The nature of our work is collaborative as our focus is on developing and implementing spectroscopic techniques to study molecular systems. Our publication lists (https://researchers.mq.edu.au/en/persons/alison-rodger) indicate many of the collaborators with whom we have enjoyed working. Many collaborations result from chance encounters and convenience of location. In addition to local Macquarie and Sydney collaborators we enjoy working with: Tim Dafforn, University of Birmingham; Bengt Nordén, Chalmers University; Louise Serpell, University of Sussex; Nikola Chmel, University of Warwick; Margaret Brimble, University of Auckland; Ravi Jagadeeshan, Monash University; Josef Kapitan, Palacky University in Olomouc; and Andrew Reason and Mark Millichip, BioPharmaSpec.
This list of projects is designed to illustrate our capability rather than be comprehensive
1. A new Raman instrument for polarized spectroscopy of biomacromolecular systems
This project is motivated by the fact that structural characterization of biomacromolecules in complex environments e.g. biological cells, membranes, or in formulation vehicles (for biopharmaceutical products) is being demanded at ever increasing levels of detail. We are particularly interested in biological membranes and sugars, including peptidoglycans, which have little or no UV–visible spectroscopy. In addition to research-drivers, the moves towards ‘Quality by Design’ and parametric release methods for biopharmaceuticals means that the biopharmaceutical industry is demanding new methods. Raman spectroscopy provides access to the wealth of information available in vibrational spectroscopy without the challenges which confront infra red absorbance where water signals dominate. We have developed a new form of Raman spectroscopy, Raman linear difference, have designed and built a new instrument based on a BioTools instrument which we are currently validating for Raman, Raman Optical Activity (ROA) and Raman Linear Difference (RLD) spectroscopy in a project funded by the Engineering and Physical Sciences Research Council, UK and are working in collaboration with Josef Kapitan, Palacky University in Olomouc. ROA is well-established but comparatively underused to probe secondary and tertiary structures of proteins and other biomacromolecules. RLD is the newly invented technique (Rodger et al. Analytical Chemistry, 2012) that gives relative orientations of subunits of complex molecular assemblies. This project builds on our success (measured by increase in publications and instrument sales over the past 10 years) in making UV–linear dichroism an available technology.
2. Bacterial cell division
A long-running project to study the structures and kinetics of bacterial cell division proteins (in collaboration with D. Roper, Warwick and T. Dafforn, Birmingham) that make up and bind to the Z-ring (the structure that causes the membrane contraction at the division site) has recently been enhanced by mathematical modelling of the kinetics and force induction and given new applications in the context of antimicrobial resistance. We continue to enhance the model with more components of the divisome complex and to use it to interpret previously unexplained experimental results, such as the behaviour of various deletion mutants, and to determine where in the division process to target new drugs.
3. Process analytical technology, quality by design, and parametric release
A challenging application area for analytical sciences is provided by the emerging biosimilars (generic biopharmaceutical drugs) market, not least of which is ‘what is similar?’. We are address the need of developing new analytical techniques for this purpose.
4. Structural probes of biomacromolecules and their interactions with ligands, proteins, membranes, nucleic acids
High resolution structure determination of soluble globular proteins relies heavily on X-ray crystallography techniques and to lesser extents on NMR. Such approaches are often ineffective for investigations into the structure of assemblies of molecules that do not crystallize and are too large or irregular for NMR. Among these are fibrous proteins (e.g. b-sheet amyloid fibres, collagen, a1-antitrypsin polymers and cytoskeletal proteins tubulin, actin and FtsZ); membrane systems (including membrane proteins and antibacterial membrane-binding peptides); nucleic acids and their complexes with small molecules or proteins. We can use our structural methodologies on different levels, most simply qualitative (which may include quantitative monitoring of reaction kinetics), semi-empirical and quantitatively. Our focus is on circular and linear dichroism spectroscopies to provide information that no other techniques can give, but quantitative analysis requires more work on the understanding the optical contributions to the measured signals and the dependence of LD signals on the degree of flow orientation. New florescence detected methods are currently being developed.