Program Degree Type Student Load Student Name 2023 Co-Supervisor Characterization and optimization of oxygenase enzymes involved in bacterial lignin degradation Doctor of Philosophy Doctorate Full Time Mr Tuhin Das 2023 Co-Supervisor Study of bacteriophage protein structures for the production of improved antimicrobial agents Master of Philosophy Master Full Time Ms Sarah Jayne Eisemann 2022 Co-Supervisor Engineering small molecule binding proteins as novel biosensors Doctor of Philosophy Doctorate Full Time Mr Alix Charles Harlington 2021 Co-Supervisor Engineering biosensors for wine spoilage Doctor of Philosophy Doctorate Full Time Mr Ranjith Manjula Meemanage Cebreco 2021 Co-Supervisor Directed evolution of heme monooxygenases using phage driven systems Doctor of Philosophy Doctorate Part Time Mr Jason Benedict Leonard 2019 Co-Supervisor Phage based antibacterial proteins Doctor of Philosophy Doctorate Full Time Miss Hannah Rose Bonham -
Other Supervision Activities
Date Role Research Topic Location Program Supervision Type Student Load Student Name 2020 - ongoing Principal Supervisor Isolating bacteriophage host binding and infection machinery University of Adelaide Masters of Biotechnology Master Full Time Diva Sinha 2017 - ongoing Other Thermal unfolding of tandem repeat protein domains University of York - Doctorate Full Time Rachael Cooper 2016 - 2016 Co-Supervisor mutagenesis, protein expression, purification and crystallisation of mutant adhesin domains from Staphylococcal surface adhesins SasG and Aap University of York B.Sc. Research Project Other Part Time Nicholas Butler 2015 - 2018 Other Structural and biophysical analysis of tandem repeat domains of Gram-positive bacteria University of York - Doctorate Full Time Lotte Van Beek 2015 - 2015 Other Cloning and purification of human Cip1 interacting zinc finger protein University of York B.Sc. Research Project Other Part Time Caroline Pearson 2012 - 2012 Other Supervision of lab work and manuscript preparation resulting in a peer reviewed publication on a human tRNA modifying enzyme. Samuel went on to be awarded a competitive and highly prestigious Wellcome Trust funded scholarship to study on the Oxford PhD program University of York B.Sc. Research Project Other Part Time Samuel Griffiths
-
Committee Memberships
Date Role Committee Institution Country 2022 - ongoing Member SET Faculty Workload Model Working Group University of Adelaide Australia 2021 - ongoing Member School of Biological Sciences Research Committee University of Adelaide Australia 2021 - 2022 Member School of Biological Sciences Review Team University of Adelaide Australia 2013 - 2016 Representative Staff Committee University of York United Kingdom -
Memberships
Date Role Membership Country 2019 - ongoing Member Australian Microscopy and Microanalysis Society Australia 2019 - ongoing Member Synthetic Biology Australasia Australia 2012 - ongoing Member Biochemical Society United Kingdom -
Community Engagement
Date Title Engagement Type Institution Country 2016 - 2016 British Heart Foundation visit day Public Community Engagement University of York United Kingdom -
Event Participation
Date Event Name Event Type Institution Country 2019 - 2019 University Open Day Function University of Adelaide Australia -
Offices Held
Date Office Name Institution Country 2020 - ongoing Adelaide SBA Node Leader Synthetic Biology Australasia Australia 2019 - 2020 EMCRA Social Media Officer EMCRA, School of Biological Sciences, University of Adelaide Australia -
Review, Assessment, Editorial and Advice
Date Title Type Institution Country 2019 - ongoing Referee: Genomics Peer Review University of Adelaide Australia 2019 - ongoing Thesis examiner - Masters of Biotechnology Thesis Review University of Adelaide Australia 2015 - ongoing Journal of Molecular Biology Peer Review University of York United Kingdom
Connect With Me
External Profiles
