Dr Joe Alexander Kaczmarski

Qualifications

2021 -
Lecturer, ARC Centre of Excellence in Synthetic Biology, Research School of Biology
The Australian National University, Canberra

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

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 (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

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

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).”

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.”
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

Teaching Experience

2019-current Direct supervision of 9 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

2019-current 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)
2017-2018 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

Songya Zhang, Lin Zhang, Anja Greule, Julien Tailhades, Edward Marschall, Panward Prasongpholchai, Daniel J. Leng, Jingfan Zhang, Jing Zhu, Joe A Kaczmarski, Ralf B. Schittenhelm, Oliver Einsle, Colin J. Jackson, Fabrizio Alberti, Andreas Bechthold, Youming Zhang, Manuela Tosin, Tong Si, Max J Cryle. 2023. P450-mediated dehydrotyrosine formation during WS9326 biosynthesis proceeds via dehydrogenation of a specific acylated dipeptide substrate. Acta Pharmaceutica Sinica B https://doi.org/10.1016/j.apsb.2023.03.021
Nicholas J. East, Ben E. Clifton, Colin J. Jackson, Joe A Kaczmarski. 2022. The role of oligomerization in the optimization of cyclohexadienyl dehydratase conformational dynamics and catalytic activity. Protein Science 16 Nov. https://doi.org/10.1002/pro.4510
Cagla Ergun Ayva, Maria M.Fiorito, Zhong Guo, Selvakumar Edwardraja, Joe A Kaczmarski, Dejan Gagoski, Patricia Walden, Wayne A.Johnston, Colin J.Jackson, TomNebl, Kirill Alexandrov. 2022. Exploring Performance Parameters of Artificial Allosteric Protein Switches. Journal of Molecular Biology 15 Sept. https://doi.org/10.1016/j.jmb.2022.167678
Yvonne Joho, Vanessa Vongsouthi, Matthew A. Spence, Jennifer Ton, Chloe Gomez, Li Lynn Tan, Joe A Kaczmarski, Alessandro T. Caputo, Santana Royan, Colin J. Jackson, and Albert Ardevol. 2022. Ancestral Sequence Reconstruction Identifies Structural Changes Underlying the Evolution of Ideonella sakaiensis PETase and Variants with Improved Stability and Activity Biochemistry Aug 11. https://doi.org/10.1021/acs.biochem.2c00323
Daniel J Ford, Nisharnthi M Duggan, Sarah E Fry, Jorge Ripoll-Rozada, Stijn M Agten, Wenyu Liu, Leo Corcilius, Tilman M Hackeng, Rene van Oerle, Henri MH Spronk, Anneliese S Ashhurst, Vishnu Mini Sasi, Joe A Kaczmarski, Colin J Jackson, Pedro José Barbosa Pereira, Toby Passioura, Hiroaki Suga, Richard J Payne. 2021. Potent Cyclic Peptide Inhibitors of FXIIa Discovered by mRNA Display with Genetic Code Reprogramming. Journal of Medicinal Chemistry May 27. doi: 10.1021/acs.jmedchem.1c00651.
Spence MA^*, Kaczmarski JA^*, Saunders JW & Jackson CJ. 2021. Ancestral sequence reconstruction for protein engineers. Curr. Opin. Struct. Biol. 12: 2511.
Izoré, T, Candace H, 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. 2021. Structures of a non-ribosomal peptide synthetase condensation domain suggest the basis of substrate selectivity. Nature Communications 12: 2511.
Chatterjee D, Lewis FJ, Sutton HJ, Kaczmarski JA, Gao X, Cai Y, McNamara HA, Jackson CJ, Cockburn IA. 2021. Avid binding by B cells to the Plasmodium circumsporozoite protein repeat suppresses responses to protective subdominant epitopes. Cell Reports 35(2):108996
Kaczmarski JA, Mahawaththa MC, Feintuch A, Clifton BE, Adams LA, Goldfarb D, Otting G, Jackson CJ. 2020. Altered conformational sampling along an evolutionary trajectory changes the catalytic activity of an enzyme. Nature Communications 11:5945
Kaczmarski JA, Hong NS, Mukherjee B, Wey LT, Rourke L, Förster B, Peat TS, Price GD, Jackson CJ. 2019. Structural basis for the allosteric regulation of the SbtA bicarbonate transporter by the PII-like protein, SbtB, from Cyanobium sp. PCC7001. Biochemistry 58:5030–5039.
Kaczmarski JA, Mitchell JA, Spence MA, Vongsouthi V, Jackson CJ. 2019. Structural and evolutionary approaches to the design and optimization of fluorescence-based small molecule biosensors. Curr Opin Struct Biol 57:31–38.
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. 2019. Kistamicin biosynthesis reveals the biosynthetic requirements for production of highly crosslinked glycopeptide antibiotics. Nat Commun 10:2613.
Izoré T, Tailhades J, Hansen MH, Kaczmarski JA, Jackson CJ, Cryle MJ. 2019. Drosophila melanogaster nonribosomal peptide synthetase Ebony encodes an atypical condensation domain. Proc Natl Acad Sci USA 116:2913–2918.
Clifton BE, Kaczmarski JA, Carr PD, Gerth ML, Tokuriki N, Jackson CJ. 2018. Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein. Nat Chem Biol 14:542–547.
Fisher CR, Sutton HJ, Kaczmarski JA, McNamara HA, Clifton B, Mitchell J, Cai Y, Dups JN, D’Arcy NJ, Singh M, Chuah A, Peat TS, Jackson CJ, Cockburn IA. 2017. T-dependent B cell responses to Plasmodium induce antibodies that form a high-avidity multivalent complex with the circumsporozoite protein. PLoS Pathog 13:1–23.
Kaczmarski JA, Corry B. 2014. Investigating the size and dynamics of voltage-gated sodium channel fenestrations: A molecular dynamics study. Channels 8:264–277.

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.