Fiona Whelan

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) - email supervisor to discuss availability.

Based at the University of York, UK, my research has been focused on the structural biology of viral and bacterial nucleic acid binding proteins; and 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, SEC-MALS, CD spectroscopy, small angle X-ray scattering, force unfolding AFM to determine the relationship between the structure and the function of target proteins. I recently relocated to the University of Adelaide where I have been developing the use of cryo electron microscopy in analysis of bacteriophage transcriptional regulators.

I am now using my expertise 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. One aim of this work is to select for new sensor/small molecule binding by building bacterial circuitry to select for sensor activation. Investing in the synthetic biology approach to design, build, test and learn will 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.

  • 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
    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.
    DOI
    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.
    DOI Scopus2 WoS2 Europe PMC1
    2020 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.
    DOI
    2019 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.
    DOI Scopus5 WoS5 Europe PMC4
    2017 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.
    DOI Scopus32 WoS30 Europe PMC12
    2016 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.
    DOI Scopus16 WoS15 Europe PMC12
    2015 Whelan, F., & Potts, J. (2015). Two repetitive, biofilm-forming proteins from Staphylococci: From disorder to extension. Biochemical Society Transactions, 43(5), 861-866.
    DOI Scopus5 WoS4 Europe PMC4
    2015 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.
    DOI Scopus29 WoS27 Europe PMC19
    2015 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.
    DOI Scopus38 WoS35 Europe PMC23
    2015 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.
    DOI Scopus10 WoS10 Europe PMC5
    2015 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.
    DOI Scopus8 WoS7 Europe PMC7
    2013 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.
    DOI Scopus16 WoS15 Europe PMC14
    2012 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.
    DOI Scopus11 WoS11 Europe PMC11
    2012 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.
    DOI Scopus4 WoS4 Europe PMC1
    2010 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.
    DOI Scopus18 WoS15 Europe PMC15
    2009 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.
    DOI Scopus12 WoS10 Europe PMC4
    2009 Furness, S., & 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.
    DOI Scopus52 WoS46 Europe PMC36
    2001 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.
    DOI
    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.
    DOI Scopus60 WoS57 Europe PMC43

  • 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.
    DOI
    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.
    DOI

  • 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.
    DOI
    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.
    DOI
    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.
    DOI
    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.
    DOI

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

 

Biology Department Summer Research Funding – June 2013

Chief Investigator

Department of Biology

University of York

Total awarded $7180

Lecturer – Cancer, Stem cells and Development – B.Sc. 3rd Year cohort – 3 lectures, 4 tutorials, Semester 2, 2020

Molecular and Biomedical Science, University of Adelaide

 

Lecturer – Advanced Research Platforms – M.Sc (Biotechnology) – 1 lecture, Semester 1, 2020

Molecular and Biomedical Science, University of Adelaide

 

Panel member - M.Sc. Major review panel, June 2020

Jill Chmielewski, 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
    2021 Co-Supervisor Engineering biosensors for wine spoilage Doctor of Philosophy Doctorate Full Time Mr Ranjith Manjula Meemanage Cebreco
    2021 Co-Supervisor Engineering small molecule binding proteins as novel biosensors Master of Philosophy Master Full Time Mr Alix Charles Harlington
    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
  • Position: Grant-Funded Researcher (B)
  • Phone: 83135362
  • Email: fiona.whelan@adelaide.edu.au
  • Campus: North Terrace
  • Building: Molecular Life Sciences, floor 2
  • Org Unit: School of Biological Sciences
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