Qualifications
2021 -
Lecturer, ARC Centre of Excellence in Synthetic Biology, Research School of Biology
The Australian National University, Canberra
- Lecturing & designing/running workshops in CHEM2211 Chemical Biology 1 + CHEM2208 Chemical Biology 2
- Supervision of Undergraduate, Honours and PhD student projects
- Co-established new Canberra node of the ARC CoE for Syn Bio at RSB
- [6 months parental leave in 2024]
2020 - 2021
Postdoctoral Researcher, Research School of Chemistry
The Australian National University, Canberra
2016 - 2020
PhD, Research School of Chemistry
The Australian National University, Canberra
Thesis: The structure, dynamics, function and evolution of binding proteins
Supervisor: Professor Colin Jackson
2011 - 2014
Bachelor of Philosophy (First Class Honours in Protein Chemistry)
The Australian National University, Canberra
A competitive, research-focused science degree
🏅University Medal in Chemistry
Honours, Awards & Funding
2022 EMCR Seed Funding Scheme, Australian Research Council Centre of Excellence in Synthetic Biology & Research School of Biology: “Establishing a Vibrio natriegens-based expression system for the rapid production and purification of secreted recombinant protein targets from growth media.”
2022 Two Successful Major Equipment Grant Applications @ Research School of Biology, ANU
2021 BioPlatforms Australia Research Project Funding: “A solute-binding protein library for the rapid development of small-molecule biosensors.”
2021 ARC Centre of Excellence in Synthetic Biology Pitch Competition Winner ($10,000 seed grant)
2021 CSL Behring/Cicada Innovations Plasma Protein Purification Challenge 2nd Place ($15,000 seed grant + mentoring)
2021 Nominated by Australian Academy of Science to attend the JSPS 13th HOPE Meeting with Nobel Laureates
2019 Australian Society for Biochemistry and Molecular Biology Fellowship
2016-2018 Research School of Chemistry Postgraduate Teaching Fellowship
2016-2020 Research School of Chemistry PhD Scholarship
2016-2020 Australian Government Research Training Program Stipend Scholarship
2017 Vice Chancellor’s Travel Grant
2014 University Medal in Chemistry
2011-2014 National Undergraduate Scholarship
2012-2013 Summer Research Program Scholarship
Key Skills
Laboratory-based X-ray crystallography, protein expression, protein purification, isothermal titration calorimetry, cloning (traditional, Gibson Assembly), in-cell assay development, circular dichroism, enzyme kinetics, differential scanning fluorimetry, surface-plasmon resonance.
Computer-based (science) Protein design & stabilisation, molecular dynamics (Desmond, Gromacs, NAMD), molecular docking (AF3, Glide, AutoDock), ancestral protein reconstruction, phylogenetic analysis, homology modelling and AlphaFold modelling.
Computer-based (other) Microsoft Office, R, Python, photo & video editing, website design & management, social media management, Adobe Creative Suite.
Other Science communication, teaching & student supervision, leadership.
Research Presentations
Oral presentations
- 2023 Canberra Protein Group, Canberra. “Getting started with ColabDesign & ProteinMPNN”
- 2022 ANU RSB EMCR Symposium, “Periplasmic binding proteins – evolution & engineering”
- 2022 HOPE Meeting with Nobel Laureates. “Altered conformational sampling along an evolutionary trajectory increases the catalytic activity of a new enzyme”
- 2021 FAOBMB Congress “Altered conformational sampling along an evolutionary trajectory increases the catalytic activity of a new enzyme”
- 2021 FAOBMB Young Scientists Programme “Altered conformational sampling along an evolutionary trajectory increases the catalytic activity of a new enzyme”
- 2021 ARC Centre of Excellence in Synthetic Biology Seminar Series. “Altered conformational sampling along an evolutionary trajectory increases the catalytic activity of a new enzyme”
- 2021 Lorne Protein Conference. “Altered conformational sampling along an evolutionary trajectory changes the catalytic activity of an enzyme”
- 2017 Biomolecular Machines Conference, Banff, Canada. “Conformational sampling is altered during the emergence and evolution of new enzyme activity”. Best Student Talk Award.🏆
- 2017 Research School of Chemistry’s Celebration of HDR Chemistry. “The molecular machines of life”. Best Presentation Award.🏆
Poster presentations
- 2023 ASBMB Annual Conference, Canberra. TEVp2.0: A soluble, stable & active proteinMPNN generated TEV-protease”
- 2023 Gordon Research Conference in Protein Engineering, US. “TEVp2.0: A soluble, stable & active proteinMPNN generated TEV-protease”
- 2023 Protein Society Annual Meeting, Boston, US. TEVp2.0: A soluble, stable & active proteinMPNN generated TEV-protease”
- 2022 ComBio 2022. “The role of oligomerisation during the evolution &optimisation of an enzyme”
- 2021 ARC Centre of Excellence in Synthetic Biology Workshop. “Evolution-based approaches for protein engineers”
- 2019 Lorne Protein Conference. “Molecular basis for the regulation of bicarbonate transport by the cyanobacterial PII-like protein, SbtB”. Poster Prize.🏆
- 2018 Lorne Protein Conference. “From binding protein to enzyme. Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein”. Poster Prize.🏆
- 2017 Melbourne Protein Group Symposium. “Introducing catalysis into non-catalytic protein folds: how nature does it”.
- 2017 Synthetic Biology: Evolution, Engineering & Design Conference, Vancouver, Canada. “From binding protein to enzyme. Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein”.
- 2017 Gordon Research Conference: Molecular Mechanisms in Evolution. “From binding protein to enzyme. Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein”.
- 2017 Lorne Protein Conference. “From binding protein to enzyme: Investigating the emergence of cyclohexadienyl dehydratase activity from non-catalytic ancestral proteins”. asdfasdas
- 2016 ComBio Conference, Brisbane. “From binding protein to enzyme: Investigating the emergence of cyclohexadienyl dehydratase activity from non-catalytic ancestral proteins.” ASBMB Poster Prize.🏆
- 2012 Australian Society for Biophysics Membrane Transport Satellite Meeting. “Investigating the interactions of sontochin and analogues with the Plasmodium falciparum Chloroquine Resistance Transporter (PfCRT).”
Teaching Experience
2022 - 2023 Lecturer, Chem2211 Chemical Biology 1 (~120 students). Australian National University
2022 - 2023 Lecturer, Chem2208 Chemical Biology 2 (~120 students). Australian National University
2019-current Direct supervision of 11 Undergraduate & Honours Project Students
2013-2020 Tutor/Lab Demonstrator/Exam marker, Chemistry (1st year course), Chemical Biology (2nd year course), Protein Engineering (2nd year and 3rd year courses).
2017-2018 Lecturer, Chemistry Bridging Course, ANU
Leadership, Service & Community Involvement
2024 Session chair “Protein Design” at BioMolecular Horizons 2024
2023 2023 ASBMB Annual Conference Organising Committee - raised >$30,000 in funding from Industry partners
2023 Session chair “Protein Engineering & Design” at ASBMB23 Meeting
2022 Session chair “Protein Engineering” at ComBio Conference
2022 Australasian Synthetic Biology Challenge Executive Committee (Education)
2019-2023 ASBMB Australian Biochemist Editorial Board Member
2020 Meristem Volunteer
2018-2020 Canberra Protein Group Committee Member (ASBMB)
2019 “Shirty Science” Participant (National Science Week, outreach program)
2017-2019 Jackson Lab Website & Social Media Manager
2017-2018 Research School of Chemistry Higher Degree Research Student Representative Committee Member
2016-2020 ANU Open Day Volunteer
2011-current National Youth Science Forum Volunteer & Alumni Representative
Publications
- Sandhu M, Chen J, Matthews D, Spence M, Pulsford SB, Gall B, Nichols J, Kaczmarski J, Tokuriki N, Jackson CJ. Computational and Experimental Exploration of Protein Fitness Landscapes: Navigating Smooth and Rugged Terrains}. arXiv, 2024 [author list requires fixing]
- Gall B, Pulsford SB, Matthews D, Spence MA, Kaczmarski J, Chen JZ, Sandhu M, Stone E, Nichols J, Jackson CJ. Protein Evolution as a Complex System. arXiv, 2024
- Miton C, Campbell E, Kaczmarski J, Feixas F, Romero‐Rivera A, Sandhu M, Anderson DW, Shatani N, Osuna S, Jackson C, Tokuriki N. Origin of evolutionary bifurcation in an enzyme. bioRxiv, 2023
- Matthews DS, Spence M, Mater AC, Nichols J, Pulsford SB, Sandhu M, Kaczmarski J, Miton C, Tokuriki N, Jackson C. Leveraging ancestral sequence reconstruction for protein representation learning. Nature Machine Intelligence, 2024
- Smith OB, Frkic RL, Rahman MG, Jackson CJ, Kaczmarski JA. Identification and Characterization of a Bacterial Periplasmic Solute Binding Protein That Binds l-Amino Acid Amides. Biochemistry, 2024, 63, 1322–1334
- Ho Y, Izoré T, Kaczmarski J, Marschall E, Ratnayake MS, Tailhades J, Steer D, Schittenhelm R, Tosin M, Jackson C, Cryle M. Exploring the selectivity and engineering potential of an NRPS condensation domain involved in the biosynthesis of the thermophilic siderophore fuscachelin. Frontiers in Catalysis, 2023
- Ho Y, Kaczmarski J, Tailhades J, Izoré T, Steer D, Schittenhelm R, Tosin M, Jackson C, Cryle M. Not always an innocent bystander: the impact of stabilised phosphopantetheine moieties when studying nonribosomal peptide biosynthesis. Chemical Communications, 2023
- Zhang S, Zhang L, Greule A, Tailhades J, Marschall E, Prasongpholchai P, Leng DJ, Zhang J, Zhu J, Kaczmarski J, Schittenhelm R, Einsle O, Jackson C, Alberti F, Bechthold A, Zhang Y, Tosin M, Si T, Cryle M. P450-mediated dehydrotyrosine formation during WS9326 biosynthesis proceeds via dehydrogenation of a specific acylated dipeptide substrate. Acta Pharmaceutica Sinica B, 2023
- Förster B, Mukherjee B, Rourke LM, Kaczmarski JA, Jackson CJ, Price GD. Adenylnucleotide-mediated binding of the PII-like protein SbtB contributes to controlling activity of the cyanobacterial bicarbonate transporter SbtA. eLife, 2023, 12
- Joho Y, Vongsouthi V, Spence M, Ton J, Gomez C, Tan L, Kaczmarski J, Caputo A, Royan S, Jackson C, Ardevol A. Ancestral Sequence Reconstruction Identifies Structural Changes Underlying the Evolution of Ideonella sakaiensis PETase and Variants with Improved Stability and Activity. Biochemistry, 2022
- East NJ, Clifton BE, Jackson CJ, Kaczmarski JA. The role of oligomerization in the optimization of cyclohexadienyl dehydratase conformational dynamics and catalytic activity. Protein Science, 2022, 31, e4510–e4510
- Ayva CE, Fiorito MM, Guo Z, Edwardraja S, Kaczmarski JA, Gagoski D, Walden P, Johnston WA, Jackson CJ, Nebl T, Alexandrov K. Exploring performance parameters of artificial allosteric protein switches. Journal of Molecular Biology, 2022, 167678–167678
- Spence MA, Kaczmarski JA, Saunders JW, Jackson CJ. Ancestral sequence reconstruction for protein engineers. Current Opinion in Structural Biology, 2021, 69, 131–141
- Izoré T, Ho YTC, Ho YTC, Kaczmarski JA, Gavriilidou A, Chow KH, Steer DL, Goode RJA, Schittenhelm RB, Tailhades J, Tosin M, Challis GL, Krenske EH, Ziemert N, Jackson CJ, Cryle MJ. Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity. Nature Communications, 2021, 12, 2511–2511
- Ford DJ, Duggan NM, Fry SE, Ripoll-Rozada J, Agten SM, Liu W, Corcilius L, Hackeng TM, van Oerle R, Spronk HMH, Ashhurst AS, Sasi VM, Kaczmarski JA, Jackson CJ, Pereira P, Passioura T, Suga H, Payne RJ. Potent Cyclic Peptide Inhibitors of FXIIa Discovered by mRNA Display with Genetic Code Reprogramming. Journal of Medicinal Chemistry, 2021, 64, 7853–7876
- Chatterjee D, Lewis FJ, Sutton HJ, Kaczmarski JA, Gao X, Cai Y, McNamara HA, Jackson CJ, Cockburn IA. Avid binding by B cells to the Plasmodium circumsporozoite protein repeat suppresses responses to protective subdominant epitopes. Cell Reports, 2021, 35, 108996–108996
- Kaczmarski JA, Mahawaththa MC, Feintuch A, Clifton BE, Adams LA, Goldfarb D, Otting G, Jackson CJ. altered conformational sampling along an evolutionary trajectory changes the catalytic activity of an enzyme. Nature Communications, 2020, 11, 5945
- Kaczmarski JA, Mitchell JA, Spence MA, Vongsouthi V, Jackson CJ. Structural and evolutionary approaches to the design and optimization of fluorescence-based small molecule biosensors. Current Opinion in Structural Biology, 2019, 57, 31–38
- Kaczmarski JA, Hong N-S, Mukherjee B, Wey LT, Rourke L, Förster B, Peat TS, Price GD, Jackson CJ. Structural Basis for the Allosteric Regulation of the SbtA Bicarbonate Transporter by the PII-like Protein, SbtB, from Cyanobium sp. PCC7001. Biochemistry, 2019
- Izoré T, Tailhades J, Hansen MH, Kaczmarski JA, Jackson CJ, Cryle MJ. Drosophila melanogaster nonribosomal peptide synthetase Ebony encodes an atypical condensation domain. Proceedings of the National Academy of Sciences of the United States of America, 2019, 116, 2913–2918
- Greule A, Izoré T, Iftime D, Tailhades J, Schoppet M, Zhao Y, Peschke M, Ahmed I, Kulik A, Adamek M, Goode RJA, Schittenhelm RB, Kaczmarski JA, Jackson CJ, Ziemert N, Krenske EH, De Voss JJ, Stegmann E, Cryle MJ. Kistamicin biosynthesis reveals the biosynthetic requirements for production of highly crosslinked glycopeptide antibiotics. Nature Communications, 2019, 10, 2613–2613
- Clifton BE, Kaczmarski JA, Carr PD, Gerth ML, Tokuriki N, Jackson CJ. Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein. Nature Chemical Biology, 2018, 14, 542–547
- Fisher C, Sutton HJ, Kaczmarski JA, McNamara HA, Clifton BE, Mitchell JA, Cai Y, Dups JN, D’Arcy NJ, Singh M, Chuah A, Peat TS, Jackson CJ, Cockburn IA. T-dependent B cell responses to Plasmodium induce antibodies that form a high-avidity multivalent complex with the circumsporozoite protein. PLOS Pathogens, 2017, 13
- Kaczmarski JA, Corry B. Investigating the size and dynamics of voltage-gated sodium channel fenestrations. Channels, 2014, 8, 264–277
Pre-Prints
Peer-Reviewed Publications
* authors contributed equally
Employment History (other)
2014 – 2016 Tour guide & bus driver, Bruny Island Safaris
2008 – 2011 Wilderness Tour Guide, Tasmanian Walking company
Referees
Referee contact details and/or reference letters are available upon request.