Publications

  • Zaucha, J. & Heddle, J. G. (2017) Resurrecting the Dead (Molecules). Comp. Struc. Biotech. J. [Science Direct]
    In this work we considered the sceince 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. (The American Chemical Society) In The Press
  • 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]