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Bionanoscience and Biochemistry Laboratory

The full Heddle lab homepage is here

 

Prof. Jonathan Heddle

·         T +48 12 664 61 19

·         F +48

·         jonathan.heddle[a.t]uj.edu.pl

·         MCB, Gronostajowa 7a str

Bionanoscience

Our overall goal is to understand, harness, manipulate and eventually build complex bionano machines or bionano robots.  This work spans a wide range of research from basic research to applied research. In basic research we are designing and building a toolbox of novel shapes and structures using biological molecules. Our primary building materials are proteins and nucleic acids (DNA and RNA). We hope to discover new methods of building and to produce new structures and ultimately new nanomachines that are compatible with living systems and so useful for medical applications. In our more applied research we are investigating existing nanomachines such as topoisomerases and recombinases both for insights into how natural nanomachines (enzymes) function and to exploit them as useful targets for discovery and development of new drugs.

            In our lab we utilize a wide range of biochemical, molecular biology, structural biology and biophysical techniques to achieve our goals.

 

The 8 nm diameter, ring shaped TRAP protein (a, pdb 1QAW) can be modified in different ways to produce hollow spheres approx. 20 nm in diameter (b) or a protein nanotube approx. 10 nm in diameter and up to several micrometres in length (c). Scale bar in (c) is 10 nm (a) is adapted from Malay et al., 2012, (b) is adapted from Imamura et al., 2015 and (c) is adapted from Miranda et al., 2012

 

Predicted structure of the GyrA A protein dimer from P. falciparum, a cause of  malaria (shown in blue and dark grey) using  the known structure of E. coli ParC (light grey and cyan, pdb 1ZVU) as a model. See also Nagano et al., 2014

 

Other Interests

The lab has other interests including aging and age-related diseases and we ultimately see this merging with the bionanoscience work whereby an understanding of age-related disease processes and mastery of bionanoscience leads to effective treatment using smart therapeutics.

Job Opportunities

We are always seeking for interested and highly motivated Master, PhD or Postdoc candidates. Please contact us for further details (jonathan.heddle[a.t]uj.edu.pl).

Selection of Relevant Publications

Topoisomerases and recombinases
 

  1. Heddle, J. G., Lu, T., Zhao, X., Drlica, K. & Maxwell, A. 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, (2001).
  2. Heddle, J. G., Mitelheiser, S., Maxwell, A. & Thomson, N. H. Nucleotide binding to DNA gyrase causes loss of DNA wrap. J. Mol. Biol. 337, 597-610, (2004).
  3. Nagano, S., Lin, T., Reddy, J. & Heddle, J. Unique features of apicoplast DNA gyrases from Toxoplasma gondii and Plasmodium falciparum. BMC Bioinformatics 15, 416, (2014).
  4. Lin, Ting-Yu, Soshichiro Nagano, and Jonathan Gardiner Heddle. "Functional analyses of the Toxoplasma gondii DNA gyrase holoenzyme: a janus topoisomerase with supercoiling and decatenation abilities." Scientific reports 5 (2015): 14491.

DNA origami

  1. Yamazaki, T., Heddle, J. G., Kuzuya, A. & Komiyama, M. Orthogonal enzyme arrays on a DNA origami scaffold bearing size-tunable wells. Nanoscale 6, 9122-9126, (2014).
  2. A DNA aptamer recognising a malaria protein biomarker can function as part of a DNA origami assembly." Scientific reports 6 (2016): 21266
  3. Shiu, Simon Chi‐Chin, et al. "The Three S's for Aptamer‐Mediated Control of DNA Nanostructure Dynamics: Shape, Self‐Complementarity, and Spatial Flexibility." ChemBioChem19.18 (2018): 1900-1906
  4. Balakrishnan, Dhanasekaran, Gerrit D. Wilkens, and Jonathan G. Heddle. "Delivering DNA origami to cells." Nanomedicine00 (2019)

Protein nanotechnology

  1. Heddle, J. G., Yokoyama, T., Yamashita, I., Park, S. Y. & Tame, J. R. Rounding up: Engineering 12-membered rings from the cyclic 11-mer TRAP. Structure 14, 925-933, (2006).
  2. Heddle, J. G. et al. Using the ring-shaped protein TRAP to capture and confine gold nanodots on a surface. Small 3, 1950-1956, (2007).
  3. Miranda, F. F. et al. A Self-Assembled Protein Nanotube with High Aspect Ratio. Small 5, 2077-2084, (2009).
  4. Watanabe, M. et al. The nature of the TRAP-Anti-TRAP complex. Proc. Natl. Acad. Sci. USA 106, 2176-2181, (2009).
  5. Malay, A. D., Watanabe, M., Heddle, J. G. & Tame, J. R. H. Crystal structure of unliganded TRAP: implications for dynamic allostery. Biochem. J. 434, 429-434, (2011).
  6. Heddle, J. G. & Tame, J. R. H. in Amino Acids, Peptides and Proteins Vol. 37  (eds E. Farkas & M. Ryadnov)  151-189 (The Royal Society of Chemistry, 2012).
  7. Malay, A. D. et al. Gold Nanoparticle-Induced Formation of Artificial Protein Capsids. Nano Lett. 12, 2056-2059, (2012).
  8. Shah, S. & Heddle, J. G. Squaring up to DNA: pentapeptide repeat proteins and DNA mimicry. Appl Microbiol Biotechnol 98, 9545-9560, (2014).
  9. Shah, S. N., Shah, S. S., Ito, E. & Heddle, J. G. Template-free, hollow and porous platinum nanotubes derived from tobamovirus and their three-dimensional structure at the nanoscale. RSC Advances 4, 39305-39311, (2014).
  10. Shah, S. S., Shah, S. N. & Heddle, J. G. Polymer-Mediated Dual Mineralization of a Plant Virus: A Platinum Nanowire Encapsulated by Iron Oxide. Chem. Lett. 44, 79-81, (2015)
  11. Imamura, M. et al. Probing structural dynamics of an artificial protein cage using high-speed atomic force microscopy. Nano Lett 15, 1331-1335, (2015).
  12. Nagano, Soshichiro, et al. "Understanding the assembly of an artificial protein nanotube." Advanced Materials Interfaces3.24 (2016): 1600846.