Publications

---

• See an up-to-date publication list on my Google Scholar profile Google Scholar

---

Pre-Prints

1. 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]
2. 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
3. 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



Peer-Reviewed Publications

1. 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
2. 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
3. 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
4. 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
5. 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
6. 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
7. 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
8. 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
9. 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
10. Spence MA, Kaczmarski JA, Saunders JW, Jackson CJ. Ancestral sequence reconstruction for protein engineers. Current Opinion in Structural Biology, 2021, 69, 131–141
11. 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
12. 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
13. 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
14. 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
15. 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
16. 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
17. 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
18. 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
19. 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
20. 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
21. Kaczmarski JA, Corry B. Investigating the size and dynamics of voltage-gated sodium channel fenestrations. Channels, 2014, 8, 264–277

^* authors contributed equally

---