Structural Biology and Molecular Characterisation

Structural biology and molecular characterisation

Understanding molecular mechanisms of disease requires detailed knowledge of the structure of the relevant biological macromolecules. Our researchers employ experimental approaches such as X-ray crystallography and cryo-electron microscopy and combine them with computational approaches to unravel the structure of proteins and better understand their function.

Research groups

The development and application of high-resolution mass spectrometry imaging methods to study localized chemical processes occurring within complex surfaces such as biological tissue and cells. MSI developments focus on are (i) improving spatial resolution; (ii) the types of molecules that can be detected using MALDI-based approaches; and (iii) techniques to unambiguously identify the detected molecules. Key application areas include visualizing and understanding alterations in lipid biochemistry occurring throughout heterogeneous tissues, and more generally,  disease-induced bimolecular alterations that occurring within diseased tissues.

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View Dr Shane Ellis` Scholars

Life is driven by chemistry. Digesting food, contracting muscle, eyesight, and all of the other processes that keep us alive are driven by it. Physicist Richard Feynman said “it is very easy to answer many of these fundamental biological questions; you just look at the thing!” Knowing the three-dimensional shapes of important biological molecules can help us understand how they work. Knowing their structure can inform the discovery of therapeutic agents. So how do we “see” the structures of biological molecules? We use a technique called X-ray diffraction and computational techniques to study the structure and dynamics of two important classes biological molecules: proteins and nucleic acids.

Our research is exemplified by the following projects:

  • Bacterial DNA clamps are proteins that slide along DNA. They are required for bacterial survival and represent an excellent target for antibiotic development. With Prof Nick Dixon and A/Prof Michael Kelso (SCMB), and Dr Andy McElroy (The Research Network, UK) we are developing compounds that block important interactions involving bacterial DNA clamps.
  • Human glutathione transferase Omega 1 (GSTO1-1) plays an essential role in bacterial lipopolysaccharide (LPS) stimulated inflammatory responses through Toll-like receptor 4 (TLR4). This protein is a target for the development of inhibitors that could limit the massive innate immune response that produces damaging inflammatory cytokines and reactive oxygen species. We are working with the John Curtin School of Medical Research and the Monash Institute of Pharmaceutical Sciences to develop inhibitors.

View Associate Professor Aaron Oakley's Scholars page

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The Tolun group studies the bio-nano-machines carrying out processes involving nucleic acids such as DNA recombination, replication, repair and RNA transcription. We use molecular imaging (electron microscopy), structural biology (Cryo-EM), biochemistry and molecular biology.

Tolun Group members standing out the front of the Molecular Horizons Building

The main technique utilised in my group is electron microscopy (EM). In addition to the state-of-the-art cryo-EM, we also use the classical EM techniques such as shadow-casting (i.e., metal shadowing) and negative staining. Shadow-casting is a technique ideally suited for visualising DNA and DNA-protein complexes at the single-molecule level.

DNA Recombination

Single strand annealing homologous DNA recombination (SSA) is a process found in virtually all life. It is particularly important in the double-strand DNA (dsDNA) viruses, such as the oncogenic viruses Epstein-Barr Virus (EBV) Kaposi's sarcoma-associated herpesvirus (KSHV), and Herpes Simplex Virus 1 (HSV-1). SSA is catalysed by a protein complex called a two-component recombinase (TCR), composed of an exonuclease and an annealase. The exonuclease generates a single-strand DNA (ssDNA) overhang, and the annealase binds to this nascent ssDNA and anneals it to a homologous ssDNA strand.

My research group is using a multi-disciplinary approach to better understand how this machinery works, with a focus on cryo-EM. We are interested in determining the structures of proteins and protein complexes involved in SSA, using cryo-EM.

DNA Replication

In collaboration with the research groups of Nick Dixon, Antoine van Oijen, and Aaron Oakley, we are studying DNA replication to better understand the molecular mechanistic details of this process.


We are a very collaborative group, and in addition to our main interests above, we also work on many collaboration projects to determine the cryo-EM structures of proteins or complexes from other systems. Some of the topics we are working on with our collaborators include transcription, snake venom toxins and chaperons.    

View Dr Gökhan Tolun's Scholars page

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Our research efforts focus on developing and applying theoretical and computational tools to understand the structure-dynamics-function relationship in the complex (bio)molecular and nanoscale systems. Complementary to experimental investigations, such studies can gain new insights at the atomic level into the underlying mechanism and provide necessary knowledge for molecular engineering and discovery of novel therapeutics. Current research projects include computational studies of protein-ligand interactions, mechanistic studies of enzymatic reactions, and computer-aided enzyme design. 

View Associate Professor Haibo Yu’s Scholar page

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