Browsing by Author "Panjikar, S"

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    The Australian Synchrotron in the international Year of Crystallography
    (Australian Institute of Physics, 2014-09-01) James, M; Brand, HEA; Panjikar, S
    The Australian Synchrotron has been providing world quality X-ray diffraction instrumentation and expertise to the scientific community via the Powder Diffraction and two Macromolecular Crystallography beamlines since 2007. These capabilities reach across the scientific landscape from studies of advanced materials for applications such as electronics displays and new energy technologies, to development of new pharmaceuticals, studies of disease and other fundamental biological processes. © 2014 Australian Institute of Physics Inc.
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    Chemical crystallography at the Australian Synchrotron MX Beamlines
    (SCANZ, 2017-12-03) Price, JR; Aishima, J; Aragao, D; Eriksson, D; Panjikar, S; Riboldi-Tunnicliffe, A; Williamson, R; Caradoc-Davies, TT
    The macromolecular (MX) beamlines at the Australian synchrotron are mixed use between the structural biology and chemical crystallography (CX) communities. Since commissioning the high throughput MX1 bending magnet and the MX2 microfocus undulator beamlines have proven very successful for both communities. The deployment of a 16M Eiger detector (funded by Australian Structural Biology laboratories and Australian Cancer Research Foundation) has changed the ‘standard’ MX2 collection for CX from 1° oscillation in 1 second over 360°, which takes ~15 min with the beam attenuated to give a balance of resolution vs detector overloads to a new shutter less 360° oscillation yielding 3600 frames in 36 sec. This increase in data volume and experiment turnaround time has led to a number of challenges for the workflow for the users and highlighted the biggest dead time for beam is now: search and secure for hand mounting, and robot sample change time for automated sample handling including remote use. Indicative use of MX2 from completed search and secure in a 24-hour experiment with hand mounting (preferred by CX) was 188 completed searches. Maximum robot-mounted samples over the same duration is 288. There is a robot upgrade under development to take sample change times from ~4 min to ~30 sec, and it is anticipated that MX1 will also receive a detector upgrade. This increase in throughput is having a significant impact on our ability to return analysis on the experiment in real time, as well as deliver auto-processed data in a timely fashion (new computational hardware is on its way). Given these dramatic increases in experimental throughput, what are the addition opportunities that may be embraced by the crystallographic community in Australia? What is the future for chemical crystallography at the MX beamlines? A review of the current developments that are underway and some discussion of what may lie in the future will be presented.
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    Crystal structure of posnjakite formed in the first crystal water-cooling line of the ANSTO Melbourne Australian Synchrotron MX1 Double Crystal Monochromator
    (International Union of Crystallography (IUCr), 2020-06-30T14:00:00Z) Mills, SJ; Aishima, J; Aragao, D; Caradoc-Davies, TT; Cowieson, NP; Gee, CL; Ericsson, D; Harrop, SJ; Panjikar, S; Smith, KML; Riboldi-Tunnicliffe, A; Williamson, R; Price, JR
    Exceptionally large crystals of posnjakite, CuSO(OH)(HO), formed during corrosion of a Swagelock(tm) Snubber copper gasket within the MX1 beamline at the ANSTO-Melbourne, Australian Synchrotron. The crystal structure was solved using synchrotron radiation to = 0.029 and revealed a structure based upon [Cu(OH)(HO)O] sheets, which contain Jahn-Teller-distorted Cu octa-hedra. The sulfate tetra-hedra are bonded to one side of the sheet corner sharing and linked to successive sheets extensive hydrogen bonds. The sulfate tetra-hedra are split and rotated, which enables additional hydrogen bonds. © Mills et al. 2020.
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    Data evaluation on the fly: Auto-Rickshaw at the MX beamlines of the Australian Synchrotron
    (International Union of Crystallography, 2021-08-14) Panjikar, S
    Auto-Rickshaw [1,2] is a system for automated crystal structure determination. It provides computer coded decision-makers for successive and automated execution of a number of existing macromolecular crystallographic computer programs thus forming a software pipeline for automated and efficient crystal structure determination. Auto-Rickshaw (AR) is freely accessible to the crystallography community through the EMBL-Hamburg AR Server [3]. Recently, it has been installed at the ASCI cluster at the Australian Synchrotron which uses Docker and Kubernetes system for launching AR jobs in high-throughput manner. The synchrotron AR server is accessible to users from the MX beamline computers. AR at the MX beamlines can be invoked through command line or a web-based graphical user interface (GUI) for data and parameter input and for monitoring the progress of structure determination. It can be also invoked via automatic data processing if the parameter inputs have been pre set at the AR-GUI during X-ray diffraction experiment. A large number of possible structure solution paths are encoded in the system and the optimal path is selected as the structure solution evolves. The platform can carry out experimental (SAD, SIRAS, RIP or various MAD) and MR phasing or combination of experimental and MR phasing. The system has extended extensively for evaluation of multiple datasets for various phasing protocols as well as for evaluation of ligand binding and fragment screening. The new implementation and features will be discussed during the presentation. © 2022 The Author
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    Recent and future developments on the Australian Synchrotron MX2 beamline driven by the Eiger 16M detector deployment
    (Society of Crystallographers in Australia and New Zealand, 2017-12-03) Aragao, D; Aishima, J; Clarken, R; Eriksson, D; Macedo, S; Moll, A; Mudie, N; Panjikar, S; Price, JR; Riboldi-Tunnicliffe, A; Williamson, R; Caradoc-Davies, TT
    The new pixel array detector — Eiger 16M — deployed on MX2 in February 2017 has now generated more than 152 Tb of data compared with 18 Tb in the same period last year using a CCD based detector. This has not only revolutionised the speed that datasets are collected but also put challenges in the way we collect, take notes, process and store data. Here we will present how some of these challenges have been tackled and what are the future developments already being worked on for deployment in the next 12 months. We will also briefly describe one of the most common traps on collecting data on the Eiger 16M.
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    Repurposed inhibitor of bacterial dihydrodipicolinate reductase exhibits effective herbicidal activity.
    (Springer Nature, 2023-05-22) Mackie, ERR; Barrow, AS; Giel, MC; Hulett, MD; Gendall, AR; Panjikar, S; Soares da Costa, TP
    Herbicide resistance represents one of the biggest threats to our natural environment and agricultural sector. Thus, new herbicides are urgently needed to tackle the rise in herbicide-resistant weeds. Here, we employed a novel strategy to repurpose a 'failed' antibiotic into a new and target-specific herbicidal compound. Specifically, we identified an inhibitor of bacterial dihydrodipicolinate reductase (DHDPR), an enzyme involved in lysine biosynthesis in plants and bacteria, that exhibited no antibacterial activity but severely attenuated germination of the plant Arabidopsis thaliana. We confirmed that the inhibitor targets plant DHDPR orthologues in vitro, and exhibits no toxic effects against human cell lines. A series of analogues were then synthesised with improved efficacy in germination assays and against soil-grown A. thaliana. We also showed that our lead compound is the first lysine biosynthesis inhibitor with activity against both monocotyledonous and dicotyledonous weed species, by demonstrating its effectiveness at reducing the germination and growth of Lolium rigidum (rigid ryegrass) and Raphanus raphanistrum (wild radish). These results provide proof-of-concept that DHDPR inhibition may represent a much-needed new herbicide mode of action. Furthermore, this study exemplifies the untapped potential of repurposing 'failed' antibiotic scaffolds to fast-track the development of herbicide candidates targeting the respective plant enzymes. © The Authors - Open Access Creative Commons Attribution 4.0 International Licence.
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    Uncovering the structures and mechanisms for the largest group of bacterial surface virulence factors
    (International Union of Crystallography, 2021-08-14) Paxman, J; Vo, JL; Martínez Ortiz, G; Totsika, M; Lo, AW; Hor, L; Panjikar, S; Schembri, MA; Heras, B
    We know so little about how bacteria utilise surface virulence factors to colonise, infect, persist and cause disease in their hosts. The largest group of these virulence factors are the autotransporters, where although they employ a simple process for translocation to the bacterial surface, their functional passenger domains show a diverse range of pathogenic functions such as promoting adhesion, biofilm formation, invasion and tissue destruction. Despite extensive international efforts at the genotype-phenotype level that have confirmed the association of autotransporters with bacterial pathogenesis, less than 0.6 % of their structures have been determined with very little information on their molecular mechanisms of action. With 10 new structures of autotransporter passenger domains over the past few years our group has been leading this area of research. Taking advantage of many autotransporter passenger domains being based upon large >500 residue β-solenoid structures, we have successfully employed Xenon derivatisation at the Australian Synchrotron to acquire anomalous signal for structure determination by single isomorphous replacement. More importantly, we have used our crystal structures to inform a comprehensive array of biophysical, biochemical and microbiological approaches to uncover the mode of action of the autotransporters and their roles in bacterial pathogenesis. Using this approach, we were the first to determine the molecular mechanism of an autotransporter adhesin1. We found that this Ag43 adhesin from Uropathogenic E. coli (UPEC) promoted bacterial biofilms through a self-association mechanism between neighbouring E. coli cell surfaces. This knowledge on biofilms is critical given their contribution to bacterial chronic infections and the development of antibiotic resistance. Here we present the first crystal structure and mechanism of action of an autotransporter adhesin that binds to host tissue to facilitate bacterial colonisation2. The crystal structure of UpaB from UPEC was found to display significant modifications to its β-helix that creates two different binding sites, allowing it to interact simultaneously with both host surface proteins and polysaccharides. As shown in live animal models, both sites co-operate to achieve bacterial colonisation. In contrast to Ag43 that forms self-associations that lead to biofilms, UpaB through directly binding host factors to facilitate colonisation creates a second mechanistic group of the autotransporter adhesins. Returning to Ag43, we also investigate the conservation of its self-association mechanism with 3 new crystal structures of Ag43 homologues from widespread E. coli pathogens3. We show that adaptations to this mechanism of action alter the kinetics of bacterial aggregation and biofilm formation, presumably to suit the different E. coli pathogens to their specific infection sites. Even more importantly, we are using our molecular knowledge on autotransporters such as Ag43 to develop new classes of anti-bacterial inhibitors. To date we have developed and patented a successful inhibitor that targets Ag43 to prevent pathogenic E. coli biofilms4. Again using X-ray crystallography, we have determined the structure of the first autotransporter adhesin-inhibitor complex to fully understand how this novel inhibitor interacts with Ag43 and blocks its function. © The Authors