Joe Kaczmarski

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.