Publications

  • Tang, M. S., Shiu, S. C-C., Godonoga, M., Cheung, Y-W., Liang, S., Dirkzwager, R. M., Kinghorn, A. B., Fraser, L. A., Heddle, J. G.*, Tanner, J. A.* (2018) An aptamer-enabled DNA nanobox for protein sensing, Nanomedicine. In The Press
  • Banwell, E. F., Piette, B., Taormina, A., Heddle, J. G. (2018) Reciprocal Nucleopeptides as the Ancestral Darwinian Self-Replicator, Molec. Biol. Evol. 35 404-416. [OUP]
    Before cells there were simple molecular replicators. What were they made of? A popular theory (RNA World) suggests that the initial replicators were RNA. Peptides have also been suggested as candidates. Here we demonstrate that, just like in todays cells, the initial replicator could have had a nucleic acid andi> a peptide component
  • Zaucha, J. & Heddle, J. G. (2017) Resurrecting the Dead (Molecules). Comp. Struc. Biotech. J. [Science Direct]
    In this work we considered the science of "Molecular Paleontology" and how understanding long-extinct molecules is useful not only in understanding evolution but also in designing new molecules.
  • Heddle, J. G. (2017) TRAPped Structures: Making Artificial Cages With a Ring Protein in Advances in Bioinspired and Biomedical Materials. Volume 1 (pp. 3-17). (The American Chemical Society). [ACS]
    A summary of our bionanoscience work with TRAP up to 2017.
  • Heddle, J. G., Chakraborti, S., Iwasaki, K. (2017) Natural and Artificial Protein Cages: Design, Structure and Therapeutic Applications. Curr. Opin. Struc. Biol. 43:148-155 [Science Direct]
    In this review we looked a the relationship between advances in cryo-EM techniques, their application to understanding virus capsid structres and how these data can be used in strcutural synthetic biology for designing artificial protein cage structures.
  • Nagano, S.; Banwell, E. F.; Iwasaki, K.; Michalak, M.; Pałka, R.; Zhang, K. Y. J.; Voet, A. R. D.; Heddle, J. G. (2016) Understanding the Assembly of an Artificial Protein Nanotube Adv. Mater. Interfaces 3 [Wiley]
  • Godonoga, M., Lin, T.-Y., Oshima, A., Sumitomo, K., Tang, M. S. L., Cheung, Y.-W., Kinghorn, A. B., Dirkzwager, R. M., Zhou, C., Kuzuya, A., Tanner, J. A., Heddle, J. G. (2016) A DNA aptamer recognising a malaria protein biomarker can function as part of a DNA origami assembly Sci. Rep 6: 21266. [Nature]
  • Shah, s., Khan, A., Espinosa, A., Garcia, M., Nuansing, W., Ungureanu, M., Heddle, J. G., Chuvilin, A., Wege, C., Bittner, A. (2016) Virus-Templated Near-Amorphous Iron Oxide Nanotubes. Langmuir 32 5899-5908 [ACS]
  • Nagano, S., Seki, E., Lin, T-Y., Shirouzu, M., Yokoyama, S., Heddle, J. G. (2015) Investigating the roles of the C-terminal domain of Plasmodium falciparum GyrA. PLOS ONE, 0(11): e0142313 [Pubmed]
  • Lin, T.-Y., Nagano, S. & Gardiner Heddle, J. (2015).Functional Analyses of the Toxoplasma gondii DNA Gyrase Holoenzyme: A Janus Topoisomerase with Supercoiling and Decatenation Abilities. Sci. Rep. 5 14491 [Pubmed]
  • Imamura, M., Uchihashi, T., Ando, T., Arisaka, F., Malay, A.D. and Heddle, J.G. (2015) Probing Structural Dynamics of an Artificial Protein Cage Using High-Speed Atomic Force Microscopy Nano Lett. 15 1331–1335 [ACS]
  • Shah, S. S., Shah, S. N. & Heddle, J. G. (2015) Polymer-Mediated Dual Mineralization of a Plant Virus: A Platinum Nanowire Encapsulated by Iron Oxide. Chem. Lett. 44, 79-81 [CSJ]
  • Nagano, S., Lin, T., Reddy, J., Heddle, J. G. (2014) Unique Features of Apicoplast DNA Gyrases from Toxoplasma gondii and Plasmodium falciparum. BMC Bioinformatics. 15, 416 [Pubmed]
  • Shah, S. & Heddle, J. G. (2014) Squaring up to DNA: pentapeptide repeat proteins and DNA mimicry. Appl. Microbiol. and Biot. 98, 9545-9560 [Springer]
  • Shah, S. N., Shah, S. S., Ito, E., Heddle, J. G. (2014) Template-Free, Hollow and Porous Platinum Nanotube Derived from Tobamovirus and its Three-Dimensional Structure at the Nanoscale. RSC Advances 4, 39305-39311.[RSC]
  • Curtis, F. A. et al. (2014) Phage Orf family recombinases: conservation of activities and involvement of the central channel in DNA binding. PLOS ONE (2014). [PLOS]
  • Yamazaki, T., Heddle, J.G. Kuzuya, A. and Komiyama, M. (2014) Orthogonal Enzyme Arrays on a DNA Origami Scaffold Bearing Size-Tunable Wells. Nanoscale 6, 9122-9126 [RSC]
  • Matsubara, K., Malay, A. D., Curtis, F. A. Sharples, G. J., Heddle, J. G. (2013). Structural and functional characterization of the Redβ recombinase from bacteriophage λ. PLOS ONE 8, e78869 [PLOS]
  • Tsukamoto, R., Godonoga, M., Matsuyama, R., Igarashi, M., Heddle, J.G., Samukawa, S. and Yamashita, I. (2013) The effect of PEGylation on Controllably-Spaced Adsorption of Ferritin Molecules. Langmuir 29, 12737-12743 [ACS]
  • Trindade, L. S., Aigaki, T., Peixoto, A. A., Balduino, A., da Cruz, I. B. M., nica & Heddle, J. G. (2013). A novel classification system for aging theories. Frontiers Genet. 4. [Froniters]
  • Voet, A., Banwell, E. F., Sahu, K. K., Heddle, J. G. & Zhang, K. Y. (2013). Protein Interface Pharmacophore Mapping Tools for Small Molecule Protein:Protein Interaction Inhibitor Discovery. Curr. Top. Med. Chem. 13, 989-1001 [Pubmed]
  • Heddle, J. G., (2013). Gold Nanoparticle-Biological Molecule Interactions and Catalysis. Catalysts 3. 683-708[Full Text]
  • Malay, A. D., Heddle, J. G*., Tomita, S., Iwasaki, K., Miyazaki, N., Sumitomo, K., Yanagi, H., Yamashita, I. & Uraoka, Y. (2012). Gold Nanoparticle-Induced Formation of Artificial Protein Capsids. Nano Lett. 12, 2056-2059 [PDF]
  • Heddle, J. G.* & Tame, J. R. H. (2012). Protein nanotubes, channels and cages. In Amino Acids, Peptides and Proteins (Farkas, E. & Ryadnov, M., eds.), Vol. 37, pp. 151-189. The Royal Society of Chemistry, Cambridge [RSC]
  • Trindade, L., Balduino, A., Aigaki, T. and Heddle, J. (2012) Senemorphism: a novel perspective on aging patterns and its implication for diet-related biology. Biogerontology, 13, 457-466. [PUBMED
  • Malay, A. D., Watanabe, M., Heddle, J. G*. & Tame, J. R. H. (2011). Crystal structure of unliganded TRAP: implications for dynamic allostery. Biochem. J. 434, 429-434. [PUBMED]
  • Watanabe, M., Heddle, J. G#., Kikuchi, K., Unzai, S., Akashi, S., Park, S. Y. & Tame, J. R. (2009). The nature of the TRAP-Anti-TRAP complex. Proc. Natl. Acad. Sci. USA 106, 2176-2181. [PUBMED]
  • Miranda, F. F., Iwasaki, K., Akashi, S., Sumitomo, K., Kobayashi, M., Yamashita, I., Tame, J. R. H. & Heddle, J. G. (2009). A Self-Assembled Protein Nanotube with High Aspect Ratio. Small 5, 2077-2084. [PUBMED]
  • Akashi, S., Watanabe, M., Heddle, J. G., Unzai, S., Park, S. Y. & Tame, J. R. (2009). RNA and Protein Complexes of trp RNA-Binding Attenuation Protein Characterized by Mass Spectrometry. Anal. Chem. 81, 2218-2226. [PUBMED]
  • Watanabe, M., Mishima, Y., Yamashita, I., Park, S.-Y., Tame, J. R. H. & Heddle, J. G. (2008). Intersubunit linker length as a modifier of protein stability: Crystal structures and thermostability of mutant TRAP. Protein Sci. 17, 518-526. [WILEY]
  • Heddle, J. G. (2008). Protein cages,rings and tubes:useful components of future nanodevices? Nanotechnology, Science and Applications 1, 67-78. [NCBI]
  • Yoshizawa, K., Mishima, Y., Park, S. Y., Heddle, J. G., Tame, J. R., Iwahori, K., Kobayashi, M. & Yamashita, I. (2007). Effect of N-terminal residues on the structural stability of recombinant horse L-chain apoferritin in an acidic environment. J. Biochem. (Tokyo) 142, 707-713. [PUBMED]
  • Heddle, J. G*., Okajima, T., Scott, D. J., Akashi, S., Park, S. Y. & Tame, J. R. (2007). Dynamic allostery in the ring protein TRAP. J. Mol. Biol. 371, 154-167. [ScienceDirect]
  • Heddle, J. G*., Fujiwara, I., Yamadaki, H., Yoshii, S., Nishio, K., Addy, C., Yamashita, I. & Tame, J. R. (2007). Using the ring-shaped protein TRAP to capture and confine gold nanodots on a surface. Small 3, 1950-6. [PUBMED]
  • Addy, C., Ohara, M., Kawai, F., Kidera, A., Ikeguchi, M., Fuchigami, S., Osawa, M., Shimada, I., Park, S. Y., Tame, J. R. & Heddle, J. G. (2007). Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography. Acta. Crystallogr. D. Bio.l Crystallogr. 63, 221-229. [PUBMED]
  • Heddle, J. G., Yokoyama, T., Yamashita, I., Park, S. Y. & Tame, J. R. (2006). Rounding up: Engineering 12-membered rings from the cyclic 11-mer TRAP. Structure 14, 925-33. [ScienceDirect]
  • Rajesh, S., Heddle, J. G., Kurashima-Ito, K., Nietlispach, D., Shirakawa, M., Tame, J. R. & Ito, Y. (2005). Backbone 1H, 13C, and 15N assignments of a 56 kDa E. coli nickel binding protein NikA. J, Biomol. NMR 32, 177. [PUBMED]
  • Otto, B. R., Sijbrandi, R., Luirink, J., Oudega, B., Heddle, J. G., Mizutani, K., Park, S. Y. & Tame, J. R. (2005). Crystal structure of hemoglobin protease, a heme binding autotransporter protein from pathogenic Escherichia coli. J. Biol. Chem. 280, 17339-17345. [JBC]
  • Heddle, J. G., Mitelheiser, S., Maxwell, A. & Thomson, N. H. (2004). Nucleotide binding to DNA gyrase causes loss of DNA wrap. J. Mol. Biol. 337, 597-610. [PUBMED]
  • Heddle, J., Scott, D. J., Unzai, S., Park, S. Y. & Tame, J. R. (2003). Crystal structures of the liganded and unliganded nickel-binding protein NikA from Escherichia coli. J. Biol. Chem. 278, 50322-50329. [PUBMED]
  • Strumberg, D., Nitiss, J. L., Dong, J., Walker, J., Nicklaus, M. C., Kohn, K. W., Heddle, J. G., Maxwell, A., Seeber, S. & Pommier, Y. (2002). Importance of the fourth alpha-helix within the CAP homology domain of type II topoisomerase for DNA cleavage site recognition and quinolone action. Antimicrob. Agents Chemother. 46, 2735-2746. [PUBMED]
  • Heddle, J. & Maxwell, A. (2002). Quinolone-binding pocket of DNA gyrase: role of GyrB. Antimicrob Agents Chemother 46, 1805-1815. [PUBMED]
  • Zamble, D. B., Miller, D. A., Heddle, J. G., Maxwell, A., Walsh, C. T. & Hollfelder, F. (2001). In vitro characterization of DNA gyrase inhibition by microcin B17 analogs with altered bisheterocyclic sites. Proc. Natl. Acad. Sci. USA 98, 7712-7717. [PNAS]
  • Heddle, J. G., Lu, T., Zhao, X., Drlica, K. & Maxwell, A. (2001). gyrB-225, a mutation of DNA gyrase that compensates for topoisomerase I deficiency: investigation of its low activity and quinolone hypersensitivity. J. Mol. Biol. 309, 1219-1231. [ScienceDirect]
  • Heddle, J. G., Blance, S. J., Zamble, D. B., Hollfelder, F., Miller, D. A., Wentzell, L. M., Walsh, C. T. & Maxwell, A. (2001). The antibiotic microcin B17 is a DNA gyrase poison: characterisation of the mode of inhibition. J. Mol. Biol. 307, 1223-1234. [PUBMED]
  • Heddle, J. G., Barnard, F. M., Wentzell, L. M. & Maxwell, A. (2000). The interaction of drugs with DNA gyrase: a model for the molecular basis of quinolone action. Nucleosides Nucleotides Nucleic Acids 19, 1249-1264. [PUBMED]