UC Spark

Dr Renwick Charles Joseph Dobson

Biological Sciences; Biomolecular Interaction Centre

Fields of Research

  • Enzymology
  • Enzyme evolution and Enzyme design
  • Structural biology
  • Biophysics

Researcher Summary

Research in our lab focuses on the structure, function and inhibition of key enzymes involved in infection and disease.  We are also interested in the evolution of enzyme function, and conversely its design and manipulation.

We study a variety of enzymes: from those responsible for the biosynthesis of amino acids, in particular lysine, since these are validated drug targets; to glycolytic enzymes, such as pyruvate kinase, since these are tractable model systems to understand enzyme allostery.  The list is ever increasing.

A common theme in the lab is the role protein-protein interactions in a variety of biological systems, mostly derived from bacteria, but more recently including eukaryotic proteins involved in cancer, where we hope to address the twin problems of how and why proteins form complexes and the functional consequences of these associations.

Subject Area: Disciplines

Research Groups

Key Methodologies

  • Macromolecular crystallography
  • Analytical ultracentrifugation
  • Protein and Enzyme engineering
  • Molecular Biology (PCR, gene sub-cloning and over-expression)
  • Protein expression and purification
  • Small angle X-ray and neutron scattering
  • Multiangle laser light scattering (MALLS)
  • Mass spectrometry
  • Circular dichroism
  • Fluorescence spectroscopy
  • Isothermal titration microcalorimetry
  • Protein dynamics (NMR and MD simulations, via collaborations)

Affiliations

Prizes and Awards

  • Awarded the Prestigious C.R. Roper Senior Research Fellow, Department of Biochemistry and Molecular Biology, University of Melbourne. (2009-2012)
  • US ARO Research Fellowship, Department of Biochemistry and Molecular Biology, University of Melbourne (2007-2009)

Research Service

  • Principle Investigator and Theme Leader (Macromolecular Interactions), Biomolecular Interaction Centre (BIC), University of Canterbury. (see http://www.bic.canterbury.ac.nz/) (2010-present)

Publications


Journal Article
  • Sikorski, A., Argüello-Astorga, G.R., Dayaram, A., Dobson, R.C.J. and Varsani, A. (2013) Discovery of a novel circular single-stranded DNA virus from porcine faeces. Archives of Virology 158(1): 283-289. http://dx.doi.org/10.1007/s00705-012-1470-0.
  • Cross, P.J., Allison, T.M., Dobson, R.C.J., Jameson, G.B. and Parker, E.J. (2013) Engineering allosteric control to an unregulated enzyme by transfer of a regulatory domain. Proceedings of the National Academy of Sciences of the United States of America 110(6): 2111-2116.
  • Mercadante, D., Melton, L.D., Norris, G.E., Loo, T.S., Williams, M.A.K., Dobson, R.C.J. and Jameson, G.B. (2012) Bovine ß-Lactoglobulin is dimeric under imitative physiological conditions: Dissociation equilibrium and rate constants over the pH range of 2.5-7.5. Biophysical Journal 103(2): 303-312. http://dx.doi.org/10.1016/j.bpj.2012.05.041.
  • Atkinson, S.C., Dogovski, C., Downton, M.T., Pearce, F.G., Reboul, C.F., Buckle, A.M., Gerrard, J.A., Dobson, R.C.J., Wagner, J. and Perugini, M.A. (2012) Crystal, Solution and In silico Structural Studies of Dihydrodipicolinate Synthase from the Common Grapevine. PLoS ONE 7(6): e38318. http://dx.doi.org/10.1371/journal.pone.0038318.
  • Nachar, V.R., Savka, F.C., McGroty, S.E., Donovan, K.A., North, R.A., Dobson, R.C.J., Buckley, L.J. and Hudson, A.O. (2012) Genomic and biochemical analysis of the diaminopimelate and lysine biosynthesis pathway in Verrucomicrobium spinosum: identification and partial characterization of L,L-diaminopimelate aminotransferase and UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-meso-diaminopimelate ligase. Frontiers in Evolutionary and Genomic Microbiology 3: Online. http://dx.doi.org/10.3389/fmicb.2012.00183.
  • Dayaram, A., Opong, A., Jäschke, A., Hadfield, J., Baschiera, M., Dobson, R.C.J., Offei, S.K., Shepherd, D.N., Martin, D.P. and Varsani, A. (2012) Molecular characterisation of a novel cassava associated circular ssDNA virus. Virus Research 166(1-2): 130-135. http://dx.doi.org/10.1016/j.virusres.2012.03.009.
  • Boughton, B.A., Dobson, R.C.J. and Hutton, C.A. (2012) The crystal structure of dihydrodipicolinate synthase from Escherichia coli with bound pyruvate and succinic acid semialdehyde: Unambiguous resolution of the stereochemistry of the condensation product. Proteins 80(8): 2117-2122. http://dx.doi.org/10.1002/prot.24106/pdf.
  • Evans, G., Schuldt, L., Griffin, M.D.W., Devenish, S.R.A., Pearce, F.G., Perugini, M.A., Dobson, R.C.J., Jameson, G.B., Weiss, M.S. and Gerrard, J.A. (2011) A tetrameric structure is not essential for activity in dihydrodipicolinate synthase (DHDPS) from Mycobacterium tuberculosis. Archives of Biochemistry and Biophysics 512(2): 154-159. http://dx.doi.org/10.1016/j.abb.2011.05.014.
  • Pearce, F.G., Dobson, R.C.J., Jameson, G.B., Perugini, M.A. and Gerrard J.A. (2011) Characterisation of monomeric dihydrodipicolinate synthase variant reveals the importance of substrate binding in optimizing oligomerisation. Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics 1814(12): 1900-1909. http://dx.doi.org/10.1016/j.bbapap.2011.07.016.
  • Atkinson, S.C., Dogovski, C., Newman, J., Dobson, R.C.J. and Perugini, M.A. (2011) Cloning, expression, purification and crystallization of dihydrodipicolinate synthase from the grapevine Vitis vinifera. Acta crystallographica Section F: Structural biology and crystallization communications 67(12): 1537-1541. http://dx.doi.org/10.1107/S1744309111038395.
  • Griffin, M.D., Billakanti, J.M., Gerrard, J.A., Dobson, R.C.J. and Pearce, F.G. (2011) Crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase 2 from Arabidopsis thaliana. Acta crystallographica Section F: Structural biology and crystallization communications 67(11): 1386-1390. http://dx.doi.org/10.1107/S1744309111033276.
  • Hudson, A.O., Girón, I. and Dobson, R.C. (2011) Crystallization and preliminary X-ray diffraction analysis of l,l-diaminopimelate aminotransferase (DapL) from Chlamydomonas reinhardtii. Acta Crystallographica Section F: Structural Biology and Crystallization Communications 67(1): 140-143. http://dx.doi.org/10.1107/S174430911004844X.
  • Hudson A.O., Klartag A., Gilvarg C., Dobson R.C.J. and Marques F.G., Leustek T. (2011) Dual diaminopimelate biosynthesis pathways in Bacteroides fragilis and Clostridium thermocellum. Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics 1814(9): 1162-1168. http://dx.doi.org/10.1016/j.bbapap.2011.04.019.
  • Veldhuis N.A., Kuiper M.J., Dobson R.C.J., Pearson R.B. and Camakaris J. (2011) In silico modeling of the Menkes copper-translocating P-type ATPase 3rd metal binding domain predicts that phosphorylation regulates copper-binding. Biometals 24(3): 477-487. http://dx.doi.org/10.1007/s10534-011-9410-0.
  • Dobson, R.C., Girón, I. and Hudson, A.O. (2011) L,L-Diaminopimelate Aminotransferase from Chlamydomonas reinhardtii: A Target for Algaecide Development. PLoS One 6(5): e20439 (13pp). http://dx.doi.org/10.1371/journal.pone.0020439.
  • Gunn, N.J., Gorman, M.A., Dobson, R.C.J., Parker, M.W. and Mulhern, T.D. (2011) Purification, crystallization, small-angle X-ray scattering and preliminary X-ray diffraction analysis of the SH2 domain of the Csk-homologous kinase. Acta Crystallographica Section F: Structural Biology and Crystallization Communications 67(3): 336-339. http://dx.doi.org/10.1107/S1744309110053728.
  • Cross P.J., Dobson R.C.J. and Patchett M.L., Parker E.J. (2011) Tyrosine Latching of a Regulatory Gate Affords Allosteric Control of Aromatic Amino Acid Biosynthesis. The Journal of Biological Chemistry 286(12): 10216-10224. http://dx.doi.org/10.1074/jbc.M110.209924.
  • Dommaraju, S., Gorman, M.A., Dogovski, C., Pearce, F.G., Gerrard, J.A., Dobson, R.C.J., Parker, M.W. and Perugini, M.A. (2010) Cloning, expression and crystallization of dihydrodipicolinate reductase from methicillin-resistant Staphylococcus aureus. Acta Crystallographica Section F: Structural Biology and Crystallization Communications 66(1): 57-60. http://dx.doi.org/10.1107/s1744309109047964.
  • Wubben, J.M., Dogovski, C., Dobson, R.C., Codd, R., Gerrard, J.A., Parker, M.W. and Perugini, M.A. (2010) Cloning, expression, purification and crystallization of dihydrodipicolinate synthase from the psychrophile Shewanella benthica. Acta Crystallographica Section F: Structural Biology and Crystallization Communications 66(11): 1511-1516. http://dx.doi.org/10.1107/S1744309110036791.
  • Hor, L., Dobson, R.C.J., Dogovski, C., Hutton, C.A. and Perugini, M.A. (2010) Crystallization and preliminary X-ray diffraction analysis of diaminopimelate epimerase from Escherichia coli. Acta Crystallographica Section F: Structural Biology and Crystallization Communications 66(1): 37-40. http://dx.doi.org/10.1107/S1744309109047708.
  • Chan, K.C., Lio, D.S., Dobson, R.C.J., Jarasrassamee, B., Hossain, M.I., Roslee, A.K., Ia, K.K., Perugini, M.A. and Cheng, H.C. (2010) Development of the procedures for high-yield expression and rapid purification of active recombinant Csk-homologous kinase (CHK): Comparison of the catalytic activities of CHK and CSK. Protein Expression and Purification 74(2): 139-147. http://dx.doi.org/10.1016/j.pep.2010.07.007.
  • Muscroft-Taylor, A.C., Catchpole, R.J., Dobson, R.C.J., Pearce, F.G., Perugini, M.A. and Gerrard, J.A. (2010) Disruption of quaternary structure in Escherichia coli dihydrodipicolinate synthase (DHDPS) generates a functional monomer that is no longer inhibited by lysine. Archives of Biochemistry and Biophysics 503: 202-206. http://dx.doi.org/10.1016/j.abb.2010.08.009.
  • Griffin, M.D.W., Dobson, R.C.J., Gerrard, J.A. and Perugini, M.A. (2010) Exploring the dihydrodipicolinate synthase tetramer: how resilient is the dimer-dimer interface? Archives of Biochemistry and Biophysics 494(1): 58-63. http://dx.doi.org/10.1016/j.abb.2009.11.014.
  • Soares da Costa, T.P., Muscroft-Taylor, A.C., Dobson, R.C.J., Devenish, S.R.A., Jameson, G.B. and Gerrard, J.A. (2010) How essential is the 'essential' active-site lysine in dihydrodipicolinate synthase? Biochimie 92(7): 837-845. http://www.ncbi.nlm.nih.gov/pubmed/20353808.
  • Voss, J.E., Scally, S.W., Taylor, N.L., Atkinson, S.C., Griffin, M.D.W., Hutton, C.A., Parker, M.W., Alderton, M.R., Gerrard, J.A., Dobson, R.C.J., Dogovski, C. and Perugini, M.A. (2010) Substrate-mediated stabilization of a tetrameric drug target reveals Achilles heel in anthrax. The Journal of Biological Chemistry 285(8): 5188-5195. http://dx.doi.org/10.1074/jbc.M109.038166.
  • Zhu, T., Bailey, M.F., Angley, L.M., Cooper, T.F. and Dobson, R.C.J. (2010) The quaternary structure of pyruvate kinase type 1 from Escherichia coli at low nanomolar concentrations. Biochimie 92(1): 116-120. http://dx.doi.org/10.1016/j.biochi.2009.09.016.
  • James, P.F., Dogovski, C., Dobson, R.C.J., Bailey, M.F., Goldie, K.N., Karas, J.A., Scanlon, R., O'Hair, J. and Perugini, A. (2009) Aromatic residues in the C-terminal helix of human apoC-I mediate phospholipid interactions and particle morphology. The Journal of Lipid Research 50(7): 1384–1394. http://dx.doi.org/10.1194/jlr.M800529-JLR200.
  • Domigan, L.J., Scally, S.W., Fogg, M.J., Hutton, C.A., Perugini, M.A., Dobson, R.C.J., Muscroft-Taylor, A.C., Gerrard, J.A. and Devenish, S.R.A. (2009) Characterisation of dihydrodipicolinate synthase (DHDPS) from Bacillus anthracis. Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics 1794(10): 1510-1516. http://dx.doi.org/10.1016/j.bbapap.2009.06.020.
  • Dommaraju, S.R., Gorman, M.A., Dogovski, C., Pearce, F.G., Gerrard, J.A., Dobson, R.C.J., Parker, M.W. and Perugini, M.A. (2009) Cloning expression and crystallization of Dihydrodipicolinate reductase from Methicillin-resistant Staphylococcus aureus. Acta Crystallographica Section F: Structural Biology and Crystallization Communications 66(1): 57-60.
  • Atkinson, S.C., Dobson, R.C.J., Newman, J.M., Gorman, M.A., Dogovski, C. and Parker, M.W. (2009) Crystallization and preliminary X-ray analysis of dihydrodipicolinate synthase from Clostridium botulinum in the presence of its substrate pyruvate. Acta Crystallographica Section F: Structural Biology and Crystallization Communications 65(3): 253–255. http://dx.doi.org/10.1107/S1744309108039018.
  • Voss, J.E., Scally, S.W., Taylor, N.L., Dogovski, C., Alderton, M.R., Hutton, C.A., Gerrard, J.A., Parker, M.W., Dobson, R.C.J. and Perugini, M.A. (2009) Expression, purification, crystallization and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Bacillus anthracis in the presence of pyruvate. Acta Crystallographica Section F: Structural Biology and Crystallization Communications 65(2): 181-191.
  • Dobson, R.C.J., Perugini, M.A., Jameson, G.B. and Gerrard, J.A. (2009) Specificity versus catalytic potency: the role of threonine 44 in Escherichia coli dihydrodipicolinate synthase mediated catalysis. Biochimie 91(8): 1036-1044. http://dx.doi.org/10.1016/j.biochi.2009.05.013.
  • Guo, B.B.B., Devenish, S.R.A., Dobson, R.C.J., Muscroft-Taylor, A.C. and Gerrard, J.A. (2009) The C-terminal domain of Escherichia coli dihydrodipicolinate synthase (DHDPS) is essential for maintenance of quaternary structure and efficient catalysis. Biochemical and Biophysical Research Communications 380(4): 802-806. http://dx.doi.org/10.1016/j.bbrc.2009.01.169.
  • Boughton, B.A., Dobson, R.C.J., Gerrard, J.A. and Hutton, C.A. (2008) Conformationally constrained diketopimelic acid analogues as inhibitors of dihydrodipicolinate synthase. Bioorganic & Medicinal Chemistry Letters 18: 460-463. http://dx.doi.org/10.1016/j.bmcl.2007.11.108.
  • Dobson, R.C.J., Griffin, M.D.W., Devenish, S.R.A., Pearce, F.G., Hutton, C.A., Gerrard, J.A., Jameson, G.B. and Perugini, M.A. (2008) Conserved main-chain peptide distortions: a proposed role for Ile203 in catalysis by dihydrodipicolinate synthase. Protein Science 17(12): 2080-2090. http://dx.doi.org/10.1110/ps.037440.108.
  • Kefala, G., Evans, G.L., Griffin, M.D.W., Devenish, S.R.A., Pearce, F.G., Perugini, M.A., Gerrard, J.A., Weiss, M.S. and Dobson, R.C.J. (2008) Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis. Biochemical Journal 411(2): 351-360. http://dx.doi.org/10.1042/BJ20071360.
  • Griffin, M.D.W., Dobson, R.C.J., Pearce, F.G., Antonio, L., Whitten, A.E., Liew, C.K., Mackay, J.P., Trewhella, J., Jameson, G.B., Perugini, M.A. and Gerrard, J.A. (2008) Evolution of quaternary structure in a homotetrameric enzyme. Journal of Molecular Biology 380(4): 691-703. http://dx.doi.org/10.1016/j.jmb.2008.05.038.
  • Androulakis, S., Schmidberger, J., Bate, M.A., DeGori, R., Beitz, A., Keong, C., Cameron, B., McGowan, S., Porter, C.J., Harrison, A., Hunter, J., Martin, J.L., Kobe, B., Dobson, R.C.J., Parker, M.W., Whisstock, J.C., Gray, J., Treloar, A., Groenewegen, D., Dickson, N. and Buckle, A. (2008) Federated repositories of X-ray diffraction images. Acta Crystallographica Section D: Biological Crystallography 64(7): 810-814. http://dx.doi.org/10.1107/S0907444908015540.
  • Mitsakos, V., Dobson, R.C.J., Pearce, F.G., Devenish, S.R., Evans, G.L., Burgess, B.R., Perugini, M.A., Gerrard, J.A. and Hutton, C.A. (2008) Inhibiting dihydrodipicolinate synthase across species: Towards specificity for pathogens? Bioorganic & Medicinal Chemistry Letters 18(2): 842-844. /http://dx.doi.org/10.1016/j.bmcl.2007.11.026.
  • Boughton, B.A., Grifftin, D.W., O'Donnell, P.A., Dobson, R.C.J., Perugini, M.A., Gerrard, J.A. and Hutton, C.A. (2008) Irreversible inhibition of dihydrodipicolinate synthase by 4-oxo-heptenedioic acid analogues. Bioorganic & Medicinal Chemistry 16: 9975-9983. http://dx.doi.org/10.1016/j.bmc.2008.10.026.
  • Pearce, F.G., Dobson, R.C.J., Weber, A., Lane, L.A., McCammon, M.G., Squire, M.A., Perugini, M.A., Jameson, G.B., Robinson, C.V. and Gerrard, J.A. (2008) Mutating the tight-dimer interface of dihydrodipicolinate synthase disrupts the enzyme quaternary structure: Toward a monomeric enzyme. Biochemistry 47(46): 12108-12117. http://dx.doi.org/10.1021/bi801094t.
  • Burgess, B.R., Dobson, R.C.J., Dogovski, C., Jameson, G.B., Parker, M.W. and Perugini, M.A. (2008) Purification, crystallization and preliminary X-ray diffraction studies to near-atomic resolution of dihydrodipicolinate synthase from methicillin-resistant Staphylococcus aureus. Acta Crystallographica Section F: Structural Biology and Crystallization Communications 64(7): 659-661. http://dx.doi.org/10.1107/S1744309108016746.
  • Burgess, B.R., Dobson, R.C.J., Bailey, M.F., Atkinson, S.C., Griffin, M.D.W., Jameson, G.B., Parker, M.W., Gerrard, J.A. and Perugini, M.A. (2008) Structure and evolution of a novel dimeric enzyme from a clinically important bacterial pathogen. The Journal of Biological Chemistry 283(41): 27598-27603. http://dx.doi.org/10.1074/jbc.M804231200.
  • Devenish, S.R., Gerrard, J.A., Jameson, G.B. and Dobson, R.C.J. (2008) The high-resolution structure of dihydrodipicolinate synthase from Escherichia coli bound to its first substrate, pyruvate. Acta Crystallographica Section F: Structural Biology and Crystallization Communications F64(12): 1092-1095. http://dx.doi.org/10.1107/S1744309108033654.
  • Dobson, R.C.J., Atkinson, S.C., Gorman, M.A., Newman, J.M., Parker, M.W. and Perugini, M.A. (2008) The purification, crystallisation, and preliminary X-ray diffraction analysis of dihydrodipicolinate synthase from Clostridium botulinum. Acta Crystallographica Section F: Structural Biology and Crystallization Communications 64(3): 206-208. http://dx.doi.org/10.1107/S1744309108002819.
  • Dobson, R.C.J., Devenish, S.R.A., Turner, L.A., Clifford, V.R., Pearce, F.G., Jameson, G.B. and Gerrard, J.A. (2005) Role of Arginine 138 in the catalysis and regulation of Escherichia coli dihydrodipicolinate synthase. Biochemistry 44: 13007-13013.
  • Dobson, R.C.J., Griffin, M.D.W., Jameson, G.B. and Gerrard, J.A. (2005) The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance. Acta Crystallographica Section D: Biological Crystallography 61: 1116-1124.
  • Turner, J.J., Healy, J.P., Dobson, R.C.J., Gerrard, J.A. and Hutton, C.A. (2005) Two new irreversible inhibitors of dihydrodipicolinate synthase: diethyl (E,E)-4-oxo-2,5-heptadienedioate and diethyl (E)-4-oxo-2-heptenedioate. Bioorganic and Medicinal Chemistry Letters 15: 995-998.
  • Dobson, R.C.J., Griffin, M.D.W., Roberts, S.J. and Gerrard, J.A. (2004) Dihydrodipicolinate synthase (DHDPS) from Escherichia coli displays partial mixed inhibition with respect to its first substrate, pyruvate. Biochimie 86(4-5): 311-315.
  • Dobson, R.C.J., Gerrard, J.A. and Pearce, F.G. (2004) Dihydrodipicolinate synthase is not inhibited by its substrate, (S)-aspartate beta-semialdehyde. Biochemical Journal 377: 757-762.
  • Dobson, R.C.J., Valegard, K. and Gerrard, J.A. (2004) The Crystal Structure of Three Site-directed Mutants of Escherichia coli Dihydrodipicolinate Synthase: Further Evidence for a Catalytic Triad. Journal of Molecular Biology 338(2): 329-339.
  • Roberts, S.J., Morris, J.C., Dobson, R.C.J., Baxter, C.L. and Gerrard, J.A. (2004) Two complete syntheses of (S)-aspartate semi-aldehyde and demonstration that Δ2-tetrahydroisophthalic acid is a non-competitive inhibitor of dihydrodipicolinate synthase. Arkivoc 2004(10): 166-177. http://www.arkat-usa.org.
  • Roberts, S.J., Morris, J.C., Dobson, R.C.J. and Gerrard, J.A. (2003) The preparation of (S)-Aspartate semi-aldehyde appropriate for use in biochemical studies. Bioorganic and Medicinal Chemistry Letters 13(2): 265-267.
Chapter in Book
  • Dogovski, C., Atkinson, S.C., Dommaraju, S.R., Dobson, R.C.J., Perugini, M.A., Hor, L., Huton, C.A. and Gerrard, J.A. (2009) Lysine biosynthesis in bacteria - An unchartered pathway for novel antibiotic design. In H.W. Doelle and S. Rokem (Ed.), Biotechnology Volume XI: 146-166. Oxford: Eolss Publishers.
Conference Contribution - Paper in published proceedings
  • Zhu T., Fei N., Perugini M.A., Cooper T.F. and Dobson R.C.J. (2008) In vivo evolution of Escherichia coli pyruvate kinase type I: how does genotypic evolution affect phenotype? Cairns, Australia: The Joint 2nd Pacific Rim International Conference on Protein Science and 4th Asian-Oceania Human Proteome Organization, 22-26 June 2008. In Journal of Proteomics & Bioinformatics 01 237-238.
Thesis - Doctor of Philosophy
  • Dobson, R.C.J. (2004) Investigating the catalytic and regulatory mechanisms of dihydrodipicolinate synthase. PhD, University of Canterbury, Christchurch, New Zealand.
Additional Publications
  • Giron, I.O., Dobson, R.C.J. and Hudson, AO. (2011) Characterization of L,L-diaminopimelate aminotransferase from Chlamydomonas reinhardtii. Minneapolis, WI, USA: Plant Biology 2011, 6-10 Aug 2011.