Dr Fiona Whelan
Grant-Funded Researcher (B)
Research Infrastructure and Platforms
Division of Research and Innovation
Eligible to supervise Masters and PhD - email supervisor to discuss availability.
- My Research
- Career
- Publications
- Grants and Funding
- Teaching
- Supervision
- Professional Activities
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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, commenced 2023.
In press: PhD candidate Alix Harlington is the driving force behind this study into the structure, specificity and green chemistry catalytic potential of this unique P450 enzyme, SyoA, a S-lignin-derived monolignol specific O-demethylase. Published online 20th Feb, 2025.
And for the story behind the paper, head to Research Communities.
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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 -
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Journals
Year Citation 2025 Harlington, A. C., Das, T., Shearwin, K. E., Bell, S. G., & Whelan, F. (2025). Structural insights into S-lignin O-demethylation via a rare class of heme peroxygenase enzymes. Nature Communications, 16(1), 1815-1-1815-12.
Scopus22025 Dehkhoda, F., Ringuet, M. T., Whitfield, E. A., Mutunduwe, K., Whelan, F., Nowell, C. J., . . . Furness, S. G. B. (2025). Constitutive ghrelin receptor activity enables reversal of dopamine D2 receptor signaling. Molecular Cell, 85(11), 2246-2260.e10.
Scopus12024 Lee, J. H. Z., Coleman, T., Mclean, M. A., Podgorski, M. N., Hayball, E. F., Stone, I. S. J., . . . Bell, S. G. (2024). Selective α-Hydroxyketone Formation and Subsequent C-C Bond Cleavage by Cytochrome P450 Monooxygenase Enzymes. ACS Catalysis, 14(11), 8958-8971.
Scopus6 Europe PMC22024 Akter, J., Lee, J. H. Z., Whelan, F., De Voss, J. J., & Bell, S. G. (2024). Characterisation of the Cytochrome P450 Monooxygenase CYP116B46 from Tepidiphilus thermophilus as a Homogentisic Acid Generating Enzyme and its Conversion to a Peroxygenase.. Chembiochem, 26(5), e202400880-1-e202400880-12.
Scopus2 Europe PMC12023 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 non-canonical legume-like lectin adhesin domains from the bacterial surface.. The Journal of biological chemistry, 299(3), 102936.
Scopus7 WoS1 Europe PMC92022 Whelan, F. (2022). The long and the short of Periscope Proteins. Biochemical Society Transactions, 50(5), 1293-1302.
Scopus1 WoS1 Europe PMC22022 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.
Scopus27 WoS1 Europe PMC72021 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.
Scopus13 WoS10 Europe PMC172020 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.
Scopus4 WoS2 Europe PMC22019 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.
Scopus17 WoS11 Europe PMC142017 Devine, P. W. A., Fisher, H. C., Calabrese, A. N., Whelan, F., Higazi, D. R., Potts, J. R., . . . Ashcroft, A. E. (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.
Scopus47 WoS40 Europe PMC262016 Gruszka, D. T., Mendonça, C. A. T. F., Paci, E., Whelan, F., Hawkhead, J., Potts, J. R., & 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.
Scopus24 WoS15 Europe PMC232015 Whelan, F., & Potts, J. R. (2015). Two repetitive, biofilm-forming proteins from Staphylococci: From disorder to extension. Biochemical Society Transactions, 43(5), 861-866.
Scopus6 WoS4 Europe PMC62015 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.
Scopus41 WoS29 Europe PMC332015 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.
Scopus52 WoS38 Europe PMC432015 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.
Scopus18 WoS11 Europe PMC132015 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.
Scopus10 WoS7 Europe PMC102013 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 PMC162012 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.
Scopus5 WoS4 Europe PMC52010 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.
Scopus21 WoS17 Europe PMC182009 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 PMC72009 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.
Scopus55 WoS46 Europe PMC382001 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.
Scopus65 WoS57 Europe PMC53 -
Conference Papers
Year Citation 2016 Bilder, R. M., Loo, S., McGough, J. J., Whelan, F., Helleman, G., Sugar, C., . . . McCracken, J. T. (2016). Cognitive Effects of Stimulant, Guanfacine, and Combined Treatment in Child and Adolescent Attention-Deficit/Hyperactivity Disorder. In BIOLOGICAL PSYCHIATRY Vol. 79 (pp. 158S). ELSEVIER SCIENCE INC. 2015 Gruszka, D. T., Whelan, F., Paci, E., Brockwell, D. J., Potts, J. R., & 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). MD, Baltimore: CELL PRESS.
DOI2014 Whelan, F., Gruszka, D. T., Clarke, J., & Potts, J. R. (2014). The SasG E-G5 Protein Fold Forms A Stable Contiguous Rigid Nanorod Of Tunable Length. In PROTEIN SCIENCE Vol. 23 (pp. 134-135). CA, San Diego: WILEY-BLACKWELL. 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.
DOI2008 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.
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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. CA, San Francisco: CELL PRESS.
DOI2018 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. CA, San Francisco: CELL PRESS.
DOI2017 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.
DOI2016 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. CA, Los Angeles: CELL PRESS.
DOI2016 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. CA, Los Angeles: CELL PRESS.
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Preprint
Year Citation 2024 Harlington, A. C., Das, T., Shearwin, K. E., Bell, S. G., & Whelan, F. (2024). The S-lignin<i>O</i>-demethylase SyoA: Structural insights into a new class of heme peroxygenase enzymes.
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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 2022-2024
Molecular and Biomedical Science, University of Adelaide
Lecturer – Cancer, Stem cells and Development/Biochemistry III – B.Sc. 3rd Year cohort – 3 lectures, 3 tutorials, Semester 1/2, 2020-2024
Molecular and Biomedical Science, University of Adelaide
Lecturer – Advanced Research Platforms – M.Sc (Biotechnology) – 1 lecture, Semester 1, 2020-2024
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
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Current Higher Degree by Research Supervision (University of Adelaide)
Date Role Research Topic Program Degree Type Student Load Student Name 2025 Co-Supervisor Exploring Cold-Adapted Cytochrome P450 Enzymes from Psychrophilic Organisms: Production, Characterization, and Biotechnological Applications. Doctor of Philosophy Doctorate Full Time Miss Rabia Mehmood 2025 Co-Supervisor Study of bacteriophage protein structures for the production of improved antimicrobial
agentsDoctor of Philosophy Doctorate Full Time Ms Sarah Jayne Eisemann 2023 Co-Supervisor Characterization and Structural Study of Cytochrome P450 enzymes from thermophilic bacteria Doctor of Philosophy Doctorate Full Time Mr Tuhin Das 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 Part Time Mr Ranjith Manjula Meemanage Cebreco -
Past Higher Degree by Research Supervision (University of Adelaide)
Date Role Research Topic Program Degree Type Student Load Student Name 2019 - 2024 Co-Supervisor Development of the PHEARLESS system and its application for directed protein mutagenesis and characterisation of putative endolysin activity 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
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Committee Memberships
Date Role Committee Institution Country 2024 - ongoing Member Australian Biocommons Computational Structural Biology Node Australian Biocommons Australia 2024 - ongoing Member Australian Microscopy and Microanalysis Society CryOz Executive Australian Microscopy and Microanalysis Society Australia 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
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